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Sample records for computational studies reveal

  1. Revealing Stepwise Mechanisms in Dipolar Cycloaddition Reactions: Computational Study of the Reaction between Nitrones and Isocyanates.

    PubMed

    Darù, Andrea; Roca-López, David; Tejero, Tomás; Merino, Pedro

    2016-01-15

    The mechanism of cycloaddition reactions of nitrones with isocyanates has been studied using density functional theory (DFT) methods at the M06-2X/cc-pVTZ level of theory. The exploration of the potential energy surfaces associated with two reactive channels leading to 1,2,4-oxadiazolidin-5-ones and 1,4,2-dioxazolidines revealed that the cycloaddition reaction takes place through a concerted mechanism in gas phase and in apolar solvents but a stepwise mechanism in polar solvents. In stepwise mechanisms, the first step of the reaction is a rare case in which the nitrone oxygen acts as a nucleophile by attacking the central carbon atom of the isocyanate (interacting with the π-system of the C═O bond) to give an intermediate. The corresponding transition structure is stabilized by an attractive electrostatic interaction favored in a polar medium. The second step of the reaction is the rate-limiting one in which the formation of 1,2,4-oxadiazolidin-5-ones or 1,4,2-dioxazolidines is decided. Calculations indicate that formation of 1,2,4-oxadiazolidin-5-ones is favored both kinetically and thermodynamically independently of the solvent, in agreement with experimental observations. Noncovalent interactions (NCI) and topological analysis of the gradient field of electron localization function (ELF) bonding confirmed the observed interactions.

  2. Revealing Stepwise Mechanisms in Dipolar Cycloaddition Reactions: Computational Study of the Reaction between Nitrones and Isocyanates.

    PubMed

    Darù, Andrea; Roca-López, David; Tejero, Tomás; Merino, Pedro

    2016-01-15

    The mechanism of cycloaddition reactions of nitrones with isocyanates has been studied using density functional theory (DFT) methods at the M06-2X/cc-pVTZ level of theory. The exploration of the potential energy surfaces associated with two reactive channels leading to 1,2,4-oxadiazolidin-5-ones and 1,4,2-dioxazolidines revealed that the cycloaddition reaction takes place through a concerted mechanism in gas phase and in apolar solvents but a stepwise mechanism in polar solvents. In stepwise mechanisms, the first step of the reaction is a rare case in which the nitrone oxygen acts as a nucleophile by attacking the central carbon atom of the isocyanate (interacting with the π-system of the C═O bond) to give an intermediate. The corresponding transition structure is stabilized by an attractive electrostatic interaction favored in a polar medium. The second step of the reaction is the rate-limiting one in which the formation of 1,2,4-oxadiazolidin-5-ones or 1,4,2-dioxazolidines is decided. Calculations indicate that formation of 1,2,4-oxadiazolidin-5-ones is favored both kinetically and thermodynamically independently of the solvent, in agreement with experimental observations. Noncovalent interactions (NCI) and topological analysis of the gradient field of electron localization function (ELF) bonding confirmed the observed interactions. PMID:26682934

  3. Structural and computational studies of the Staphylococcus aureus sortase B-substrate complex reveal a substrate-stabilized oxyanion hole.

    PubMed

    Jacobitz, Alex W; Wereszczynski, Jeff; Yi, Sung Wook; Amer, Brendan R; Huang, Grace L; Nguyen, Angelyn V; Sawaya, Michael R; Jung, Michael E; McCammon, J Andrew; Clubb, Robert T

    2014-03-28

    Sortase cysteine transpeptidases covalently attach proteins to the bacterial cell wall or assemble fiber-like pili that promote bacterial adhesion. Members of this enzyme superfamily are widely distributed in Gram-positive bacteria that frequently utilize multiple sortases to elaborate their peptidoglycan. Sortases catalyze transpeptidation using a conserved active site His-Cys-Arg triad that joins a sorting signal located at the C terminus of their protein substrate to an amino nucleophile located on the cell surface. However, despite extensive study, the catalytic mechanism and molecular basis of substrate recognition remains poorly understood. Here we report the crystal structure of the Staphylococcus aureus sortase B enzyme in a covalent complex with an analog of its NPQTN sorting signal substrate, revealing the structural basis through which it displays the IsdC protein involved in heme-iron scavenging from human hemoglobin. The results of computational modeling, molecular dynamics simulations, and targeted amino acid mutagenesis indicate that the backbone amide of Glu(224) and the side chain of Arg(233) form an oxyanion hole in sortase B that stabilizes high energy tetrahedral catalytic intermediates. Surprisingly, a highly conserved threonine residue within the bound sorting signal substrate facilitates construction of the oxyanion hole by stabilizing the position of the active site arginine residue via hydrogen bonding. Molecular dynamics simulations and primary sequence conservation suggest that the sorting signal-stabilized oxyanion hole is a universal feature of enzymes within the sortase superfamily.

  4. [Pneumothorax revealed by postoperative computed tomography].

    PubMed

    Ikeda, Shizuka; Katori, Kiyoshi; Fujimoto, Minoru; Nitahara, Keiichi; Higa, Kazuo

    2005-11-01

    We report a case of pneumothorax revealed by postoperative computed tomography. A 39-year-old obese woman (height 153 cm, weight 70 kg) with fractures of the radius, ulna, clavicle, and femur in a traffic accident, was scheduled for osteosynthesis. Anesthesia was induced with thiopental and maintained with 50% nitrous oxide in oxygen and sevoflurane. The Spo2 decreased from 99% to 94% during the surgery. Bilateral chest sounds were symmetrical. The Spo2 increased to 100% after discontinuation of nitrous oxide. Pneumothorax was not evident on a postoperative chest X-ray, but computed tomography of the chest demonstrated right-sided pneumothorax. An ECG electrode had overlapped the fractured rib on the preoperative chest X-ray.

  5. Computational models reveal genotype-phenotype associations in Saccharomyces cerevisiae.

    PubMed

    Franco-Duarte, Ricardo; Mendes, Inês; Umek, Lan; Drumonde-Neves, João; Zupan, Blaz; Schuller, Dorit

    2014-07-01

    Genome sequencing is essential to understand individual variation and to study the mechanisms that explain relations between genotype and phenotype. The accumulated knowledge from large-scale genome sequencing projects of Saccharomyces cerevisiae isolates is being used to study the mechanisms that explain such relations. Our objective was to undertake genetic characterization of 172 S. cerevisiae strains from different geographical origins and technological groups, using 11 polymorphic microsatellites, and computationally relate these data with the results of 30 phenotypic tests. Genetic characterization revealed 280 alleles, with the microsatellite ScAAT1 contributing most to intrastrain variability, together with alleles 20, 9 and 16 from the microsatellites ScAAT4, ScAAT5 and ScAAT6. These microsatellite allelic profiles are characteristic for both the phenotype and origin of yeast strains. We confirm the strength of these associations by construction and cross-validation of computational models that can predict the technological application and origin of a strain from the microsatellite allelic profile. Associations between microsatellites and specific phenotypes were scored using information gain ratios, and significant findings were confirmed by permutation tests and estimation of false discovery rates. The phenotypes associated with higher number of alleles were the capacity to resist to sulphur dioxide (tested by the capacity to grow in the presence of potassium bisulphite) and the presence of galactosidase activity. Our study demonstrates the utility of computational modelling to estimate a strain technological group and phenotype from microsatellite allelic combinations as tools for preliminary yeast strain selection.

  6. African Studies Computer Resources.

    ERIC Educational Resources Information Center

    Kuntz, Patricia S.

    African studies computer resources that are readily available in the United States with linkages to Africa are described, highlighting those most directly corresponding to African content. Africanists can use the following four fundamental computer systems: (1) Internet/Bitnet; (2) Fidonet; (3) Usenet; and (4) dial-up bulletin board services. The…

  7. Remote-Stereocontrol in Dienamine Catalysis: Z-Dienamine Preferences and Electrophile-Catalyst Interaction Revealed by NMR and Computational Studies.

    PubMed

    Seegerer, Andreas; Hioe, Johnny; Hammer, Michael M; Morana, Fabio; Fuchs, Patrick J W; Gschwind, Ruth M

    2016-08-10

    Catalysis with remote-stereocontrol provides special challenges in design and comprehension. One famous example is the dienamine catalysis, for which high ee values are reported despite insufficient shielding of the second double bond. Especially for dienamines with variable Z/E-ratios of the second double bond, no correlations to the ee values are found. Therefore, the structures, thermodynamics, and kinetics of dienamine intermediates in SN-type reactions are investigated. The NMR studies show that the preferred dienamine conformation provides an effective shielding if large electrophiles are used. Calculations at SCS-MP2/CBS-level of theory and experimental data of the dienamine formation show kinetic preference for the Z-isomer of the second double bond and a slow isomerization toward the thermodynamically preferred E-isomer. Modulations of the rate-determining step, by variation of the concentration of the electrophile, allow the conversion of dienamines to be observed. With electrophiles, a faster reaction of Z- than of E-isomers is observed experimentally. Calculations corroborate these results by correlating ee values of three catalysts with the kinetics of the electrophilic attack and reveal the significance of CH-π and stacking interactions in the transition states. Thus, for the first time a comprehensive understanding of the remote stereocontrol in γ-functionalization reactions of dienamines and an explanation to the "Z/E-dilemma" are presented. The combination of bulky catalyst subsystems and large electrophiles provides a shielding of one face and causes different reactivities of E/Z-dienamines in nucleophilic attacks from the other face. Kinetic preferences for the formation of Z-dienamines and their unfavorable thermodynamics support high ee values. PMID:27430865

  8. Remote-Stereocontrol in Dienamine Catalysis: Z-Dienamine Preferences and Electrophile-Catalyst Interaction Revealed by NMR and Computational Studies.

    PubMed

    Seegerer, Andreas; Hioe, Johnny; Hammer, Michael M; Morana, Fabio; Fuchs, Patrick J W; Gschwind, Ruth M

    2016-08-10

    Catalysis with remote-stereocontrol provides special challenges in design and comprehension. One famous example is the dienamine catalysis, for which high ee values are reported despite insufficient shielding of the second double bond. Especially for dienamines with variable Z/E-ratios of the second double bond, no correlations to the ee values are found. Therefore, the structures, thermodynamics, and kinetics of dienamine intermediates in SN-type reactions are investigated. The NMR studies show that the preferred dienamine conformation provides an effective shielding if large electrophiles are used. Calculations at SCS-MP2/CBS-level of theory and experimental data of the dienamine formation show kinetic preference for the Z-isomer of the second double bond and a slow isomerization toward the thermodynamically preferred E-isomer. Modulations of the rate-determining step, by variation of the concentration of the electrophile, allow the conversion of dienamines to be observed. With electrophiles, a faster reaction of Z- than of E-isomers is observed experimentally. Calculations corroborate these results by correlating ee values of three catalysts with the kinetics of the electrophilic attack and reveal the significance of CH-π and stacking interactions in the transition states. Thus, for the first time a comprehensive understanding of the remote stereocontrol in γ-functionalization reactions of dienamines and an explanation to the "Z/E-dilemma" are presented. The combination of bulky catalyst subsystems and large electrophiles provides a shielding of one face and causes different reactivities of E/Z-dienamines in nucleophilic attacks from the other face. Kinetic preferences for the formation of Z-dienamines and their unfavorable thermodynamics support high ee values.

  9. A Social Studies Computer Lab.

    ERIC Educational Resources Information Center

    Stevens, Lawrence

    1993-01-01

    Describes a variety of computer software programs and student activities utilizing the computer to help teach secondary social studies. Suggests using word processors, painting programs, and computer simulations for history and government courses. Concludes that successful use of computers in social studies instruction depends on the design of…

  10. Computational mechanics needs study

    NASA Technical Reports Server (NTRS)

    Griffin, O. Hayden, Jr.

    1993-01-01

    In order to assess the needs in computational mechanics over the next decade, we formulated a questionnaire and contacted computational mechanics researchers and users in industry, government, and academia. As expected, we found a wide variety of computational mechanics usage and research. This report outlines the activity discussed with those contacts, as well as that in our own organizations. It should be noted that most of the contacts were made before the recent decline of the defense industry. Therefore, areas which are strongly defense-oriented may decrease in relative importance. In order to facilitate updating of this study, names of a few key researchers in each area are included as starting points for future literature surveys. These lists of names are not intended to represent those persons doing the best research in that area, nor are they intended to be comprehensive. They are, as previously stated, offered as starting points for future literature searches. Overall, there is currently a broad activity in computational mechanics in this country, with the breadth and depth increasing as more sophisticated software and faster computers become more available. The needs and desires of the workers in this field are as diverse as their background and organizational products. There seems to be some degree of software development in any organization (although the level of activity is highly variable from one organization to another) which has any research component in its mission. It seems, however, that there is considerable use of commercial software in almost all organizations. In most industrial research organizations, it appears that very little actual software development is contracted out, but that most is done in-house, using a mixture of funding sources. Government agencies vary widely in the ratio of in-house to out-house ratio. There is a considerable amount of experimental verification in most, but not all, organizations. Generally, the amount of

  11. Pupillary dynamics reveal computational cost in sentence planning.

    PubMed

    Sevilla, Yamila; Maldonado, Mora; Shalóm, Diego E

    2014-01-01

    This study investigated the computational cost associated with grammatical planning in sentence production. We measured people's pupillary responses as they produced spoken descriptions of depicted events. We manipulated the syntactic structure of the target by training subjects to use different types of sentences following a colour cue. The results showed higher increase in pupil size for the production of passive and object dislocated sentences than for active canonical subject-verb-object sentences, indicating that more cognitive effort is associated with more complex noncanonical thematic order. We also manipulated the time at which the cue that triggered structure-building processes was presented. Differential increase in pupil diameter for more complex sentences was shown to rise earlier as the colour cue was presented earlier, suggesting that the observed pupillary changes are due to differential demands in relatively independent structure-building processes during grammatical planning. Task-evoked pupillary responses provide a reliable measure to study the cognitive processes involved in sentence production.

  12. Fractional charge revealed in computer simulations of resonant tunneling in the fractional quantum Hall regime.

    PubMed

    Tsiper, E V

    2006-08-18

    The concept of fractional charge is central to the theory of the fractional quantum Hall effect. Here I use exact diagonalization as well as configuration space renormalization to study finite clusters which are large enough to contain two independent edges. I analyze the conditions of resonant tunneling between the two edges. The "computer experiment" reveals a periodic sequence of resonant tunneling events consistent with the experimentally observed fractional quantization of electric charge in units of e/3 and e/5.

  13. Computed tomography: Will the slices reveal the truth

    PubMed Central

    Haridas, Harish; Mohan, Abarajithan; Papisetti, Sravanthi; Ealla, Kranti K. R.

    2016-01-01

    With the advances in the field of imaging sciences, new methods have been developed in dental radiology. These include digital radiography, density analyzing methods, cone beam computed tomography (CBCT), magnetic resonance imaging, ultrasound, and nuclear imaging techniques, which provide high-resolution detailed images of oral structures. The current review aims to critically elaborate the use of CBCT in endodontics.

  14. Computed tomography: Will the slices reveal the truth.

    PubMed

    Haridas, Harish; Mohan, Abarajithan; Papisetti, Sravanthi; Ealla, Kranti K R

    2016-08-01

    With the advances in the field of imaging sciences, new methods have been developed in dental radiology. These include digital radiography, density analyzing methods, cone beam computed tomography (CBCT), magnetic resonance imaging, ultrasound, and nuclear imaging techniques, which provide high-resolution detailed images of oral structures. The current review aims to critically elaborate the use of CBCT in endodontics. PMID:27652253

  15. Computed tomography: Will the slices reveal the truth

    PubMed Central

    Haridas, Harish; Mohan, Abarajithan; Papisetti, Sravanthi; Ealla, Kranti K. R.

    2016-01-01

    With the advances in the field of imaging sciences, new methods have been developed in dental radiology. These include digital radiography, density analyzing methods, cone beam computed tomography (CBCT), magnetic resonance imaging, ultrasound, and nuclear imaging techniques, which provide high-resolution detailed images of oral structures. The current review aims to critically elaborate the use of CBCT in endodontics. PMID:27652253

  16. Insights into enzymatic halogenation from computational studies

    PubMed Central

    Senn, Hans M.

    2014-01-01

    The halogenases are a group of enzymes that have only come to the fore over the last 10 years thanks to the discovery and characterization of several novel representatives. They have revealed the fascinating variety of distinct chemical mechanisms that nature utilizes to activate halogens and introduce them into organic substrates. Computational studies using a range of approaches have already elucidated many details of the mechanisms of these enzymes, often in synergistic combination with experiment. This Review summarizes the main insights gained from these studies. It also seeks to identify open questions that are amenable to computational investigations. The studies discussed herein serve to illustrate some of the limitations of the current computational approaches and the challenges encountered in computational mechanistic enzymology. PMID:25426489

  17. Insights into enzymatic halogenation from computational studies

    NASA Astrophysics Data System (ADS)

    Senn, Hans

    2014-11-01

    The halogenases are a group of enzymes that have only come to the fore over the last ten years thanks to the discovery and characterization of several of novel representatives. They have re-vealed the fascinating variety of distinct chemical mechanisms that nature utilizes to activate and introduce halogens into organic substrates. Computational studies using a range of approaches have already elucidated many details of the mechanisms of these enzymes, often in synergistic combination with experiment. This Review summarizes the main insights gained from these stud-ies. It also seeks to identify open questions that are amenable to computational investigations. The studies discussed herein also serve to illustrate some of the limitations of the current computa-tional approaches and the challenges encountered in computational mechanistic enzymology.

  18. Diffraction computed tomography reveals the inner structure of complex biominerals

    NASA Astrophysics Data System (ADS)

    Leemreize, Hanna; Birkbak, Mie; Frølich, Simon; Kenesei, Peter; Almer, Jonathan D.; Stock, Stuart R.; Birkedal, Henrik

    2014-09-01

    Biological materials are complex and their investigation demands advanced characterization tools capable of elucidating their structure in three dimensions without the need for complicated sample preparation. Herein, we discuss our implementation of diffraction/scattering computed tomography (DSCT). DSCT is based on the use of diffraction information for tomographic reconstructions rather than linear attenuation as in regular μ-CT. This provides much additional information on the material under investigation. We illustrate the use of DSCT by discussion of data on a biomineralized attachment organ from a marine mussel. DSCT allowed mapping the spatial distribution of calcium carbonate polymorphs aragonite and calcite even though they were indistinguishable in absorption tomography. Detailed analysis of reconstructed diffraction patterns may provide additional insights as exemplified in the present case by mapping of the degree of chemical substitution in calcite.

  19. Reveal protein dynamics by combining computer simulation and neutron scattering

    NASA Astrophysics Data System (ADS)

    Hong, Liang; Smith, Jeremy; CenterMolecular Biophysics Team

    2014-03-01

    Protein carries out most functions in living things on the earth through characteristic modulation of its three-dimensional structure over time. Understanding the microscopic nature of the protein internal motion and its connection to the function and structure of the biomolecule is a central topic in biophysics, and of great practical importance for drug design, study of diseases, and the development of renewable energy, etc. Under physiological conditions, protein exhibits a complex dynamics landscape, i.e., a variety of diffusive and conformational motions occur on similar time and length scales. This variety renders difficult the derivation of a simplified description of protein internal motions in terms of a small number of distinct, additive components. This difficulty is overcome by our work using a combined approach of Molecular Dynamics (MD) simulations and the Neutron Scattering experiments. Our approach enables distinct protein motions to be characterized separately, furnishing an in-depth understanding of the connection between protein structure, dynamics and function.

  20. Advanced flight computer. Special study

    NASA Technical Reports Server (NTRS)

    Coo, Dennis

    1995-01-01

    This report documents a special study to define a 32-bit radiation hardened, SEU tolerant flight computer architecture, and to investigate current or near-term technologies and development efforts that contribute to the Advanced Flight Computer (AFC) design and development. An AFC processing node architecture is defined. Each node may consist of a multi-chip processor as needed. The modular, building block approach uses VLSI technology and packaging methods that demonstrate a feasible AFC module in 1998 that meets that AFC goals. The defined architecture and approach demonstrate a clear low-risk, low-cost path to the 1998 production goal, with intermediate prototypes in 1996.

  1. Computational Studies of Glutamate Transporters

    PubMed Central

    Setiadi, Jeffry; Heinzelmann, Germano; Kuyucak, Serdar

    2015-01-01

    Glutamate is the major excitatory neurotransmitter in the human brain whose binding to receptors on neurons excites them while excess glutamate are removed from synapses via transporter proteins. Determination of the crystal structures of bacterial aspartate transporters has paved the way for computational investigation of their function and dynamics at the molecular level. Here, we review molecular dynamics and free energy calculation methods used in these computational studies and discuss the recent applications to glutamate transporters. The focus of the review is on the insights gained on the transport mechanism through computational methods, which otherwise is not directly accessible by experimental probes. Recent efforts to model the mammalian glutamate and other amino acid transporters, whose crystal structures have not been solved yet, are included in the review. PMID:26569328

  2. Computational Studies of Flame Structures

    NASA Astrophysics Data System (ADS)

    Amin, Vaishali

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

  3. A computer program for sample size computations for banding studies

    USGS Publications Warehouse

    Wilson, K.R.; Nichols, J.D.; Hines, J.E.

    1989-01-01

    Sample sizes necessary for estimating survival rates of banded birds, adults and young, are derived based on specified levels of precision. The banding study can be new or ongoing. The desired coefficient of variation (CV) for annual survival estimates, the CV for mean annual survival estimates, and the length of the study must be specified to compute sample sizes. A computer program is available for computation of the sample sizes, and a description of the input and output is provided.

  4. Computational studies of energetic nitramines

    NASA Astrophysics Data System (ADS)

    Politzer, Peter

    1991-09-01

    This final report summarizes our computational investigations of energetic materials carried out over a six-year period. It is divided into seven main sections, describing the major themes of this project. First, factors important in designing molecules with high specific impulse values and in determining the sensitivities of energetic systems are discussed, followed by a review of our analysis of reaction energetics (carried out primarily using a local density functional approach). Next, studies aimed at providing insight into possible synthetic routes are summarized, followed by a section on fundamental molecular properties of nitramines. Surface electrostatic potentials of the four known CL-20 polymorphs show significant differences in their tendencies for intermolecular interactions. We have calculated structures and reactive properties for a variety of new energetic materials, including heterocyclic, ionic, mesoionic and zwitterionic systems. We have shown that correlations exist between key calculated properties (the electrostatic potential V(r) and the average local ionization energy I(r)) and a number of experimentally-based indices of reactivity.

  5. Computational dissection of human episodic memory reveals mental process-specific genetic profiles

    PubMed Central

    Luksys, Gediminas; Fastenrath, Matthias; Coynel, David; Freytag, Virginie; Gschwind, Leo; Heck, Angela; Jessen, Frank; Maier, Wolfgang; Milnik, Annette; Riedel-Heller, Steffi G.; Scherer, Martin; Spalek, Klara; Vogler, Christian; Wagner, Michael; Wolfsgruber, Steffen; Papassotiropoulos, Andreas; de Quervain, Dominique J.-F.

    2015-01-01

    Episodic memory performance is the result of distinct mental processes, such as learning, memory maintenance, and emotional modulation of memory strength. Such processes can be effectively dissociated using computational models. Here we performed gene set enrichment analyses of model parameters estimated from the episodic memory performance of 1,765 healthy young adults. We report robust and replicated associations of the amine compound SLC (solute-carrier) transporters gene set with the learning rate, of the collagen formation and transmembrane receptor protein tyrosine kinase activity gene sets with the modulation of memory strength by negative emotional arousal, and of the L1 cell adhesion molecule (L1CAM) interactions gene set with the repetition-based memory improvement. Furthermore, in a large functional MRI sample of 795 subjects we found that the association between L1CAM interactions and memory maintenance revealed large clusters of differences in brain activity in frontal cortical areas. Our findings provide converging evidence that distinct genetic profiles underlie specific mental processes of human episodic memory. They also provide empirical support to previous theoretical and neurobiological studies linking specific neuromodulators to the learning rate and linking neural cell adhesion molecules to memory maintenance. Furthermore, our study suggests additional memory-related genetic pathways, which may contribute to a better understanding of the neurobiology of human memory. PMID:26261317

  6. Computational dissection of human episodic memory reveals mental process-specific genetic profiles.

    PubMed

    Luksys, Gediminas; Fastenrath, Matthias; Coynel, David; Freytag, Virginie; Gschwind, Leo; Heck, Angela; Jessen, Frank; Maier, Wolfgang; Milnik, Annette; Riedel-Heller, Steffi G; Scherer, Martin; Spalek, Klara; Vogler, Christian; Wagner, Michael; Wolfsgruber, Steffen; Papassotiropoulos, Andreas; de Quervain, Dominique J-F

    2015-09-01

    Episodic memory performance is the result of distinct mental processes, such as learning, memory maintenance, and emotional modulation of memory strength. Such processes can be effectively dissociated using computational models. Here we performed gene set enrichment analyses of model parameters estimated from the episodic memory performance of 1,765 healthy young adults. We report robust and replicated associations of the amine compound SLC (solute-carrier) transporters gene set with the learning rate, of the collagen formation and transmembrane receptor protein tyrosine kinase activity gene sets with the modulation of memory strength by negative emotional arousal, and of the L1 cell adhesion molecule (L1CAM) interactions gene set with the repetition-based memory improvement. Furthermore, in a large functional MRI sample of 795 subjects we found that the association between L1CAM interactions and memory maintenance revealed large clusters of differences in brain activity in frontal cortical areas. Our findings provide converging evidence that distinct genetic profiles underlie specific mental processes of human episodic memory. They also provide empirical support to previous theoretical and neurobiological studies linking specific neuromodulators to the learning rate and linking neural cell adhesion molecules to memory maintenance. Furthermore, our study suggests additional memory-related genetic pathways, which may contribute to a better understanding of the neurobiology of human memory. PMID:26261317

  7. Computer technology forecast study for general aviation

    NASA Technical Reports Server (NTRS)

    Seacord, C. L.; Vaughn, D.

    1976-01-01

    A multi-year, multi-faceted program is underway to investigate and develop potential improvements in airframes, engines, and avionics for general aviation aircraft. The objective of this study was to assemble information that will allow the government to assess the trends in computer and computer/operator interface technology that may have application to general aviation in the 1980's and beyond. The current state of the art of computer hardware is assessed, technical developments in computer hardware are predicted, and nonaviation large volume users of computer hardware are identified.

  8. Computational studies of doped nanostructures

    NASA Astrophysics Data System (ADS)

    Chelikowsky, James R.; Alemany, M. M. G.; Chan, T.-L.; Dalpian, G. M.

    2011-04-01

    One of the most challenging issues in materials physics is to predict the properties of defects in matter. Such defects play an important role in functionalizing materials for use in electronic and optical devices. As the length scale for such devices approaches the nano-regime, the interplay of dimensionality, quantum confinement and defects can be complex. In particular, the usual rules for describing defects in bulk may be inoperative, i.e. a shallow defect level in bulk may become a deep level at the nanoscale. The development of computational methods to describe the properties of nanoscale defects is a formidable challenge. Nanoscale systems may contain numerous electronic and nuclear degrees of freedom, and often possess little symmetry. In this review, we focus on new computational methods, which allow one to predict the role of quantum confinement on the electronic, magnetic and structural properties of functionalized nanostructures. We illustrate how these methods can be applied to nanoscale systems, and present calculations for the electronic, magnetic and structural properties of dopants in semiconductor nanocrystals and nanowires.

  9. Computer-Assisted Study Skills Improvement Program.

    ERIC Educational Resources Information Center

    Brown, William F.; Forristall, Dorothy Z.

    The Computer-Assisted Study Skills Improvement Program (CASSIP) is designed to help students develop effective study skills and academic attitudes, thus increasing their potential for scholastic success. The program contains four integrated items: Study Skills Surveys; Study Skills Modules, Study Skills Notebook; and Study Skills Test. The surveys…

  10. Evaluating Computer-Tutors: A Protocol Study.

    ERIC Educational Resources Information Center

    Strickland, James

    A protocol study investigated whether computer tutors (programs that interactively guide writers while they freewrite with a word processing program) promote or hinder a richer understanding of the composing process. The analysis focused on writers' attitudes toward computer tutors in the invention process. Data were collected by tape recording a…

  11. Study on global cloud computing research trend

    NASA Astrophysics Data System (ADS)

    Ma, Feicheng; Zhan, Nan

    2014-01-01

    Since "cloud computing" was put forward by Google , it quickly became the most popular concept in IT industry and widely permeated into various areas promoted by IBM, Microsoft and other IT industry giants. In this paper the methods of bibliometric analysis were used to investigate the global cloud computing research trend based on Web of Science (WoS) database and the Engineering Index (EI) Compendex database. In this study, the publication, countries, institutes, keywords of the papers was deeply studied in methods of quantitative analysis, figures and tables are used to describe the production and the development trends of cloud computing.

  12. Computational study of lattice models

    NASA Astrophysics Data System (ADS)

    Zujev, Aleksander

    This dissertation is composed of the descriptions of a few projects undertook to complete my doctorate at the University of California, Davis. Different as they are, the common feature of them is that they all deal with simulations of lattice models, and physics which results from interparticle interactions. As an example, both the Feynman-Kikuchi model (Chapter 3) and Bose-Fermi mixture (Chapter 4) deal with the conditions under which superfluid transitions occur. The dissertation is divided into two parts. Part I (Chapters 1-2) is theoretical. It describes the systems we study - superfluidity and particularly superfluid helium, and optical lattices. The numerical methods of working with them are described. The use of Monte Carlo methods is another unifying theme of the different projects in this thesis. Part II (Chapters 3-6) deals with applications. It consists of 4 chapters describing different projects. Two of them, Feynman-Kikuchi model, and Bose-Fermi mixture are finished and published. The work done on t - J model, described in Chapter 5, is more preliminary, and the project is far from complete. A preliminary report on it was given on 2009 APS March meeting. The Isentropic project, described in the last chapter, is finished. A report on it was given on 2010 APS March meeting, and a paper is in preparation. The quantum simulation program used for Bose-Fermi mixture project was written by our collaborators Valery Rousseau and Peter Denteneer. I had written my own code for the other projects.

  13. Use of Computers in Home Study.

    ERIC Educational Resources Information Center

    Ancarrow, Janice S.

    Based on data gathered and analyzed for the Home Information Technology Study (HITS), which was jointly sponsored by the Center for Education Statistics in the U.S. Department of Education and the Corporation for Public Broadcasting to study informal, nonschool learning in households, this report focuses on the use of computers in home study. The…

  14. Aerodynamic optimization studies on advanced architecture computers

    NASA Technical Reports Server (NTRS)

    Chawla, Kalpana

    1995-01-01

    The approach to carrying out multi-discipline aerospace design studies in the future, especially in massively parallel computing environments, comprises of choosing (1) suitable solvers to compute solutions to equations characterizing a discipline, and (2) efficient optimization methods. In addition, for aerodynamic optimization problems, (3) smart methodologies must be selected to modify the surface shape. In this research effort, a 'direct' optimization method is implemented on the Cray C-90 to improve aerodynamic design. It is coupled with an existing implicit Navier-Stokes solver, OVERFLOW, to compute flow solutions. The optimization method is chosen such that it can accomodate multi-discipline optimization in future computations. In the work , however, only single discipline aerodynamic optimization will be included.

  15. Computational bacterial genome-wide analysis of phylogenetic profiles reveals potential virulence genes of Streptococcus agalactiae.

    PubMed

    Lin, Frank Po-Yen; Lan, Ruiting; Sintchenko, Vitali; Gilbert, Gwendolyn L; Kong, Fanrong; Coiera, Enrico

    2011-04-04

    The phylogenetic profile of a gene is a reflection of its evolutionary history and can be defined as the differential presence or absence of a gene in a set of reference genomes. It has been employed to facilitate the prediction of gene functions. However, the hypothesis that the application of this concept can also facilitate the discovery of bacterial virulence factors has not been fully examined. In this paper, we test this hypothesis and report a computational pipeline designed to identify previously unknown bacterial virulence genes using group B streptococcus (GBS) as an example. Phylogenetic profiles of all GBS genes across 467 bacterial reference genomes were determined by candidate-against-all BLAST searches,which were then used to identify candidate virulence genes by machine learning models. Evaluation experiments with known GBS virulence genes suggested good functional and model consistency in cross-validation analyses (areas under ROC curve, 0.80 and 0.98 respectively). Inspection of the top-10 genes in each of the 15 virulence functional groups revealed at least 15 (of 119) homologous genes implicated in virulence in other human pathogens but previously unrecognized as potential virulence genes in GBS. Among these highly-ranked genes, many encode hypothetical proteins with possible roles in GBS virulence. Thus, our approach has led to the identification of a set of genes potentially affecting the virulence potential of GBS, which are potential candidates for further in vitro and in vivo investigations. This computational pipeline can also be extended to in silico analysis of virulence determinants of other bacterial pathogens.

  16. Computer Networks and African Studies Centers.

    ERIC Educational Resources Information Center

    Kuntz, Patricia S.

    The use of electronic communication in the 12 Title VI African Studies Centers is discussed, and the networks available for their use are reviewed. It is argued that the African Studies Centers should be on the cutting edge of contemporary electronic communication and that computer networks should be a fundamental aspect of their programs. An…

  17. Cross-domain adaptation reveals that a common mechanism computes stereoscopic (cyclopean) and luminance plaid motion.

    PubMed

    Bowd, C; Donnelly, M; Shorter, S; Patterson, R

    2000-01-01

    Across three experiments, this study investigated the visual processing of moving stereoscopic plaid patterns (plaids created with cyclopean components defined by moving binocular disparity embedded in a dynamic random-dot stereogram). Results showed that adaptation to a moving stereoscopic plaid or its components affected the perceived coherence of a luminance test plaid, and vice versa. Cross-domain adaptation suggests that stereoscopic and luminance motion signals feed into a common pattern-motion mechanism, consistent with the idea that stereoscopic motion signals are computed early in the motion processing stream.

  18. Computer vision profiling of neurite outgrowth dynamics reveals spatiotemporal modularity of Rho GTPase signaling

    PubMed Central

    Fusco, Ludovico; Lefort, Riwal; Smith, Kevin; Benmansour, Fethallah; Gonzalez, German; Barillari, Caterina; Rinn, Bernd; Fleuret, Francois; Fua, Pascal

    2016-01-01

    Rho guanosine triphosphatases (GTPases) control the cytoskeletal dynamics that power neurite outgrowth. This process consists of dynamic neurite initiation, elongation, retraction, and branching cycles that are likely to be regulated by specific spatiotemporal signaling networks, which cannot be resolved with static, steady-state assays. We present NeuriteTracker, a computer-vision approach to automatically segment and track neuronal morphodynamics in time-lapse datasets. Feature extraction then quantifies dynamic neurite outgrowth phenotypes. We identify a set of stereotypic neurite outgrowth morphodynamic behaviors in a cultured neuronal cell system. Systematic RNA interference perturbation of a Rho GTPase interactome consisting of 219 proteins reveals a limited set of morphodynamic phenotypes. As proof of concept, we show that loss of function of two distinct RhoA-specific GTPase-activating proteins (GAPs) leads to opposite neurite outgrowth phenotypes. Imaging of RhoA activation dynamics indicates that both GAPs regulate different spatiotemporal Rho GTPase pools, with distinct functions. Our results provide a starting point to dissect spatiotemporal Rho GTPase signaling networks that regulate neurite outgrowth. PMID:26728857

  19. A Computing Infrastructure for Supporting Climate Studies

    NASA Astrophysics Data System (ADS)

    Yang, C.; Bambacus, M.; Freeman, S. M.; Huang, Q.; Li, J.; Sun, M.; Xu, C.; Wojcik, G. S.; Cahalan, R. F.; NASA Climate @ Home Project Team

    2011-12-01

    Climate change is one of the major challenges facing us on the Earth planet in the 21st century. Scientists build many models to simulate the past and predict the climate change for the next decades or century. Most of the models are at a low resolution with some targeting high resolution in linkage to practical climate change preparedness. To calibrate and validate the models, millions of model runs are needed to find the best simulation and configuration. This paper introduces the NASA effort on Climate@Home project to build a supercomputer based-on advanced computing technologies, such as cloud computing, grid computing, and others. Climate@Home computing infrastructure includes several aspects: 1) a cloud computing platform is utilized to manage the potential spike access to the centralized components, such as grid computing server for dispatching and collecting models runs results; 2) a grid computing engine is developed based on MapReduce to dispatch models, model configuration, and collect simulation results and contributing statistics; 3) a portal serves as the entry point for the project to provide the management, sharing, and data exploration for end users; 4) scientists can access customized tools to configure model runs and visualize model results; 5) the public can access twitter and facebook to get the latest about the project. This paper will introduce the latest progress of the project and demonstrate the operational system during the AGU fall meeting. It will also discuss how this technology can become a trailblazer for other climate studies and relevant sciences. It will share how the challenges in computation and software integration were solved.

  20. Hospital study reveals strategies for improving media relations.

    PubMed

    Fitzgerald, P E; Embrey-Wahl, L

    1987-01-01

    A nationwide study revealed that hospital administrators feel inadequate when dealing with the media, and also think the media does not understand the hospital business. Many strategies are available to counter these problems, including some that emphasize issues related to bed size. PMID:3583722

  1. A Systematic Computational Study on Flavonoids

    PubMed Central

    Aparicio, Santiago

    2010-01-01

    17 selected flavones derivatives, flavonoids, were analyzed through a systematic B3LYP/6-311++G** computational study with the aim of understanding the molecular factors that determine their structural and energetic properties in gas phase. Flavonoids were selected in a systematic way to infer the effect of the number and relative positions of hydroxyl groups on molecular properties. Different conformers for each flavonoid were analyzed and the strength and topology of the intramolecular hydrogen bonds studied through the computation of the corresponding torsional profiles. Atoms in a Molecule, and Natural Bond Orbital methodology was applied to the analysis of charge distribution along the studied molecules, and the intramolecular hydrogen bonds. Molecular shapes were studied through full geometry optimization, and the position of the catechol ring analyzed through dihedral scans. PMID:20559499

  2. "Compressed graphite" formed during C60 to diamond transformation as revealed by scattering computed tomography.

    PubMed

    Álvarez-Murga, M; Bleuet, P; Garbarino, G; Salamat, A; Mezouar, M; Hodeau, J L

    2012-07-13

    The collapsing of C60 into polycrystalline diamond has been studied after nonhydrostatic pressurization at ambient temperature using x-ray scattering computed tomography. Using this selective structural probe we provide evidence of concentric coexistence of "compressed graphite" (d(00l)∼3.09-3.11  Å), sp2-graphitelike phase (d(00l)∼3.35-3.42  Å), and sp3-like amorphous carbon surrounding polycrystalline diamond (a∼3.56-3.59  Å). The so-called "compressed graphite" exhibits a collapsed c axis and is textured with disordered layers. This latter phase is better described as a short interlayered carbon phase with buckled sp2-sp3 layers with possible interlayer bonding. Additionally, our 3D maps of phase distribution and of the residual stress retained in the polycrystalline diamond phase support the importance of stressed synthesis conditions for diamond formation.

  3. Computational Image Analysis Reveals Intrinsic Multigenerational Differences between Anterior and Posterior Cerebral Cortex Neural Progenitor Cells

    PubMed Central

    Winter, Mark R.; Liu, Mo; Monteleone, David; Melunis, Justin; Hershberg, Uri; Goderie, Susan K.; Temple, Sally; Cohen, Andrew R.

    2015-01-01

    Summary Time-lapse microscopy can capture patterns of development through multiple divisions for an entire clone of proliferating cells. Images are taken every few minutes over many days, generating data too vast to process completely by hand. Computational analysis of this data can benefit from occasional human guidance. Here we combine improved automated algorithms with minimized human validation to produce fully corrected segmentation, tracking, and lineaging results with dramatic reduction in effort. A web-based viewer provides access to data and results. The improved approach allows efficient analysis of large numbers of clones. Using this method, we studied populations of progenitor cells derived from the anterior and posterior embryonic mouse cerebral cortex, each growing in a standardized culture environment. Progenitors from the anterior cortex were smaller, less motile, and produced smaller clones compared to those from the posterior cortex, demonstrating cell-intrinsic differences that may contribute to the areal organization of the cerebral cortex. PMID:26344906

  4. Computational Analysis Reveals a Key Regulator of Cryptococcal Virulence and Determinant of Host Response

    PubMed Central

    Gish, Stacey R.; Maier, Ezekiel J.; Haynes, Brian C.; Santiago-Tirado, Felipe H.; Srikanta, Deepa L.; Ma, Cynthia Z.; Li, Lucy X.; Williams, Matthew; Crouch, Erika C.; Khader, Shabaana A.

    2016-01-01

    ABSTRACT Cryptococcus neoformans is a ubiquitous, opportunistic fungal pathogen that kills over 600,000 people annually. Here, we report integrated computational and experimental investigations of the role and mechanisms of transcriptional regulation in cryptococcal infection. Major cryptococcal virulence traits include melanin production and the development of a large polysaccharide capsule upon host entry; shed capsule polysaccharides also impair host defenses. We found that both transcription and translation are required for capsule growth and that Usv101 is a master regulator of pathogenesis, regulating melanin production, capsule growth, and capsule shedding. It does this by directly regulating genes encoding glycoactive enzymes and genes encoding three other transcription factors that are essential for capsule growth: GAT201, RIM101, and SP1. Murine infection with cryptococci lacking Usv101 significantly alters the kinetics and pathogenesis of disease, with extended survival and, unexpectedly, death by pneumonia rather than meningitis. Our approaches and findings will inform studies of other pathogenic microbes. PMID:27094327

  5. Revealing the Elephant: The Use and Misuse of Computers in Education.

    ERIC Educational Resources Information Center

    Kay, Alan

    1996-01-01

    Discusses the need for children to become fluent in logical argument and systems dynamics. Examines the "create an embedded environment and support classroom teachers with visiting experts" strategy in music and technology education. Describes the distinction between meaningless activities with computers and computer literacy. (AEF)

  6. Experimental and computational studies of nanofluids

    NASA Astrophysics Data System (ADS)

    Vajjha, Ravikanth S.

    The goals of this dissertation were (i) to experimentally investigate the fluid dynamic and heat transfer performance of nanofluids in a circular tube, (ii) to study the influence of temperature and particle volumetric concentration of nanofluids on thermophysical properties, heat transfer and pumping power, (iii) to measure the rheological properties of various nanofluids and (iv) to investigate using a computational fluid dynamic (CFD) technique the performance of nanofluids in the flat tube of a radiator. Nanofluids are a new class of fluids prepared by dispersing nanoparticles with average sizes of less than 100 nm in traditional heat transfer fluids such as water, oil, ethylene glycol and propylene glycol. In cold regions of the world, the choice of base fluid for heat transfer applications is an ethylene glycol or propylene glycol mixed with water in different proportions. In the present research, a 60% ethylene glycol (EG) or propylene glycol (PG) and 40% water (W) by mass fluid mixture (60:40 EG/W or 60:40 PG/W) was used as a base fluid, which provides freeze protection to a very low level of temperature. Experiments were conducted to measure the convective heat transfer coefficient and pressure loss of nanofluids flowing in a circular tube in the fully developed turbulent regime. The experimental measurements were carried out for aluminum oxide (Al2O3), copper oxide (CuO) and silicon dioxide (SiO2) nanoparticles dispersed in 60:40 EG/W base fluid. Experiments revealed that the heat transfer coefficient of nanofluids showed an increase with the particle volumetric concentration. Pressure loss was also observed to increase with the nanoparticle volumetric concentration. New correlations for the Nusselt number and the friction factor were developed. The effects of temperature and particle volumetric concentration on different thermophysical properties (e.g. viscosity, thermal conductivity, specific heat and density) and subsequently on the Prandtl number

  7. Computational modeling of tuberculous meningitis reveals an important role for tumor necrosis factor-α

    PubMed Central

    El-Kebir, M.; van der Kuip, M.; van Furth, A.M.; Kirschner, D.E.

    2013-01-01

    Tuberculosis is a global health issue with annually about 1.5 million deaths and 2 billion infected people worldwide. Extra pulmonary tuberculosis comprises 13% of all cases of which tuberculous meningitis is the most severe. It has a high mortality and is often diagnosed once irreversible neurological damage has already occurred. Development of diagnostic and treatment strategies requires a thorough understanding of the pathogenesis of tuberculous meningitis. This disease is characterized by the formation of a cerebral granuloma, which is a collection of immune cells that attempt to immunologically restrain, and physically contain bacteria. The cytokine tumor necrosis factor-α is known for its important role in granuloma formation. Because traditional experimental animal studies exploring tuberculous meningitis are difficult and expensive, another approach is needed to begin to address this important and significant disease outcome. Here, we present an in silico model capturing the unique immunological environment of the brain that allows us to study the key mechanisms driving granuloma formation in time. Uncertainty and sensitivity analysis reveal a dose-dependent effect of tumor necrosis factor-α on bacterial load and immune cell numbers thereby influencing the onset of tuberculous meningitis. Insufficient levels result in bacterial overgrowth, whereas high levels lead to uncontrolled inflammation being detrimental to the host. These findings have important implications for the development of immuno-modulating treatment strategies for tuberculous meningitis. PMID:23542051

  8. Elucidating graphene - Ionic Liquid interfacial region: a combined experimental and computational study

    SciTech Connect

    Vijayakumar, M.; Schwenzer, Birgit; Shutthanandan, V.; Hu, Jian Z.; Liu, Jun; Aksay, Ilhan A.

    2014-01-10

    The interfacial region between graphene and an imidazolium based ionic liquid is studied using spectroscopic analysis and computational modelling. This combined approach reveals that the molecular level structure of the interfacial region is significantly influenced by functional group defects on the graphene surface.The combined experimental and computational study reveals that the molecular structure at interfacial region between graphene and imidazolium based ionic liquid is defined by the hydroxyl functional groups on the graphene surface

  9. Asymmetric energy flow in liquid alkylbenzenes: A computational study

    SciTech Connect

    Leitner, David M.; Pandey, Hari Datt

    2015-10-14

    Ultrafast IR-Raman experiments on substituted benzenes [B. C. Pein et al., J. Phys. Chem. B 117, 10898–10904 (2013)] reveal that energy can flow more efficiently in one direction along a molecule than in others. We carry out a computational study of energy flow in the three alkyl benzenes, toluene, isopropylbenzene, and t-butylbenzene, studied in these experiments, and find an asymmetry in the flow of vibrational energy between the two chemical groups of the molecule due to quantum mechanical vibrational relaxation bottlenecks, which give rise to a preferred direction of energy flow. We compare energy flow computed for all modes of the three alkylbenzenes over the relaxation time into the liquid with energy flow through the subset of modes monitored in the time-resolved Raman experiments and find qualitatively similar results when using the subset compared to all the modes.

  10. Supermodeled sabercat, predatory behavior in Smilodon fatalis revealed by high-resolution 3D computer simulation.

    PubMed

    McHenry, Colin R; Wroe, Stephen; Clausen, Philip D; Moreno, Karen; Cunningham, Eleanor

    2007-10-01

    The American sabercat Smilodon fatalis is among the most charismatic of fossil carnivores. Despite broad agreement that its extraordinary anatomy reflects unique hunting techniques, after >150 years of study, many questions remain concerning its predatory behavior. Were the "sabers" used to take down large prey? Were prey killed with an eviscerating bite to the abdomen? Was its bite powerful or weak compared with that of modern big cats? Here we quantitatively assess the sabercat's biomechanical performance using the most detailed computer reconstructions yet developed for the vertebrate skull. Our results demonstrate that bite force driven by jaw muscles was relatively weak in S. fatalis, one-third that of a lion (Panthera leo) of comparable size, and its skull was poorly optimized to resist the extrinsic loadings generated by struggling prey. Its skull is better optimized for bites on restrained prey where the bite is augmented by force from the cervical musculature. We conclude that prey were brought to ground and restrained before a killing bite, driven in large part by powerful cervical musculature. Because large prey is easier to restrain if its head is secured, the killing bite was most likely directed to the neck. We suggest that the more powerful jaw muscles of P. leo may be required for extended, asphyxiating bites and that the relatively low bite forces in S. fatalis might reflect its ability to kill large prey more quickly, avoiding the need for prolonged bites.

  11. X-Ray Computed Tomography Reveals the Response of Root System Architecture to Soil Texture.

    PubMed

    Rogers, Eric D; Monaenkova, Daria; Mijar, Medhavinee; Nori, Apoorva; Goldman, Daniel I; Benfey, Philip N

    2016-07-01

    Root system architecture (RSA) impacts plant fitness and crop yield by facilitating efficient nutrient and water uptake from the soil. A better understanding of the effects of soil on RSA could improve crop productivity by matching roots to their soil environment. We used x-ray computed tomography to perform a detailed three-dimensional quantification of changes in rice (Oryza sativa) RSA in response to the physical properties of a granular substrate. We characterized the RSA of eight rice cultivars in five different growth substrates and determined that RSA is the result of interactions between genotype and growth environment. We identified cultivar-specific changes in RSA in response to changing growth substrate texture. The cultivar Azucena exhibited low RSA plasticity in all growth substrates, whereas cultivar Bala root depth was a function of soil hardness. Our imaging techniques provide a framework to study RSA in different growth environments, the results of which can be used to improve root traits with agronomic potential. PMID:27208237

  12. Computational analysis of stochastic heterogeneity in PCR amplification efficiency revealed by single molecule barcoding.

    PubMed

    Best, Katharine; Oakes, Theres; Heather, James M; Shawe-Taylor, John; Chain, Benny

    2015-10-13

    The polymerase chain reaction (PCR) is one of the most widely used techniques in molecular biology. In combination with High Throughput Sequencing (HTS), PCR is widely used to quantify transcript abundance for RNA-seq, and in the context of analysis of T and B cell receptor repertoires. In this study, we combine DNA barcoding with HTS to quantify PCR output from individual target molecules. We develop computational tools that simulate both the PCR branching process itself, and the subsequent subsampling which typically occurs during HTS sequencing. We explore the influence of different types of heterogeneity on sequencing output, and compare them to experimental results where the efficiency of amplification is measured by barcodes uniquely identifying each molecule of starting template. Our results demonstrate that the PCR process introduces substantial amplification heterogeneity, independent of primer sequence and bulk experimental conditions. This heterogeneity can be attributed both to inherited differences between different template DNA molecules, and the inherent stochasticity of the PCR process. The results demonstrate that PCR heterogeneity arises even when reaction and substrate conditions are kept as constant as possible, and therefore single molecule barcoding is essential in order to derive reproducible quantitative results from any protocol combining PCR with HTS.

  13. Computational analysis of stochastic heterogeneity in PCR amplification efficiency revealed by single molecule barcoding

    PubMed Central

    Best, Katharine; Oakes, Theres; Heather, James M.; Shawe-Taylor, John; Chain, Benny

    2015-01-01

    The polymerase chain reaction (PCR) is one of the most widely used techniques in molecular biology. In combination with High Throughput Sequencing (HTS), PCR is widely used to quantify transcript abundance for RNA-seq, and in the context of analysis of T and B cell receptor repertoires. In this study, we combine DNA barcoding with HTS to quantify PCR output from individual target molecules. We develop computational tools that simulate both the PCR branching process itself, and the subsequent subsampling which typically occurs during HTS sequencing. We explore the influence of different types of heterogeneity on sequencing output, and compare them to experimental results where the efficiency of amplification is measured by barcodes uniquely identifying each molecule of starting template. Our results demonstrate that the PCR process introduces substantial amplification heterogeneity, independent of primer sequence and bulk experimental conditions. This heterogeneity can be attributed both to inherited differences between different template DNA molecules, and the inherent stochasticity of the PCR process. The results demonstrate that PCR heterogeneity arises even when reaction and substrate conditions are kept as constant as possible, and therefore single molecule barcoding is essential in order to derive reproducible quantitative results from any protocol combining PCR with HTS. PMID:26459131

  14. A Preliminary Study of the Burgers Equation with Symbolic Computation

    NASA Astrophysics Data System (ADS)

    Derickson, Russell G.; Pielke, Roger A.

    2000-07-01

    A novel approach based on recursive symbolic computation is introduced for the approximate analytic solution of the Burgers equation. Once obtained, appropriate numerical values can be inserted into the symbolic solution to explore parametric variations. The solution is valid for both inviscid and viscous cases, covering the range of Reynolds number from 500 to infinity, whereas current direct numerical simulation (DNS) methods are limited to Reynolds numbers no greater than 4000. What further distinguishes the symbolic approach from numerical and traditional analytic techniques is the ability to reveal and examine direct nonlinear interactions between waves, including the interplay between inertia and viscosity. Thus, preliminary efforts suggest that symbolic computation may be quite effective in unveiling the “anatomy” of the myriad interactions that underlie turbulent behavior. However, due to the tendency of nonlinear symbolic operations to produce combinatorial explosion, future efforts will require the development of improved filtering processes to select and eliminate computations leading to negligible high order terms. Indeed, the initial symbolic computations present the character of turbulence as a problem in combinatorics. At present, results are limited in time evolution, but reveal the beginnings of the well-known “saw tooth” waveform that occurs in the inviscid case (i.e., Re=∞). Future efforts will explore more fully developed 1-D flows and investigate the potential to extend symbolic computations to 2-D and 3-D. Potential applications include the development of improved subgrid scale (SGS) parameterizations for large eddy simulation (LES) models, and studies that complement DNS in exploring fundamental aspects of turbulent flow behavior.

  15. Computational Modeling Reveals Optimal Strategy for Kinase Transport by Microtubules to Nerve Terminals

    PubMed Central

    Koon, Yen Ling; Koh, Cheng Gee; Chiam, Keng-Hwee

    2014-01-01

    Intracellular transport of proteins by motors along cytoskeletal filaments is crucial to the proper functioning of many eukaryotic cells. Since most proteins are synthesized at the cell body, mechanisms are required to deliver them to the growing periphery. In this article, we use computational modeling to study the strategies of protein transport in the context of JNK (c-JUN NH2-terminal kinase) transport along microtubules to the terminals of neuronal cells. One such strategy for protein transport is for the proteins of the JNK signaling cascade to bind to scaffolds, and to have the whole protein-scaffold cargo transported by kinesin motors along microtubules. We show how this strategy outperforms protein transport by diffusion alone, using metrics such as signaling rate and signal amplification. We find that there exists a range of scaffold concentrations for which JNK transport is optimal. Increase in scaffold concentration increases signaling rate and signal amplification but an excess of scaffolds results in the dilution of reactants. Similarly, there exists a range of kinesin motor speeds for which JNK transport is optimal. Signaling rate and signal amplification increases with kinesin motor speed until the speed of motor translocation becomes faster than kinase/scaffold-motor binding. Finally, we suggest experiments that can be performed to validate whether, in physiological conditions, neuronal cells do indeed adopt such an optimal strategy. Understanding cytoskeletal-assisted protein transport is crucial since axonal and cell body accumulation of organelles and proteins is a histological feature in many human neurodegenerative diseases. In this paper, we have shown that axonal transport performance changes with altered transport component concentrations and transport speeds wherein these aspects can be modulated to improve axonal efficiency and prevent or slowdown axonal deterioration. PMID:24691408

  16. Computational studies of plasma lipoprotein lipids.

    PubMed

    Pan, Lurong; Segrest, Jere P

    2016-10-01

    Plasma lipoproteins are macromolecular assemblies of proteins and lipids found in the blood. The lipid components of lipoproteins are amphipathic lipids such as phospholipids (PLs), and unesterified cholesterols (UCs) and hydrophobic lipids such as cholesteryl esters (CEs) and triglycerides (TGs). Since lipoproteins are soft matter supramolecular assemblies easily deformable by thermal fluctuations and they also exist in varying densities and protein/lipid components, a detailed understanding of their structure/function is experimentally difficult. Molecular dynamics (MD) simulation has emerged as a particularly promising way to explore the structure and dynamics of lipoproteins. The purpose of this review is to survey the current status of computational studies of the lipid components of the lipoproteins. Computational studies aim to explore three levels of complexity for the 3-dimensional structural dynamics of lipoproteins at various metabolic stages: (i) lipoprotein particles consist of protein with minimal lipid; (ii) lipoprotein particles consist of PL-rich discoidal bilayer-like lipid particles; (iii) mature circulating lipoprotein particles consist of CE-rich or TG-rich spheroidal lipid-droplet-like particles. Due to energy barriers involved in conversion between these species, other biomolecules also participate in lipoprotein biological assembly. For example: (i) lipid-poor apolipoprotein A-I (apoA-I) interacts with ATP-binding cassette transporter A1 (ABCA1) to produce nascent discoidal high density lipoprotein (dHDL) particles; (ii) lecithin-cholesterol acyltransferase (LCAT) mediates the conversion of UC to CE in dHDL, driving spheroidal HDL (sHDL) formation; (iii) transfer proteins, cholesterol ester transfer protein (CETP) and phospholipid transfer protein (PLTP), transfer both CE and TG and PL, respectively, between lipoprotein particles. Computational studies have the potential to explore different lipoprotein particles at each metabolic stage in

  17. A computational study of the topology of vortex breakdown

    NASA Technical Reports Server (NTRS)

    Spall, Robert E.; Gatski, Thomas B.

    1991-01-01

    A fully three-dimensional numerical simulation of vortex breakdown using the unsteady, incompressible Navier-Stokes equations has been performed. Solutions to four distinct types of breakdown are identified and compared with experimental results. The computed solutions include weak helical, double helix, spiral, and bubble-type breakdowns. The topological structure of the various breakdowns as well as their interrelationship are studied. The data reveal that the asymmetric modes of breakdown may be subject to additional breakdowns as the vortex core evolves in the streamwise direction. The solutions also show that the freestream axial velocity distribution has a significant effect on the position and type of vortex breakdown.

  18. Fibrous twists and turns: early ceramic technology revealed through computed tomography

    NASA Astrophysics Data System (ADS)

    Sanger, Matthew; Thostenson, James; Hill, Morgan; Cain, Hannah

    2013-06-01

    While the emergence of pottery manufacturing is a wide-spread historical occurrence, and one that has garnered the attention of archaeologists for decades, we know very little about how these ancient vessels were created. Through the application of radiographic scanning and computed tomography this paper provides insights into the manufacturing techniques used by the earliest potters in North America. While x-rays have been used to investigate ceramic manufacturing techniques for decades, this paper provides a reassessment of radiography in light of advances in both computed tomography and reconstructive software.

  19. Ethiopian population dermatoglyphic study reveals linguistic stratification of diversity.

    PubMed

    Yohannes, Seile; Bekele, Endashaw

    2015-01-01

    The manifestation of ethnic, blood type, & gender-wise population variations regarding Dermatoglyphic manifestations are of interest to assess intra-group diversity and differentiation. The present study reports on the analysis of qualitaive and quantitative finger Dermatoglyphic traits of 382 individuals cross-sectionally sampled from an administrative region of Ethiopia, consisting of five ethnic cohorts from the Afro-Asiatic & Nilo-Saharan affiliations. These Dermatoglyphic parameters were then applied in the assessment of diversity & differentiation, including Heterozygosity, Fixation, Panmixia, Wahlund's variance, Nei's measure of genetic diversity, and thumb & finger pattern genotypes, which were inturn used in homology inferences as summarized by a Neighbour-Joining tree constructed from Nei's standard genetic distance. Results revealed significant correlation between Dermatoglyphics & population parameters that were further found to be in concordance with the historical accounts of the ethnic groups. Such inductions as the ancient north-eastern presence and subsequent admixure events of the Oromos (PII= 15.01), the high diversity of the Amharas (H= 0.1978, F= 0.6453, and P= 0.4144), and the Nilo-Saharan origin of the Berta group (PII= 10.66) are evidences to this. The study has further tested the possibility of applying Dermatoglyphics in population genetic & anthropologic research, highlighting on the prospect of developing a method to trace back population origins & ancient movement patterns. Additionally, linguistic clustering was deemed significant for the Ethiopian population, coinciding with recent genome wide studies that have ascertained that linguistic clustering as to being more crucial than the geographical patterning in the Ethiopian context. Finally, Dermatoglyphic markers have been proven to be endowed with a strong potential as non-invasive preliminary tools applicable prior to genetic studies to analyze ethnically sub-divided populations and

  20. Ethiopian Population Dermatoglyphic Study Reveals Linguistic Stratification of Diversity

    PubMed Central

    2015-01-01

    The manifestation of ethnic, blood type, & gender-wise population variations regarding Dermatoglyphic manifestations are of interest to assess intra-group diversity and differentiation. The present study reports on the analysis of qualitaive and quantitative finger Dermatoglyphic traits of 382 individuals cross-sectionally sampled from an administrative region of Ethiopia, consisting of five ethnic cohorts from the Afro-Asiatic & Nilo-Saharan affiliations. These Dermatoglyphic parameters were then applied in the assessment of diversity & differentiation, including Heterozygosity, Fixation, Panmixia, Wahlund’s variance, Nei’s measure of genetic diversity, and thumb & finger pattern genotypes, which were inturn used in homology inferences as summarized by a Neighbour-Joining tree constructed from Nei’s standard genetic distance. Results revealed significant correlation between Dermatoglyphics & population parameters that were further found to be in concordance with the historical accounts of the ethnic groups. Such inductions as the ancient north-eastern presence and subsequent admixure events of the Oromos (PII= 15.01), the high diversity of the Amharas (H= 0.1978, F= 0.6453, and P= 0.4144), and the Nilo-Saharan origin of the Berta group (PII= 10.66) are evidences to this. The study has further tested the possibility of applying Dermatoglyphics in population genetic & anthropologic research, highlighting on the prospect of developing a method to trace back population origins & ancient movement patterns. Additionally, linguistic clustering was deemed significant for the Ethiopian population, coinciding with recent genome wide studies that have ascertained that linguistic clustering as to being more crucial than the geographical patterning in the Ethiopian context. Finally, Dermatoglyphic markers have been proven to be endowed with a strong potential as non-invasive preliminary tools applicable prior to genetic studies to analyze ethnically sub

  1. Ethiopian population dermatoglyphic study reveals linguistic stratification of diversity.

    PubMed

    Yohannes, Seile; Bekele, Endashaw

    2015-01-01

    The manifestation of ethnic, blood type, & gender-wise population variations regarding Dermatoglyphic manifestations are of interest to assess intra-group diversity and differentiation. The present study reports on the analysis of qualitaive and quantitative finger Dermatoglyphic traits of 382 individuals cross-sectionally sampled from an administrative region of Ethiopia, consisting of five ethnic cohorts from the Afro-Asiatic & Nilo-Saharan affiliations. These Dermatoglyphic parameters were then applied in the assessment of diversity & differentiation, including Heterozygosity, Fixation, Panmixia, Wahlund's variance, Nei's measure of genetic diversity, and thumb & finger pattern genotypes, which were inturn used in homology inferences as summarized by a Neighbour-Joining tree constructed from Nei's standard genetic distance. Results revealed significant correlation between Dermatoglyphics & population parameters that were further found to be in concordance with the historical accounts of the ethnic groups. Such inductions as the ancient north-eastern presence and subsequent admixure events of the Oromos (PII= 15.01), the high diversity of the Amharas (H= 0.1978, F= 0.6453, and P= 0.4144), and the Nilo-Saharan origin of the Berta group (PII= 10.66) are evidences to this. The study has further tested the possibility of applying Dermatoglyphics in population genetic & anthropologic research, highlighting on the prospect of developing a method to trace back population origins & ancient movement patterns. Additionally, linguistic clustering was deemed significant for the Ethiopian population, coinciding with recent genome wide studies that have ascertained that linguistic clustering as to being more crucial than the geographical patterning in the Ethiopian context. Finally, Dermatoglyphic markers have been proven to be endowed with a strong potential as non-invasive preliminary tools applicable prior to genetic studies to analyze ethnically sub-divided populations and

  2. Seismically induced soft-sediment deformation structures revealed by X-ray computed tomography of boring cores

    NASA Astrophysics Data System (ADS)

    Nakashima, Yoshito; Komatsubara, Junko

    2016-06-01

    X-ray computed tomography (CT) allows us to visualize three-dimensional structures hidden in boring cores nondestructively. We applied medical X-ray CT to cores containing seismically induced soft-sediment deformation structures (SSDSs) obtained from the Kanto region of Japan, where the 2011 off the Pacific coast of Tohoku Earthquake occurred. The CT images obtained clearly revealed various types of the seismically induced SSDSs embedded in the cores: a propagating sand dyke bent complexly by the preexisting geological structure, deformed laminations of fluidized sandy layers, and two types of downward mass movement (ductile downward folding and brittle normal faulting) as compensation for upward sand transport through sand dykes. Two advanced image analysis techniques were applied to the sand dyke CT images for the first time. The GrowCut algorithm, a specific digital image segmentation technique that uses cellular automata, was used successfully to extract the three-dimensional complex sand dyke structures embedded in the sandy sediments, which would have been difficult to achieve using a conventional image processing technique. Local autocorrelation image analysis was performed to detect the flow pattern aligned along the sand dykes objectively. The results demonstrate that X-ray CT coupled with advanced digital image analysis techniques is a promising approach to studying the seismically induced SSDSs in boring cores.

  3. Changes in bone macro- and microstructure in diabetic obese mice revealed by high resolution microfocus X-ray computed tomography

    PubMed Central

    Kerckhofs, G.; Durand, M.; Vangoitsenhoven, R.; Marin, C.; Van der Schueren, B.; Carmeliet, G.; Luyten, F. P.; Geris, L.; Vandamme, K.

    2016-01-01

    High resolution microfocus X-ray computed tomography (HR-microCT) was employed to characterize the structural alterations of the cortical and trabecular bone in a mouse model of obesity-driven type 2 diabetes (T2DM). C57Bl/6J mice were randomly assigned for 14 weeks to either a control diet-fed (CTRL) or a high fat diet (HFD)-fed group developing obesity, hyperglycaemia and insulin resistance. The HFD group showed an increased trabecular thickness and a decreased trabecular number compared to CTRL animals. Midshaft tibia intracortical porosity was assessed at two spatial image resolutions. At 2 μm scale, no change was observed in the intracortical structure. At 1 μm scale, a decrease in the cortical vascular porosity of the HFD bone was evidenced. The study of a group of 8 week old animals corresponding to animals at the start of the diet challenge revealed that the decreased vascular porosity was T2DM-dependant and not related to the ageing process. Our results offer an unprecedented ultra-characterization of the T2DM compromised skeletal micro-architecture and highlight an unrevealed T2DM-related decrease in the cortical vascular porosity, potentially affecting the bone health and fragility. Additionally, it provides some insights into the technical challenge facing the assessment of the rodent bone structure using HR-microCT imaging. PMID:27759061

  4. Computational study of hydroxyapatite structures, properties and defects

    NASA Astrophysics Data System (ADS)

    Bystrov, V. S.; Coutinho, J.; Bystrova, A. V.; Dekhtyar, Yu D.; Pullar, R. C.; Poronin, A.; Palcevskis, E.; Dindune, A.; Alkan, B.; Durucan, C.; Paramonova, E. V.

    2015-03-01

    Hydroxyapatite (HAp) was studied from a first principle approach using the local density approximation (LDA) method in AIMPRO code, in combination with various quantum mechanical (QM) and molecular mechanical (MM) methods from HypemChem 7.5/8.0. The data obtained were used for studies of HAp structures, the physical properties of HAp (density of electronic states—DOS, bulk modulus etc) and defects in HAp. Computed data confirmed that HAp can co-exist in different phases—hexagonal and monoclinic. Ordered monoclinic structures, which could reveal piezoelectric properties, are of special interest. The data obtained allow us to characterize the properties of the following defects in HAp: O, H and OH vacancies; H and OH interstitials; substitutions of Ca by Mg, Sr, Mn or Se, and P by Si. These properties reveal the appearance of additional energy levels inside the forbidden zone, shifts of the top of the valence band or the bottom of the conduction band, and subsequent changes in the width of the forbidden zone. The data computed are compared with other known data, both calculated and experimental, such as alteration of the electron work functions under different influences of various defects and treatments, obtained by photoelectron emission. The obtained data are very useful, and there is an urgent need for such analysis of modified HAp interactions with living cells and tissues, improvement of implant techniques and development of new nanomedical applications.

  5. Vertebral Pneumaticity in the Ornithomimosaur Archaeornithomimus (Dinosauria: Theropoda) Revealed by Computed Tomography Imaging and Reappraisal of Axial Pneumaticity in Ornithomimosauria

    PubMed Central

    Watanabe, Akinobu; Eugenia Leone Gold, Maria; Brusatte, Stephen L.; Benson, Roger B. J.; Choiniere, Jonah; Davidson, Amy; Norell, Mark A.

    2015-01-01

    Among extant vertebrates, pneumatization of postcranial bones is unique to birds, with few known exceptions in other groups. Through reduction in bone mass, this feature is thought to benefit flight capacity in modern birds, but its prevalence in non-avian dinosaurs of variable sizes has generated competing hypotheses on the initial adaptive significance of postcranial pneumaticity. To better understand the evolutionary history of postcranial pneumaticity, studies have surveyed its distribution among non-avian dinosaurs. Nevertheless, the degree of pneumaticity in the basal coelurosaurian group Ornithomimosauria remains poorly known, despite their potential to greatly enhance our understanding of the early evolution of pneumatic bones along the lineage leading to birds. Historically, the identification of postcranial pneumaticity in non-avian dinosaurs has been based on examination of external morphology, and few studies thus far have focused on the internal architecture of pneumatic structures inside the bones. Here, we describe the vertebral pneumaticity of the ornithomimosaur Archaeornithomimus with the aid of X-ray computed tomography (CT) imaging. Complementary examination of external and internal osteology reveals (1) highly pneumatized cervical vertebrae with an elaborate configuration of interconnected chambers within the neural arch and the centrum; (2) anterior dorsal vertebrae with pneumatic chambers inside the neural arch; (3) apneumatic sacral vertebrae; and (4) a subset of proximal caudal vertebrae with limited pneumatic invasion into the neural arch. Comparisons with other theropod dinosaurs suggest that ornithomimosaurs primitively exhibited a plesiomorphic theropod condition for axial pneumaticity that was extended among later taxa, such as Archaeornithomimus and large bodied Deinocheirus. This finding corroborates the notion that evolutionary increases in vertebral pneumaticity occurred in parallel among independent lineages of bird

  6. Vertebral Pneumaticity in the Ornithomimosaur Archaeornithomimus (Dinosauria: Theropoda) Revealed by Computed Tomography Imaging and Reappraisal of Axial Pneumaticity in Ornithomimosauria.

    PubMed

    Watanabe, Akinobu; Eugenia Leone Gold, Maria; Brusatte, Stephen L; Benson, Roger B J; Choiniere, Jonah; Davidson, Amy; Norell, Mark A

    2015-01-01

    Among extant vertebrates, pneumatization of postcranial bones is unique to birds, with few known exceptions in other groups. Through reduction in bone mass, this feature is thought to benefit flight capacity in modern birds, but its prevalence in non-avian dinosaurs of variable sizes has generated competing hypotheses on the initial adaptive significance of postcranial pneumaticity. To better understand the evolutionary history of postcranial pneumaticity, studies have surveyed its distribution among non-avian dinosaurs. Nevertheless, the degree of pneumaticity in the basal coelurosaurian group Ornithomimosauria remains poorly known, despite their potential to greatly enhance our understanding of the early evolution of pneumatic bones along the lineage leading to birds. Historically, the identification of postcranial pneumaticity in non-avian dinosaurs has been based on examination of external morphology, and few studies thus far have focused on the internal architecture of pneumatic structures inside the bones. Here, we describe the vertebral pneumaticity of the ornithomimosaur Archaeornithomimus with the aid of X-ray computed tomography (CT) imaging. Complementary examination of external and internal osteology reveals (1) highly pneumatized cervical vertebrae with an elaborate configuration of interconnected chambers within the neural arch and the centrum; (2) anterior dorsal vertebrae with pneumatic chambers inside the neural arch; (3) apneumatic sacral vertebrae; and (4) a subset of proximal caudal vertebrae with limited pneumatic invasion into the neural arch. Comparisons with other theropod dinosaurs suggest that ornithomimosaurs primitively exhibited a plesiomorphic theropod condition for axial pneumaticity that was extended among later taxa, such as Archaeornithomimus and large bodied Deinocheirus. This finding corroborates the notion that evolutionary increases in vertebral pneumaticity occurred in parallel among independent lineages of bird

  7. Non-Determinism: An Abstract Concept in Computer Science Studies

    ERIC Educational Resources Information Center

    Armoni, Michal; Gal-Ezer, Judith

    2007-01-01

    Non-determinism is one of the most important, yet abstract, recurring concepts of Computer Science. It plays an important role in Computer Science areas such as formal language theory, computability theory, distributed computing, and operating systems. We conducted a series of studies on the perception of non-determinism. In the current research,…

  8. Endocranial features of Australopithecus africanus revealed by 2- and 3-D computed tomography.

    PubMed

    Conroy, G C; Vannier, M W; Tobias, P V

    1990-02-16

    The earliest hominid from South Africa, Australopithecus africanus, is known from only six specimens in which accurate assessment of endocranial capacity and cranial venous outflow pattern can be obtained. This places a severe limit on a number of hypotheses concerning early hominid evolution, particularly those involving brain-body size relationships and adaptations of the circulatory system to evolving upright posture. Advances in high-resolution two- and three-dimensional computed tomography (CT) now allow the inclusion of another important specimen to this list, MLD 37/38 from Makapansgat. A new computer imaging technique is described that "reconstructs" the missing portions of the endocranial cavity in order to determine endocranial capacity. In addition, CT evaluation allows assessment of cranial venous outflow pattern even in cases where the endocranial cavity is completely filled with stone matrix. Results show that endocranial capacity in this specimen is less than originally proposed and also support the view that gracile and robust australopithecines evolved different cranial venous outflow patterns in response to upright postures. PMID:2305255

  9. Overcoming computational uncertainties to reveal chemical sensitivity in single molecule conduction calculations

    NASA Astrophysics Data System (ADS)

    Solomon, Gemma C.; Reimers, Jeffrey R.; Hush, Noel S.

    2005-06-01

    In the calculation of conduction through single molecule's approximations about the geometry and electronic structure of the system are usually made in order to simplify the problem. Previously [G. C. Solomon, J. R. Reimers, and N. S. Hush, J. Chem. Phys. 121, 6615 (2004)], we have shown that, in calculations employing cluster models for the electrodes, proper treatment of the open-shell nature of the clusters is the most important computational feature required to make the results sensitive to variations in the structural and chemical features of the system. Here, we expand this and establish a general hierarchy of requirements involving treatment of geometrical approximations. These approximations are categorized into two classes: those associated with finite-dimensional methods for representing the semi-infinite electrodes, and those associated with the chemisorption topology. We show that ca. 100 unique atoms are required in order to properly characterize each electrode: using fewer atoms leads to nonsystematic variations in conductivity that can overwhelm the subtler changes. The choice of binding site is shown to be the next most important feature, while some effects that are difficult to control experimentally concerning the orientations at each binding site are actually shown to be insignificant. Verification of this result provides a general test for the precision of computational procedures for molecular conductivity. Predictions concerning the dependence of conduction on substituent and other effects on the central molecule are found to be meaningful only when they exceed the uncertainties of the effects associated with binding-site variation.

  10. Overcoming computational uncertainties to reveal chemical sensitivity in single molecule conduction calculations.

    PubMed

    Solomon, Gemma C; Reimers, Jeffrey R; Hush, Noel S

    2005-06-01

    In the calculation of conduction through single molecule's approximations about the geometry and electronic structure of the system are usually made in order to simplify the problem. Previously [G. C. Solomon, J. R. Reimers, and N. S. Hush, J. Chem. Phys. 121, 6615 (2004)], we have shown that, in calculations employing cluster models for the electrodes, proper treatment of the open-shell nature of the clusters is the most important computational feature required to make the results sensitive to variations in the structural and chemical features of the system. Here, we expand this and establish a general hierarchy of requirements involving treatment of geometrical approximations. These approximations are categorized into two classes: those associated with finite-dimensional methods for representing the semi-infinite electrodes, and those associated with the chemisorption topology. We show that ca. 100 unique atoms are required in order to properly characterize each electrode: using fewer atoms leads to nonsystematic variations in conductivity that can overwhelm the subtler changes. The choice of binding site is shown to be the next most important feature, while some effects that are difficult to control experimentally concerning the orientations at each binding site are actually shown to be insignificant. Verification of this result provides a general test for the precision of computational procedures for molecular conductivity. Predictions concerning the dependence of conduction on substituent and other effects on the central molecule are found to be meaningful only when they exceed the uncertainties of the effects associated with binding-site variation.

  11. Computational Analysis Reveals a Successive Adaptation of Multiple Inositol Polyphosphate Phosphatase 1 in Higher Organisms Through Evolution

    PubMed Central

    Kilaparty, Surya P; Singh, Awantika; Baltosser, William H; Ali, Nawab

    2014-01-01

    Multiple inositol polyphosphate phosphatase 1 (Minpp1) in higher organisms dephosphorylates InsP6, the most abundant inositol phosphate. It also dephosphorylates less phosphorylated InsP5 and InsP4 and more phosphorylated InsP7 or InsP8. Minpp1 is classified as a member of the histidine acid phosphatase super family of proteins with functional resemblance to phytases found in lower organisms. This study took a bioinformatics approach to explore the extent of evolutionary diversification in Minpp1 structure and function in order to understand its physiological relevance in higher organisms. The human Minpp1 amino acid (AA) sequence was BLAST searched against available national protein databases. Phylogenetic analysis revealed that Minpp1 was widely distributed from lower to higher organisms. Further, we have identified that there exist four isoforms of Minpp1. Multiple computational tools were used to identify key functional motifs and their conservation among various species. Analyses showed that certain motifs predominant in higher organisms were absent in lower organisms. Variation in AA sequences within motifs was also analyzed. We found that there is diversification of key motifs and thus their functions present in Minpp1 from lower organisms to higher organisms. Another interesting result of this analysis was the presence of a glucose-1-phosphate interaction site in Minpp1; the functional significance of which has yet to be determined experimentally. The overall findings of our study point to an evolutionary adaptability of Minpp1 functions from lower to higher life forms. PMID:25574123

  12. Computational Studies of Magnetic Nozzle Performance

    NASA Technical Reports Server (NTRS)

    Ebersohn, Frans H.; Longmier, Benjamin W.; Sheehan, John P.; Shebalin, John B.; Raja, Laxminarayan

    2013-01-01

    An extensive literature review of magnetic nozzle research has been performed, examining previous work, as well as a review of fundamental principles. This has allow us to catalog all basic physical mechanisms which we believe underlie the thrust generation process. Energy conversion mechanisms include the approximate conservation of the magnetic moment adiabatic invariant, generalized hall and thermoelectric acceleration, swirl acceleration, thermal energy transformation into directed kinetic energy, and Joule heating. Momentum transfer results from the interaction of the applied magnetic field with currents induced in the plasma plume., while plasma detachment mechanisms include resistive diffusion, recombination and charge exchange collisions, magnetic reconnection, loss of adiabaticity, inertial forces, current closure, and self-field detachment. We have performed a preliminary study of Hall effects on magnetic nozzle jets with weak guiding magnetic fields and weak expansions (p(sub jet) approx. = P(sub background)). The conclusion from this study is that the Hall effect creates an azimuthal rotation of the plasma jet and, more generally, creates helical structures in the induced current, velocity field, and magnetic fields. We have studied plasma jet expansion to near vacuum without a guiding magnetic field, and are presently including a guiding magnetic field using a resistive MHD solver. This research is progressing toward the implementation of a full generalized Ohm's law solver. In our paper, we will summarize the basic principle, as well as the literature survey and briefly review our previous results. Our most recent results at the time of submittal will also be included. Efforts are currently underway to construct an experiment at the University of Michigan Plasmadynamics and Electric Propulsion Laboratory (PEPL) to study magnetic nozzle physics for a RF-thruster. Our computational study will work directly with this experiment to validate the numerical

  13. Approximate Bayesian computation reveals the factors that influence genetic diversity and population structure of foxsnakes.

    PubMed

    Row, J R; Brooks, R J; MacKinnon, C A; Lawson, A; Crother, B I; White, M; Lougheed, S C

    2011-11-01

    Contemporary geographical range and patterns of genetic diversity within species reflect complex interactions between multiple factors acting across spatial and temporal scales, and it is notoriously difficult to disentangle causation. Here, we quantify patterns of genetic diversity and genetic population structure using mitochondrial DNA sequences (101 individuals, cytochrome b) and microsatellites (816 individuals, 12 loci) and use Approximate Bayesian computation methods to test competing models of the demographic history of eastern and western foxsnakes. Our analyses indicate that post-glacial colonization and past population declines, probably caused by the infilling of deciduous forest and cooler temperatures since the mid-Holocene, largely underpin large-scale genetic patterns for foxsnakes. At finer geographical scales, our results point to more recent anthropogenic habitat loss as having accentuated genetic population structure by causing further declines and fragmentation.

  14. Computer Simulations Reveal Multiple Functions for Aromatic Residues in Cellulase Enzymes (Fact Sheet)

    SciTech Connect

    Not Available

    2012-07-01

    NREL researchers use high-performance computing to demonstrate fundamental roles of aromatic residues in cellulase enzyme tunnels. National Renewable Energy Laboratory (NREL) computer simulations of a key industrial enzyme, the Trichoderma reesei Family 6 cellulase (Cel6A), predict that aromatic residues near the enzyme's active site and at the entrance and exit tunnel perform different functions in substrate binding and catalysis, depending on their location in the enzyme. These results suggest that nature employs aromatic-carbohydrate interactions with a wide variety of binding affinities for diverse functions. Outcomes also suggest that protein engineering strategies in which mutations are made around the binding sites may require tailoring specific to the enzyme family. Cellulase enzymes ubiquitously exhibit tunnels or clefts lined with aromatic residues for processing carbohydrate polymers to monomers, but the molecular-level role of these aromatic residues remains unknown. In silico mutation of the aromatic residues near the catalytic site of Cel6A has little impact on the binding affinity, but simulation suggests that these residues play a major role in the glucopyranose ring distortion necessary for cleaving glycosidic bonds to produce fermentable sugars. Removal of aromatic residues at the entrance and exit of the cellulase tunnel, however, dramatically impacts the binding affinity. This suggests that these residues play a role in acquiring cellulose chains from the cellulose crystal and stabilizing the reaction product, respectively. These results illustrate that the role of aromatic-carbohydrate interactions varies dramatically depending on the position in the enzyme tunnel. As aromatic-carbohydrate interactions are present in all carbohydrate-active enzymes, the results have implications for understanding protein structure-function relationships in carbohydrate metabolism and recognition, carbon turnover in nature, and protein engineering strategies for

  15. Using the Computer in Evolution Studies

    ERIC Educational Resources Information Center

    Mariner, James L.

    1973-01-01

    Describes a high school biology exercise in which a computer greatly reduces time spent on calculations. Genetic equilibrium demonstrated by the Hardy-Weinberg principle and the subsequent effects of violating any of its premises are more readily understood when frequencies of alleles through many generations are calculated by the computer. (JR)

  16. Computer Competency: A 7-Year Study to Identify Gaps in Student Computer Skills

    ERIC Educational Resources Information Center

    Shuster, George F.; Pearl, Mona

    2011-01-01

    Computer competency is crucial to student success in higher education. Assessment of student knowledge related to specific computer competencies can provide faculty with important information about the strengths and weaknesses of their students' computer competency skills. The purpose of this study was to identify the competency level of two…

  17. Computational gene expression profiling under salt stress reveals patterns of co-expression

    PubMed Central

    Sanchita; Sharma, Ashok

    2016-01-01

    Plants respond differently to environmental conditions. Among various abiotic stresses, salt stress is a condition where excess salt in soil causes inhibition of plant growth. To understand the response of plants to the stress conditions, identification of the responsible genes is required. Clustering is a data mining technique used to group the genes with similar expression. The genes of a cluster show similar expression and function. We applied clustering algorithms on gene expression data of Solanum tuberosum showing differential expression in Capsicum annuum under salt stress. The clusters, which were common in multiple algorithms were taken further for analysis. Principal component analysis (PCA) further validated the findings of other cluster algorithms by visualizing their clusters in three-dimensional space. Functional annotation results revealed that most of the genes were involved in stress related responses. Our findings suggest that these algorithms may be helpful in the prediction of the function of co-expressed genes. PMID:26981411

  18. Single molecule studies reveal new mechanisms for microtubule severing

    NASA Astrophysics Data System (ADS)

    Ross, Jennifer; Diaz-Valencia, Juan Daniel; Morelli, Margaret; Zhang, Dong; Sharp, David

    2011-03-01

    Microtubule-severing enzymes are hexameric complexes made from monomeric enzyme subunits that remove tubulin dimers from the microtubule lattice. Severing proteins are known to remodel the cytoskeleton during interphase and mitosis, and are required in proper axon morphology and mammalian bone and cartilage development. We have performed the first single molecule imaging to determine where and how severing enzymes act to cut microtubules. We have focused on the original member of the group, katanin, and the newest member, fidgetin to compare their biophysical activities in vitro. We find that, as expected, severing proteins localize to areas of activity. Interestingly, the association is very brief: they do not stay bound nor do they bind cooperatively at active sites. The association duration changes with the nucleotide content, implying that the state in the catalytic cycle dictates binding affinity with the microtubule. We also discovered that, at lower concentrations, both katanin and fidgetin can depolymerize taxol-stabilized microtubules by removing terminal dimers. These studies reveal the physical regulation schemes to control severing activity in cells, and ultimately regulate cytoskeletal architecture. This work is supported by the March of Dimes Grant #5-FY09-46.

  19. CeleST: computer vision software for quantitative analysis of C. elegans swim behavior reveals novel features of locomotion.

    PubMed

    Restif, Christophe; Ibáñez-Ventoso, Carolina; Vora, Mehul M; Guo, Suzhen; Metaxas, Dimitris; Driscoll, Monica

    2014-07-01

    In the effort to define genes and specific neuronal circuits that control behavior and plasticity, the capacity for high-precision automated analysis of behavior is essential. We report on comprehensive computer vision software for analysis of swimming locomotion of C. elegans, a simple animal model initially developed to facilitate elaboration of genetic influences on behavior. C. elegans swim test software CeleST tracks swimming of multiple animals, measures 10 novel parameters of swim behavior that can fully report dynamic changes in posture and speed, and generates data in several analysis formats, complete with statistics. Our measures of swim locomotion utilize a deformable model approach and a novel mathematical analysis of curvature maps that enable even irregular patterns and dynamic changes to be scored without need for thresholding or dropping outlier swimmers from study. Operation of CeleST is mostly automated and only requires minimal investigator interventions, such as the selection of videotaped swim trials and choice of data output format. Data can be analyzed from the level of the single animal to populations of thousands. We document how the CeleST program reveals unexpected preferences for specific swim "gaits" in wild-type C. elegans, uncovers previously unknown mutant phenotypes, efficiently tracks changes in aging populations, and distinguishes "graceful" from poor aging. The sensitivity, dynamic range, and comprehensive nature of CeleST measures elevate swim locomotion analysis to a new level of ease, economy, and detail that enables behavioral plasticity resulting from genetic, cellular, or experience manipulation to be analyzed in ways not previously possible. PMID:25033081

  20. CeleST: Computer Vision Software for Quantitative Analysis of C. elegans Swim Behavior Reveals Novel Features of Locomotion

    PubMed Central

    Vora, Mehul M.; Guo, Suzhen; Metaxas, Dimitris; Driscoll, Monica

    2014-01-01

    In the effort to define genes and specific neuronal circuits that control behavior and plasticity, the capacity for high-precision automated analysis of behavior is essential. We report on comprehensive computer vision software for analysis of swimming locomotion of C. elegans, a simple animal model initially developed to facilitate elaboration of genetic influences on behavior. C. elegans swim test software CeleST tracks swimming of multiple animals, measures 10 novel parameters of swim behavior that can fully report dynamic changes in posture and speed, and generates data in several analysis formats, complete with statistics. Our measures of swim locomotion utilize a deformable model approach and a novel mathematical analysis of curvature maps that enable even irregular patterns and dynamic changes to be scored without need for thresholding or dropping outlier swimmers from study. Operation of CeleST is mostly automated and only requires minimal investigator interventions, such as the selection of videotaped swim trials and choice of data output format. Data can be analyzed from the level of the single animal to populations of thousands. We document how the CeleST program reveals unexpected preferences for specific swim “gaits” in wild-type C. elegans, uncovers previously unknown mutant phenotypes, efficiently tracks changes in aging populations, and distinguishes “graceful” from poor aging. The sensitivity, dynamic range, and comprehensive nature of CeleST measures elevate swim locomotion analysis to a new level of ease, economy, and detail that enables behavioral plasticity resulting from genetic, cellular, or experience manipulation to be analyzed in ways not previously possible. PMID:25033081

  1. CeleST: computer vision software for quantitative analysis of C. elegans swim behavior reveals novel features of locomotion.

    PubMed

    Restif, Christophe; Ibáñez-Ventoso, Carolina; Vora, Mehul M; Guo, Suzhen; Metaxas, Dimitris; Driscoll, Monica

    2014-07-01

    In the effort to define genes and specific neuronal circuits that control behavior and plasticity, the capacity for high-precision automated analysis of behavior is essential. We report on comprehensive computer vision software for analysis of swimming locomotion of C. elegans, a simple animal model initially developed to facilitate elaboration of genetic influences on behavior. C. elegans swim test software CeleST tracks swimming of multiple animals, measures 10 novel parameters of swim behavior that can fully report dynamic changes in posture and speed, and generates data in several analysis formats, complete with statistics. Our measures of swim locomotion utilize a deformable model approach and a novel mathematical analysis of curvature maps that enable even irregular patterns and dynamic changes to be scored without need for thresholding or dropping outlier swimmers from study. Operation of CeleST is mostly automated and only requires minimal investigator interventions, such as the selection of videotaped swim trials and choice of data output format. Data can be analyzed from the level of the single animal to populations of thousands. We document how the CeleST program reveals unexpected preferences for specific swim "gaits" in wild-type C. elegans, uncovers previously unknown mutant phenotypes, efficiently tracks changes in aging populations, and distinguishes "graceful" from poor aging. The sensitivity, dynamic range, and comprehensive nature of CeleST measures elevate swim locomotion analysis to a new level of ease, economy, and detail that enables behavioral plasticity resulting from genetic, cellular, or experience manipulation to be analyzed in ways not previously possible.

  2. Computational analysis of translational readthrough proteins in Drosophila and yeast reveals parallels to alternative splicing

    PubMed Central

    Pancsa, Rita; Macossay-Castillo, Mauricio; Kosol, Simone; Tompa, Peter

    2016-01-01

    In translational readthrough (TR) the ribosome continues extending the nascent protein beyond the first in-frame termination codon. Due to the lack of dedicated analyses of eukaryotic TR cases, the associated functional-evolutionary advantages are still unclear. Here, based on a variety of computational methods, we describe the structural and functional properties of previously proposed D. melanogaster and S. cerevisiae TR proteins and extensions. We found that in D. melanogaster TR affects long proteins in mainly regulatory roles. Their TR-extensions are structurally disordered and rich in binding motifs, which, together with their cell-type- and developmental stage-dependent inclusion, suggest that similarly to alternatively spliced exons they rewire cellular interaction networks in a temporally and spatially controlled manner. In contrast, yeast TR proteins are rather short and fulfil mainly housekeeping functions, like translation. Yeast extensions usually lack disorder and linear motifs, which precludes elucidating their functional relevance with sufficient confidence. Therefore we propose that by being much more restricted and by lacking clear functional hallmarks in yeast as opposed to fruit fly, TR shows remarkable parallels with alternative splicing. Additionally, the lack of conservation of TR extensions among orthologous TR proteins suggests that TR-mediated functions may be generally specific to lower taxonomic levels. PMID:27561673

  3. Approximate Bayesian Computation Reveals the Crucial Role of Oceanic Islands for the Assembly of Continental Biodiversity.

    PubMed

    Patiño, Jairo; Carine, Mark; Mardulyn, Patrick; Devos, Nicolas; Mateo, Rubén G; González-Mancebo, Juana M; Shaw, A Jonathan; Vanderpoorten, Alain

    2015-07-01

    The perceived low levels of genetic diversity, poor interspecific competitive and defensive ability, and loss of dispersal capacities of insular lineages have driven the view that oceanic islands are evolutionary dead ends. Focusing on the Atlantic bryophyte flora distributed across the archipelagos of the Azores, Madeira, the Canary Islands, Western Europe, and northwestern Africa, we used an integrative approach with species distribution modeling and population genetic analyses based on approximate Bayesian computation to determine whether this view applies to organisms with inherent high dispersal capacities. Genetic diversity was found to be higher in island than in continental populations, contributing to mounting evidence that, contrary to theoretical expectations, island populations are not necessarily genetically depauperate. Patterns of genetic variation among island and continental populations consistently fitted those simulated under a scenario of de novo foundation of continental populations from insular ancestors better than those expected if islands would represent a sink or a refugium of continental biodiversity. We, suggest that the northeastern Atlantic archipelagos have played a key role as a stepping stone for transoceanic migrants. Our results challenge the traditional notion that oceanic islands are the end of the colonization road and illustrate the significant role of oceanic islands as reservoirs of novel biodiversity for the assembly of continental floras.

  4. Computer-Assisted Identification of Protoplasts Responsible for Rare Division Events Reveals Guard-Cell Totipotency.

    PubMed Central

    Hall, R. D.; Verhoeven, H. A.; Krens, F. A.

    1995-01-01

    With the use of a computer-controlled microscope system to assist in the positioning and rapid relocation of large numbers of cultured cells, we were able to identify those protoplasts with the capacity to divide within a highly recalcitrant culture in which only a tiny fraction of the total population proceeds to produce viable microcalli. In the cultures used, comprising Beta vulgaris L. (sugar beet) leaf protoplasts, it was confirmed that these cells can be recognized solely on the basis of morphological characters. Therefore, a direct link exists between competence for cell division in vitro and cell type. Divergent callus morphologies and totipotent potential could also be ascribed to distinct protoplast types and hence to cells with a specific origin. The progenitors of the totipotent protoplasts in these cultures have been confirmed as being stomatal guard cells. Consequently, in plants even the most highly adapted living cells clearly retain and can reactivate all of the functional genetic information necessary to recreate the whole organism; an extreme degree of cytodifferentiation is, therefore, no hindrance to expressing totipotent potential. In addition to the considerable practical value of these findings, their implications concerning our understanding of both the control of gene expression and plant cell differentiation and its reversibility are of fundamental significance. PMID:12228442

  5. Computational analysis of translational readthrough proteins in Drosophila and yeast reveals parallels to alternative splicing.

    PubMed

    Pancsa, Rita; Macossay-Castillo, Mauricio; Kosol, Simone; Tompa, Peter

    2016-01-01

    In translational readthrough (TR) the ribosome continues extending the nascent protein beyond the first in-frame termination codon. Due to the lack of dedicated analyses of eukaryotic TR cases, the associated functional-evolutionary advantages are still unclear. Here, based on a variety of computational methods, we describe the structural and functional properties of previously proposed D. melanogaster and S. cerevisiae TR proteins and extensions. We found that in D. melanogaster TR affects long proteins in mainly regulatory roles. Their TR-extensions are structurally disordered and rich in binding motifs, which, together with their cell-type- and developmental stage-dependent inclusion, suggest that similarly to alternatively spliced exons they rewire cellular interaction networks in a temporally and spatially controlled manner. In contrast, yeast TR proteins are rather short and fulfil mainly housekeeping functions, like translation. Yeast extensions usually lack disorder and linear motifs, which precludes elucidating their functional relevance with sufficient confidence. Therefore we propose that by being much more restricted and by lacking clear functional hallmarks in yeast as opposed to fruit fly, TR shows remarkable parallels with alternative splicing. Additionally, the lack of conservation of TR extensions among orthologous TR proteins suggests that TR-mediated functions may be generally specific to lower taxonomic levels. PMID:27561673

  6. Computer simulations reveal complex distribution of haemodynamic forces in a mouse retina model of angiogenesis.

    PubMed

    Bernabeu, Miguel O; Jones, Martin L; Nielsen, Jens H; Krüger, Timm; Nash, Rupert W; Groen, Derek; Schmieschek, Sebastian; Hetherington, James; Gerhardt, Holger; Franco, Claudio A; Coveney, Peter V

    2014-10-01

    There is currently limited understanding of the role played by haemodynamic forces on the processes governing vascular development. One of many obstacles to be overcome is being able to measure those forces, at the required resolution level, on vessels only a few micrometres thick. In this paper, we present an in silico method for the computation of the haemodynamic forces experienced by murine retinal vasculature (a widely used vascular development animal model) beyond what is measurable experimentally. Our results show that it is possible to reconstruct high-resolution three-dimensional geometrical models directly from samples of retinal vasculature and that the lattice-Boltzmann algorithm can be used to obtain accurate estimates of the haemodynamics in these domains. We generate flow models from samples obtained at postnatal days (P) 5 and 6. Our simulations show important differences between the flow patterns recovered in both cases, including observations of regression occurring in areas where wall shear stress (WSS) gradients exist. We propose two possible mechanisms to account for the observed increase in velocity and WSS between P5 and P6: (i) the measured reduction in typical vessel diameter between both time points and (ii) the reduction in network density triggered by the pruning process. The methodology developed herein is applicable to other biomedical domains where microvasculature can be imaged but experimental flow measurements are unavailable or difficult to obtain.

  7. Chromatin structure revealed by X-ray scattering analysis and computational modeling.

    PubMed

    Maeshima, Kazuhiro; Imai, Ryosuke; Hikima, Takaaki; Joti, Yasumasa

    2014-12-01

    It remains unclear how the 2m of human genomic DNA is organized in each cell. The textbook model has long assumed that the 11-nm-diameter nucleosome fiber (beads-on-a-string), in which DNA is wrapped around core histones, is folded into a 30-nm chromatin fiber. One of the classical models assumes that the 30-nm chromatin fiber is further folded helically to form a larger fiber. Small-angle X-ray scattering (SAXS) is a powerful method for investigating the bulk structure of interphase chromatin and mitotic chromosomes. SAXS can detect periodic structures in biological materials in solution. In our SAXS results, no structural feature larger than 11 nm was detected. Combining this with a computational analysis of "in silico condensed chromatin" made it possible to understand more about the X-ray scattering profiles and suggested that the chromatin in interphase nuclei and mitotic chromosomes essentially consists of irregularly folded nucleosome fibers lacking the 30-nm chromatin structure. In this article, we describe the experimental details of our SAXS and modeling systems. We also discuss other methods for investigating the chromatin structure in cells. PMID:25168089

  8. Computational Study of Multiple Hydrokinetic Turbine Performance

    NASA Astrophysics Data System (ADS)

    Jonas, Joseph David

    The k-omega Shear Stress Transport turbulence model was used to determine the performance of a pair of horizontal-axis hydrokinetic turbines. By varying the separation distance perpendicular to the flow direction between these turbines and computing both power and drag coefficients, the relationship between these outputs and the separation distance as an input was discovered. This study used a rotating reference frame, steady state approximation over three separation distances and two different mesh sizes to verify mesh independence. Once this meshing methodology was verified, two more separation distances were run using the same steady-state approximations at the coarse mesh size to better understand turbine performance at greater separation distances. The results of these simulations show that, at a given separation distance, the left and right turbines have very similar performance. The power and drag coefficients were both found to decrease on the order of 8% as the turbines are brought closer together, which means that, in an infinite and uniform flow field, turbines should be placed as far apart as is feasible to maximize resultant combined power output.

  9. Computational studies on intermolecular interactions in solvation

    NASA Astrophysics Data System (ADS)

    Song, Weiping

    This thesis presents the results of computational studies of intermolecular interactions in various contexts. We first investigated the relation between solute-solvent intermolecular interactions and local density augmentation in supercritical solvation. The phenomenon of interest is the excess density that exists in the neighborhood of an attractive solute in a supercritical solvent in the vicinity of the critical point. In Chapter 2, we examined the ability of various measures of the strength of solute-solvent interactions, calculated from all-atom potential functions, to correlate the extent of local density augmentation in both experimental and model solvents. The Gibbs Ensemble Monte Carlo (GEMC) method enables us to calculate phase equilibrium in pure substances and mixtures. It provides a convenient way to test and develop model potentials. In Chapter 3 we present some methodological aspects of such calculations, the issues related to approach to critical points and finite-size effects and applications to simple fluids. Chapter 4 then describes a simplified 2-site potential model for simulating supercritical fluoroform. The GEMC method was used to simulate the vapor-liquid coexistence curve of the model fluid and the dynamic properties were studied by performing NVT molecular dynamics (MD) simulations. The results show that despite its simplicity, this model is able to reproduce many important properties of supercritical fluoroform, making it useful in molecular simulations of supercritical solvation. In the above two studies, the intermolecular interactions are described by a sum of pair-wise additive Lennard-Jones + Coulomb terms. The standard Lorentz-Berthelot combining rules (geometric mean rule for well depth and arithmetic mean rule for collision diameter) are commonly applied to account for the unlike pair Lennard-Jones parameters. In Chapter 5, we examined the applicability of the combining rules for modeling alkane-perfluoroalkane interactions. It

  10. Reaction Mechanism of Glutamate Carboxypeptidase II Revealed by Mutagenesis, X-ray Crystallography, and Computational Methods

    SciTech Connect

    Klusak, Vojtech; Barinka, Cyril; Plechanovova, Anna; Mlcochova, Petra; Konvalinka, Jan; Rulisek, Lubomir; Lubkowski, Jacek

    2009-05-29

    Glutamate carboxypeptidase II (GCPII, EC 3.4.17.21) is a zinc-dependent exopeptidase and an important therapeutic target for neurodegeneration and prostate cancer. The hydrolysis of N-acetyl-l-aspartyl-l-glutamate (N-Ac-Asp-Glu), the natural dipeptidic substrate of the GCPII, is intimately involved in cellular signaling within the mammalian nervous system, but the exact mechanism of this reaction has not yet been determined. To investigate peptide hydrolysis by GCPII in detail, we constructed a mutant of human GCPII [GCPII(E424A)], in which Glu424, a putative proton shuttle residue, is substituted with alanine. Kinetic analysis of GCPII(E424A) using N-Ac-Asp-Glu as substrate revealed a complete loss of catalytic activity, suggesting the direct involvement of Glu424 in peptide hydrolysis. Additionally, we determined the crystal structure of GCPII(E424A) in complex with N-Ac-Asp-Glu at 1.70 {angstrom} resolution. The presence of the intact substrate in the GCPII(E424A) binding cavity substantiates our kinetic data and allows a detailed analysis of GCPII/N-Ac-Asp-Glu interactions. The experimental data are complemented by the combined quantum mechanics/molecular mechanics calculations (QM/MM) which enabled us to characterize the transition states, including the associated reaction barriers, and provided detailed information concerning the GCPII reaction mechanism. The best estimate of the reaction barrier was calculated to be {Delta}G {approx} 22({+-}5) kcal{center_dot}mol{sup -1}, which is in a good agreement with the experimentally observed reaction rate constant (k{sub cat} {approx} 1 s{sup -1}). Combined together, our results provide a detailed and consistent picture of the reaction mechanism of this highly interesting enzyme at the atomic level.

  11. Pheromone component patterns of moth evolution revealed by computer analysis of the Pherolist.

    PubMed

    Byer, John A

    2006-03-01

    1. The Pherolist internet site listing moth sex pheromone components reported in the literature was downloaded and processed by a basic program into a database with 2931 combinations of 377 unique chemical names of sex pheromone attractants used by 1572 moth species in 619 genera and 49 families. Names of pheromone compounds were analysed for aliphatic chain length, unsaturation position, geometric configuration, functional group (aldehyde, alcohol, acetate, epoxide, methyl-branched and hydrocarbon) and number of instances such combinations are used by species and families. 2. The analyses revealed pheromone blends of species ranged from one to eight components (45% species with one component, 36% two, 12% three, 5% four, 1% five, < or = 0.5% for > or = six). The numbers of different components of various chain lengths and functional groups, the numbers of instances such compounds are used by species and the numbers of species using such compounds are presented. 3. The average number of pheromone components per species increased as the number of species in a family increased based on linear regression of components in the 10 largest families, with species numbers ranging from 19 to 461. Pooling the four largest families gave a mean of 1.96 components per species that was significantly greater than the mean of the next 14 smaller families (1.63). Because related species in a large family would need more communication channels, this suggests that these species on average evolved to produce and detect more components in their pheromone blends to achieve a unique communication channel than was needed by species in smaller families. 4. Speciation in moths would entail evolutionary changes in both pheromone biosynthetic and sensory systems that avoided competition for communication channels of existing species. Regression analysis indicated that the more species in a family the more unique pheromone components, but the increase diminishes progressively. This suggests

  12. Computational Mutagenesis Studies of Hammerhead Ribozyme Catalysis

    PubMed Central

    Lee, Tai-Sung; York, Darrin M.

    2010-01-01

    Computational studies of the mutational effects at the C3, G8, and G5 positions of the hammerhead ribozyme (HHR) are reported based on a series of twenty four 100-ns molecular dynamics simulations of the native and mutated HHR in the reactant state and in an activated precursor state (G8:2′OH deprotonated). Invoking the assumptions that G12 acts as the general base while the 2′OH of G8 acts as a general acid, the simulations are able to explain the origins of experimentally observed mutational effects, including several that are not easily inferred from the crystal structure. Simulations suggest that the Watson-Crick base-pairing between G8 and C3, the hydrogen bond network between C17 and G5, and the base stacking interactions between G8 and C1.1, collectively, are key to maintaining an active site structure conducive for catalytic activity. Mutation-induced disruption of any of these interactions will adversely affect activity. The simulation results predict that the C3U/G8D double mutant, where D is 2,6-diaminopurine, will have a rescue effect relative to the corresponding single mutations. Two general conclusions about the simulations emerge from this work. Firstly, mutation simulations may require 30 ns or more to suitably relax such that the mutational effects become apparent. Secondly, in some cases, it is necessary to look beyond the reactant state in order to interpret mutational effects in terms of catalytically active structure. The present simulation results lead to better understanding of the origin of experimental mutational effects, and provide insight into the key conserved features necessary to maintain the integrity of the active site architecture. PMID:20812715

  13. Computational Approaches to Study Microbes and Microbiomes

    PubMed Central

    Greene, Casey S.; Foster, James A.; Stanton, Bruce A.; Hogan, Deborah A.; Bromberg, Yana

    2016-01-01

    Technological advances are making large-scale measurements of microbial communities commonplace. These newly acquired datasets are allowing researchers to ask and answer questions about the composition of microbial communities, the roles of members in these communities, and how genes and molecular pathways are regulated in individual community members and communities as a whole to effectively respond to diverse and changing environments. In addition to providing a more comprehensive survey of the microbial world, this new information allows for the development of computational approaches to model the processes underlying microbial systems. We anticipate that the field of computational microbiology will continue to grow rapidly in the coming years. In this manuscript we highlight both areas of particular interest in microbiology as well as computational approaches that begin to address these challenges. PMID:26776218

  14. Wrist Hypothermia Related to Continuous Work with a Computer Mouse: A Digital Infrared Imaging Pilot Study.

    PubMed

    Reste, Jelena; Zvagule, Tija; Kurjane, Natalja; Martinsone, Zanna; Martinsone, Inese; Seile, Anita; Vanadzins, Ivars

    2015-08-07

    Computer work is characterized by sedentary static workload with low-intensity energy metabolism. The aim of our study was to evaluate the dynamics of skin surface temperature in the hand during prolonged computer mouse work under different ergonomic setups. Digital infrared imaging of the right forearm and wrist was performed during three hours of continuous computer work (measured at the start and every 15 minutes thereafter) in a laboratory with controlled ambient conditions. Four people participated in the study. Three different ergonomic computer mouse setups were tested on three different days (horizontal computer mouse without mouse pad; horizontal computer mouse with mouse pad and padded wrist support; vertical computer mouse without mouse pad). The study revealed a significantly strong negative correlation between the temperature of the dorsal surface of the wrist and time spent working with a computer mouse. Hand skin temperature decreased markedly after one hour of continuous computer mouse work. Vertical computer mouse work preserved more stable and higher temperatures of the wrist (>30 °C), while continuous use of a horizontal mouse for more than two hours caused an extremely low temperature (<28 °C) in distal parts of the hand. The preliminary observational findings indicate the significant effect of the duration and ergonomics of computer mouse work on the development of hand hypothermia.

  15. Wrist Hypothermia Related to Continuous Work with a Computer Mouse: A Digital Infrared Imaging Pilot Study

    PubMed Central

    Reste, Jelena; Zvagule, Tija; Kurjane, Natalja; Martinsone, Zanna; Martinsone, Inese; Seile, Anita; Vanadzins, Ivars

    2015-01-01

    Computer work is characterized by sedentary static workload with low-intensity energy metabolism. The aim of our study was to evaluate the dynamics of skin surface temperature in the hand during prolonged computer mouse work under different ergonomic setups. Digital infrared imaging of the right forearm and wrist was performed during three hours of continuous computer work (measured at the start and every 15 minutes thereafter) in a laboratory with controlled ambient conditions. Four people participated in the study. Three different ergonomic computer mouse setups were tested on three different days (horizontal computer mouse without mouse pad; horizontal computer mouse with mouse pad and padded wrist support; vertical computer mouse without mouse pad). The study revealed a significantly strong negative correlation between the temperature of the dorsal surface of the wrist and time spent working with a computer mouse. Hand skin temperature decreased markedly after one hour of continuous computer mouse work. Vertical computer mouse work preserved more stable and higher temperatures of the wrist (>30 °C), while continuous use of a horizontal mouse for more than two hours caused an extremely low temperature (<28 °C) in distal parts of the hand. The preliminary observational findings indicate the significant effect of the duration and ergonomics of computer mouse work on the development of hand hypothermia. PMID:26262633

  16. Writing Apprehension, Computer Anxiety and Telecomputing: A Pilot Study.

    ERIC Educational Resources Information Center

    Harris, Judith; Grandgenett, Neal

    1992-01-01

    A study measured graduate students' writing apprehension and computer anxiety levels before and after using electronic mail, computer conferencing, and remote database searching facilities during an educational technology course. Results indicted postcourse computer anxiety levels significantly related to usage statistics. Precourse writing…

  17. A Study of Computing Undergraduates Undertaking a Systematic Literature Review

    ERIC Educational Resources Information Center

    Brereton, P.

    2011-01-01

    Teaching computing students about the importance of evidence and about the use of empirical methods for evaluating computing technologies can be difficult, especially within dual honors undergraduate degree programs. The aims of this study were to explore the effectiveness of second-year undergraduate computing students in carrying out a…

  18. RESQme studies for SDC regional computing centers

    SciTech Connect

    Day, C.T.

    1993-02-01

    The Technical Design Report for the SDC proposes a model for offline computing which includes a computing center at the SSCL, containing all of the physics data, together with a number of regional computing centers around the world. These regional centers would contain subsets of the data, and would support the daily work of most physicists. For large or unusual requests, where the data are not held at the regional center, the requests would automatically be forwarded to the SSCL. It is assumed that the closeness'' of the regional centers and their reduced demand from fewer users would result in improved system performance. Such a system is too complex to model analytically; simulation is the only viable approach. However, Monte Carlo models built from scratch for complicated systems are very difficult to maintain and hard to modify. Fortunately, we have obtained from IBM a modeling framework, RESQme, explicitly designed for building statistical models of computer systems. This note describes a first pass at modeling the proposed offline system.

  19. RESQme studies for SDC regional computing centers

    SciTech Connect

    Day, C.T.

    1993-02-01

    The Technical Design Report for the SDC proposes a model for offline computing which includes a computing center at the SSCL, containing all of the physics data, together with a number of regional computing centers around the world. These regional centers would contain subsets of the data, and would support the daily work of most physicists. For large or unusual requests, where the data are not held at the regional center, the requests would automatically be forwarded to the SSCL. It is assumed that the ``closeness`` of the regional centers and their reduced demand from fewer users would result in improved system performance. Such a system is too complex to model analytically; simulation is the only viable approach. However, Monte Carlo models built from scratch for complicated systems are very difficult to maintain and hard to modify. Fortunately, we have obtained from IBM a modeling framework, RESQme, explicitly designed for building statistical models of computer systems. This note describes a first pass at modeling the proposed offline system.

  20. Assessing Moderator Variables: Two Computer Simulation Studies.

    ERIC Educational Resources Information Center

    Mason, Craig A.; And Others

    1996-01-01

    A strategy is proposed for conceptualizing moderating relationships based on their type (strictly correlational and classically correlational) and form, whether continuous, noncontinuous, logistic, or quantum. Results of computer simulations comparing three statistical approaches for assessing moderator variables are presented, and advantages of…

  1. Computational Chemistry Studies on the Carbene Hydroxymethylene

    ERIC Educational Resources Information Center

    Marzzacco, Charles J.; Baum, J. Clayton

    2011-01-01

    A density functional theory computational chemistry exercise on the structure and vibrational spectrum of the carbene hydroxymethylene is presented. The potential energy curve for the decomposition reaction of the carbene to formaldehyde and the geometry of the transition state are explored. The results are in good agreement with recent…

  2. Where Computer Science and Cultural Studies Collide

    ERIC Educational Resources Information Center

    Kirschenbaum, Matthew

    2009-01-01

    Most users have no more knowledge of what their computer or code is actually doing than most automobile owners have of their carburetor or catalytic converter. Nor is any such knowledge necessarily needed. But for academics, driven by an increasing emphasis on the materiality of new media--that is, the social, cultural, and economic factors…

  3. Requirement for transient metal ions revealed through computational analysis for DNA polymerase going in reverse.

    PubMed

    Perera, Lalith; Freudenthal, Bret D; Beard, William A; Shock, David D; Pedersen, Lee G; Wilson, Samuel H

    2015-09-22

    DNA polymerases facilitate faithful insertion of nucleotides, a central reaction occurring during DNA replication and repair. DNA synthesis (forward reaction) is "balanced," as dictated by the chemical equilibrium by the reverse reaction of pyrophosphorolysis. Two closely spaced divalent metal ions (catalytic and nucleotide-binding metals) provide the scaffold for these reactions. The catalytic metal lowers the pKa of O3' of the growing primer terminus, and the nucleotide-binding metal facilitates substrate binding. Recent time-lapse crystallographic studies of DNA polymerases have identified an additional metal ion (product metal) associated with pyrophosphate formation, leading to the suggestion of its possible involvement in the reverse reaction. Here, we establish a rationale for a role of the product metal using quantum mechanical/molecular mechanical calculations of the reverse reaction in the confines of the DNA polymerase β active site. Additionally, site-directed mutagenesis identifies essential residues and metal-binding sites necessary for pyrophosphorolysis. The results indicate that the catalytic metal site must be occupied by a magnesium ion for pyrophosphorolysis to occur. Critically, the product metal site is occupied by a magnesium ion early in the pyrophosphorolysis reaction path but must be removed later. The proposed dynamic nature of the active site metal ions is consistent with crystallographic structures. The transition barrier for pyrophosphorolysis was estimated to be significantly higher than that for the forward reaction, consistent with kinetic activity measurements of the respective reactions. These observations provide a framework to understand how ions and active site changes could modulate the internal chemical equilibrium of a reaction that is central to genome stability.

  4. Novel features of end-gas aotoignition revealed by computational fluid dynamics

    SciTech Connect

    Griffiths, J.F.; Rose, D.J. ); Schreiber, M.; Meyer, J.; Knoche, K.F. )

    1992-11-01

    Autoignition of the end-gas in the combustion chamber is believed to be a primary cause of knock in spark ignition engines. Fundamental studies of the autoignition of hydrocarbon + air mixtures has been performed successfully in rapid compression machines. There has also been considerable progress towards the numerical modeling of these phenomena, but applications to combustion in a rapid compression machine have been based only on a spatially uniform well-mixed condition. The authors report in this paper the implementation of a fluid dynamics code in conjunction with the Shell generalized (or reduced) kinetic model, which represents the exothermic oxidation of the alkane components of gasoline, to predict the development of autoignition in the combustion chamber. The numerical simulations reported in this paper were matched to the performance of the rapid compression apparatus in use at Leeds. In this system, combustion occurred in a cylindrical chamber, the flat, end faces of which were the piston crown and cylinder head. The reactants were compressed by a piston, which was then brought to rest at the end of its stroke. The geometric configuration of the combustion chamber of the rapid compression machine is fully axisymmetric. This permitted a two-dimensional treatment of spatial conditions on a plane representing piston displacement and half radius. Reactive gas flows were simulated on a 14 [times] 50 mesh at the start of compression, which was reduced to 14 [times] 10 cells as the piston reached top-dead-center. The resolution within the vicinity of the cylinder wall was enhanced by a nonequidistant grid structure.

  5. Requirement for transient metal ions revealed through computational analysis for DNA polymerase going in reverse

    PubMed Central

    Perera, Lalith; Freudenthal, Bret D.; Beard, William A.; Shock, David D.; Pedersen, Lee G.; Wilson, Samuel H.

    2015-01-01

    DNA polymerases facilitate faithful insertion of nucleotides, a central reaction occurring during DNA replication and repair. DNA synthesis (forward reaction) is “balanced,” as dictated by the chemical equilibrium by the reverse reaction of pyrophosphorolysis. Two closely spaced divalent metal ions (catalytic and nucleotide-binding metals) provide the scaffold for these reactions. The catalytic metal lowers the pKa of O3′ of the growing primer terminus, and the nucleotide-binding metal facilitates substrate binding. Recent time-lapse crystallographic studies of DNA polymerases have identified an additional metal ion (product metal) associated with pyrophosphate formation, leading to the suggestion of its possible involvement in the reverse reaction. Here, we establish a rationale for a role of the product metal using quantum mechanical/molecular mechanical calculations of the reverse reaction in the confines of the DNA polymerase β active site. Additionally, site-directed mutagenesis identifies essential residues and metal-binding sites necessary for pyrophosphorolysis. The results indicate that the catalytic metal site must be occupied by a magnesium ion for pyrophosphorolysis to occur. Critically, the product metal site is occupied by a magnesium ion early in the pyrophosphorolysis reaction path but must be removed later. The proposed dynamic nature of the active site metal ions is consistent with crystallographic structures. The transition barrier for pyrophosphorolysis was estimated to be significantly higher than that for the forward reaction, consistent with kinetic activity measurements of the respective reactions. These observations provide a framework to understand how ions and active site changes could modulate the internal chemical equilibrium of a reaction that is central to genome stability. PMID:26351676

  6. Study of basic computer competence among public health nurses in Taiwan.

    PubMed

    Yang, Kuei-Feng; Yu, Shu; Lin, Ming-Sheng; Hsu, Chia-Ling

    2004-03-01

    Rapid advances in information technology and media have made distance learning on the Internet possible. This new model of learning allows greater efficiency and flexibility in knowledge acquisition. Since basic computer competence is a prerequisite for this new learning model, this study was conducted to examine the basic computer competence of public health nurses in Taiwan and explore factors influencing computer competence. A national cross-sectional randomized study was conducted with 329 public health nurses. A questionnaire was used to collect data and was delivered by mail. Results indicate that basic computer competence of public health nurses in Taiwan is still needs to be improved (mean = 57.57 +- 2.83, total score range from 26-130). Among the five most frequently used software programs, nurses were most knowledgeable about Word and least knowledgeable about PowerPoint. Stepwise multiple regression analysis revealed eight variables (weekly number of hours spent online at home, weekly amount of time spent online at work, weekly frequency of computer use at work, previous computer training, computer at workplace and Internet access, job position, education level, and age) that significantly influenced computer competence, which accounted for 39.0 % of the variance. In conclusion, greater computer competence, broader educational programs regarding computer technology, and a greater emphasis on computers at work are necessary to increase the usefulness of distance learning via the Internet in Taiwan. Building a user-friendly environment is important in developing this new media model of learning for the future. PMID:15136958

  7. Optimizing Classroom Acoustics Using Computer Model Studies.

    ERIC Educational Resources Information Center

    Reich, Rebecca; Bradley, John

    1998-01-01

    Investigates conditions relating to the maximum useful-to-detrimental sound ratios present in classrooms and determining the optimum conditions for speech intelligibility. Reveals that speech intelligibility is more strongly influenced by ambient noise levels and that the optimal location for sound absorbing material is on a classroom's upper…

  8. Computer aided design study of hypermixing nozzles

    NASA Technical Reports Server (NTRS)

    Mefferd, L. A.; Bevilacqua, P. M.

    1979-01-01

    The development of a nozzle which combines the hypermixing and lobe mechanisms to achieve further increases in jet entrainment and ejector performance is investigated. A computer program which incorporates a two equation turbulence model and is used to predict and compare the evolution of jets from various nozzle designs is discussed. Increasing the length of the nozzle lobes and an alternating lobe nozzle are a methods examined for increasing the entrainment rate.

  9. Examining the architecture of cellular computing through a comparative study with a computer.

    PubMed

    Wang, Degeng; Gribskov, Michael

    2005-06-22

    The computer and the cell both use information embedded in simple coding, the binary software code and the quadruple genomic code, respectively, to support system operations. A comparative examination of their system architecture as well as their information storage and utilization schemes is performed. On top of the code, both systems display a modular, multi-layered architecture, which, in the case of a computer, arises from human engineering efforts through a combination of hardware implementation and software abstraction. Using the computer as a reference system, a simplistic mapping of the architectural components between the two is easily detected. This comparison also reveals that a cell abolishes the software-hardware barrier through genomic encoding for the constituents of the biochemical network, a cell's "hardware" equivalent to the computer central processing unit (CPU). The information loading (gene expression) process acts as a major determinant of the encoded constituent's abundance, which, in turn, often determines the "bandwidth" of a biochemical pathway. Cellular processes are implemented in biochemical pathways in parallel manners. In a computer, on the other hand, the software provides only instructions and data for the CPU. A process represents just sequentially ordered actions by the CPU and only virtual parallelism can be implemented through CPU time-sharing. Whereas process management in a computer may simply mean job scheduling, coordinating pathway bandwidth through the gene expression machinery represents a major process management scheme in a cell. In summary, a cell can be viewed as a super-parallel computer, which computes through controlled hardware composition. While we have, at best, a very fragmented understanding of cellular operation, we have a thorough understanding of the computer throughout the engineering process. The potential utilization of this knowledge to the benefit of systems biology is discussed. PMID:16849179

  10. Computational Studies in Molecular Geochemistry and Biogeochemistry

    SciTech Connect

    Felmy, Andrew R.; Bylaska, Eric J.; Dixon, David A.; Dupuis, Michel; Halley, James W.; Kawai, R.; Rosso, Kevin M.; Rustad, James R.; Smith, Paul E.; Straatsma, TP; Voth, Gregory A.; Weare, John H.; Yuen, David A.

    2006-04-18

    The ability to predict the transport and transformations of contaminants within the subsurface is critical for decisions on virtually every waste disposal option facing the Department of Energy (DOE), from remediation technologies such as in situ bioremediation to evaluations of the safety of nuclear waste repositories. With this fact in mind, the DOE has recently sponsored a series of workshops on the development of a Strategic Simulation Plan on applications of high perform-ance computing to national problems of significance to the DOE. One of the areas selected for application was in the area of subsurface transport and environmental chemistry. Within the SSP on subsurface transport and environmental chemistry several areas were identified where applications of high performance computing could potentially significantly advance our knowledge of contaminant fate and transport. Within each of these areas molecular level simulations were specifically identified as a key capability necessary for the development of a fundamental mechanistic understanding of complex biogeochemical processes. This effort consists of a series of specific molecular level simulations and program development in four key areas of geochemistry/biogeochemistry (i.e., aqueous hydrolysis, redox chemistry, mineral surface interactions, and microbial surface properties). By addressing these four differ-ent, but computationally related, areas it becomes possible to assemble a team of investigators with the necessary expertise in high performance computing, molecular simulation, and geochemistry/biogeochemistry to make significant progress in each area. The specific targeted geochemical/biogeochemical issues include: Microbial surface mediated processes: the effects of lipopolysacchardies present on gram-negative bacteria. Environmental redox chemistry: Dechlorination pathways of carbon tetrachloride and other polychlorinated compounds in the subsurface. Mineral surface interactions: Describing

  11. Jugular foramen: anatomic and computed tomographic study

    SciTech Connect

    Daniels, D.L.; Williams, A.L.; Haughton, V.M.

    1984-01-01

    The computed tomographic (CT) appearance of the jugular foramen was examined in detail, and anatomic and CT sections were correlated. The pars nervosa and pars vascularis were identified, and, with intravenous contrast enhancement, a rapid sequence of scans at a gantry angle of +30/sup 0/ to the canthomeatal line demonstrated cranial nerves IX, X, and XI. The osseous margins of the jugular foramen were best shown by CT at planes of sections parallel and positive (0/sup 0/-30/sup 0/) to the canthomeatal line. CT can be used to evaluate osseous anatomy and the jugular foramen with precision sufficient to confidently exclude an intracanalicular mass.

  12. Computer Simulation Studies of Gramicidin Channel

    NASA Astrophysics Data System (ADS)

    Song, Hyundeok; Beck, Thomas

    2009-04-01

    Ion channels are large membrane proteins, and their function is to facilitate the passage of ions across biological membranes. Recently, Dr. John Cuppoletti's group at UC showed that the gramicidin channel could function at high temperatures (360 -- 390K) with significant currents. This finding may have large implications for fuel cell technology. In this project, we will examine the experimental system by computer simulation. We will investigate how the temperature affects the current and differences in magnitude of the currents between two forms of Gramicidin, A and D. This research will help to elucidate the underlying molecular mechanism in this promising new technology.

  13. Synchrotron-radiation-based X-ray micro-computed tomography reveals dental bur debris under dental composite restorations.

    PubMed

    Hedayat, Assem; Nagy, Nicole; Packota, Garnet; Monteith, Judy; Allen, Darcy; Wysokinski, Tomasz; Zhu, Ning

    2016-05-01

    Dental burs are used extensively in dentistry to mechanically prepare tooth structures for restorations (fillings), yet little has been reported on the bur debris left behind in the teeth, and whether it poses potential health risks to patients. Here it is aimed to image dental bur debris under dental fillings, and allude to the potential health hazards that can be caused by this debris when left in direct contact with the biological surroundings, specifically when the debris is made of a non-biocompatible material. Non-destructive micro-computed tomography using the BioMedical Imaging & Therapy facility 05ID-2 beamline at the Canadian Light Source was pursued at 50 keV and at a pixel size of 4 µm to image dental bur fragments under a composite resin dental filling. The bur's cutting edges that produced the fragment were also chemically analyzed. The technique revealed dental bur fragments of different sizes in different locations on the floor of the prepared surface of the teeth and under the filling, which places them in direct contact with the dentinal tubules and the dentinal fluid circulating within them. Dispersive X-ray spectroscopy elemental analysis of the dental bur edges revealed that the fragments are made of tungsten carbide-cobalt, which is bio-incompatible.

  14. Children as Educational Computer Game Designers: An Exploratory Study

    ERIC Educational Resources Information Center

    Baytak, Ahmet; Land, Susan M.; Smith, Brian K.

    2011-01-01

    This study investigated how children designed computer games as artifacts that reflected their understanding of nutrition. Ten 5th grade students were asked to design computer games with the software "Game Maker" for the purpose of teaching 1st graders about nutrition. The results from the case study show that students were able to express their…

  15. Academic Computing at Worcester Polytechnic Institute. A Case Study.

    ERIC Educational Resources Information Center

    Hunter, Beverly

    This case study is one of a series focusing on computers as everyday learning and teaching tools which is addressed to administrators, teachers, staff, and students who wish to plan or improve the uses of computers at their own institutions. Following a brief description of the purpose and selection of cases for the overall study, the report…

  16. International Computer and Information Literacy Study: Assessment Framework

    ERIC Educational Resources Information Center

    Fraillon, Julian; Schulz, Wolfram; Ainley, John

    2013-01-01

    The purpose of the International Computer and Information Literacy Study 2013 (ICILS 2013) is to investigate, in a range of countries, the ways in which young people are developing "computer and information literacy" (CIL) to support their capacity to participate in the digital age. To achieve this aim, the study will assess student…

  17. Computer Simulation in the Social Sciences/Social Studies.

    ERIC Educational Resources Information Center

    Klassen, Daniel L.

    Computers are beginning to be used more frequently as instructional tools in secondary school social studies. This is especially true of "new social studies" programs; i.e., programs which subordinate mere mastery of factual content to the recognition of and ability to deal with the social imperatives of the future. Computer-assisted instruction…

  18. Advances in computational studies of energy materials.

    PubMed

    Catlow, C R A; Guo, Z X; Miskufova, M; Shevlin, S A; Smith, A G H; Sokol, A A; Walsh, A; Wilson, D J; Woodley, S M

    2010-07-28

    We review recent developments and applications of computational modelling techniques in the field of materials for energy technologies including hydrogen production and storage, energy storage and conversion, and light absorption and emission. In addition, we present new work on an Sn2TiO4 photocatalyst containing an Sn(II) lone pair, new interatomic potential models for SrTiO3 and GaN, an exploration of defects in the kesterite/stannite-structured solar cell absorber Cu2ZnSnS4, and report details of the incorporation of hydrogen into Ag2O and Cu2O. Special attention is paid to the modelling of nanostructured systems, including ceria (CeO2, mixed Ce(x)O(y) and Ce2O3) and group 13 sesquioxides. We consider applications based on both interatomic potential and electronic structure methodologies; and we illustrate the increasingly quantitative and predictive nature of modelling in this field. PMID:20566517

  19. Microscopic study reveals the singular origins of growth

    NASA Astrophysics Data System (ADS)

    Yaari, G.; Nowak, A.; Rakocy, K.; Solomon, S.

    2008-04-01

    Anderson [Science 177, 293 (1972)] proposed the concept of complexity in order to describe the emergence and growth of macroscopic collective patterns out of the simple interactions of many microscopic agents. In the physical sciences this paradigm was implemented systematically and confirmed repeatedly by successful confrontation with reality. In the social sciences however, the possibilities to stage experiments to validate it are limited. During the 90's a series of dramatic political and economic events have provided the opportunity to do so. We exploit the resulting empirical evidence to validate a simple agent based alternative to the classical logistic dynamics. The post-liberalization empirical data from Poland confirm the theoretical prediction that the dynamics is dominated by singular rare events which insure the resilience and adaptability of the system. We have shown that growth is led by few singular “growth centers" (Fig. 1), that initially developed at a tremendous rate (Fig. 3), followed by a diffusion process to the rest of the country and leading to a positive growth rate uniform across the counties. In addition to the interdisciplinary unifying potential of our generic formal approach, the present work reveals the strong causal ties between the “softer" social conditions and their “hard" economic consequences.

  20. Computational and experimental study of laminar flames

    SciTech Connect

    Smooke, Mitchell

    2015-05-29

    During the past three years, our research has centered on an investigation of the effects of complex chemistry and detailed transport on the structure and extinction of hydrocarbon flames in coflowing axisymmetric configurations. We have pursued both computational and experimental aspects of the research in parallel on both steady-state and time-dependent systems. The computational work has focused on the application of accurate and efficient numerical methods for the solution of the steady-state and time-dependent boundary value problems describing the various reacting systems. Detailed experimental measurements were performed on axisymmetric coflow flames using two-dimensional imaging techniques. Previously, spontaneous Raman scattering, chemiluminescence, and laser-induced fluorescence were used to measure the temperature, major and minor species profiles. Particle image velocimetry (PIV) has been used to investigate velocity distributions and for calibration of time-varying flames. Laser-induced incandescence (LII) with an extinction calibration was used to determine soot volume fractions, while soot surface temperatures were measured with three-color optical pyrometry using a color digital camera. A blackbody calibration of the camera allows for determination of soot volume fraction as well, which can be compared with the LII measurements. More recently, we have concentrated on a detailed characterization of soot using a variety of techniques including time-resolved LII (TiRe-LII) for soot primary particles sizes, multi-angle light scattering (MALS) for soot radius of gyration, and spectrally-resolved line of sight attenuation (spec-LOSA). Combining the information from all of these soot measurements can be used to determine the soot optical properties, which are observed to vary significantly depending on spatial location and fuel dilution. Our goal has been to obtain a more fundamental understanding of the important fluid dynamic and chemical interactions in

  1. Trifluoperazine regulation of calmodulin binding to Fas: a computational study.

    PubMed

    Pan, Di; Yan, Qi; Chen, Yabing; McDonald, Jay M; Song, Yuhua

    2011-08-01

    Death-inducing signaling complex (DISC) formation is a critical step in Fas-mediated signaling for apoptosis. Previous experiments have demonstrated that the calmodulin (CaM) antagonist, trifluoperazine (TFP) regulates CaM-Fas binding and affects Fas-mediated DISC formation. In this study, we investigated the anti-cooperative characteristics of TFP binding to CaM and the effect of TFP on the CaM-Fas interaction from both structural and thermodynamic perspectives using combined molecular dynamics simulations and binding free energy analyses. We studied the interactions of different numbers of TFP molecules with CaM and explored the effects of the resulting conformational changes in CaM on CaM-Fas binding. Results from these analyses showed that the number of TFP molecules bound to CaM directly influenced α-helix formation and hydrogen bond occupancy within the α-helices of CaM, contributing to the conformational and motion changes in CaM. These changes affected CaM binding to Fas, resulting in secondary structural changes in Fas and conformational and motion changes of Fas in CaM-Fas complexes, potentially perturbing the recruitment of Fas-associated death domain for DISC formation. The computational results from this study reveal the structural and molecular mechanisms that underlie the role of the CaM antagonist, TFP, in regulation of CaM-Fas binding and Fas-mediated DISC formation in a concentration-dependent manner.

  2. A review of Computer Science resources for learning and teaching with K-12 computing curricula: an Australian case study

    NASA Astrophysics Data System (ADS)

    Falkner, Katrina; Vivian, Rebecca

    2015-10-01

    To support teachers to implement Computer Science curricula into classrooms from the very first year of school, teachers, schools and organisations seek quality curriculum resources to support implementation and teacher professional development. Until now, many Computer Science resources and outreach initiatives have targeted K-12 school-age children, with the intention to engage children and increase interest, rather than to formally teach concepts and skills. What is the educational quality of existing Computer Science resources and to what extent are they suitable for classroom learning and teaching? In this paper, an assessment framework is presented to evaluate the quality of online Computer Science resources. Further, a semi-systematic review of available online Computer Science resources was conducted to evaluate resources available for classroom learning and teaching and to identify gaps in resource availability, using the Australian curriculum as a case study analysis. The findings reveal a predominance of quality resources, however, a number of critical gaps were identified. This paper provides recommendations and guidance for the development of new and supplementary resources and future research.

  3. Implementing Japanese Lesson Study in Foreign Countries: Misconceptions Revealed

    ERIC Educational Resources Information Center

    Fujii, Toshiakira

    2014-01-01

    This paper is based on data gathered during visits to Uganda and Malawi, conducted by the International Math-teacher Professionalization Using Lesson Study (IMPULS) project and the Japanese International Cooperation Agency (JICA). The author's observations and experiences highlighted misconceptions about lesson study. The paper concludes that…

  4. Study Reveals Brain Biology behind Self-Control

    ERIC Educational Resources Information Center

    Sparks, Sarah D.

    2011-01-01

    A new neuroscience twist on a classic psychology study offers some clues to what makes one student able to buckle down for hours of homework before a test while his classmates party. The study published in the September 2011 edition of "Proceedings of the National Academy of Science," suggests environmental cues may "hijack" the brain's mechanisms…

  5. A Qualitative Study of ESL College Students' Attitudes about Computer-Assisted Writing Classes

    ERIC Educational Resources Information Center

    Ghandoura, Waleed A.

    2012-01-01

    The purpose of this qualitative study was to examine a sample of 13 English as a second language (ESL) students' attitudes about a computer-aided composition (WebCT) class. Participants were enrolled in an introductory writing course. Data from student diaries revealed that students enjoyed and valued the WebCT course and that the course…

  6. Preferred computer activities among individuals with dementia: a pilot study.

    PubMed

    Tak, Sunghee H; Zhang, Hongmei; Hong, Song Hee

    2015-03-01

    Computers offer new activities that are easily accessible, cognitively stimulating, and enjoyable for individuals with dementia. The current descriptive study examined preferred computer activities among nursing home residents with different severity levels of dementia. A secondary data analysis was conducted using activity observation logs from 15 study participants with dementia (severe = 115 logs, moderate = 234 logs, and mild = 124 logs) who participated in a computer activity program. Significant differences existed in preferred computer activities among groups with different severity levels of dementia. Participants with severe dementia spent significantly more time watching slide shows with music than those with both mild and moderate dementia (F [2,12] = 9.72, p = 0.003). Preference in playing games also differed significantly across the three groups. It is critical to consider individuals' interests and functional abilities when computer activities are provided for individuals with dementia. A practice guideline for tailoring computer activities is detailed.

  7. A Study of Factors Promoting Success in Computer Science Including Gender Differences

    NASA Astrophysics Data System (ADS)

    Cantwell Wilson, Brenda

    2002-03-01

    This study was conducted to determine factors that promote success in an introductory college computer science course and to determine what, if any, differences appear between genders on those factors. The model included math background, attribution for success/failure, self-efficacy, encouragement, comfort level in the course, work style preference, previous programming experience, previous non-programming computer experience, and gender as possible predictive factors for success in the computer science course. Subjects included 105 students enrolled in an introductory computer science course. The study revealed three predictive factors in the following order of importance: comfort level (with a positive influence), math background (with a positive influence), and attribution to luck (with a negative influence). No significant gender differences were found in these three factors. The study also revealed that both a formal class in programming (which had a positive correlation) and game playing (which had a negative correlation) were predictive of success. The study revealed a significant gender difference in game playing with males reporting more experience with playing games on the computer than females reported.

  8. Multitargeting by curcumin as revealed by molecular interaction studies

    PubMed Central

    Gupta, Subash C.; Prasad, Sahdeo; Kim, Ji Hye; Patchva, Sridevi; Webb, Lauren J.; Priyadarsini, Indira K.

    2012-01-01

    Curcumin (diferuloylmethane), the active ingredient in turmeric (Curcuma longa), is a highly pleiotropic molecule with anti-inflammatory, anti-oxidant, chemopreventive, chemosensitization, and radiosensitization activities. The pleiotropic activities attributed to curcumin come from its complex molecular structure and chemistry, as well as its ability to influence multiple signaling molecules. Curcumin has been shown to bind by multiple forces directly to numerous signaling molecules, such as inflammatory molecules, cell survival proteins, protein kinases, protein reductases, histone acetyltransferase, histone deacetylase, glyoxalase I, xanthine oxidase, proteasome, HIV1 integrase, HIV1 protease, sarco (endo) plasmic reticulum Ca2+ ATPase, DNA methyltransferases 1, FtsZ protofilaments, carrier proteins, and metal ions. Curcumin can also bind directly to DNA and RNA. Owing to its β-diketone moiety, curcumin undergoes keto–enol tautomerism that has been reported as a favorable state for direct binding. The functional groups on curcumin found suitable for interaction with other macromolecules include the α, β-unsaturated β-diketone moiety, carbonyl and enolic groups of the β-diketone moiety, methoxy and phenolic hydroxyl groups, and the phenyl rings. Various biophysical tools have been used to monitor direct interaction of curcumin with other proteins, including absorption, fluorescence, Fourier transform infrared (FTIR) and circular dichroism (CD) spectroscopy, surface plasmon resonance, competitive ligand binding, Forster type fluorescence resonance energy transfer (FRET), radiolabeling, site-directed mutagenesis, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), immunoprecipitation, phage display biopanning, electron microscopy, 1-anilino-8-naphthalene-sulfonate (ANS) displacement, and co-localization. Molecular docking, the most commonly employed computational tool for calculating binding affinities and predicting

  9. Academic computer science and gender: A naturalistic study investigating the causes of attrition

    NASA Astrophysics Data System (ADS)

    Declue, Timothy Hall

    Far fewer women than men take computer science classes in high school, enroll in computer science programs in college, or complete advanced degrees in computer science. The computer science pipeline begins to shrink for women even before entering college, but it is at the college level that the "brain drain" is the most evident numerically, especially in the first class taken by most computer science majors called "Computer Science 1" or CS-I. The result, for both academia and industry, is a pronounced technological gender disparity in academic and industrial computer science. The study revealed the existence of several factors influencing success in CS-I. First, and most clearly, the effect of attribution processes seemed to be quite strong. These processes tend to work against success for females and in favor of success for males. Likewise, evidence was discovered which strengthens theories related to prior experience and the perception that computer science has a culture which is hostile to females. Two unanticipated themes related to the motivation and persistence of successful computer science majors. The findings did not support the belief that females have greater logistical problems in computer science than males, or that females tend to have a different programming style than males which adversely affects the females' ability to succeed in CS-I.

  10. A computer simulation study of racemic mixtures

    NASA Astrophysics Data System (ADS)

    Largo, J.; Vega, C.; MacDowell, L. G.; Solana, J. R.

    A simple model for a chiral molecule is proposed. The model consists of a central atom bonded to four different atoms in tetrahedral coordination. Two different potentials were used to describe the pair potentials between atoms: the hard sphere potential and the Lennard-Jones potential. For both the hard sphere and the Lennard-Jones chiral models, computer simulations have been performed for the pure enantiomers and also for the racemic mixture. The racemic mixture consisted of an equimolar mixture of the two optically active enantiomers. It is found that the equations of state are the same, within statistical uncertainty, for the pure enantiomer fluid and for the racemic mixture. Only at high pressures does the racemic mixture seem to have a higher density, for a given pressure, than the pure enantiomer. Concering the structure, no difference is found in the site-site correlation functions between like and unlike molecules in the racemic mixture either at low or at high densities. However, small differences are found for the site-site correlations of the pure enantiomer and those of the racemic mixtures. In the Lennard-Jones model, similar conclusions are drawn. The extension of Wertheim's first-order perturbation theory, denoted bonded hard sphere theory (ARCHER, A. L., and JACKSON, G., 1991, Molec. Phys. , 73 , 881; AMOS, M. D., and JACKSON, G., 1992, J. chem. Phys. , 96 , 4604), successfully reproduces the simulation results for the hard chiral model. Virial coefficients of the hard chiral model up to the fourth have also been evaluated. Again, no differences are found between virial coefficients of the pure fluid and of the racemic mixture. All the results of this work illustrate the quasi-ideal behaviour of racemic mixtures in the fluid phase.

  11. Developmental palaeontology of Reptilia as revealed by histological studies.

    PubMed

    Scheyer, Torsten M; Klein, Nicole; Sander, P Martin

    2010-06-01

    Among the fossilized ontogenetic series known for tetrapods, only more basal groups like temnospondyl amphibians have been used extensively in developmental studies, whereas reptilian and synapsid data have been largely neglected so far. However, before such ontogenetic series can be subject to study, the relative age and affiliation of putative specimens within a series has to be verified. Bone histology has a long-standing tradition as being a source of palaeobiological and growth history data in fossil amniotes and indeed, the analysis of bone microstructures still remains the most important and most reliable tool for determining the absolute ontogenetic age of fossil vertebrates. It is also the only direct way to reconstruct life histories and growth strategies for extinct animals. Herein the record of bone histology among Reptilia and its application to elucidate and expand fossilized ontogenies as a source of developmental data are reviewed.

  12. Recent advances in maize nuclear proteomic studies reveal histone modifications.

    PubMed

    Casati, Paula

    2012-01-01

    The nucleus of eukaryotic organisms is highly dynamic and complex, containing different types of macromolecules including DNA, RNA, and a wide range of proteins. Novel proteomic applications have led to a better overall determination of nucleus protein content. Although nuclear plant proteomics is only at the initial phase, several studies have been reported and are summarized in this review using different plants species, such as Arabidopsis thaliana, rice, cowpea, onion, garden cress, and barrel clover. These include the description of the total nuclear or phospho-proteome (i.e., Arabidopsis, cowpea, onion), or the analysis of the differential nuclear proteome under different growth environments (i.e., Arabidopsis, rice, cowpea, onion, garden cress, and barrel clover). However, only few reports exist on the analysis of the maize nuclear proteome or its changes under various conditions. This review will present recent data on the study of the nuclear maize proteome, including the analysis of changes in posttranslational modifications in histone proteins. PMID:23248634

  13. An Exploratory Study of Apache Middle School Students' Computer Animation.

    ERIC Educational Resources Information Center

    Stokrocki, Mary; Buckpitt, Marcia

    The paper describes a participant observation study of a 3 week summer art program for Apache middle school students on the White Mountain Reservation. Computer art skills, specifically animation using a menu-driven computer paint program, were the focus of the investigation. Because it was in the context of a summer program, instruction was…

  14. Computer-Tutors and a Freshman Writer: A Protocol Study.

    ERIC Educational Resources Information Center

    Strickland, James

    Although there are many retrospective accounts from teachers and professional writers concerning the effect of computers on their writing, there are few real-time accounts of students struggling to simultaneously develop as writers and cope with computers. To fill this void in "testimonial data," a study examining talking-aloud protocols from a…

  15. Study Guide in Digital Computing and Related Mathematics.

    ERIC Educational Resources Information Center

    Stanford Univ., CA. School Mathematics Study Group.

    This SMSG study guide is designed to aid the teacher in acquiring familiarity with digital computer concepts or to further his/her knowledge of the field. Suitable references for important topics are categorized as central, peripheral, or advanced. Topics covered include: (1) nature and organization of computers; (2) problem analysis; (3)…

  16. NASA Computational Case Study: The Flight of Friendship 7

    NASA Technical Reports Server (NTRS)

    Simpson, David G.

    2012-01-01

    In this case study, we learn how to compute the position of an Earth-orbiting spacecraft as a function of time. As an exercise, we compute the position of John Glenn's Mercury spacecraft Friendship 7 as it orbited the Earth during the third flight of NASA's Mercury program.

  17. Predicting Computer Science Ph.D. Completion: A Case Study

    ERIC Educational Resources Information Center

    Cox, G. W.; Hughes, W. E., Jr.; Etzkorn, L. H.; Weisskopf, M. E.

    2009-01-01

    This paper presents the results of an analysis of indicators that can be used to predict whether a student will succeed in a Computer Science Ph.D. program. The analysis was conducted by studying the records of 75 students who have been in the Computer Science Ph.D. program of the University of Alabama in Huntsville. Seventy-seven variables were…

  18. Studying an Eulerian Computer Model on Different High-performance Computer Platforms and Some Applications

    NASA Astrophysics Data System (ADS)

    Georgiev, K.; Zlatev, Z.

    2010-11-01

    The Danish Eulerian Model (DEM) is an Eulerian model for studying the transport of air pollutants on large scale. Originally, the model was developed at the National Environmental Research Institute of Denmark. The model computational domain covers Europe and some neighbour parts belong to the Atlantic Ocean, Asia and Africa. If DEM model is to be applied by using fine grids, then its discretization leads to a huge computational problem. This implies that such a model as DEM must be run only on high-performance computer architectures. The implementation and tuning of such a complex large-scale model on each different computer is a non-trivial task. Here, some comparison results of running of this model on different kind of vector (CRAY C92A, Fujitsu, etc.), parallel computers with distributed memory (IBM SP, CRAY T3E, Beowulf clusters, Macintosh G4 clusters, etc.), parallel computers with shared memory (SGI Origin, SUN, etc.) and parallel computers with two levels of parallelism (IBM SMP, IBM BlueGene/P, clusters of multiprocessor nodes, etc.) will be presented. The main idea in the parallel version of DEM is domain partitioning approach. Discussions according to the effective use of the cache and hierarchical memories of the modern computers as well as the performance, speed-ups and efficiency achieved will be done. The parallel code of DEM, created by using MPI standard library, appears to be highly portable and shows good efficiency and scalability on different kind of vector and parallel computers. Some important applications of the computer model output are presented in short.

  19. Computational Assay of H7N9 Influenza Neuraminidase Reveals R292K Mutation Reduces Drug Binding Affinity

    NASA Astrophysics Data System (ADS)

    Woods, Christopher J.; Malaisree, Maturos; Long, Ben; McIntosh-Smith, Simon; Mulholland, Adrian J.

    2013-12-01

    The emergence of a novel H7N9 avian influenza that infects humans is a serious cause for concern. Of the genome sequences of H7N9 neuraminidase available, one contains a substitution of arginine to lysine at position 292, suggesting a potential for reduced drug binding efficacy. We have performed molecular dynamics simulations of oseltamivir, zanamivir and peramivir bound to H7N9, H7N9-R292K, and a structurally related H11N9 neuraminidase. They show that H7N9 neuraminidase is structurally homologous to H11N9, binding the drugs in identical modes. The simulations reveal that the R292K mutation disrupts drug binding in H7N9 in a comparable manner to that observed experimentally for H11N9-R292K. Absolute binding free energy calculations with the WaterSwap method confirm a reduction in binding affinity. This indicates that the efficacy of antiviral drugs against H7N9-R292K will be reduced. Simulations can assist in predicting disruption of binding caused by mutations in neuraminidase, thereby providing a computational `assay.'

  20. Studies of Ancient Lice Reveal Unsuspected Past Migrations of Vectors

    PubMed Central

    Drali, Rezak; Mumcuoglu, Kosta Y.; Yesilyurt, Gonca; Raoult, Didier

    2015-01-01

    Lice are among the oldest parasites of humans representing an excellent marker of the evolution and migration of our species over time. Here, we analyzed by real-time polymerase chain reaction (RT-PCR) developed in this study the mitochondrial DNA of seven ancient head louse eggs found on hair remains recovered from two sites in Israel: 1) five nits dating from Chalcolithic period (4,000 bc) were found in the Cave of the Treasure located at Nahal Mishmar, in the Judean Desert and 2) two nits dating from Early Islamic Period (ad 650–810) were found in Nahal Omer in the Arava Valley (between Dead Sea and Red Sea). Our results suggest that these eggs belonged to people originating from west Africa based on identification of the louse mitochondrial sub-clade specific to that region. PMID:26078317

  1. Epistatic study reveals two genetic interactions in blood pressure regulation

    PubMed Central

    2013-01-01

    Background Although numerous candidate gene and genome-wide association studies have been performed on blood pressure, a small number of regulating genetic variants having a limited effect have been identified. This phenomenon can partially be explained by possible gene-gene/epistasis interactions that were little investigated so far. Methods We performed a pre-planned two-phase investigation: in phase 1, one hundred single nucleotide polymorphisms (SNPs) in 65 candidate genes were genotyped in 1,912 French unrelated adults in order to study their two-locus combined effects on blood pressure (BP) levels. In phase 2, the significant epistatic interactions observed in phase 1 were tested in an independent population gathering 1,755 unrelated European adults. Results Among the 9 genetic variants significantly associated with systolic and diastolic BP in phase 1, some may act through altering the corresponding protein levels: SNPs rs5742910 (Padjusted≤0.03) and rs6046 (Padjusted =0.044) in F7 and rs1800469 (Padjusted ≤0.036) in TGFB1; whereas some may be functional through altering the corresponding protein structure: rs1800590 (Padjusted =0.028, SE=0.088) in LPL and rs2228570 (Padjusted ≤9.48×10-4) in VDR. The two epistatic interactions found for systolic and diastolic BP in the discovery phase: VCAM1 (rs1041163) * APOB (rs1367117), and SCGB1A1 (rs3741240) * LPL (rs1800590), were tested in the replication population and we observed significant interactions on DBP. In silico analyses yielded putative functional properties of the SNPs involved in these epistatic interactions trough the alteration of corresponding protein structures. Conclusions These findings support the hypothesis that different pathways and then different genes may act synergistically in order to modify BP. This could highlight novel pathophysiologic mechanisms underlying hypertension. PMID:23298194

  2. Toxin Diversity Revealed by a Transcriptomic Study of Ornithoctonus huwena

    PubMed Central

    He, Quanze; Liu, Jinyan; Luo, Ji; Zhu, Li; Lu, Shanshan; Huang, Pengfei; Chen, Xinyi; Zeng, Xiongzhi; Liang, Songping

    2014-01-01

    Spider venom comprises a mixture of compounds with diverse biological activities, which are used to capture prey and defend against predators. The peptide components bind a broad range of cellular targets with high affinity and selectivity, and appear to have remarkable structural diversity. Although spider venoms have been intensively investigated over the past few decades, venomic strategies to date have generally focused on high-abundance peptides. In addition, the lack of complete spider genomes or representative cDNA libraries has presented significant limitations for researchers interested in molecular diversity and understanding the genetic mechanisms of toxin evolution. In the present study, second-generation sequencing technologies, combined with proteomic analysis, were applied to determine the diverse peptide toxins in venom of the Chinese bird spider Ornithoctonus huwena. In total, 626 toxin precursor sequences were retrieved from transcriptomic data. All toxin precursors clustered into 16 gene superfamilies, which included six novel superfamilies and six novel cysteine patterns. A surprisingly high number of hypermutations and fragment insertions/deletions were detected, which accounted for the majority of toxin gene sequences with low-level expression. These mutations contribute to the formation of diverse cysteine patterns and highly variable isoforms. Furthermore, intraspecific venom variability, in combination with variable transcripts and peptide processing, contributes to the hypervariability of toxins in venoms, and associated rapid and adaptive evolution of toxins for prey capture and defense. PMID:24949878

  3. A Trade-Off Study Revealing Nested Timescales of Constraint

    PubMed Central

    Wijnants, M. L.; Cox, R. F. A.; Hasselman, F.; Bosman, A. M. T.; Van Orden, G.

    2012-01-01

    This study investigates human performance in a cyclic Fitts task at three different scales of observation, either in the presence (difficult condition) or in the absence (easy condition) of a speed–accuracy trade-off. At the fastest scale, the harmonicity of the back and forth movements, which reflects the dissipation of mechanical energy, was measured within the timeframe of single trials. At an intermediate scale, speed and accuracy measures were determined over a trial. The slowest scale pertains to the temporal structure of movement variability, which evolves over multiple trials. In the difficult condition, reliable correlations across each of the measures corroborated a coupling of nested scales of performance. Participants who predominantly emphasized the speed-side of the trade-off (despite the instruction to be both fast and accurate) produced more harmonic movements and clearer 1/f scaling in the produced movement time series, but were less accurate and produced more random variability in the produced movement amplitudes (vice versa for more accurate participants). This implied that speed–accuracy trade-off was accompanied by a trade-off between temporal and spatial streams of 1/f scaling, as confirmed by entropy measures. In the easy condition, however, no trade-offs nor couplings among scales of performance were observed. Together, these results suggest that 1/f scaling is more than just a byproduct of cognition. These findings rather support the claim that interaction-dominant dynamics constitute a coordinative basis for goal-directed behavior. PMID:22654760

  4. A computed tomographic study of schizophrenia.

    PubMed

    Siddharatha; Lal, N; Tewari, S C; Dalal, P K; Kohli, N; Srivastava, S

    1997-04-01

    Fifty schizophrenic patients fulfilling DSM-III-R criteria, and group matched normal healthy controls were selected for the study The case and control groups have been compared in terms of VBR, WSF and WTF. In the study schizophrenics have been divided into positive, negative and mixed subgroups on basis of SAPS and SANS, and these subgroups are compared with each other for VBR, WSF & WTF. Tomographic abnormalities were noted in schizophrenics, particularly with negative and mixed subtypes, when compared to controls. PMID:21584057

  5. Educational NASA Computational and Scientific Studies (enCOMPASS)

    NASA Technical Reports Server (NTRS)

    Memarsadeghi, Nargess

    2013-01-01

    Educational NASA Computational and Scientific Studies (enCOMPASS) is an educational project of NASA Goddard Space Flight Center aimed at bridging the gap between computational objectives and needs of NASA's scientific research, missions, and projects, and academia's latest advances in applied mathematics and computer science. enCOMPASS achieves this goal via bidirectional collaboration and communication between NASA and academia. Using developed NASA Computational Case Studies in university computer science/engineering and applied mathematics classes is a way of addressing NASA's goals of contributing to the Science, Technology, Education, and Math (STEM) National Objective. The enCOMPASS Web site at http://encompass.gsfc.nasa.gov provides additional information. There are currently nine enCOMPASS case studies developed in areas of earth sciences, planetary sciences, and astrophysics. Some of these case studies have been published in AIP and IEEE's Computing in Science and Engineering magazines. A few university professors have used enCOMPASS case studies in their computational classes and contributed their findings to NASA scientists. In these case studies, after introducing the science area, the specific problem, and related NASA missions, students are first asked to solve a known problem using NASA data and past approaches used and often published in a scientific/research paper. Then, after learning about the NASA application and related computational tools and approaches for solving the proposed problem, students are given a harder problem as a challenge for them to research and develop solutions for. This project provides a model for NASA scientists and engineers on one side, and university students, faculty, and researchers in computer science and applied mathematics on the other side, to learn from each other's areas of work, computational needs and solutions, and the latest advances in research and development. This innovation takes NASA science and

  6. Open-Source Software in Computational Research: A Case Study

    DOE PAGES

    Syamlal, Madhava; O'Brien, Thomas J.; Benyahia, Sofiane; Gel, Aytekin; Pannala, Sreekanth

    2008-01-01

    A case study of open-source (OS) development of the computational research software MFIX, used for multiphase computational fluid dynamics simulations, is presented here. The verification and validation steps required for constructing modern computational software and the advantages of OS development in those steps are discussed. The infrastructure used for enabling the OS development of MFIX is described. The impact of OS development on computational research and education in gas-solids flow, as well as the dissemination of information to other areas such as geophysical and volcanology research, is demonstrated. This study shows that the advantages of OS development were realized inmore » the case of MFIX: verification by many users, which enhances software quality; the use of software as a means for accumulating and exchanging information; the facilitation of peer review of the results of computational research.« less

  7. Osmosis : a molecular dynamics computer simulation study

    NASA Astrophysics Data System (ADS)

    Lion, Thomas

    Osmosis is a phenomenon of critical importance in a variety of processes ranging from the transport of ions across cell membranes and the regulation of blood salt levels by the kidneys to the desalination of water and the production of clean energy using potential osmotic power plants. However, despite its importance and over one hundred years of study, there is an ongoing confusion concerning the nature of the microscopic dynamics of the solvent particles in their transfer across the membrane. In this thesis the microscopic dynamical processes underlying osmotic pressure and concentration gradients are investigated using molecular dynamics (MD) simulations. I first present a new derivation for the local pressure that can be used for determining osmotic pressure gradients. Using this result, the steady-state osmotic pressure is studied in a minimal model for an osmotic system and the steady-state density gradients are explained using a simple mechanistic hopping model for the solvent particles. The simulation setup is then modified, allowing us to explore the timescales involved in the relaxation dynamics of the system in the period preceding the steady state. Further consideration is also given to the relative roles of diffusive and non-diffusive solvent transport in this period. Finally, in a novel modification to the classic osmosis experiment, the solute particles are driven out-of-equilibrium by the input of energy. The effect of this modification on the osmotic pressure and the osmotic ow is studied and we find that active solute particles can cause reverse osmosis to occur. The possibility of defining a new "osmotic effective temperature" is also considered and compared to the results of diffusive and kinetic temperatures..

  8. Enrique: A case study of a gifted computer user

    SciTech Connect

    Sesko, S C

    2000-03-17

    The author has been investigating the affective and intellectual views that gifted children have about computers. These studies have used various methodological approaches in order to develop a broad perspective on the issues involved in this topic. The author has used survey instruments (Sesko, 1998) and interview techniques (Sesko, 1999) to capture both statistical and narrative data. The objective of this study is to explore in depth the interactions that one student has with the machine and its applications. The driver for this and the previous studies was the paucity of research in the area of gifted and talented children and their involvement with what has become the primary intellectual tool of the century (Turkel, 1984). The second reason is that it has been posited that the intellectual characteristics of gifted children should enable those who are interested in computers to achieve a high level of proficiency with either computer applications or programming. Further, the ability to learn things at a young age should allow gifted children who use computers to develop a large variety of computer-based activities. The author has shown evidence to support these ideas in previous work. Finally, as Hausman (1985) claims, facilities with computers should allow these children to create new activities for using computers. The author found no published research to demonstrate whether they do; but still believes the results of this case study strongly support Hausman's contentions.

  9. Experimental and computational study of thaumasite structure

    SciTech Connect

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

    2014-05-01

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

  10. Computational studies of quantum spin systems

    NASA Astrophysics Data System (ADS)

    Wang, Ling

    Quantum spin models are important for studying the magnetic behavior of strongly correlated electronic insulators. Specifically, the 2D S = 1/2 Heisenberg model closely captures the antiferromagnetic state of CuO2 layers of the high-Tc superconductor parent compounds at half band filling. Introducing competing interactions or disorder can drive quantum phase transitions to other new states. I use the stochastic series expansion (SSE) quantum Monte Carlo (QMC) method and finite-size scaling to study the quantum critical points of two Heisenberg bilayers, each with intra- and inter-plane couplings J and J⊥. Tuning the inter- to intra-layer coupling constant ratio g = J⊥ /J drives a quantum phase transition between the Neel ordered state and a quantum disordered state. I discuss the ground-state finite-size scaling properties of three different quantities and extract the critical value of the coupling ratio gc. The results improve gc by more than an order of magnitude over the previous best estimates. Upon doping with static non-magnetic impurities, (e.g., substituting Cu with Zn), the cuprate layer is driven through a percolation phase transition. While the static properties are described by 2D classical percolation, the dynamical properties are quantum mechanical. I use exact diagonalization to calculate the lowest excitation gap Delta and use SSE to study an upper bound for Delta obtained from sum rules. Scaling the gap distribution with the cluster length L, a dynamic exponent z ≈ 2Df is obtained, where Df is the fractal dimensionality of the percolating cluster. I present several arguments showing that the low-energy excitations are due to weakly coupled effective moments formed owing to local imbalance in sublattice occupation. Many interesting quantum spin models lead to negative signs in the importance weight used in QMC sampling, and thus this method cannot be used. Matrix product states (MPSs) and tensor product states (TPSs) have recently been

  11. Computational Studies of Venom Peptides Targeting Potassium Channels.

    PubMed

    Chen, Rong; Chung, Shin-Ho

    2015-12-01

    Small peptides isolated from the venom of animals are potential scaffolds for ion channel drug discovery. This review article mainly focuses on the computational studies that have advanced our understanding of how various toxins interfere with the function of K⁺ channels. We introduce the computational tools available for the study of toxin-channel interactions. We then discuss how these computational tools have been fruitfully applied to elucidate the mechanisms of action of a wide range of venom peptides from scorpions, spiders, and sea anemone. PMID:26633507

  12. Computational Studies of Venom Peptides Targeting Potassium Channels

    PubMed Central

    Chen, Rong; Chung, Shin-Ho

    2015-01-01

    Small peptides isolated from the venom of animals are potential scaffolds for ion channel drug discovery. This review article mainly focuses on the computational studies that have advanced our understanding of how various toxins interfere with the function of K+ channels. We introduce the computational tools available for the study of toxin-channel interactions. We then discuss how these computational tools have been fruitfully applied to elucidate the mechanisms of action of a wide range of venom peptides from scorpions, spiders, and sea anemone. PMID:26633507

  13. The effect of infected external computers on the spread of viruses: A compartment modeling study

    NASA Astrophysics Data System (ADS)

    Yang, Lu-Xing; Yang, Xiaofan

    2013-12-01

    Inevitably, there exist infected computers outside of the Internet. This paper aims to understand how infected external computers affect the spread of computer viruses. For that purpose, a new virus-antivirus spreading model, which takes into account the effect of infected/immune external computers, is established. A systematic study shows that, unlike most previous models, the proposed model admits no virus-free equilibrium and admits a globally asymptotically stable viral equilibrium. This result implies that it would be practically impossible to eradicate viruses on the Internet. As a result, inhibiting the virus prevalence to below an acceptable level would be the next best thing. A theoretical study reveals the effect of different parameters on the steady virus prevalence. On this basis, a number of suggestions are made so as to contain virus spreading.

  14. A study of computer-related upper limb discomfort and computer vision syndrome.

    PubMed

    Sen, A; Richardson, Stanley

    2007-12-01

    Personal computers are one of the commonest office tools in Malaysia today. Their usage, even for three hours per day, leads to a health risk of developing Occupational Overuse Syndrome (OOS), Computer Vision Syndrome (CVS), low back pain, tension headaches and psychosocial stress. The study was conducted to investigate how a multiethnic society in Malaysia is coping with these problems that are increasing at a phenomenal rate in the west. This study investigated computer usage, awareness of ergonomic modifications of computer furniture and peripherals, symptoms of CVS and risk of developing OOS. A cross-sectional questionnaire study of 136 computer users was conducted on a sample population of university students and office staff. A 'Modified Rapid Upper Limb Assessment (RULA) for office work' technique was used for evaluation of OOS. The prevalence of CVS was surveyed incorporating a 10-point scoring system for each of its various symptoms. It was found that many were using standard keyboard and mouse without any ergonomic modifications. Around 50% of those with some low back pain did not have an adjustable backrest. Many users had higher RULA scores of the wrist and neck suggesting increased risk of developing OOS, which needed further intervention. Many (64%) were using refractive corrections and still had high scores of CVS commonly including eye fatigue, headache and burning sensation. The increase of CVS scores (suggesting more subjective symptoms) correlated with increase in computer usage spells. It was concluded that further onsite studies are needed, to follow up this survey to decrease the risks of developing CVS and OOS amongst young computer users. PMID:18572794

  15. Linking Different Cultures by Computers: A Study of Computer-Assisted Music Notation Instruction.

    ERIC Educational Resources Information Center

    Chen, Steve Shihong; Dennis, J. Richard

    1993-01-01

    Describes a study that investigated the feasibility of using computers to teach music notation systems to Chinese students, as well as to help Western educators study Chinese music and its number notation system. Topics discussed include students' learning sequences; HyperCard software; hypermedia and graphic hypertext indexing; and the…

  16. Synthesis, spectral, computational and thermal analysis studies of metallocefotaxime antibiotics.

    PubMed

    Masoud, Mamdouh S; Ali, Alaa E; Elasala, Gehan S

    2015-01-01

    Cefotaxime metal complexes of Cr(III), Mn(II), Fe(III), Co(II), Ni(II), Cu(II), Zn(II), Cd(II), Hg(II) and two mixed metals complexes of (Fe,Cu) and (Fe,Ni) were synthesized and characterized by elemental analysis, IR, electronic spectra, magnetic susceptibility and ESR spectra. The studies proved that cefotaxime may act as mono, bi, tri and tetra-dentate ligand through oxygen atoms of lactam carbonyl, carboxylic or amide carbonyl groups and nitrogen atom of thiazole ring. From the magnetic measurements and electronic spectral data, octahedral structures were proposed for all complexes. Quantum chemical methods have been performed for cefotaxime to calculate charges, bond lengths, bond angles, dihedral angles, electronegativity (χ), chemical potential (μ), global hardness (η), softness (σ) and the electrophilicity index (ω). The thermal decomposition of the prepared metals complexes was studied by TGA, DTA and DSC techniques. Thermogravimetric studies revealed the presence of lattice or coordinated water molecules in all the prepared complexes. The decomposition mechanisms were suggested. The thermal decomposition of the complexes ended with the formation of metal oxides and carbon residue as a final product except in case of Hg complex, sublimation occur at the temperature range 376.5-575.0 °C so, only carbon residue was produced during thermal decomposition. The orders of chemical reactions (n) were calculated via the peak symmetry method and the activation parameters were computed from the thermal decomposition data. The geometries of complexes may be converted from Oh to Td during the thermal decomposition steps.

  17. Calorimetric and computational study of indanones.

    PubMed

    Matos, M Agostinha R; Miranda, Margarida S; Monte, Manuel J S; Santos, Luís M N B F; Morais, Victor M F; Chickos, James S; Umnahanant, Patamaporn; Liebman, Joel F

    2007-11-01

    Condensed phase standard (p degrees = 0.1 MPa) molar enthalpies of formation for 1-indanone, 2-indanone, and 1,3-indandione were derived from the standard molar enthalpies of combustion, in oxygen, at T = 298.15 K, measured by static bomb combustion calorimetry. The standard molar enthalpies of sublimation for 1-indanone and 2-indanone, at T = 298.15 K, were measured both by correlation-gas chromatography and by Calvet microcalorimetry leading to a mean value for each compound. For 1,3-indandione, the standard molar enthalpy of sublimation was derived from the vapor pressure dependence on temperature. The following enthalpies of formation in gas phase, at T = 298.15 K, were then derived: 1-indanone, -64.0 +/- 3.8 kJ mol(-1); 2-indanone, -56.6 +/- 4.8 kJ mol(-1); 1,3-indandione, -165.0 +/- 2.6 kJ mol(-1). The vaporization and fusion enthalpies of the indanones studied are also reported. In addition, theoretical calculations using the density functional theory with the B3LYP and MPW1B95 energy functionals and the 6-311G** and cc-pVTZ basis sets have been performed for these molecules and the corresponding one-ring species to obtain the most stable geometries and to access their energetic stabilities. PMID:17929782

  18. Cluster Mechanism of Homogeneous Crystallization (Computer Study)

    NASA Astrophysics Data System (ADS)

    Belashchenko, D. K.

    2008-12-01

    A molecular dynamics (MD) study of homogeneous crystallization of liquid rubidium is conducted with an inter-particle pair potential. The equilibrium crystallization temperature of the models was 313 K. Models consisted of 500, 998, and 1968 particles in a basic cube. The main investigation method was as follows: to detect (along the MD run) the atoms with Voronoi polyhedrons (VP) of 0608 type (“0608-atoms,” as in a bcc crystal) and to detect the bound groups of 0608-atoms (“0608-clusters”) that could play the role of the seeds in crystallization. Full crystallization was observed only at temperatures lower than 185 K with the creation of a predominant bcc crystal. The crystallization mechanism of Rb models differs drastically from the mechanism adopted in classical nucleation theory. It consists of the growth of the total number of 0608-atoms on cooling and the formation of 0608-clusters, analogous to the case of coagulation of solute for a supersaturated two-component solution. At the first stage of the process the clusters have a very loose structure (something like medusa or octopus with many tentacles) and include inside atoms with other Voronoi polyhedron types. The dimensions of clusters quickly increase and approach those of the basic cube. 0608-atoms play the leading role in the crystallization process and activate the transition of the atoms involved in the 0608-coordination. The fast growth of the maximum cluster begins after it attains a critical size (about 150 0608-atoms). The fluctuations of cluster sizes are very important in the creation of a 0608-cluster of critical (threshold) size. These fluctuations are especially large in the interval from 180 K to 185 K.

  19. Hispanic women overcoming deterrents to computer science: A phenomenological study

    NASA Astrophysics Data System (ADS)

    Herling, Lourdes

    The products of computer science are important to all aspects of society and are tools in the solution of the world's problems. It is, therefore, troubling that the United States faces a shortage in qualified graduates in computer science. The number of women and minorities in computer science is significantly lower than the percentage of the U.S. population which they represent. The overall enrollment in computer science programs has continued to decline with the enrollment of women declining at a higher rate than that of men. This study addressed three aspects of underrepresentation about which there has been little previous research: addressing computing disciplines specifically rather than embedding them within the STEM disciplines, what attracts women and minorities to computer science, and addressing the issues of race/ethnicity and gender in conjunction rather than in isolation. Since women of underrepresented ethnicities are more severely underrepresented than women in general, it is important to consider whether race and ethnicity play a role in addition to gender as has been suggested by previous research. Therefore, this study examined what attracted Hispanic women to computer science specifically. The study determines whether being subjected to multiple marginalizations---female and Hispanic---played a role in the experiences of Hispanic women currently in computer science. The study found five emergent themes within the experiences of Hispanic women in computer science. Encouragement and role models strongly influenced not only the participants' choice to major in the field, but to persist as well. Most of the participants experienced a negative atmosphere and feelings of not fitting in while in college and industry. The interdisciplinary nature of computer science was the most common aspect that attracted the participants to computer science. The aptitudes participants commonly believed are needed for success in computer science are the Twenty

  20. Vector computer implementation of power flow outage studies

    SciTech Connect

    Granelli, G.P.; Montagna, M.; Pasini, G.L. ); Marannino, P. )

    1992-05-01

    This paper presents an application of vector and parallel processing to power flow outage studies on large-scale networks. Standard sparsity programming is not well suited to the capabilities of vector and parallel computers because of the extremely short vectors processed in load flow studies. In order to improve computation efficiency, the operations required to perform both forward/backward solution and power residual calculation are gathered in the form of long FORTRAN DO loops. Two algorithms are proposed and compared with the results of a program written for scalar processing. Simulations for the outage studies on IEEE standard networks and some different configurations of the Italian and European (UCPTE) EHV systems are run on a CRAY Y-MP8/432 vector computer (and partially on a IBM 3090/200S VF). The multitasking facility of the CRAY computer is also exploited in order to shorten the wall clock time required by a complete outage simulation.

  1. A Case Study on the Use of Blended Learning to Encourage Computer Science Students to Study

    ERIC Educational Resources Information Center

    Perez-Marin, Diana; Pascual-Nieto, Ismael

    2012-01-01

    Students tend to procrastinate. In particular, Computer Science students tend to reduce the number of hours devoted to study concepts after class. In this paper, a case study on the use of Blended Learning to encourage Computer Science students to study is described. Furthermore, an experiment in which the reaction of 131 Computer Science…

  2. Computer-assisted image analysis of human cilia and Chlamydomonas flagella reveals both similarities and differences in axoneme structure.

    PubMed

    O'Toole, Eileen T; Giddings, Thomas H; Porter, Mary E; Ostrowski, Lawrence E

    2012-08-01

    In the past decade, investigations from several different fields have revealed the critical role of cilia in human health and disease. Because of the highly conserved nature of the basic axonemal structure, many different model systems have proven useful for the study of ciliopathies, especially the unicellular, biflagellate green alga Chlamydomonas reinhardtii. Although the basic axonemal structure of cilia and flagella is highly conserved, these organelles often perform specialized functions unique to the cell or tissue in which they are found. These differences in function are likely reflected in differences in structural organization. In this work, we directly compare the structure of isolated axonemes from human cilia and Chlamydomonas flagella to identify similarities and differences that potentially play key roles in determining their functionality. Using transmission electron microscopy and 2D image averaging techniques, our analysis has confirmed the overall structural similarity between these two species, but also revealed clear differences in the structure of the outer dynein arms, the central pair projections, and the radial spokes. We also show how the application of 2D image averaging can clarify the underlying structural defects associated with primary ciliary dyskinesia (PCD). Overall, our results document the remarkable similarity between these two structures separated evolutionarily by over a billion years, while highlighting several significant differences, and demonstrate the potential of 2D image averaging to improve the diagnosis and understanding of PCD.

  3. A Reflective Study into Children's Cognition When Making Computer Games

    ERIC Educational Resources Information Center

    Allsop, Yasemin

    2016-01-01

    In this paper, children's mental activities when making digital games are explored. Where previous studies have mainly focused on children's learning, this study aimed to unfold the children's thinking process for learning when making computer games. As part of an ongoing larger scale study, which adopts an ethnographic approach, this research…

  4. Nanomaterials in biological environment: a review of computer modelling studies.

    PubMed

    Makarucha, A J; Todorova, N; Yarovsky, I

    2011-02-01

    Nanotechnology is set to impact a vast range of fields, including computer science, materials technology, engineering/manufacturing and medicine. As nanotechnology grows so does exposure to nanostructured materials, thus investigation of the effects of nanomaterials on biological systems is paramount. Computational techniques can allow investigation of these systems at the nanoscale, providing insight into otherwise unexaminable properties, related to both the intentional and unintentional effects of nanomaterials. Herein, we review the current literature involving computational modelling of nanoparticles and biological systems. This literature has highlighted the common modes in which nanostructured materials interact with biological molecules such as membranes, peptides/proteins and DNA. Hydrophobic interactions are the most favoured, with π-stacking of the aromatic side-chains common when binding to a carbonaceous nanoparticle or surface. van der Waals forces are found to dominate in the insertion process of DNA molecules into carbon nanotubes. Generally, nanoparticles have been observed to disrupt the tertiary structure of proteins due to the curvature and atomic arrangement of the particle surface. Many hydrophobic nanoparticles are found to be able to transverse a lipid membrane, with some nanoparticles even causing mechanical damage to the membrane, thus potentially leading to cytotoxic effects. Current computational techniques have revealed how some nanoparticles interact with biological systems. However, further research is required to determine both useful applications and possible cytotoxic effects that nanoparticles may have on DNA, protein and membrane structure and function within biosystems.

  5. Quantitative error analysis for computer assisted navigation: a feasibility study

    PubMed Central

    Güler, Ö.; Perwög, M.; Kral, F.; Schwarm, F.; Bárdosi, Z. R.; Göbel, G.; Freysinger, W.

    2013-01-01

    Purpose The benefit of computer-assisted navigation depends on the registration process, at which patient features are correlated to some preoperative imagery. The operator-induced uncertainty in localizing patient features – the User Localization Error (ULE) - is unknown and most likely dominating the application accuracy. This initial feasibility study aims at providing first data for ULE with a research navigation system. Methods Active optical navigation was done in CT-images of a plastic skull, an anatomic specimen (both with implanted fiducials) and a volunteer with anatomical landmarks exclusively. Each object was registered ten times with 3, 5, 7, and 9 registration points. Measurements were taken at 10 (anatomic specimen and volunteer) and 11 targets (plastic skull). The active NDI Polaris system was used under ideal working conditions (tracking accuracy 0.23 mm root mean square, RMS; probe tip calibration was 0.18 mm RMS. Variances of tracking along the principal directions were measured as 0.18 mm2, 0.32 mm2, and 0.42 mm2. ULE was calculated from predicted application accuracy with isotropic and anisotropic models and from experimental variances, respectively. Results The ULE was determined from the variances as 0.45 mm (plastic skull), 0.60 mm (anatomic specimen), and 4.96 mm (volunteer). The predicted application accuracy did not yield consistent values for the ULE. Conclusions Quantitative data of application accuracy could be tested against prediction models with iso- and anisotropic noise models and revealed some discrepancies. This could potentially be due to the facts that navigation and one prediction model wrongly assume isotropic noise (tracking is anisotropic), while the anisotropic noise prediction model assumes an anisotropic registration strategy (registration is isotropic in typical navigation systems). The ULE data are presumably the first quantitative values for the precision of localizing anatomical landmarks and implanted fiducials

  6. An Empirical Study of Pupils' Attitudes to Computers and Robots.

    ERIC Educational Resources Information Center

    Moore, J. L.

    1985-01-01

    Describes a study which utilized a Likert type questionnaire to assess seven scales of secondary pupils' attitudes toward computers and robotics (school, leisure, career, employment, social, threat, future) and investigated pupils' scores on functions of their sex, general academic ability, course of study, and microcomputer experience. (MBR)

  7. Computing requirements for S. S. C. accelerator design and studies

    SciTech Connect

    Dragt, A.; Talman, R.; Siemann, R.; Dell, G.F.; Leemann, B.; Leemann, C.; Nauenberg, U.; Peggs, S.; Douglas, D.

    1984-01-01

    We estimate the computational hardware resources that will be required for accelerator physics studies during the design of the Superconducting SuperCollider. It is found that both Class IV and Class VI facilities (1) will be necessary. We describe a user environment for these facilities that is desirable within the context of accelerator studies. An acquisition scenario for these facilities is presented.

  8. Experiences of Computer Science Curriculum Design: A Phenomenological Study

    ERIC Educational Resources Information Center

    Sloan, Arthur; Bowe, Brian

    2015-01-01

    This paper presents a qualitative study of 12 computer science lecturers' experiences of curriculum design of several degree programmes during a time of transition from year-long to semesterised courses, due to institutional policy change. The background to the study is outlined, as are the reasons for choosing the research methodology. The main…

  9. Empirical evidence for musical syntax processing? Computer simulations reveal the contribution of auditory short-term memory.

    PubMed

    Bigand, Emmanuel; Delbé, Charles; Poulin-Charronnat, Bénédicte; Leman, Marc; Tillmann, Barbara

    2014-01-01

    During the last decade, it has been argued that (1) music processing involves syntactic representations similar to those observed in language, and (2) that music and language share similar syntactic-like processes and neural resources. This claim is important for understanding the origin of music and language abilities and, furthermore, it has clinical implications. The Western musical system, however, is rooted in psychoacoustic properties of sound, and this is not the case for linguistic syntax. Accordingly, musical syntax processing could be parsimoniously understood as an emergent property of auditory memory rather than a property of abstract processing similar to linguistic processing. To support this view, we simulated numerous empirical studies that investigated the processing of harmonic structures, using a model based on the accumulation of sensory information in auditory memory. The simulations revealed that most of the musical syntax manipulations used with behavioral and neurophysiological methods as well as with developmental and cross-cultural approaches can be accounted for by the auditory memory model. This led us to question whether current research on musical syntax can really be compared with linguistic processing. Our simulation also raises methodological and theoretical challenges to study musical syntax while disentangling the confounded low-level sensory influences. In order to investigate syntactic abilities in music comparable to language, research should preferentially use musical material with structures that circumvent the tonal effect exerted by psychoacoustic properties of sounds.

  10. 11beta-Hydroxysteroid dehydrogenase 1 inhibiting constituents from Eriobotrya japonica revealed by bioactivity-guided isolation and computational approaches.

    PubMed

    Rollinger, Judith M; Kratschmar, Denise V; Schuster, Daniela; Pfisterer, Petra H; Gumy, Christel; Aubry, Evelyne M; Brandstötter, Sarah; Stuppner, Hermann; Wolber, Gerhard; Odermatt, Alex

    2010-02-15

    The inhibition of 11beta-hydroxysteroid dehydrogenase 1 (11beta-HSD1), which catalyzes the conversion of inactive 11-ketoglucocorticoids to active 11beta-hydroxyglucocorticoids, emerged as promising strategy to treat symptoms of the metabolic syndrome, including obesity and type 2 diabetes. In this study the leaves of the anti-diabetic medicinal plant loquat (Eriobotrya japonica) were phytochemically investigated following hints from a pharmacophore-based virtual screening and a bioactivity-guided approach. Determination of the 11beta-HSD1 and 11beta-HSD2 inhibitory activities in cell lysates revealed triterpenes from the ursane type as selective, low micro-molar inhibitors of 11beta-HSD1, that is, corosolic acid (1), 3-epicorosolic acid methyl ester (4), 2-alpha hydroxy-3-oxo urs-12-en-28-oic acid (6), tormentic acid methyl ester (8), and ursolic acid (9). Importantly, a mixture of loquat constituents with moderate activities displayed a pronounced additive effect. By means of molecular modeling studies and the identification of the 11beta-HSD1-inhibiting 11-keto-ursolic acid (17) and 3-acetyl-11-keto-ursolic acid (18) a structure-activity relationship was deduced for this group of pentacyclic triterpenes. The mechanism of action elucidated in the present work together with the previously determined pharmacological activities provides these natural products with an astonishing multi-targeted anti-diabetic profile.

  11. Empirical evidence for musical syntax processing? Computer simulations reveal the contribution of auditory short-term memory

    PubMed Central

    Bigand, Emmanuel; Delbé, Charles; Poulin-Charronnat, Bénédicte; Leman, Marc; Tillmann, Barbara

    2014-01-01

    During the last decade, it has been argued that (1) music processing involves syntactic representations similar to those observed in language, and (2) that music and language share similar syntactic-like processes and neural resources. This claim is important for understanding the origin of music and language abilities and, furthermore, it has clinical implications. The Western musical system, however, is rooted in psychoacoustic properties of sound, and this is not the case for linguistic syntax. Accordingly, musical syntax processing could be parsimoniously understood as an emergent property of auditory memory rather than a property of abstract processing similar to linguistic processing. To support this view, we simulated numerous empirical studies that investigated the processing of harmonic structures, using a model based on the accumulation of sensory information in auditory memory. The simulations revealed that most of the musical syntax manipulations used with behavioral and neurophysiological methods as well as with developmental and cross-cultural approaches can be accounted for by the auditory memory model. This led us to question whether current research on musical syntax can really be compared with linguistic processing. Our simulation also raises methodological and theoretical challenges to study musical syntax while disentangling the confounded low-level sensory influences. In order to investigate syntactic abilities in music comparable to language, research should preferentially use musical material with structures that circumvent the tonal effect exerted by psychoacoustic properties of sounds. PMID:24936174

  12. X-Ray Computed Tomography Reveals the Response of Root System Architecture to Soil Texture1[OPEN

    PubMed Central

    Rogers, Eric D.; Monaenkova, Daria; Mijar, Medhavinee; Goldman, Daniel I.

    2016-01-01

    Root system architecture (RSA) impacts plant fitness and crop yield by facilitating efficient nutrient and water uptake from the soil. A better understanding of the effects of soil on RSA could improve crop productivity by matching roots to their soil environment. We used x-ray computed tomography to perform a detailed three-dimensional quantification of changes in rice (Oryza sativa) RSA in response to the physical properties of a granular substrate. We characterized the RSA of eight rice cultivars in five different growth substrates and determined that RSA is the result of interactions between genotype and growth environment. We identified cultivar-specific changes in RSA in response to changing growth substrate texture. The cultivar Azucena exhibited low RSA plasticity in all growth substrates, whereas cultivar Bala root depth was a function of soil hardness. Our imaging techniques provide a framework to study RSA in different growth environments, the results of which can be used to improve root traits with agronomic potential. PMID:27208237

  13. Life under tension: Computational studies of proteins involved in mechanotransduction

    NASA Astrophysics Data System (ADS)

    Sotomayor, Marcos Manuel

    Living organisms rely on macroscopic and microscopic structures that produce and transform force: from mechanical motion of our muscles and bones to sound transduction and cell volume regulation, handling of forces is essential to life. Investigation of the microscopic machinery behind force generation and transduction in the cell has only become possible with recent advances in x-ray crystallography, nuclear magnetic resonance spectroscopy, single-molecule force spectroscopy, and computer modeling. In this thesis, molecular dynamics simulations have been used to study proteins that transform forces into biochemical signals (mechanotransduction). The first protein studied is the mechanosensitive channel of small conductance MscS. This membrane channel has been proposed to act as a safety valve during osmotic shock, facilitating the release of ions and small solutes upon increase in membrane tension, thereby preventing bacterial cells from bursting. The second set of proteins studied are ankyrin and cadherin repeats, likely forming part of the transduction apparatus in hearing and other mechanical senses. Simulations of all these proteins went beyond the standard approach in which only equilibrium properties are monitored; we adopted and developed strategies in which external electric fields and forces are used to probe their response and function and at the same time produce verifiable predictions. The outcome of the simulations performed on MscS, in close collaborations with experimentalists, allowed us to establish conduction properties of different conformations and propose structural models of MscS's open and closed states. Simulations of ankyrin and cadherin repeats focused on their elastic properties, resulting in the discovery and prediction of ankyrin's tertiary and secondary structure elasticity (later on corroborated by atomic force microscopy experiments), and the discovery of a novel form of secondary structure elasticity mediated by calcium ions in

  14. Macro- and microstructural diversity of sea urchin teeth revealed by large-scale mircro-computed tomography survey

    NASA Astrophysics Data System (ADS)

    Ziegler, Alexander; Stock, Stuart R.; Menze, Björn H.; Smith, Andrew B.

    2012-10-01

    Sea urchins (Echinodermata: Echinoidea) generally possess an intricate jaw apparatus that incorporates five teeth. Although echinoid teeth consist of calcite, their complex internal design results in biomechanical properties far superior to those of inorganic forms of the constituent material. While the individual elements (or microstructure) of echinoid teeth provide general insight into processes of biomineralization, the cross-sectional shape (or macrostructure) of echinoid teeth is useful for phylogenetic and biomechanical inferences. However, studies of sea urchin tooth macro- and microstructure have traditionally been limited to a few readily available species, effectively disregarding a potentially high degree of structural diversity that could be informative in a number of ways. Having scanned numerous sea urchin species using micro-computed tomography µCT) and synchrotron µCT, we report a large variation in macro- and microstructure of sea urchin teeth. In addition, we describe aberrant tooth shapes and apply 3D visualization protocols that permit accelerated visual access to the complex microstructure of sea urchin teeth. Our broad survey identifies key taxa for further in-depth study and integrates previously assembled data on fossil species into a more comprehensive systematic analysis of sea urchin teeth. In order to circumvent the imprecise, word-based description of tooth shape, we introduce shape analysis algorithms that will permit the numerical and therefore more objective description of tooth macrostructure. Finally, we discuss how synchrotron µCT datasets permit virtual models of tooth microstructure to be generated as well as the simulation of tooth mechanics based on finite element modeling.

  15. Applied study of optical interconnection link in computer cluster

    NASA Astrophysics Data System (ADS)

    Zhou, Ge; Tian, Jindong; Zhang, Nan; Jing, Wencai; Li, Haifeng

    2000-10-01

    In this paper, some study results to apply fiber link to a computer cluster are presented. The research is based on a ring network topology for a cluster system, which is connected by gigabit/s virtual parallel optical fiber link (VPOFLink) and its driver is for Linux Operating System, the transmission protocol of VPOFLink is compliant with Ethernet standard. We have studied the effect of different types of motherboard on transmission rate of the VPOFLink, and have analyzed the influence of optical interconnection network topology and computer networks protocol on the performance of this optical interconnection computer cluster. The round-trip transmission bandwidth of the VPOFLink have been tested, and the factors that limit transmission bandwidth, such as modes of forwarding data packets in the optical interconnection ring networks, and the size of the link buffer etc., are investigated.

  16. Genome-wide Computational Analysis Reveals Cardiomyocyte-specific Transcriptional Cis-regulatory Motifs That Enable Efficient Cardiac Gene Therapy

    PubMed Central

    Rincon, Melvin Y; Sarcar, Shilpita; Danso-Abeam, Dina; Keyaerts, Marleen; Matrai, Janka; Samara-Kuko, Ermira; Acosta-Sanchez, Abel; Athanasopoulos, Takis; Dickson, George; Lahoutte, Tony; De Bleser, Pieter; VandenDriessche, Thierry; Chuah, Marinee K

    2015-01-01

    Gene therapy is a promising emerging therapeutic modality for the treatment of cardiovascular diseases and hereditary diseases that afflict the heart. Hence, there is a need to develop robust cardiac-specific expression modules that allow for stable expression of the gene of interest in cardiomyocytes. We therefore explored a new approach based on a genome-wide bioinformatics strategy that revealed novel cardiac-specific cis-acting regulatory modules (CS-CRMs). These transcriptional modules contained evolutionary-conserved clusters of putative transcription factor binding sites that correspond to a “molecular signature” associated with robust gene expression in the heart. We then validated these CS-CRMs in vivo using an adeno-associated viral vector serotype 9 that drives a reporter gene from a quintessential cardiac-specific α-myosin heavy chain promoter. Most de novo designed CS-CRMs resulted in a >10-fold increase in cardiac gene expression. The most robust CRMs enhanced cardiac-specific transcription 70- to 100-fold. Expression was sustained and restricted to cardiomyocytes. We then combined the most potent CS-CRM4 with a synthetic heart and muscle-specific promoter (SPc5-12) and obtained a significant 20-fold increase in cardiac gene expression compared to the cytomegalovirus promoter. This study underscores the potential of rational vector design to improve the robustness of cardiac gene therapy. PMID:25195597

  17. Genome-wide computational analysis reveals cardiomyocyte-specific transcriptional Cis-regulatory motifs that enable efficient cardiac gene therapy.

    PubMed

    Rincon, Melvin Y; Sarcar, Shilpita; Danso-Abeam, Dina; Keyaerts, Marleen; Matrai, Janka; Samara-Kuko, Ermira; Acosta-Sanchez, Abel; Athanasopoulos, Takis; Dickson, George; Lahoutte, Tony; De Bleser, Pieter; VandenDriessche, Thierry; Chuah, Marinee K

    2015-01-01

    Gene therapy is a promising emerging therapeutic modality for the treatment of cardiovascular diseases and hereditary diseases that afflict the heart. Hence, there is a need to develop robust cardiac-specific expression modules that allow for stable expression of the gene of interest in cardiomyocytes. We therefore explored a new approach based on a genome-wide bioinformatics strategy that revealed novel cardiac-specific cis-acting regulatory modules (CS-CRMs). These transcriptional modules contained evolutionary-conserved clusters of putative transcription factor binding sites that correspond to a "molecular signature" associated with robust gene expression in the heart. We then validated these CS-CRMs in vivo using an adeno-associated viral vector serotype 9 that drives a reporter gene from a quintessential cardiac-specific α-myosin heavy chain promoter. Most de novo designed CS-CRMs resulted in a >10-fold increase in cardiac gene expression. The most robust CRMs enhanced cardiac-specific transcription 70- to 100-fold. Expression was sustained and restricted to cardiomyocytes. We then combined the most potent CS-CRM4 with a synthetic heart and muscle-specific promoter (SPc5-12) and obtained a significant 20-fold increase in cardiac gene expression compared to the cytomegalovirus promoter. This study underscores the potential of rational vector design to improve the robustness of cardiac gene therapy.

  18. Study of operational parameters impacting helicopter fuel consumption. [using computer techniques (computer programs)

    NASA Technical Reports Server (NTRS)

    Cross, J. L.; Stevens, D. D.

    1976-01-01

    A computerized study of operational parameters affecting helicopter fuel consumption was conducted as an integral part of the NASA Civil Helicopter Technology Program. The study utilized the Helicopter Sizing and Performance Computer Program (HESCOMP) developed by the Boeing-Vertol Company and NASA Ames Research Center. An introduction to HESCOMP is incorporated in this report. The results presented were calculated using the NASA CH-53 civil helicopter research aircraft specifications. Plots from which optimum flight conditions for minimum fuel use that can be obtained are presented for this aircraft. The results of the study are considered to be generally indicative of trends for all helicopters.

  19. Anatomy of the larynx and pharynx: effects of age, gender and height revealed by multidetector computed tomography.

    PubMed

    Inamoto, Y; Saitoh, E; Okada, S; Kagaya, H; Shibata, S; Baba, M; Onogi, K; Hashimoto, S; Katada, K; Wattanapan, P; Palmer, J B

    2015-09-01

    Although oropharyngeal and laryngeal structures are essential for swallowing, the three-dimensional (3D) anatomy is not well understood, due in part to limitations of available measuring techniques. This study uses 3D images acquired by 320-row area detector computed tomography ('320-ADCT'), to measure the pharynx and larynx and to investigate the effects of age, gender and height. Fifty-four healthy volunteers (30 male, 24 female, 23-77 years) underwent one single-phase volume scan (0.35 s) with 320-ADCT during resting tidal breathing. Six measurements of the pharynx and two of larynx were performed. Bivariate statistical methods were used to analyse the effects of gender, age and height on these measurements. Length and volume were significantly larger for men than for women for every measurement (P < 0.05) and increased with height (P < 0.05). Multiple regression analysis was performed to understand the interactions of gender, height and age. Gender, height and age each had significant effects on certain values. The volume of the larynx and hypopharynx was significantly affected by height and age. The length of pharynx was associated with gender and age. Length of the vocal folds and distance from the valleculae to the vocal folds were significantly affected by gender (P < 0.05). These results suggest that age, gender and height have independent and interacting effects on the morphology of the pharynx and larynx. Three-dimensional imaging and morphometrics using 320-ADCT are powerful tools for efficiently and reliably observing and measuring the pharynx and larynx.

  20. Computer-Based Information Services in Medicine: A Feasibility Study.

    ERIC Educational Resources Information Center

    Cox, P. H.; And Others

    The objectives of this study were to examine the need and potential demand for computer-based information services in the University of Otago medical libraries, to evaluate the various databases of interest, and to recommend the best means of access to such services. Data were collected through user and library surveys, an extensive literature…

  1. Computer-Generated Geometry Instruction: A Preliminary Study

    ERIC Educational Resources Information Center

    Kang, Helen W.; Zentall, Sydney S.

    2011-01-01

    This study hypothesized that increased intensity of graphic information, presented in computer-generated instruction, could be differentially beneficial for students with hyperactivity and inattention by improving their ability to sustain attention and hold information in-mind. To this purpose, 18 2nd-4th grade students, recruited from general…

  2. Computational fluid dynamics studies of nuclear rocket performance

    SciTech Connect

    Stubbs, R.M.; Kim, S.C.; Benson, T.J.

    1994-06-01

    A CFD analysis of a low pressure nuclear rocket concept is presented with the use of an advanced chemical kinetics, Navier-Stokes code. The computations describe the flow field in detail, including gas dynamic, thermodynamic and chemical properties, as well as global performance quantities such as specific impulse. Computational studies of several rocket nozzle shapes are conducted in an attempt to maximize hydrogen recombination. These Navier-Stokes calculations, which include real gas and viscous effects, predict lower performance values than have been reported heretofore.

  3. Computational fluid dynamics studies of nuclear rocket performance

    NASA Technical Reports Server (NTRS)

    Stubbs, Robert M.; Kim, Suk C.; Benson, Thomas J.

    1994-01-01

    A CFD analysis of a low pressure nuclear rocket concept is presented with the use of an advanced chemical kinetics, Navier-Stokes code. The computations describe the flow field in detail, including gas dynamic, thermodynamic and chemical properties, as well as global performance quantities such as specific impulse. Computational studies of several rocket nozzle shapes are conducted in an attempt to maximize hydrogen recombination. These Navier-Stokes calculations, which include real gas and viscous effects, predict lower performance values than have been reported heretofore.

  4. Crew/computer communications study. Volume 2: Appendixes

    NASA Technical Reports Server (NTRS)

    Johannes, J. D.

    1974-01-01

    The software routines developed during the crew/computer communications study are described to provide the user with an understanding of each routine, any restrictions in use, the required input data, and expected results after executing the routines. The combination of routines to generate a crew/computer communications application is also explained. The programmable keyboard and display used by the program is described, and an experiment scenario is provided to illustrate the relationship between the program frames when they are grouped into activity phases. Program descriptions and a user's guide are also presented. For Vol. 1, see N74-18843.

  5. Combining on-chip synthesis of a focused combinatorial library with computational target prediction reveals imidazopyridine GPCR ligands.

    PubMed

    Reutlinger, Michael; Rodrigues, Tiago; Schneider, Petra; Schneider, Gisbert

    2014-01-01

    Using the example of the Ugi three-component reaction we report a fast and efficient microfluidic-assisted entry into the imidazopyridine scaffold, where building block prioritization was coupled to a new computational method for predicting ligand-target associations. We identified an innovative GPCR-modulating combinatorial chemotype featuring ligand-efficient adenosine A1/2B and adrenergic α1A/B receptor antagonists. Our results suggest the tight integration of microfluidics-assisted synthesis with computer-based target prediction as a viable approach to rapidly generate bioactivity-focused combinatorial compound libraries with high success rates.

  6. Study of the TRAC Airfoil Table Computational System

    NASA Technical Reports Server (NTRS)

    Hu, Hong

    1999-01-01

    The report documents the study of the application of the TRAC airfoil table computational package (TRACFOIL) to the prediction of 2D airfoil force and moment data over a wide range of angle of attack and Mach number. The TRACFOIL generates the standard C-81 airfoil table for input into rotorcraft comprehensive codes such as CAM- RAD. The existing TRACFOIL computer package is successfully modified to run on Digital alpha workstations and on Cray-C90 supercomputers. A step-by-step instruction for using the package on both computer platforms is provided. Application of the newer version of TRACFOIL is made for two airfoil sections. The C-81 data obtained using the TRACFOIL method are compared with those of wind-tunnel data and results are presented.

  7. A Computational and Experimental Study of Slit Resonators

    NASA Technical Reports Server (NTRS)

    Tam, C. K. W.; Ju, H.; Jones, M. G.; Watson, W. R.; Parrott, T. L.

    2003-01-01

    Computational and experimental studies are carried out to offer validation of the results obtained from direct numerical simulation (DNS) of the flow and acoustic fields of slit resonators. The test cases include slits with 90-degree corners and slits with 45-degree bevel angle housed inside an acoustic impedance tube. Three slit widths are used. Six frequencies from 0.5 to 3.0 kHz are chosen. Good agreement is found between computed and measured reflection factors. In addition, incident sound waves having white noise spectrum and a prescribed pseudo-random noise spectrum are used in subsequent series of tests. The computed broadband results are again found to agree well with experimental data. It is believed the present results provide strong support that DNS can eventually be a useful and accurate prediction tool for liner aeroacoustics. The usage of DNS as a design tool is discussed and illustrated by a simple example.

  8. Using Computational and Mechanical Models to Study Animal Locomotion

    PubMed Central

    Miller, Laura A.; Goldman, Daniel I.; Hedrick, Tyson L.; Tytell, Eric D.; Wang, Z. Jane; Yen, Jeannette; Alben, Silas

    2012-01-01

    Recent advances in computational methods have made realistic large-scale simulations of animal locomotion possible. This has resulted in numerous mathematical and computational studies of animal movement through fluids and over substrates with the purpose of better understanding organisms’ performance and improving the design of vehicles moving through air and water and on land. This work has also motivated the development of improved numerical methods and modeling techniques for animal locomotion that is characterized by the interactions of fluids, substrates, and structures. Despite the large body of recent work in this area, the application of mathematical and numerical methods to improve our understanding of organisms in the context of their environment and physiology has remained relatively unexplored. Nature has evolved a wide variety of fascinating mechanisms of locomotion that exploit the properties of complex materials and fluids, but only recently are the mathematical, computational, and robotic tools available to rigorously compare the relative advantages and disadvantages of different methods of locomotion in variable environments. Similarly, advances in computational physiology have only recently allowed investigators to explore how changes at the molecular, cellular, and tissue levels might lead to changes in performance at the organismal level. In this article, we highlight recent examples of how computational, mathematical, and experimental tools can be combined to ultimately answer the questions posed in one of the grand challenges in organismal biology: “Integrating living and physical systems.” PMID:22988026

  9. Utilizing Cloud Computing to Improve Climate Modeling and Studies

    NASA Astrophysics Data System (ADS)

    Li, Z.; Yang, C.; Liu, K.; Sun, M.; XIA, J.; Huang, Q.

    2013-12-01

    Climate studies have become increasingly important due to the global climate change, one of the biggest challenges for the human in the 21st century. Climate data, not only observations data collected from various sensors but also simulated data generated from diverse climate models, are essential for scientists to explore the potential climate change patterns and analyze the complex climate dynamics. Climate modeling and simulation, a critical methodology for simulating the past and predicting the future climate conditions, can produce huge amount of data that contains potentially valuable information for climate studies. However, using modeling method in climate studies poses at least two challenges for scientists. First, running climate models is a computing intensive process, which requires large amounts of computation resources. Second, running climate models is also a data intensive process generating Big geospatial Data (model output), which demands large storage for managing the data and large computing power to process and analyze these data. This presentation introduces a novel framework to tackle the two challenges by 1) running climate models in a cloud environment in an automated fashion, and 2) managing and parallel processing Big model output Data by leveraging cloud computing technologies. A prototype system is developed based on the framework using ModelE as the climate model. Experiment results show that this framework can improve climate modeling in the research cycle by accelerating big data generation (model simulation), big data management (storage and processing) and on demand big data analytics.

  10. CFD Vision 2030 Study: A Path to Revolutionary Computational Aerosciences

    NASA Technical Reports Server (NTRS)

    Slotnick, Jeffrey; Khodadoust, Abdollah; Alonso, Juan; Darmofal, David; Gropp, William; Lurie, Elizabeth; Mavriplis, Dimitri

    2014-01-01

    This report documents the results of a study to address the long range, strategic planning required by NASA's Revolutionary Computational Aerosciences (RCA) program in the area of computational fluid dynamics (CFD), including future software and hardware requirements for High Performance Computing (HPC). Specifically, the "Vision 2030" CFD study is to provide a knowledge-based forecast of the future computational capabilities required for turbulent, transitional, and reacting flow simulations across a broad Mach number regime, and to lay the foundation for the development of a future framework and/or environment where physics-based, accurate predictions of complex turbulent flows, including flow separation, can be accomplished routinely and efficiently in cooperation with other physics-based simulations to enable multi-physics analysis and design. Specific technical requirements from the aerospace industrial and scientific communities were obtained to determine critical capability gaps, anticipated technical challenges, and impediments to achieving the target CFD capability in 2030. A preliminary development plan and roadmap were created to help focus investments in technology development to help achieve the CFD vision in 2030.

  11. Population genetic structure and approximate Bayesian computation analyses reveal the southern origin and northward dispersal of the oriental fruit moth Grapholita molesta (Lepidoptera: Tortricidae) in its native range.

    PubMed

    Wei, Shu-Jun; Cao, Li-Jun; Gong, Ya-Jun; Shi, Bao-Cai; Wang, Su; Zhang, Fan; Guo, Xiao-Jun; Wang, Yuan-Min; Chen, Xue-Xin

    2015-08-01

    The oriental fruit moth (OFM) Grapholita molesta is one of the most destructive orchard pests. Assumed to be native to China, the moth is now distributed throughout the world. However, the evolutionary history of this moth in its native range remains unknown. In this study, we explored the population genetic structure, dispersal routes and demographic history of the OFM in China and South Korea based on mitochondrial genes and microsatellite loci. The Mantel test indicated a significant correlation between genetic distance and geographical distance in the populations. Bayesian analysis of population genetic structure (baps) identified four nested clusters, while the geneland analysis inferred five genetic groups with spatial discontinuities. Based on the approximate Bayesian computation approach, we found that the OFM was originated from southern China near the Shilin area of Yunnan Province. The early divergence and dispersal of this moth was dated to the Penultimate glaciation of Pleistocene. Further dispersal from southern to northern region of China occurred before the last glacial maximum, while the expansion of population size in the derived populations in northern region of China occurred after the last glacial maximum. Our results indicated that the current distribution and structure of the OFM were complicatedly influenced by climatic and geological events and human activities of cultivation and wide dissemination of peach in ancient China. We provide an example on revealing the origin and dispersal history of an agricultural pest insect in its native range as well as the underlying factors.

  12. Recurrent largngeal nerve paralysis: a laryngographic and computed tomographic study

    SciTech Connect

    Agha, F.P.

    1983-07-01

    Vocal cord paralysis is a relatively common entity, usually resulting from a pathologic process of the vagus nerve or its recurrent larynegeal branch. It is rarely caused by intralargngeal lesions. Four teen patients with recurrent laryngeal nerve paralysis (RLNP) were evaluated by laryngography, computed tomography (CT), or both. In the evaluation of the paramedian cord, CT was limited in its ability to differentiate between tumor or RLNP as the cause of the fixed cord, but it yielded more information than laryngography on the structural abnormalities of the larynx and pre-epiglottic and paralaryngeal spaces. Laryngography revealed distinct features of RLNP and is the procedure of choice for evaluation of functional abnormalities of the larynx until further experience with faster CT scanners and dynamic scanning of the larynx is gained.

  13. Heavy Lift Vehicle (HLV) Avionics Flight Computing Architecture Study

    NASA Technical Reports Server (NTRS)

    Hodson, Robert F.; Chen, Yuan; Morgan, Dwayne R.; Butler, A. Marc; Sdhuh, Joseph M.; Petelle, Jennifer K.; Gwaltney, David A.; Coe, Lisa D.; Koelbl, Terry G.; Nguyen, Hai D.

    2011-01-01

    A NASA multi-Center study team was assembled from LaRC, MSFC, KSC, JSC and WFF to examine potential flight computing architectures for a Heavy Lift Vehicle (HLV) to better understand avionics drivers. The study examined Design Reference Missions (DRMs) and vehicle requirements that could impact the vehicles avionics. The study considered multiple self-checking and voting architectural variants and examined reliability, fault-tolerance, mass, power, and redundancy management impacts. Furthermore, a goal of the study was to develop the skills and tools needed to rapidly assess additional architectures should requirements or assumptions change.

  14. A computational study of brush seal contact loads with friction

    NASA Astrophysics Data System (ADS)

    Aksit, Mahmut Faruk

    The brush seal is emerging as a new technology to effectively control cooling and leakage flows in gas turbine engines. With their superior leakage performance, they show the potential to replace current labyrinth seals in gas turbine engines. Because the bristles slide against the rotor surface, wear at the contact becomes a major concern as it determines the life and efficiency of the seal. To optimize seal life and efficiency, an in-depth study of the factors causing the seal stiffness is needed, and a good choice of materials must be made. Although considerable research has been done on material selection and tribopairs, a brief survey reveals the lack of reliable analyses to evaluate contact loads, and to address heat transfer issues. As material pairs have been optimized for most cases, understanding and management of contact loads hold the key for further improvements in seal life. The complicated nature of bristle behavior under various combinations of pressure load and rotor interference requires computer analysis to study details that may not be available through analytical formulations. In an attempt to meet this need, this study presents a 3-D finite element model of a brush seal. The model consists of a representative bristle bundle with a backing plate and a rotor surface. Every bristle is defined by a number of 3-D quadratic beam elements. Bristles are fixed at the top nodes, while they are free to move in any direction at the tip touching the rotor surface. The model consists of 10 to 13 circumferential rows of bristles. The number of rows are based on the actual packing thickness of the seal modeled. Unlike previous analytical studies on brush seal contact loads, this work includes nonlinear frictional effects between the bristles. Frictional effects are known to drastically change the seal behavior, and are crucial in determining the contact forces. The model applies the available published experimental data to define the boundary conditions and

  15. Dynamical Approach Study of Spurious Numerics in Nonlinear Computations

    NASA Technical Reports Server (NTRS)

    Yee, H. C.; Mansour, Nagi (Technical Monitor)

    2002-01-01

    The last two decades have been an era when computation is ahead of analysis and when very large scale practical computations are increasingly used in poorly understood multiscale complex nonlinear physical problems and non-traditional fields. Ensuring a higher level of confidence in the predictability and reliability (PAR) of these numerical simulations could play a major role in furthering the design, understanding, affordability and safety of our next generation air and space transportation systems, and systems for planetary and atmospheric sciences, and in understanding the evolution and origin of life. The need to guarantee PAR becomes acute when computations offer the ONLY way of solving these types of data limited problems. Employing theory from nonlinear dynamical systems, some building blocks to ensure a higher level of confidence in PAR of numerical simulations have been revealed by the author and world expert collaborators in relevant fields. Five building blocks with supporting numerical examples were discussed. The next step is to utilize knowledge gained by including nonlinear dynamics, bifurcation and chaos theories as an integral part of the numerical process. The third step is to design integrated criteria for reliable and accurate algorithms that cater to the different multiscale nonlinear physics. This includes but is not limited to the construction of appropriate adaptive spatial and temporal discretizations that are suitable for the underlying governing equations. In addition, a multiresolution wavelets approach for adaptive numerical dissipation/filter controls for high speed turbulence, acoustics and combustion simulations will be sought. These steps are corner stones for guarding against spurious numerical solutions that are solutions of the discretized counterparts but are not solutions of the underlying governing equations.

  16. Computational and Functional Analysis of the Virus-Receptor Interface Reveals Host Range Trade-Offs in New World Arenaviruses

    PubMed Central

    Kerr, Scott A.; Jackson, Eleisha L.; Lungu, Oana I.; Meyer, Austin G.; Demogines, Ann; Ellington, Andrew D.; Georgiou, George

    2015-01-01

    ABSTRACT Animal viruses frequently cause zoonotic disease in humans. As these viruses are highly diverse, evaluating the threat that they pose remains a major challenge, and efficient approaches are needed to rapidly predict virus-host compatibility. Here, we develop a combined computational and experimental approach to assess the compatibility of New World arenaviruses, endemic in rodents, with the host TfR1 entry receptors of different potential new host species. Using signatures of positive selection, we identify a small motif on rodent TfR1 that conveys species specificity to the entry of viruses into cells. However, we show that mutations in this region affect the entry of each arenavirus differently. For example, a human single nucleotide polymorphism (SNP) in this region, L212V, makes human TfR1 a weaker receptor for one arenavirus, Machupo virus, but a stronger receptor for two other arenaviruses, Junin and Sabia viruses. Collectively, these findings set the stage for potential evolutionary trade-offs, where natural selection for resistance to one virus may make humans or rodents susceptible to other arenavirus species. Given the complexity of this host-virus interplay, we propose a computational method to predict these interactions, based on homology modeling and computational docking of the virus-receptor protein-protein interaction. We demonstrate the utility of this model for Machupo virus, for which a suitable cocrystal structural template exists. Our model effectively predicts whether the TfR1 receptors of different species will be functional receptors for Machupo virus entry. Approaches such at this could provide a first step toward computationally predicting the “host jumping” potential of a virus into a new host species. IMPORTANCE We demonstrate how evolutionary trade-offs may exist in the dynamic evolutionary interplay between viruses and their hosts, where natural selection for resistance to one virus could make humans or rodents susceptible

  17. Computational Study of Separating Flow in a Planar Subsonic Diffuser

    NASA Technical Reports Server (NTRS)

    DalBello, Teryn; Dippold, Vance, III; Georgiadis, Nicholas J.

    2005-01-01

    A computational study of the separated flow through a 2-D asymmetric subsonic diffuser has been performed. The Wind Computational Fluid Dynamics code is used to predict the separation and reattachment behavior for an incompressible diffuser flow. The diffuser inlet flow is a two-dimensional, turbulent, and fully-developed channel flow with a Reynolds number of 20,000 based on the centerline velocity and the channel height. Wind solutions computed with the Menter SST, Chien k-epsilon, Spalart-Allmaras and Explicit Algebraic Reynolds Stress turbulence models are compared with experimentally measured velocity profiles and skin friction along the upper and lower walls. In addition to the turbulence model study, the effects of grid resolution and use of wall functions were investigated. The grid studies varied the number of grid points across the diffuser and varied the initial wall spacing from y(sup +) = 0.2 to 60. The wall function study assessed the applicability of wall functions for analysis of separated flow. The SST and Explicit Algebraic Stress models provide the best agreement with experimental data, and it is recommended wall functions should only be used with a high level of caution.

  18. The Nimrod computational workbench: a case study in desktop metacomputing

    SciTech Connect

    Abramson, D.; Sosic, R.; Foster, I.; Giddy, J.; Lewis, A.; White, N.

    1996-12-31

    The coordinated use of geographically distributed computers, or metacomputing, can in principle provide more accessible and cost- effective supercomputing than conventional high-performance systems. However, we lack evidence that metacomputing systems can be made easily usable, or that there exist large numbers of applications able to exploit metacomputing resources. In this paper, we present work that addresses both these concerns. The basis for this work is a system called Nimrod that provides a desktop problem-solving environment for parametric experiments. We describe how Nimrod has been extended to support the scheduling of computational resources located in a wide-area environment, and report on an experiment in which Nimrod was used to schedule a large parametric study across the Australian Internet. The experiment provided both new scientific results and insights into Nimrod capabilities. We relate the results of this experiment to lessons learned from the I-WAY distributed computing experiment, and draw conclusions as to how Nimrod and I-WAY- like computing environments should be developed to support desktop metacomputing.

  19. Comparative study viruses with computer-aided phase microscope AIRYSCAN

    NASA Astrophysics Data System (ADS)

    Tychinsky, Vladimir P.; Koufal, Georgy E.; Perevedentseva, Elena V.; Vyshenskaia, Tatiana V.

    1996-12-01

    Traditionally viruses are studied with scanning electron microscopy (SEM) after complicated procedure of sample preparation without the possibility to study it under natural conditions. We obtained images of viruses (Vaccinia virus, Rotavirus) and rickettsias (Rickettsia provazekii, Coxiella burnetti) in native state with computer-aided phase microscope airyscan -- the interference microscope of Linnik layout with phase modulation of the reference wave with dissector image tube as coordinate-sensitive photodetector and computer processing of phase image. A light source was the He-Ne laser. The main result is coincidence of dimensions and shape of phase images with available information concerning their morphology obtained with SEM and other methods. The fine structure of surface and nuclei is observed. This method may be applied for virus recognition and express identification, investigation of virus structure and the analysis of cell-virus interaction.

  20. Helping Students Soar to Success on Computers: An Investigation of the Soar Study Method for Computer-Based Learning

    ERIC Educational Resources Information Center

    Jairam, Dharmananda; Kiewra, Kenneth A.

    2010-01-01

    This study used self-report and observation techniques to investigate how students study computer-based materials. In addition, it examined if a study method called SOAR can facilitate computer-based learning. SOAR is an acronym that stands for the method's 4 theoretically driven and empirically supported components: select (S), organize (O),…

  1. Computational analysis of the MCoTI-II plant defence knottin reveals a novel intermediate conformation that facilitates trypsin binding.

    PubMed

    Jones, Peter M; George, Anthony M

    2016-01-01

    MCoTI-I and II are plant defence proteins, potent trypsin inhibitors from the bitter gourd Momordica cochinchinensis. They are members of the Knottin Family, which display exceptional stability due to unique topology comprising three interlocked disulfide bridges. Knottins show promise as scaffolds for new drug development. A crystal structure of trypsin-bound MCoTI-II suggested that loop 1, which engages the trypsin active site, would show decreased dynamics in the bound state, an inference at odds with an NMR analysis of MCoTI-I, which revealed increased dynamics of loop 1 in the presence of trypsin. To investigate this question, we performed unrestrained MD simulations of trypsin-bound and free MCoTI-II. This analysis found that loop 1 of MCoTI-II is not more dynamic in the trypsin-bound state than in the free state. However, it revealed an intermediate conformation, transitional between the free and bound MCoTI-II states. The data suggest that MCoTI-II binding involves a process in which initial interaction with trypsin induces transitions between the free and intermediate conformations, and fluctuations between these states account for the increase in dynamics of loop 1 observed for trypsin-bound MCoTI-I. The MD analysis thus revealed new aspects of the inhibitors' dynamics that may be of utility in drug design. PMID:26975976

  2. Computational analysis of the MCoTI-II plant defence knottin reveals a novel intermediate conformation that facilitates trypsin binding.

    PubMed

    Jones, Peter M; George, Anthony M

    2016-03-15

    MCoTI-I and II are plant defence proteins, potent trypsin inhibitors from the bitter gourd Momordica cochinchinensis. They are members of the Knottin Family, which display exceptional stability due to unique topology comprising three interlocked disulfide bridges. Knottins show promise as scaffolds for new drug development. A crystal structure of trypsin-bound MCoTI-II suggested that loop 1, which engages the trypsin active site, would show decreased dynamics in the bound state, an inference at odds with an NMR analysis of MCoTI-I, which revealed increased dynamics of loop 1 in the presence of trypsin. To investigate this question, we performed unrestrained MD simulations of trypsin-bound and free MCoTI-II. This analysis found that loop 1 of MCoTI-II is not more dynamic in the trypsin-bound state than in the free state. However, it revealed an intermediate conformation, transitional between the free and bound MCoTI-II states. The data suggest that MCoTI-II binding involves a process in which initial interaction with trypsin induces transitions between the free and intermediate conformations, and fluctuations between these states account for the increase in dynamics of loop 1 observed for trypsin-bound MCoTI-I. The MD analysis thus revealed new aspects of the inhibitors' dynamics that may be of utility in drug design.

  3. Computational analysis of the MCoTI-II plant defence knottin reveals a novel intermediate conformation that facilitates trypsin binding

    PubMed Central

    Jones, Peter M.; George, Anthony M.

    2016-01-01

    MCoTI-I and II are plant defence proteins, potent trypsin inhibitors from the bitter gourd Momordica cochinchinensis. They are members of the Knottin Family, which display exceptional stability due to unique topology comprising three interlocked disulfide bridges. Knottins show promise as scaffolds for new drug development. A crystal structure of trypsin-bound MCoTI-II suggested that loop 1, which engages the trypsin active site, would show decreased dynamics in the bound state, an inference at odds with an NMR analysis of MCoTI-I, which revealed increased dynamics of loop 1 in the presence of trypsin. To investigate this question, we performed unrestrained MD simulations of trypsin-bound and free MCoTI-II. This analysis found that loop 1 of MCoTI-II is not more dynamic in the trypsin-bound state than in the free state. However, it revealed an intermediate conformation, transitional between the free and bound MCoTI-II states. The data suggest that MCoTI-II binding involves a process in which initial interaction with trypsin induces transitions between the free and intermediate conformations, and fluctuations between these states account for the increase in dynamics of loop 1 observed for trypsin-bound MCoTI-I. The MD analysis thus revealed new aspects of the inhibitors’ dynamics that may be of utility in drug design. PMID:26975976

  4. Mathematical analysis and computer program development for electromagnetic science studies

    NASA Astrophysics Data System (ADS)

    Tichovolsky, E.; Cohen, E.; Solin, R.; Dibeneditto, T.; Obrien, J. V.; Gersht, Y.; Bamforth, J.; Weiss, A.; Kerwin, N.; Krol, Y.

    1981-11-01

    This report contains representative examples of analysis and programming assignments executed for RADC technical personnel by staff of the ACRON Corporation. An assortment of analytical and computational problems as well as data processing tasks were performed relevant to Air Force projects requiring signal processing and electromagnetic theory. The core of the work pertained to LORAN-related studies, antenna theory, target detection and tracking problems, and the analysis of acoustic and magnetostatic wave devices.

  5. Teaching the Use of Computers: A Case Study.

    ERIC Educational Resources Information Center

    Atnip, Gilbert W.

    1985-01-01

    Described is a college course on the use of computers in psychology that included an introduction to computers, computing, word processing, data analysis, data acquisition, artificial intelligence, computer assisted instruction, simulation, and modeling. Students conducted independent research projects using the computer. (Author/RM)

  6. A computational study of routing algorithms for realistic transportation networks

    SciTech Connect

    Jacob, R.; Marathe, M.V.; Nagel, K.

    1998-12-01

    The authors carry out an experimental analysis of a number of shortest path (routing) algorithms investigated in the context of the TRANSIMS (Transportation Analysis and Simulation System) project. The main focus of the paper is to study how various heuristic and exact solutions, associated data structures affected the computational performance of the software developed especially for realistic transportation networks. For this purpose the authors have used Dallas Fort-Worth road network with very high degree of resolution. The following general results are obtained: (1) they discuss and experimentally analyze various one-one shortest path algorithms, which include classical exact algorithms studied in the literature as well as heuristic solutions that are designed to take into account the geometric structure of the input instances; (2) they describe a number of extensions to the basic shortest path algorithm. These extensions were primarily motivated by practical problems arising in TRANSIMS and ITS (Intelligent Transportation Systems) related technologies. Extensions discussed include--(i) time dependent networks, (ii) multi-modal networks, (iii) networks with public transportation and associated schedules. Computational results are provided to empirically compare the efficiency of various algorithms. The studies indicate that a modified Dijkstra`s algorithm is computationally fast and an excellent candidate for use in various transportation planning applications as well as ITS related technologies.

  7. A computational analysis of protein interactions in metabolic networks reveals novel enzyme pairs potentially involved in metabolic channeling.

    PubMed

    Huthmacher, Carola; Gille, Christoph; Holzhütter, Hermann-Georg

    2008-06-01

    Protein-protein interactions are operative at almost every level of cell structure and function as, for example, formation of sub-cellular organelles, packaging of chromatin, muscle contraction, signal transduction, and regulation of gene expression. Public databases of reported protein-protein interactions comprise hundreds of thousands interactions, and this number is steadily growing. Elucidating the implications of protein-protein interactions for the regulation of the underlying cellular or extra-cellular reaction network remains a great challenge for computational biochemistry. In this work, we have undertaken a systematic and comprehensive computational analysis of reported enzyme-enzyme interactions in the metabolic networks of the model organisms Escherichia coli and Saccharomyces cerevisiae. We grouped all enzyme pairs according to the topological distance that the catalyzed reactions have in the metabolic network and performed a statistical analysis of reported enzyme-enzyme interactions within these groups. We found a higher frequency of reported enzyme-enzyme interactions within the group of enzymes catalyzing reactions that are adjacent in the network, i.e. sharing at least one metabolite. As some of these interacting enzymes have already been implicated in metabolic channeling our analysis may provide a useful screening for candidates of this phenomenon. To check for a possible regulatory role of interactions between enzymes catalyzing non-neighboring reactions, we determined potentially regulatory enzymes using connectivity in the network and absolute change of Gibbs free energy. Indeed a higher portion of reported interactions pertain to such potentially regulatory enzymes.

  8. Computational methods for studying G protein-coupled receptors (GPCRs).

    PubMed

    Kaczor, Agnieszka A; Rutkowska, Ewelina; Bartuzi, Damian; Targowska-Duda, Katarzyna M; Matosiuk, Dariusz; Selent, Jana

    2016-01-01

    The functioning of GPCRs is classically described by the ternary complex model as the interplay of three basic components: a receptor, an agonist, and a G protein. According to this model, receptor activation results from an interaction with an agonist, which translates into the activation of a particular G protein in the intracellular compartment that, in turn, is able to initiate particular signaling cascades. Extensive studies on GPCRs have led to new findings which open unexplored and exciting possibilities for drug design and safer and more effective treatments with GPCR targeting drugs. These include discovery of novel signaling mechanisms such as ligand promiscuity resulting in multitarget ligands and signaling cross-talks, allosteric modulation, biased agonism, and formation of receptor homo- and heterodimers and oligomers which can be efficiently studied with computational methods. Computer-aided drug design techniques can reduce the cost of drug development by up to 50%. In particular structure- and ligand-based virtual screening techniques are a valuable tool for identifying new leads and have been shown to be especially efficient for GPCRs in comparison to water-soluble proteins. Modern computer-aided approaches can be helpful for the discovery of compounds with designed affinity profiles. Furthermore, homology modeling facilitated by a growing number of available templates as well as molecular docking supported by sophisticated techniques of molecular dynamics and quantitative structure-activity relationship models are an excellent source of information about drug-receptor interactions at the molecular level. PMID:26928552

  9. Fluid Dynamics of Competitive Swimming: A Computational Study

    NASA Astrophysics Data System (ADS)

    Mittal, Rajat; Loebbeck, Alfred; Singh, Hersh; Mark, Russell; Wei, Timothy

    2004-11-01

    The dolphin kick is an important component in competitive swimming and is used extensively by swimmers immediately following the starting dive as well as after turns. In this stroke, the swimmer swims about three feet under the water surface and the stroke is executed by performing an undulating wave-like motion of the body that is quite similar to the anguilliform propulsion mode in fish. Despite the relatively simple kinematics of this stoke, considerable variability in style and performance is observed even among Olympic level swimmers. Motivated by this, a joint experimental-numerical study has been initiated to examine the fluid-dynamics of this stroke. The current presentation will describe the computational portion of this study. The computations employ a sharp interface immersed boundary method (IBM) which allows us to simulate flows with complex moving boudnaries on stationary Cartesian grids. 3D body scans of male and female Olympic swimmers have been obtained and these are used in conjuction with high speed videos to recreate a realistic dolphin kick for the IBM solver. Preliminary results from these computations will be presented.

  10. Logic as Marr's Computational Level: Four Case Studies.

    PubMed

    Baggio, Giosuè; van Lambalgen, Michiel; Hagoort, Peter

    2015-04-01

    We sketch four applications of Marr's levels-of-analysis methodology to the relations between logic and experimental data in the cognitive neuroscience of language and reasoning. The first part of the paper illustrates the explanatory power of computational level theories based on logic. We show that a Bayesian treatment of the suppression task in reasoning with conditionals is ruled out by EEG data, supporting instead an analysis based on defeasible logic. Further, we describe how results from an EEG study on temporal prepositions can be reanalyzed using formal semantics, addressing a potential confound. The second part of the article demonstrates the predictive power of logical theories drawing on EEG data on processing progressive constructions and on behavioral data on conditional reasoning in people with autism. Logical theories can constrain processing hypotheses all the way down to neurophysiology, and conversely neuroscience data can guide the selection of alternative computational level models of cognition. PMID:25417838

  11. Sustainable Nanotechnology: Opportunities and Challenges for Theoretical/Computational Studies.

    PubMed

    Cui, Qiang; Hernandez, Rigoberto; Mason, Sara E; Frauenheim, Thomas; Pedersen, Joel A; Geiger, Franz

    2016-08-01

    For assistance in the design of the next generation of nanomaterials that are functional and have minimal health and safety concerns, it is imperative to establish causality, rather than correlations, in how properties of nanomaterials determine biological and environmental outcomes. Due to the vast design space available and the complexity of nano/bio interfaces, theoretical and computational studies are expected to play a major role in this context. In this minireview, we highlight opportunities and pressing challenges for theoretical and computational chemistry approaches to explore the relevant physicochemical processes that span broad length and time scales. We focus discussions on a bottom-up framework that relies on the determination of correct intermolecular forces, accurate molecular dynamics, and coarse-graining procedures to systematically bridge the scales, although top-down approaches are also effective at providing insights for many problems such as the effects of nanoparticles on biological membranes. PMID:27388532

  12. Logic as Marr's Computational Level: Four Case Studies.

    PubMed

    Baggio, Giosuè; van Lambalgen, Michiel; Hagoort, Peter

    2015-04-01

    We sketch four applications of Marr's levels-of-analysis methodology to the relations between logic and experimental data in the cognitive neuroscience of language and reasoning. The first part of the paper illustrates the explanatory power of computational level theories based on logic. We show that a Bayesian treatment of the suppression task in reasoning with conditionals is ruled out by EEG data, supporting instead an analysis based on defeasible logic. Further, we describe how results from an EEG study on temporal prepositions can be reanalyzed using formal semantics, addressing a potential confound. The second part of the article demonstrates the predictive power of logical theories drawing on EEG data on processing progressive constructions and on behavioral data on conditional reasoning in people with autism. Logical theories can constrain processing hypotheses all the way down to neurophysiology, and conversely neuroscience data can guide the selection of alternative computational level models of cognition.

  13. How language enables abstraction: a study in computational cultural psychology.

    PubMed

    Neuman, Yair; Turney, Peter; Cohen, Yohai

    2012-06-01

    The idea that language mediates our thoughts and enables abstract cognition has been a key idea in socio-cultural psychology. However, it is not clear what mechanisms support this process of abstraction. Peirce argued that one mechanism by which language enables abstract thought is hypostatic abstraction, the process through which a predicate (e.g., dark) turns into an object (e.g., darkness). By using novel computational tools we tested Peirce's idea. Analysis of the data provides empirical support for Peirce's mechanism and evidence of the way the use of signs enables abstraction. These conclusions are supported by the in-depth analysis of two case studies concerning the abstraction of sweet and dark. The paper concludes by discussing the findings from a broad and integrative theoretical perspective and by pointing to computational cultural psychology as a promising perspective for addressing long-lasting questions of the field.

  14. Study of tip loss corrections using CFD rotor computations

    NASA Astrophysics Data System (ADS)

    Shen, W. Z.; Zhu, W. J.; Sørensen, J. N.

    2014-12-01

    Tip loss correction is known to play an important role for engineering prediction of wind turbine performance. There are two different types of tip loss corrections: tip corrections on momentum theory and tip corrections on airfoil data. In this paper, we study the latter using detailed CFD computations for wind turbines with sharp tip. Using the technique of determination of angle of attack and the CFD results for a NordTank 500 kW rotor, airfoil data are extracted and a new tip loss function on airfoil data is derived. To validate, BEM computations with the new tip loss function are carried out and compared with CFD results for the NordTank 500 kW turbine and the NREL 5 MW turbine. Comparisons show that BEM with the new tip loss function can predict correctly the loading near the blade tip.

  15. Designing a Versatile Dedicated Computing Lab to Support Computer Network Courses: Insights from a Case Study

    ERIC Educational Resources Information Center

    Gercek, Gokhan; Saleem, Naveed

    2006-01-01

    Providing adequate computing lab support for Management Information Systems (MIS) and Computer Science (CS) programs is a perennial challenge for most academic institutions in the US and abroad. Factors, such as lack of physical space, budgetary constraints, conflicting needs of different courses, and rapid obsolescence of computing technology,…

  16. Central Computer Science Concepts to Research-Based Teacher Training in Computer Science: An Experimental Study

    ERIC Educational Resources Information Center

    Zendler, Andreas; Klaudt, Dieter

    2012-01-01

    The significance of computer science for economics and society is undisputed. In particular, computer science is acknowledged to play a key role in schools (e.g., by opening multiple career paths). The provision of effective computer science education in schools is dependent on teachers who are able to properly represent the discipline and whose…

  17. Computational studies of protegrin antimicrobial peptides: a review

    PubMed Central

    Bolintineanu, Dan S.; Kaznessis, Yiannis N.

    2010-01-01

    Antimicrobial peptides (AMPs) are small, naturally-occurring peptides that exhibit strong antibacterial properties generally believed to be a result of selective bacterial membrane disruption. As a result, there has been significant interest in the development of therapeutic antibiotics based on AMPs; however, the poor understanding of the fundamental mechanism of action of these peptides has largely hampered such efforts. We present a summary of computational and theoretical investigations of protegrin, a particularly potent peptide that is both an excellent model for the mechanism of action of AMPs and a promising therapeutic candidate. Experimental investigations have shed light on many of the key steps in the action of protegrin: protegrin monomers are known to dimerize in various lipid environments; protegrin peptides interact strongly with lipid bilayer membranes, particularly anionic lipids; protegrins have been shown to form pores in lipid bilayers, which results in uncontrolled ion transport and may be a key factor in bacterial death. In this work, we present a comprehensive review of the computational and theoretical studies that have complemented and extended the information obtained from experimental work with protegrins, as well as a brief survey of the experimental biophysical studies that are most pertinent to such computational work. We show that a consistent, mechanistic description of the bactericidal mechanism of action of protegrins is emerging, and briefly outline areas where the current understanding is deficient. We hope that the research reviewed herein offers compelling evidence of the benefits of computational investigations of protegrins and other AMPs, as well as providing a useful guide to future work in this area. PMID:20946928

  18. The rise of machine consciousness: studying consciousness with computational models.

    PubMed

    Reggia, James A

    2013-08-01

    Efforts to create computational models of consciousness have accelerated over the last two decades, creating a field that has become known as artificial consciousness. There have been two main motivations for this controversial work: to develop a better scientific understanding of the nature of human/animal consciousness and to produce machines that genuinely exhibit conscious awareness. This review begins by briefly explaining some of the concepts and terminology used by investigators working on machine consciousness, and summarizes key neurobiological correlates of human consciousness that are particularly relevant to past computational studies. Models of consciousness developed over the last twenty years are then surveyed. These models are largely found to fall into five categories based on the fundamental issue that their developers have selected as being most central to consciousness: a global workspace, information integration, an internal self-model, higher-level representations, or attention mechanisms. For each of these five categories, an overview of past work is given, a representative example is presented in some detail to illustrate the approach, and comments are provided on the contributions and limitations of the methodology. Three conclusions are offered about the state of the field based on this review: (1) computational modeling has become an effective and accepted methodology for the scientific study of consciousness, (2) existing computational models have successfully captured a number of neurobiological, cognitive, and behavioral correlates of conscious information processing as machine simulations, and (3) no existing approach to artificial consciousness has presented a compelling demonstration of phenomenal machine consciousness, or even clear evidence that artificial phenomenal consciousness will eventually be possible. The paper concludes by discussing the importance of continuing work in this area, considering the ethical issues it raises

  19. Dynamics of H2 adsorbed in porous materials as revealed by computational analysis of inelastic neutron scattering spectra.

    PubMed

    Pham, Tony; Forrest, Katherine A; Space, Brian; Eckert, Juergen

    2016-06-29

    The inelastic scattering of neutrons from adsorbed H2 is an effective and highly sensitive method for obtaining molecular level information on the type and nature of H2 binding sites in porous materials. While these inelastic neutron scattering (INS) spectra of the hindered rotational and translational excitations on the adsorbed H2 contain a significant amount of information, much of this can only be reliably extracted by means of a detailed analysis of the spectra through the utilization of models and theoretical calculations. For instance, the rotational tunneling transitions observed in the INS spectra can be related to a value for the barrier to rotation for the adsorbed H2 with the use of a simple phenomenological model. Since such an analysis is dependent on the model, it is far more desirable to use theoretical methods to compute a potential energy surface (PES), from which the rotational barriers for H2 adsorbed at a particular site can be determined. Rotational energy levels and transitions for the hindered rotor can be obtained by quantum dynamics calculations and compared directly with experiment with an accuracy subject only to the quality of the theoretical PES. In this paper, we review some of the quantum and classical mechanical calculations that have been performed on H2 adsorbed in various porous materials, such as clathrate hydrates, zeolites, and metal-organic frameworks (MOFs). The principal aims of these calculations have been the interpretation of the INS spectra for adsorbed H2 along with the extraction of atomic level details of its interaction with the host. We describe calculations of the PES used for two-dimensional quantum rotation as well as rigorous five-dimensional quantum coupled translation-rotation dynamics, and demonstrate that the combination of INS measurements and computational modeling can provide important and detailed insights into the molecular mechanism of H2 adsorption in porous materials. PMID:27160665

  20. Dynamics of H2 adsorbed in porous materials as revealed by computational analysis of inelastic neutron scattering spectra.

    PubMed

    Pham, Tony; Forrest, Katherine A; Space, Brian; Eckert, Juergen

    2016-06-29

    The inelastic scattering of neutrons from adsorbed H2 is an effective and highly sensitive method for obtaining molecular level information on the type and nature of H2 binding sites in porous materials. While these inelastic neutron scattering (INS) spectra of the hindered rotational and translational excitations on the adsorbed H2 contain a significant amount of information, much of this can only be reliably extracted by means of a detailed analysis of the spectra through the utilization of models and theoretical calculations. For instance, the rotational tunneling transitions observed in the INS spectra can be related to a value for the barrier to rotation for the adsorbed H2 with the use of a simple phenomenological model. Since such an analysis is dependent on the model, it is far more desirable to use theoretical methods to compute a potential energy surface (PES), from which the rotational barriers for H2 adsorbed at a particular site can be determined. Rotational energy levels and transitions for the hindered rotor can be obtained by quantum dynamics calculations and compared directly with experiment with an accuracy subject only to the quality of the theoretical PES. In this paper, we review some of the quantum and classical mechanical calculations that have been performed on H2 adsorbed in various porous materials, such as clathrate hydrates, zeolites, and metal-organic frameworks (MOFs). The principal aims of these calculations have been the interpretation of the INS spectra for adsorbed H2 along with the extraction of atomic level details of its interaction with the host. We describe calculations of the PES used for two-dimensional quantum rotation as well as rigorous five-dimensional quantum coupled translation-rotation dynamics, and demonstrate that the combination of INS measurements and computational modeling can provide important and detailed insights into the molecular mechanism of H2 adsorption in porous materials.

  1. Computer-Assisted Learning in UK Engineering Degree Programmes: Lessons Learned from an Extensive Case Study Programme

    ERIC Educational Resources Information Center

    Rothberg, S. J.; Lamb, F. M.; Willis, L.

    2006-01-01

    This paper gives a synopsis of an extensive programme of case studies on real uses of computer-assisted learning (CAL) materials within UK engineering degree programmes. The programme was conducted between 2000 and 2003 and followed a questionnaire-based survey looking at CAL use in the UK and in Australia. The synopsis reveals a number of key…

  2. Approximation method to compute domain related integrals in structural studies

    NASA Astrophysics Data System (ADS)

    Oanta, E.; Panait, C.; Raicu, A.; Barhalescu, M.; Axinte, T.

    2015-11-01

    Various engineering calculi use integral calculus in theoretical models, i.e. analytical and numerical models. For usual problems, integrals have mathematical exact solutions. If the domain of integration is complicated, there may be used several methods to calculate the integral. The first idea is to divide the domain in smaller sub-domains for which there are direct calculus relations, i.e. in strength of materials the bending moment may be computed in some discrete points using the graphical integration of the shear force diagram, which usually has a simple shape. Another example is in mathematics, where the surface of a subgraph may be approximated by a set of rectangles or trapezoids used to calculate the definite integral. The goal of the work is to introduce our studies about the calculus of the integrals in the transverse section domains, computer aided solutions and a generalizing method. The aim of our research is to create general computer based methods to execute the calculi in structural studies. Thus, we define a Boolean algebra which operates with ‘simple’ shape domains. This algebraic standpoint uses addition and subtraction, conditioned by the sign of every ‘simple’ shape (-1 for the shapes to be subtracted). By ‘simple’ shape or ‘basic’ shape we define either shapes for which there are direct calculus relations, or domains for which their frontiers are approximated by known functions and the according calculus is carried out using an algorithm. The ‘basic’ shapes are linked to the calculus of the most significant stresses in the section, refined aspect which needs special attention. Starting from this idea, in the libraries of ‘basic’ shapes, there were included rectangles, ellipses and domains whose frontiers are approximated by spline functions. The domain triangularization methods suggested that another ‘basic’ shape to be considered is the triangle. The subsequent phase was to deduce the exact relations for the

  3. Unexpected Regularity in Swimming Behavior of Clausocalanus furcatus Revealed by a Telecentric 3D Computer Vision System

    PubMed Central

    Bianco, Giuseppe; Botte, Vincenzo; Dubroca, Laurent; Ribera d’Alcalà, Maurizio; Mazzocchi, Maria Grazia

    2013-01-01

    Planktonic copepods display a large repertoire of motion behaviors in a three-dimensional environment. Two-dimensional video observations demonstrated that the small copepod Clausocalanus furcatus, one the most widely distributed calanoids at low to medium latitudes, presented a unique swimming behavior that was continuous and fast and followed notably convoluted trajectories. Furthermore, previous observations indicated that the motion of C. furcatus resembled a random process. We characterized the swimming behavior of this species in three-dimensional space using a video system equipped with telecentric lenses, which allow tracking of zooplankton without the distortion errors inherent in common lenses. Our observations revealed unexpected regularities in the behavior of C. furcatus that appear primarily in the horizontal plane and could not have been identified in previous observations based on lateral views. Our results indicate that the swimming behavior of C. furcatus is based on a limited repertoire of basic kinematic modules but exhibits greater plasticity than previously thought. PMID:23826331

  4. Computational study of Gleevec and G6G reveals molecular determinants of kinase inhibitor selectivity

    SciTech Connect

    Lin, Yen -Lin; Meng, Yilin; Huang, Lei; Roux, Benoît

    2014-10-22

    Gleevec is a potent inhibitor of Abl tyrosine kinase but not of the highly homologous c-Src kinase. Because the ligand binds to an inactive form of the protein in which an Asp-Phe-Gly structural motif along the activation loop adopts a so-called DFG-out conformation, it was suggested that binding specificity was controlled by a “conformational selection” mechanism. In this context, the binding affinity displayed by the kinase inhibitor G6G poses an intriguing challenge. Although it possesses a chemical core very similar to that of Gleevec, G6G is a potent inhibitor of both Abl and c-Src kinases. Both inhibitors bind to the DFG-out conformation of the kinases, which seems to be in contradiction with the conformational selection mechanism. To address this issue and display the hidden thermodynamic contributions affecting the binding selectivity, molecular dynamics free energy simulations with explicit solvent molecules were carried out. Relative to Gleevec, G6G forms highly favorable van der Waals dispersive interactions upon binding to the kinases via its triazine functional group, which is considerably larger than the corresponding pyridine moiety in Gleevec. Upon binding of G6G to c-Src, these interactions offset the unfavorable free energy cost of the DFG-out conformation. When binding to Abl, however, G6G experiences an unfavorable free energy penalty due to steric clashes with the phosphate-binding loop, yielding an overall binding affinity that is similar to that of Gleevec. Such steric clashes are absent when G6G binds to c-Src, due to the extended conformation of the phosphate-binding loop.

  5. Computational study of Gleevec and G6G reveals molecular determinants of kinase inhibitor selectivity

    DOE PAGES

    Lin, Yen -Lin; Meng, Yilin; Huang, Lei; Roux, Benoît

    2014-10-22

    Gleevec is a potent inhibitor of Abl tyrosine kinase but not of the highly homologous c-Src kinase. Because the ligand binds to an inactive form of the protein in which an Asp-Phe-Gly structural motif along the activation loop adopts a so-called DFG-out conformation, it was suggested that binding specificity was controlled by a “conformational selection” mechanism. In this context, the binding affinity displayed by the kinase inhibitor G6G poses an intriguing challenge. Although it possesses a chemical core very similar to that of Gleevec, G6G is a potent inhibitor of both Abl and c-Src kinases. Both inhibitors bind to themore » DFG-out conformation of the kinases, which seems to be in contradiction with the conformational selection mechanism. To address this issue and display the hidden thermodynamic contributions affecting the binding selectivity, molecular dynamics free energy simulations with explicit solvent molecules were carried out. Relative to Gleevec, G6G forms highly favorable van der Waals dispersive interactions upon binding to the kinases via its triazine functional group, which is considerably larger than the corresponding pyridine moiety in Gleevec. Upon binding of G6G to c-Src, these interactions offset the unfavorable free energy cost of the DFG-out conformation. When binding to Abl, however, G6G experiences an unfavorable free energy penalty due to steric clashes with the phosphate-binding loop, yielding an overall binding affinity that is similar to that of Gleevec. Such steric clashes are absent when G6G binds to c-Src, due to the extended conformation of the phosphate-binding loop.« less

  6. Implications of Ubiquitous Computing for the Social Studies Curriculum

    ERIC Educational Resources Information Center

    van Hover, Stephanie D.; Berson, Michael J.; Bolick, Cheryl Mason; Swan, Kathleen Owings

    2004-01-01

    In March 2002, members of the National Technology Leadership Initiative (NTLI) met in Charlottesville, Virginia to discuss the potential effects of ubiquitous computing on the field of education. Ubiquitous computing, or "on-demand availability of task-necessary computing power," involves providing every student with a handheld computer--a…

  7. Using Computer Databases in Student Problem Solving: A Study of Eight Social Studies Teachers' Classes.

    ERIC Educational Resources Information Center

    Ehman, Lee H.; And Others

    Recent research has shown that computer technology, including databases, is becoming a part of social studies instruction. Yet it still is not clear how teachers are using databases and what are the outcomes from such use. The research reported in this document addresses three principal questions: (1) How do teachers use computer databases in…

  8. 3D ultrasound computer tomography: update from a clinical study

    NASA Astrophysics Data System (ADS)

    Hopp, T.; Zapf, M.; Kretzek, E.; Henrich, J.; Tukalo, A.; Gemmeke, H.; Kaiser, C.; Knaudt, J.; Ruiter, N. V.

    2016-04-01

    Ultrasound Computer Tomography (USCT) is a promising new imaging method for breast cancer diagnosis. We developed a 3D USCT system and tested it in a pilot study with encouraging results: 3D USCT was able to depict two carcinomas, which were present in contrast enhanced MRI volumes serving as ground truth. To overcome severe differences in the breast shape, an image registration was applied. We analyzed the correlation between average sound speed in the breast and the breast density estimated from segmented MRIs and found a positive correlation with R=0.70. Based on the results of the pilot study we now carry out a successive clinical study with 200 patients. For this we integrated our reconstruction methods and image post-processing into a comprehensive workflow. It includes a dedicated DICOM viewer for interactive assessment of fused USCT images. A new preview mode now allows intuitive and faster patient positioning. We updated the USCT system to decrease the data acquisition time by approximately factor two and to increase the penetration depth of the breast into the USCT aperture by 1 cm. Furthermore the compute-intensive reflectivity reconstruction was considerably accelerated, now allowing a sub-millimeter volume reconstruction in approximately 16 minutes. The updates made it possible to successfully image first patients in our ongoing clinical study.

  9. Cohort study analysis with a FORTRAN computer program.

    PubMed

    Coleman, M; Douglas, A; Hermon, C; Peto, J

    1986-03-01

    We describe the analysis of cohort study data with a standard FORTRAN program which should run on most computers. It provides a summary measure of the mortality (or incidence) rate ratio between the study cohort and some standard population, based either on person-years at risk or on proportional mortality, and adjusted for age, sex and calendar period; a test of the statistical significance of the ratio; and a set of observed death rates in the study cohort. Results may also be produced in a form suitable for use with GLIM. The analysis may be subdivided into a range of time intervals since each subject was first exposed to risk. The program provides for movement of subjects between different 'level-of-exposure' subgroups within the cohort, and for various methods of censoring. It allows considerable flexibility in data management, and is available with complete documentation and a worked example. The program should enable epidemiologists with little computing experience to carry out formal analysis of cohort studies.

  10. Restricted diversity of antigen binding residues of antibodies revealed by computational alanine scanning of 227 antibody-antigen complexes.

    PubMed

    Robin, Gautier; Sato, Yoshiteru; Desplancq, Dominique; Rochel, Natacha; Weiss, Etienne; Martineau, Pierre

    2014-11-11

    Antibody molecules are able to recognize any antigen with high affinity and specificity. To get insight into the molecular diversity at the source of this functional diversity, we compiled and analyzed a non-redundant aligned collection of 227 structures of antibody-antigen complexes. Free energy of binding of all the residue side chains was quantified by computational alanine scanning, allowing the first large-scale quantitative description of antibody paratopes. This demonstrated that as few as 8 residues among 30 key positions are sufficient to explain 80% of the binding free energy in most complexes. At these positions, the residue distribution is not only different from that of other surface residues but also dependent on the role played by the side chain in the interaction, residues participating in the binding energy being mainly aromatic residues, and Gly or Ser otherwise. To question the generality of these binding characteristics, we isolated an antibody fragment by phage display using a biased synthetic repertoire with only two diversified complementarity-determining regions and solved its structure in complex with its antigen. Despite this restricted diversity, the structure demonstrated that all complementarity-determining regions were involved in the interaction with the antigen and that the rules derived from the natural antibody repertoire apply to this synthetic binder, thus demonstrating the robustness and universality of our results.

  11. Global-scale computational analysis of genomic sequences reveals the recombination pattern and coevolution dynamics of cereal-infecting geminiviruses

    PubMed Central

    Wu, Beilei; Shang, Xiaonan; Schubert, Jörg; Habekuß, Antje; Elena, Santiago F.; Wang, Xifeng

    2015-01-01

    Genetic diversity and recombination patterns were evaluated for 229 isolates of Wheat dwarf virus (WDV), which are important cereal-infecting geminiviruses. Recombination hot spots were concentrated at the boundary of the genes encoding for the replication protein (Rep), the coat protein (cp) and the movement protein (mp), as well as inside Rep and cp and in the short intergenic regions (SIR). Phylogenomic analyses confirmed that the global population of WDV clustered into two groups according to their specific host: wheat and barley, and the crucial regions for the division of two groups were mp and the large intergenic regions (LIR). The computationally inferred pattern of coevolution between amino acid residues and the predicted 3D structure for the viral proteins provided further differences among the strains or species at the genome and protein level. Pervasive interaction between Rep and Rep A proteins in WDV-wheat-specific group reflected their important and complex function in the replication and transcription of WDV. Furthermore, significant predicted interactions between CP and Rep and CP and Rep A proteins in the WDV-wheat-specific group are thought to be crucial for successful encapsidation and movement of the virus during infection. PMID:25633348

  12. A Computational and Experimental Study of Resonators in Three Dimensions

    NASA Technical Reports Server (NTRS)

    Tam, C. K. W.; Ju, H.; Jones, Michael G.; Watson, Willie R.; Parrott, Tony L.

    2009-01-01

    In a previous work by the present authors, a computational and experimental investigation of the acoustic properties of two-dimensional slit resonators was carried out. The present paper reports the results of a study extending the previous work to three dimensions. This investigation has two basic objectives. The first is to validate the computed results from direct numerical simulations of the flow and acoustic fields of slit resonators in three dimensions by comparing with experimental measurements in a normal incidence impedance tube. The second objective is to study the flow physics of resonant liners responsible for sound wave dissipation. Extensive comparisons are provided between computed and measured acoustic liner properties with both discrete frequency and broadband sound sources. Good agreements are found over a wide range of frequencies and sound pressure levels. Direct numerical simulation confirms the previous finding in two dimensions that vortex shedding is the dominant dissipation mechanism at high sound pressure intensity. However, it is observed that the behavior of the shed vortices in three dimensions is quite different from those of two dimensions. In three dimensions, the shed vortices tend to evolve into ring (circular in plan form) vortices, even though the slit resonator opening from which the vortices are shed has an aspect ratio of 2.5. Under the excitation of discrete frequency sound, the shed vortices align themselves into two regularly spaced vortex trains moving away from the resonator opening in opposite directions. This is different from the chaotic shedding of vortices found in two-dimensional simulations. The effect of slit aspect ratio at a fixed porosity is briefly studied. For the range of liners considered in this investigation, it is found that the absorption coefficient of a liner increases when the open area of the single slit is subdivided into multiple, smaller slits.

  13. Computational Design Study for Recovery of Shock Damaged Silicon Carbide

    SciTech Connect

    Iyer, K.; Dandekar, D.

    2006-07-28

    The paper presents a computational study for design of experimental configurations that may permit the recovery of weak-shock loaded high-strength brittle ceramics such as silicon carbide with controlled amounts of damage. A set of 8 configurations involving momentum traps, and subjected to a nominal shock pressure of 4 GPa, is analyzed using finite element analysis with linear elastic and damage material models. The analyses identify influences of: (i) introducing a hole in the specimen center (ii) specimen size, and (iii) impedance graded trapping.

  14. Computational study of titanium (IV) complexes with organic chromophores

    NASA Astrophysics Data System (ADS)

    Kondov, Ivan; Wang, Haobin; Thoss, Michael

    A computational study of small titanium complexes with the chromophores catechol, alizarin, and coumarin 343 is presented. Employing density functional theory (DFT), the ground-state geometries, energies, and harmonic frequencies of the different compounds are calculated. Furthermore, time-dependent DFT and the configuration interaction singles (CIS) method are used to determine excitation energies and excited-state gradients. Based on these results, the character of the excited states as well as electronic-vibrational coupling strengths are analyzed, and the implications for electron-transfer reactions at dye-semiconductor interfaces are discussed.

  15. Experimental and Analytical Studies for a Computational Materials Program

    NASA Technical Reports Server (NTRS)

    Knauss, W. G.

    1999-01-01

    The studies supported by Grant NAG1-1780 were directed at providing physical data on polymer behavior that would form the basis for computationally modeling these types of materials. Because of ongoing work in polymer characterization this grant supported part of a larger picture in this regard. Efforts went into two combined areas of their time dependent mechanical response characteristics: Creep properties on the one hand, subject to different volumetric changes (nonlinearly viscoelastic behavior) and time or frequency dependence of dilatational material behavior. The details of these endeavors are outlined sufficiently in the two appended publications, so that no further description of the effort is necessary.

  16. Computation studies into architecture and energy transfer properties of photosynthetic units from filamentous anoxygenic phototrophs

    SciTech Connect

    Linnanto, Juha Matti; Freiberg, Arvi

    2014-10-06

    We have used different computational methods to study structural architecture, and light-harvesting and energy transfer properties of the photosynthetic unit of filamentous anoxygenic phototrophs. Due to the huge number of atoms in the photosynthetic unit, a combination of atomistic and coarse methods was used for electronic structure calculations. The calculations reveal that the light energy absorbed by the peripheral chlorosome antenna complex transfers efficiently via the baseplate and the core B808–866 antenna complexes to the reaction center complex, in general agreement with the present understanding of this complex system.

  17. A computational and experimental study on mold filling

    NASA Astrophysics Data System (ADS)

    van der Graaf, G. B.; van den Akker, H. E. A.; Katgerman, L.

    2001-02-01

    Mold filling was studied for vertical, thin, plate-shaped cavities, with the liquid entering via some vertical ingate system connected to the bottom. In this study, sand molds were filled up with molten aluminum and molten cast iron, while water was used to fill up perspex models. The front walls of the sand molds were replaced by glass plates to allow observations of temperature distributions and free-surface behavior of the melt during filling. Computational fluid dynamics (CFD) simulations of the filling process were carried out to study free-surface behavior, velocity patterns, and temperature distributions. Digital particle-image velocimetry (DPIV) was used to validate the computer simulations for water. Generally, visual observations of the molten liquids, CFD simulations, and DPIV results are in good agreement. Combining the three techniques has resulted in a better understanding as to how a plate-shaped cavity is filled up. The behavior of the free surface is different for water and the molten metals. An analysis of surface waves is presented that explains these differences. Current ideas as to the role of the Weber number must be rejected. Rather, instabilities are associated with low values of the Ohnesorge number, with surface tension providing the driving force for surface instabilities and with viscosity as the damping force.

  18. Pediatric Computed Tomography. Radiation Dose in Abdominal Studies

    NASA Astrophysics Data System (ADS)

    López, X.; Ruiz-Trejo, C.; Buenfil, A. E.; Gamboa-deBuen, I.; Dies, P.

    2008-08-01

    Computed tomography is one of the most popular medical imaging modalities used in the last years. However, because is one of the techniques that delivered a considerable radiation dose, precautions should be taken into account. Pediatric patients are more radiosensitive than adults, and the probability that no desirable biological effects can occur is greater. To this, also it adds the probability that they will need more radiological studies in the future. The work consisted in determining the received dose by the pediatric patients undergoing abdominal studies in a multislice computed tomograph, according to the dosimetric quantities established by a Code of Practice published by the International Atomic Energy Agency; using a ionization chamber and a phantom that simulates the abdomen of a pediatric patient. The weighted air kerma index (Cw) was 14.3±0.4 mGy, this value is lower than the published by the American College of Radiology, 25 mGy. The multiple scan average dose (MSAD), which is a quantity established by the NOM-229-SSA1-2002 was determined, finding a value of 14.2±0.1 mGy, it is also below the value established, 25 mGy for an adult study.

  19. Pediatric Computed Tomography. Radiation Dose in Abdominal Studies

    SciTech Connect

    Lopez, X.; Ruiz-Trejo, C.; Buenfil, A. E.; Gamboa-deBuen, I.; Dies, P

    2008-08-11

    Computed tomography is one of the most popular medical imaging modalities used in the last years. However, because is one of the techniques that delivered a considerable radiation dose, precautions should be taken into account. Pediatric patients are more radiosensitive than adults, and the probability that no desirable biological effects can occur is greater. To this, also it adds the probability that they will need more radiological studies in the future. The work consisted in determining the received dose by the pediatric patients undergoing abdominal studies in a multislice computed tomograph, according to the dosimetric quantities established by a Code of Practice published by the International Atomic Energy Agency; using a ionization chamber and a phantom that simulates the abdomen of a pediatric patient. The weighted air kerma index (C{sub w}) was 14.3{+-}0.4 mGy, this value is lower than the published by the American College of Radiology, 25 mGy. The multiple scan average dose (MSAD), which is a quantity established by the NOM-229-SSA1-2002 was determined, finding a value of 14.2{+-}0.1 mGy, it is also below the value established, 25 mGy for an adult study.

  20. Experimental and computational studies on stacking faults in zinc titanate

    NASA Astrophysics Data System (ADS)

    Sun, W.; Ageh, V.; Mohseni, H.; Scharf, T. W.; Du, J.

    2014-06-01

    Zinc titanate (ZnTiO3) thin films grown by atomic layer deposition with ilmenite structure have recently been identified as an excellent solid lubricant, where low interfacial shear and friction are achieved due to intrafilm shear velocity accommodation in sliding contacts. In this Letter, high resolution transmission electron microscopy with electron diffraction revealed that extensive stacking faults are present on ZnTiO3 textured (104) planes. These growth stacking faults serve as a pathway for dislocations to glide parallel to the sliding direction and hence achieve low interfacial shear/friction. Generalized stacking fault energy plots also known as γ-surfaces were computed for the (104) surface of ZnTiO3 using energy minimization method with classical effective partial charge potential and verified by using density functional theory first principles calculations for stacking fault energies along certain directions. These two are in qualitative agreement but classical simulations generally overestimate the energies. In addition, the lowest energy path was determined to be along the [451¯] direction and the most favorable glide system is {104} ⟨451¯⟩ that is responsible for the experimentally observed sliding-induced ductility.

  1. Experimental and computational studies on stacking faults in zinc titanate

    SciTech Connect

    Sun, W.; Ageh, V.; Mohseni, H.; Scharf, T. W. E-mail: Jincheng.Du@unt.edu; Du, J. E-mail: Jincheng.Du@unt.edu

    2014-06-16

    Zinc titanate (ZnTiO{sub 3}) thin films grown by atomic layer deposition with ilmenite structure have recently been identified as an excellent solid lubricant, where low interfacial shear and friction are achieved due to intrafilm shear velocity accommodation in sliding contacts. In this Letter, high resolution transmission electron microscopy with electron diffraction revealed that extensive stacking faults are present on ZnTiO{sub 3} textured (104) planes. These growth stacking faults serve as a pathway for dislocations to glide parallel to the sliding direction and hence achieve low interfacial shear/friction. Generalized stacking fault energy plots also known as γ-surfaces were computed for the (104) surface of ZnTiO{sub 3} using energy minimization method with classical effective partial charge potential and verified by using density functional theory first principles calculations for stacking fault energies along certain directions. These two are in qualitative agreement but classical simulations generally overestimate the energies. In addition, the lowest energy path was determined to be along the [451{sup ¯}] direction and the most favorable glide system is (104) 〈451{sup ¯}〉 that is responsible for the experimentally observed sliding-induced ductility.

  2. Computational modeling reveals that a combination of chemotaxis and differential adhesion leads to robust cell sorting during tissue patterning.

    PubMed

    Tan, Rui Zhen; Chiam, Keng-Hwee

    2014-01-01

    Robust tissue patterning is crucial to many processes during development. The "French Flag" model of patterning, whereby naïve cells in a gradient of diffusible morphogen signal adopt different fates due to exposure to different amounts of morphogen concentration, has been the most widely proposed model for tissue patterning. However, recently, using time-lapse experiments, cell sorting has been found to be an alternative model for tissue patterning in the zebrafish neural tube. But it remains unclear what the sorting mechanism is. In this article, we used computational modeling to show that two mechanisms, chemotaxis and differential adhesion, are needed for robust cell sorting. We assessed the performance of each of the two mechanisms by quantifying the fraction of correct sorting, the fraction of stable clusters formed after correct sorting, the time needed to achieve correct sorting, and the size variations of the cells having different fates. We found that chemotaxis and differential adhesion confer different advantages to the sorting process. Chemotaxis leads to high fraction of correct sorting as individual cells will either migrate towards or away from the source depending on its cell type. However after the cells have sorted correctly, there is no interaction among cells of the same type to stabilize the sorted boundaries, leading to cell clusters that are unstable. On the other hand, differential adhesion results in low fraction of correct clusters that are more stable. In the absence of morphogen gradient noise, a combination of both chemotaxis and differential adhesion yields cell sorting that is both accurate and robust. However, in the presence of gradient noise, the simple combination of chemotaxis and differential adhesion is insufficient for cell sorting; instead, chemotaxis coupled with delayed differential adhesion is required to yield optimal sorting.

  3. Membrane Docking of the Synaptotagmin 7 C2A Domain: Computation Reveals Interplay between Electrostatic and Hydrophobic Contributions.

    PubMed

    Chon, Nara Lee; Osterberg, J Ryan; Henderson, Jack; Khan, Hanif M; Reuter, Nathalie; Knight, Jefferson D; Lin, Hai

    2015-09-22

    The C2A domain of synaptotagmin 7 (Syt7) is a Ca(2+) and membrane binding module that docks and inserts into cellular membranes in response to elevated intracellular Ca(2+) concentrations. Like other C2 domains, Syt7 C2A binds Ca(2+) and membranes primarily through three loop regions; however, it docks at Ca(2+) concentrations much lower than those required for other Syt C2A domains. To probe structural components of its unusually strong membrane docking, we conducted atomistic molecular dynamics simulations of Syt7 C2A under three conditions: in aqueous solution, in the proximity of a lipid bilayer membrane, and embedded in the membrane. The simulations of membrane-free protein indicate that Syt7 C2A likely binds three Ca(2+) ions in aqueous solution, consistent with prior experimental reports. Upon membrane docking, the outermost Ca(2+) ion interacts directly with lipid headgroups, while the other two Ca(2+) ions remain chelated by the protein. The membrane-bound domain was observed to exhibit large-amplitude swinging motions relative to the membrane surface, varying by up to 70° between a more parallel and a more perpendicular orientation, both during and after insertion of the Ca(2+) binding loops into the membrane. The computed orientation of the membrane-bound protein correlates well with experimental electron paramagnetic resonance measurements presented in the preceding paper ( DOI: 10.1021/acs.biochem.5b00421 ). In particular, the strictly conserved residue Phe229 inserted stably ∼4 Å below the average depth of lipid phosphate groups, providing critical hydrophobic interactions anchoring the domain in the membrane. Overall, the position and orientation of Syt7 C2A with respect to the membrane are consistent with experiments.

  4. Computational Modeling Reveals that a Combination of Chemotaxis and Differential Adhesion Leads to Robust Cell Sorting during Tissue Patterning

    PubMed Central

    Tan, Rui Zhen; Chiam, Keng-Hwee

    2014-01-01

    Robust tissue patterning is crucial to many processes during development. The "French Flag" model of patterning, whereby naïve cells in a gradient of diffusible morphogen signal adopt different fates due to exposure to different amounts of morphogen concentration, has been the most widely proposed model for tissue patterning. However, recently, using time-lapse experiments, cell sorting has been found to be an alternative model for tissue patterning in the zebrafish neural tube. But it remains unclear what the sorting mechanism is. In this article, we used computational modeling to show that two mechanisms, chemotaxis and differential adhesion, are needed for robust cell sorting. We assessed the performance of each of the two mechanisms by quantifying the fraction of correct sorting, the fraction of stable clusters formed after correct sorting, the time needed to achieve correct sorting, and the size variations of the cells having different fates. We found that chemotaxis and differential adhesion confer different advantages to the sorting process. Chemotaxis leads to high fraction of correct sorting as individual cells will either migrate towards or away from the source depending on its cell type. However after the cells have sorted correctly, there is no interaction among cells of the same type to stabilize the sorted boundaries, leading to cell clusters that are unstable. On the other hand, differential adhesion results in low fraction of correct clusters that are more stable. In the absence of morphogen gradient noise, a combination of both chemotaxis and differential adhesion yields cell sorting that is both accurate and robust. However, in the presence of gradient noise, the simple combination of chemotaxis and differential adhesion is insufficient for cell sorting; instead, chemotaxis coupled with delayed differential adhesion is required to yield optimal sorting. PMID:25302949

  5. Effects of Clinically Relevant MPL Mutations in the Transmembrane Domain Revealed at the Atomic Level through Computational Modeling

    PubMed Central

    Lee, Tai-Sung; Kantarjian, Hagop; Ma, Wanlong; Yeh, Chen-Hsiung; Giles, Francis; Albitar, Maher

    2011-01-01

    Background Mutations in the thrombopoietin receptor (MPL) may activate relevant pathways and lead to chronic myeloproliferative neoplasms (MPNs). The mechanisms of MPL activation remain elusive because of a lack of experimental structures. Modern computational biology techniques were utilized to explore the mechanisms of MPL protein activation due to various mutations. Results Transmembrane (TM) domain predictions, homology modeling, ab initio protein structure prediction, and molecular dynamics (MD) simulations were used to build structural dynamic models of wild-type and four clinically observed mutants of MPL. The simulation results suggest that S505 and W515 are important in keeping the TM domain in its correct position within the membrane. Mutations at either of these two positions cause movement of the TM domain, altering the conformation of the nearby intracellular domain in unexpected ways, and may cause the unwanted constitutive activation of MPL's kinase partner, JAK2. Conclusions Our findings represent the first full-scale molecular dynamics simulations of the wild-type and clinically observed mutants of the MPL protein, a critical element of the MPL-JAK2-STAT signaling pathway. In contrast to usual explanations for the activation mechanism that are based on the relative translational movement between rigid domains of MPL, our results suggest that mutations within the TM region could result in conformational changes including tilt and rotation (azimuthal) angles along the membrane axis. Such changes may significantly alter the conformation of the adjacent and intrinsically flexible intracellular domain. Hence, caution should be exercised when interpreting experimental evidence based on rigid models of cytokine receptors or similar systems. PMID:21858098

  6. Tungsten(VI) N-Heterocyclic Carbene Complexes: Synthetic, Structural, and Computational Study

    PubMed Central

    2011-01-01

    The reaction of WOCl4 with 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene (Idipp) leads to an orange solid whose spectroscopic data are consistent with the 1:1 adduct [WOCl4(Idipp)]. Computational studies at the DFT level further support this formulation. Exposure of this compound to the atmosphere results in rapid hydrolysis to various imidazolium salts. If air diffuses very slowly into solutions of [WOCl4(Idipp)], it also undergoes slow hydrolysis to form [WO2Cl2(Idipp)]. This has been crystallographically characterized and is the first five-coordinate, 1:1 adduct of WO2Cl2. This complex has also been subject to DFT calculations, and its metal–ligand bonding has been explored. The carbene–metal interaction is primarily σ-donor in nature. The mechanism of the hydrolysis has also been probed by computational methods, revealing a plausible, low-energy reaction pathway. PMID:24882916

  7. Using computer simulations to study relativistic heavy ion collisions

    NASA Astrophysics Data System (ADS)

    Murray, Joelle Lynn

    1998-12-01

    One of the most exciting topics in high-energy nuclear physics is the study of the potential phase transition between hadronic and partonic matter. Information about this transition, if it exists and can be experimentally determined, would be vital in understanding confinement of quarks and gluons inside hadrons. New accelerators, RHIC and LIIC, will be online in the next few years and will focus on finding evidence for this transition. RHIC will collide Au on Au at center of mass energies equal to 200 GeV/nucleon and create a high density, high temperature state of matter. To study the large particle multiplicities that will occur at these experiments, computer simulations are being developed. Within this thesis, one type of simulation will be detailed and used to study the invariant mass spectrum of leptons pairs measured at CERN SPS and several hadronic observables that could be measured at RHIC.

  8. Computational study of stall flutter in linear cascades

    SciTech Connect

    Abdelrahim, A.; Sisto, F.; Thangam, S. . Dept. of Mechanical Engineering)

    1993-01-01

    Aeroelastic interaction in turbomachinery is of prime interest to operators, designers, and aeroelasticans. Operation at off-design conditions may promote blade stall; eventually the stall pattern will propagate around the blade annulus. The unsteady periodic nature of propagating stall will force blade vibration and blade flutter may occur if the stall propagation frequency is entrained by the blade natural frequency. In this work a computational scheme based on the vortex method is used to simulate the flow over a linear cascade of airfoils. The viscous effect is confined to a thin layer, which determines the separation points on the airfoil surfaces. The preliminary structural model is a two-dimensional characteristic section with a single degree of freedom in either bending or torsion. A study of the relationship between the stall propagation frequency and the blade natural frequency has been conducted. The study shows that entrainment, or frequency synchronization, occurs, resulting in pure torsional flutter over a certain interval of reduced frequency. A severe blade torsional amplitude (of order 20 deg) has been computed in the entrainment region, reaching its largest value in the center of the interval. However, in practice, compressor blades will not sustain this vibration and blade failure may occur before reaching such a large amplitude. Outside the entrainment interval the stall propagation is shown to be independent of the blade natural frequency. In addition, computational results show that there is no entrainment in the pure bending mode. Rather, de-entrainment occurs with similar flow conditions and similar stall frequencies, resulting in blade buffeting in pure bending.

  9. Exemplary Social Studies Teachers Use of Computer-Supported Instruction in the Classroom

    ERIC Educational Resources Information Center

    Acikalin, Mehmet

    2010-01-01

    Educators increasingly support the use of computer-supported instruction in social studies education. However few studies have been conducted to study teacher use of computer-supported instruction in social studies education. This study was therefore designed to examine the use of exemplary social studies teachers' computer-supported instruction…

  10. Student Perceptions in the Design of a Computer Card Game for Learning Computer Literacy Issues: A Case Study

    ERIC Educational Resources Information Center

    Kordaki, Maria; Papastergiou, Marina; Psomos, Panagiotis

    2016-01-01

    The aim of this work was twofold. First, an empirical study was designed aimed at investigating the perceptions that entry-level non-computing majors--namely Physical Education and Sport Science (PESS) undergraduate students--hold about basic Computer Literacy (CL) issues. The participants were 90 first-year PESS students, and their perceptions…

  11. Self-Concept, Computer Anxiety, Gender and Attitude towards Interactive Computer Technologies: A Predictive Study among Nigerian Teachers

    ERIC Educational Resources Information Center

    Agbatogun, Alaba Olaoluwakotansibe

    2010-01-01

    Interactive Computer Technologies (ICTs) have crept into education industry, thus dramatically causing transformation in instructional process. This study examined the relative and combined contributions of computer anxiety, self-concept and gender to teachers' attitude towards the use of ICT(s). 454 Nigerian teachers constituted the sample. Three…

  12. Computer modeling reveals that modifications of the histone tail charges define salt-dependent interaction of the nucleosome core particles.

    PubMed

    Yang, Ye; Lyubartsev, Alexander P; Korolev, Nikolay; Nordenskiöld, Lars

    2009-03-18

    Coarse-grained Langevin molecular dynamics computer simulations were conducted for systems that mimic solutions of nucleosome core particles (NCPs). The NCP was modeled as a negatively charged spherical particle representing the complex of DNA and the globular part of the histones combined with attached strings of connected charged beads modeling the histone tails. The size, charge, and distribution of the tails relative to the core were built to match real NCPs. Three models of NCPs were constructed to represent different extents of covalent modification on the histone tails: (nonmodified) recombinant (rNCP), acetylated (aNCP), and acetylated and phosphorylated (paNCP). The simulation cell contained 10 NCPs in a dielectric continuum with explicit mobile counterions and added salt. The NCP-NCP interaction is decisively dependent on the modification state of the histone tails and on salt conditions. Increasing the monovalent salt concentration (KCl) from salt-free to physiological concentration leads to NCP aggregation in solution for rNCP, whereas NCP associates are observed only occasionally in the system of aNCPs. In the presence of divalent salt (Mg(2+)), rNCPs form dense stable aggregates, whereas aNCPs form aggregates less frequently. Aggregates are formed via histone-tail bridging and accumulation of counterions in the regions of NCP-NCP contacts. The paNCPs do not show NCP-NCP interaction upon addition of KCl or in the presence of Mg(2+). Simulations for systems with a gradual substitution of K(+) for Mg(2+), to mimic the Mg(2+) titration of an NCP solution, were performed. The rNCP system showed stronger aggregation that occurred at lower concentrations of added Mg(2+), compared to the aNCP system. Additional molecular dynamics simulations performed with a single NCP in the simulation cell showed that detachment of the tails from the NCP core was modest under a wide range of salt concentrations. This implies that salt-induced tail dissociation of the

  13. A Computational Study of the Flow Physics of Acoustic Liners

    NASA Technical Reports Server (NTRS)

    Tam, Christopher

    2006-01-01

    The present investigation is a continuation of a previous joint project between the Florida State University and the NASA Langley Research Center Liner Physics Team. In the previous project, a study of acoustic liners, in two dimensions, inside a normal incidence impedance tube was carried out. The study consisted of two parts. The NASA team was responsible for the experimental part of the project. This involved performing measurements in an impedance tube with a large aspect ratio slit resonator. The FSU team was responsible for the computation part of the project. This involved performing direct numerical simulation (DNS) of the NASA experiment in two dimensions using CAA methodology. It was agreed that upon completion of numerical simulation, the computed values of the liner impedance were to be sent to NASA for validation with experimental results. On following this procedure good agreements were found between numerical results and experimental measurements over a wide range of frequencies and sound-pressure-level. Broadband incident sound waves were also simulated numerically and measured experimentally. Overall, good agreements were also found.

  14. Size effects on insect hovering aerodynamics: an integrated computational study.

    PubMed

    Liu, H; Aono, H

    2009-03-01

    Hovering is a miracle of insects that is observed for all sizes of flying insects. Sizing effect in insect hovering on flapping-wing aerodynamics is of interest to both the micro-air-vehicle (MAV) community and also of importance to comparative morphologists. In this study, we present an integrated computational study of such size effects on insect hovering aerodynamics, which is performed using a biology-inspired dynamic flight simulator that integrates the modelling of realistic wing-body morphology, the modelling of flapping-wing and body kinematics and an in-house Navier-Stokes solver. Results of four typical insect hovering flights including a hawkmoth, a honeybee, a fruit fly and a thrips, over a wide range of Reynolds numbers from O(10(4)) to O(10(1)) are presented, which demonstrate the feasibility of the present integrated computational methods in quantitatively modelling and evaluating the unsteady aerodynamics in insect flapping flight. Our results based on realistically modelling of insect hovering therefore offer an integrated understanding of the near-field vortex dynamics, the far-field wake and downwash structures, and their correlation with the force production in terms of sizing and Reynolds number as well as wing kinematics. Our results not only give an integrated interpretation on the similarity and discrepancy of the near- and far-field vortex structures in insect hovering but also demonstrate that our methods can be an effective tool in the MAVs design. PMID:19258688

  15. Size effects on insect hovering aerodynamics: an integrated computational study.

    PubMed

    Liu, H; Aono, H

    2009-03-01

    Hovering is a miracle of insects that is observed for all sizes of flying insects. Sizing effect in insect hovering on flapping-wing aerodynamics is of interest to both the micro-air-vehicle (MAV) community and also of importance to comparative morphologists. In this study, we present an integrated computational study of such size effects on insect hovering aerodynamics, which is performed using a biology-inspired dynamic flight simulator that integrates the modelling of realistic wing-body morphology, the modelling of flapping-wing and body kinematics and an in-house Navier-Stokes solver. Results of four typical insect hovering flights including a hawkmoth, a honeybee, a fruit fly and a thrips, over a wide range of Reynolds numbers from O(10(4)) to O(10(1)) are presented, which demonstrate the feasibility of the present integrated computational methods in quantitatively modelling and evaluating the unsteady aerodynamics in insect flapping flight. Our results based on realistically modelling of insect hovering therefore offer an integrated understanding of the near-field vortex dynamics, the far-field wake and downwash structures, and their correlation with the force production in terms of sizing and Reynolds number as well as wing kinematics. Our results not only give an integrated interpretation on the similarity and discrepancy of the near- and far-field vortex structures in insect hovering but also demonstrate that our methods can be an effective tool in the MAVs design.

  16. Hydrogen generation from weak acids: electrochemical and computational studies of a diiron hydrogenase mimic.

    PubMed

    Felton, Greg A N; Vannucci, Aaron K; Chen, Jinzhu; Lockett, L Tori; Okumura, Noriko; Petro, Benjamin J; Zakai, Uzma I; Evans, Dennis H; Glass, Richard S; Lichtenberger, Dennis L

    2007-10-17

    Extended investigation of electrocatalytic generation of dihydrogen using [(mu-1,2-benzenedithiolato)][Fe(CO)3]2 has revealed that weak acids, such as acetic acid, can be used. The catalytic reduction producing dihydrogen occurs at approximately -2 V for several carboxylic acids and phenols resulting in overpotentials of only -0.44 to -0.71 V depending on the weak acid used. This unusual catalytic reduction occurs at a potential at which the starting material, in the absence of a proton source, does not show a reduction peak. The mechanism for this process and structures for the intermediates have been discerned by electrochemical and computational analysis. These studies reveal that the catalyst is the monoanion of the starting material and an ECEC mechanism occurs. PMID:17894491

  17. Study on the application of mobile internet cloud computing platform

    NASA Astrophysics Data System (ADS)

    Gong, Songchun; Fu, Songyin; Chen, Zheng

    2012-04-01

    The innovative development of computer technology promotes the application of the cloud computing platform, which actually is the substitution and exchange of a sort of resource service models and meets the needs of users on the utilization of different resources after changes and adjustments of multiple aspects. "Cloud computing" owns advantages in many aspects which not merely reduce the difficulties to apply the operating system and also make it easy for users to search, acquire and process the resources. In accordance with this point, the author takes the management of digital libraries as the research focus in this paper, and analyzes the key technologies of the mobile internet cloud computing platform in the operation process. The popularization and promotion of computer technology drive people to create the digital library models, and its core idea is to strengthen the optimal management of the library resource information through computers and construct an inquiry and search platform with high performance, allowing the users to access to the necessary information resources at any time. However, the cloud computing is able to promote the computations within the computers to distribute in a large number of distributed computers, and hence implement the connection service of multiple computers. The digital libraries, as a typical representative of the applications of the cloud computing, can be used to carry out an analysis on the key technologies of the cloud computing.

  18. Computer Literacy and Social Studies Teacher Education: Changes in Form and Content.

    ERIC Educational Resources Information Center

    Napier, John D.

    The impact of teaching computer literacy on the social studies curriculum, instruction, and teacher education is discussed. Social studies computer literacy objectives are organized into three components: awareness, understanding how computer technology affects individuals and society; acquisition, knowing how computers work and how to operate a…

  19. To What Degree Are Undergraduate Students Using Their Personal Computers to Support Their Daily Study Practices?

    ERIC Educational Resources Information Center

    Sim, KwongNui; Butson, Russell

    2014-01-01

    This scoping study examines the degree to which twenty two undergraduate students used their personal computers to support their academic study. The students were selected based on their responses to a questionnaire aimed at gauging their degree of computer skill. Computer activity data was harvested from the personal computers of eighteen…

  20. Computer Assisted Language Learning. Routledge Studies in Computer Assisted Language Learning

    ERIC Educational Resources Information Center

    Pennington, Martha

    2011-01-01

    Computer-assisted language learning (CALL) is an approach to language teaching and learning in which computer technology is used as an aid to the presentation, reinforcement and assessment of material to be learned, usually including a substantial interactive element. This books provides an up-to date and comprehensive overview of…

  1. Inquiry-Based Learning Case Studies for Computing and Computing Forensic Students

    ERIC Educational Resources Information Center

    Campbell, Jackie

    2012-01-01

    Purpose: The purpose of this paper is to describe and discuss the use of specifically-developed, inquiry-based learning materials for Computing and Forensic Computing students. Small applications have been developed which require investigation in order to de-bug code, analyse data issues and discover "illegal" behaviour. The applications are based…

  2. A calorimetric and computational study of aminomethoxybenzoic acids.

    PubMed

    Almeida, Ana R R P; Matos, M Agostinha R; Morais, Victor M F; Monte, Manuel J S

    2010-09-01

    The standard (p(0) = 0.1 MPa) molar enthalpies of formation, in the crystalline phase, of five aminomethoxybenzoic acids, at T = 298.15 K, were derived from the standard molar energies of combustion in oxygen, measured by static-bomb combustion calorimetry. Combining these results with literature results of the standard molar enthalpies of sublimation, at T = 298.15 K, the standard molar enthalpies of formation, in the gaseous phase, were derived. Additionally, the enthalpies of formation of the ten possible isomers of aminomethoxybenzoic acid were estimated using accurate Double Hybrid Density Functional Theory (DHDFT) computational methods. The good agreement between the experimental and estimated values of the enthalpies of formation of the five isomers studied experimentally allows us to be confident on the estimated values for the other five isomers. A quantitative evaluation and analysis of the aromatic character of all the studied isomers based on the calculation of Nucleus Independent Chemical Shifts (NICS) was also conducted. PMID:20718458

  3. Computational studies of polysiloxanes : oxidation potentials and decomposition reactions.

    SciTech Connect

    Assary, R. S.; Curtiss, L. A.; Redfern, P. C.; Zhang, Z.; Amine, K.

    2011-06-23

    Silicon-containing solvents have tremendous potential for application as electrolytes for electrical energy storage devices such as lithium-ion (air) batteries and supercapacitors. Quantum chemical methods were employed to investigate trends in oxidation potentials and decomposition reactions of a series of polysiloxanes. Various electron-donating and -withdrawing substituents can be used to tune the oxidation potential in shorter chain siloxanes but not in longer ones. Decomposition reactions of siloxanes in their oxidized states were investigated and compared against their carbon analogues. These studies suggest that the Si-O group provides added stability for siloxanes over their carbon analogues. Computational studies have also been performed for various disiloxanes and siloxanes with spacer groups to understand their thermochemical stability and oxidation potentials.

  4. The utilization of Computer Mediated Communication for case study collaboration.

    PubMed

    Gwozdek, Anne E; Klausner, Christine P; Kerschbaum, Wendy E

    2008-01-01

    Computer Mediated Communication (CMC) can be used as an effective tool for student communication and collaboration. First-year, first-semester dental hygiene students self-selected groups to develop dental hygiene process of care treatment plans, written reports, and oral case presentations based on assigned clinical cases. In consultation with the University of Michigan (UM) Digital Media Commons Collaborative Technologies Teams, CMC options were identified. Two chat rooms were established within the UM's Course Management System (CTools) to provide opportunities for synchronous (simultaneous, real-time) communication. One course blog site and 8 case blog sites were developed to provide students and instructors with electronic asynchronous (nonsimultaneous) communication formats. The purpose of this study was to evaluate the effectiveness of these technologies during group case study projects. CMC has the potential to provide an effective means of collaboration and communication when the technologies align with the purpose of the project and compliment the dynamics of student groups.

  5. Computational study of anterior communicating artery hemodynamics before aneurysm formation

    NASA Astrophysics Data System (ADS)

    Castro, Marcelo A.; Putman, Christopher M.; Cebral, Juan R.

    2012-03-01

    It is widely accepted that complexity in the flow pattern at the anterior communicating artery (AComA) is associated with the high rate of aneurysm formation in that location observed in large studies. A previous computational hemodynamic study showed a possible association between high maximum intraaneurysmal wall shear stress (WSS) at the systolic peak with rupture in a cohort of AComA aneurysms. In another study it was observed a connection between location of aneurysm blebs and regions of high WSS in models where blebs were virtually removed. However, others reported associations between low WSS and either rupture or blister formation. The purpose of this work is to study associations between hemodynamic patterns and AComA aneurysm initiation by comparing hemodynamics in the aneurysm and the normal model where the aneurysm was computationally removed. Vascular models of both right and left circulation were independently reconstructed from three-dimensional rotational angiography images using deformable models, and fused using a surface merging algorithm. The geometric models were then used to generate high-quality volumetric finite element grids of tetrahedra with an advancing front technique. For each patient, the second anatomical model was created by digitally removing the aneurysm. It was iteratively achieved by applying a Laplacian smoothing filter and remeshing the surface. Finite element blood flow numerical simulations were performed. It was observed that aneurysms initiated in regions of high and moderate WSS in the counterpart normal models. Adjacent or close to those regions, low WSS portions of the arterial wall were not affected by the disease.

  6. Hispanic Women Overcoming Deterrents to Computer Science: A Phenomenological Study

    ERIC Educational Resources Information Center

    Herling, Lourdes

    2011-01-01

    The products of computer science are important to all aspects of society and are tools in the solution of the world's problems. It is, therefore, troubling that the United States faces a shortage in qualified graduates in computer science. The number of women and minorities in computer science is significantly lower than the percentage of the…

  7. Case Studies in Computer Adaptive Test Design through Simulation.

    ERIC Educational Resources Information Center

    Eignor, Daniel R.; And Others

    The extensive computer simulation work done in developing the computer adaptive versions of the Graduate Record Examinations (GRE) Board General Test and the College Board Admissions Testing Program (ATP) Scholastic Aptitude Test (SAT) is described in this report. Both the GRE General and SAT computer adaptive tests (CATs), which are fixed length…

  8. A Sample Survey of Attitudes to Computer Studies.

    ERIC Educational Resources Information Center

    Gardner, J. R.; And Others

    1986-01-01

    Discusses survey of 1,441 lower sixth-form Northern Ireland students which explored attitudes toward computing and computers, aspirations towards computer-related careers, and attitudes toward programming and game playing activities. Statistical tests were applied to results to identify overall trends and assess significance of boy-girl agreement…

  9. Integrating Computer Ethics across the Curriculum: A Case Study

    ERIC Educational Resources Information Center

    Ben-Jacob, Marion G.

    2005-01-01

    There is an increased use of computers in the educational environment of today that compels educators and learners to be informed about computer ethics and the related social and legal issues. This paper addresses different approaches for integrating computer ethics across the curriculum. Included are ideas for online and on-site workshops, the…

  10. A Study on the Role of Computers in Adult Education

    ERIC Educational Resources Information Center

    Giannoukos, Georgios; Besas, Georgios; Hioctour, Vasilios; Georgas, Thomas

    2016-01-01

    This paper discusses how knowledge of computers can affect our daily personal life as well as in the workplace in Greece. Our research is concerned with how useful the knowledge of computers is in the everyday life and work of adults and attempts to investigate the interest of adults for learning computer programmes and different subjects via…

  11. Improving Computer Literacy of Business Management Majors: A Case Study

    ERIC Educational Resources Information Center

    Johnson, David W.; Bartholomew, Kimberly W.; Miller, Duane

    2006-01-01

    Stakeholders, such as future employers, parents, and educators, have raised their expectations of college graduates in the area of computer literacy. Computer skills and understanding are especially critical for business management graduates, who are expected to use computer technology as a tool in every aspect of their career. Business students…

  12. Are implicit motives revealed in mere words? Testing the marker-word hypothesis with computer-based text analysis

    PubMed Central

    Schultheiss, Oliver C.

    2013-01-01

    Traditionally, implicit motives (i.e., non-conscious preferences for specific classes of incentives) are assessed through semantic coding of imaginative stories. The present research tested the marker-word hypothesis, which states that implicit motives are reflected in the frequencies of specific words. Using Linguistic Inquiry and Word Count (LIWC; Pennebaker et al., 2001), Study 1 identified word categories that converged with a content-coding measure of the implicit motives for power, achievement, and affiliation in picture stories collected in German and US student samples, showed discriminant validity with self-reported motives, and predicted well-validated criteria of implicit motives (gender difference for the affiliation motive; in interaction with personal-goal progress: emotional well-being). Study 2 demonstrated LIWC-based motive scores' causal validity by documenting their sensitivity to motive arousal. PMID:24137149

  13. Fundamental studies in hypersonic aeroelasticity using computational methods

    NASA Astrophysics Data System (ADS)

    Thuruthimattam, Biju James

    This dissertation describes the aeroelastic analysis of a generic hypersonic vehicle using methods in computational aeroelasticity. This objective is achieved by first considering the behavior of a representative configuration, namely a two degree-of-freedom typical cross-section, followed by that of a three-dimensional model of the generic vehicle, operating at very high Mach numbers. The typical cross-section of a hypersonic vehicle is represented by a double-wedge cross-section, having pitch and plunge degrees of freedom. The flutter boundaries of the typical cross-section are first generated using third-order piston theory, to serve as a basis for comparison with the refined calculations. Prior to the refined calculations, the time-step requirements for the reliable computation of the unsteady airloads using Euler and Navier-Stokes aerodynamics are identified. Computational aeroelastic response results are used to obtain frequency and damping characteristics, and compared with those from piston theory solutions for a variety of flight conditions. A parametric study of offsets, wedge angles; and static angle of attack is conducted. All the solutions are fairly close below the flutter boundary, and differences between the various models increase when the flutter boundary is approached. For this geometry, differences between viscous and inviscid aeroelastic behavior are not substantial. The effects of aerodynamic heating on the aeroelastic behavior of the typical cross-section are incorporated in an approximate manner, by considering the response of a heated wing. Results indicate that aerodynamic heating reduces aeroelastic stability. This analysis was extended to a generic hypersonic vehicle, restrained such that the rigid-body degrees of freedom are absent. The aeroelastic stability boundaries of the canted fin alone were calculated using third-order piston theory. The stability boundaries for the generic vehicle were calculated at different altitudes using

  14. Computational studies of transport in ion channels using metadynamics.

    PubMed

    Furini, Simone; Domene, Carmen

    2016-07-01

    Molecular dynamics simulations have played a fundamental role in numerous fields of science by providing insights into the structure and dynamics of complex systems at the atomistic level. However, exhaustive sampling by standard molecular dynamics is in most cases computationally prohibitive, and the time scales accessible remain significantly shorter than many biological processes of interest. In particular, in the study of ion channels, realistic models to describe permeation and gating require accounting for large numbers of particles and accurate interaction potentials, which severely limits the length of the simulations. To overcome such limitations, several advanced methods have been proposed among which is metadynamics. In this algorithm, an external bias potential to accelerate sampling along selected collective variables is introduced. This bias potential discourages visiting regions of the configurational space already explored. In addition, the bias potential provides an estimate of the free energy as a function of the collective variables chosen once the simulation has converged. In this review, recent contributions of metadynamics to the field of ion channels are discussed, including how metadynamics has been used to search for transition states, predict permeation pathways, treat conformational flexibility that underlies the coupling between gating and permeation, or compute free energy of permeation profiles. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.

  15. Computational Study on Temperature Control Systems for Thermoelectric Refrigerators

    NASA Astrophysics Data System (ADS)

    Astrain, D.; Martínez, A.; Gorraiz, J.; Rodríguez, A.; Pérez, G.

    2012-06-01

    Thermoelectric refrigeration has the outstanding advantage of allowing accurate temperature control. However, on the market there are thermoelectric refrigerators which include on/off temperature control systems, because of their simplicity and low cost. The major problem with this system is that, when the thermoelectric modules are switched off, the heat stored in the heat exchanger at the hot end of the modules goes back into the refrigerator, forming a thermal bridge. In this work, we use a computational model, presented and validated in previous papers, to study alternative control systems. A new system is introduced based on idling voltages; that is, once the temperature of the refrigerator reaches the lower limit, the thermoelectric modules are not switched off but supplied with minimum voltage. Computational results prove that this system reduces the electric power consumption of the refrigerator by at least 40% with respect to that obtained with on/off control systems, and the coefficient of performance increases close to the maximum provided by any other control system.

  16. Enzymatic Halogenases and Haloperoxidases: Computational Studies on Mechanism and Function.

    PubMed

    Timmins, Amy; de Visser, Sam P

    2015-01-01

    Despite the fact that halogenated compounds are rare in biology, a number of organisms have developed processes to utilize halogens and in recent years, a string of enzymes have been identified that selectively insert halogen atoms into, for instance, a CH aliphatic bond. Thus, a number of natural products, including antibiotics, contain halogenated functional groups. This unusual process has great relevance to the chemical industry for stereoselective and regiospecific synthesis of haloalkanes. Currently, however, industry utilizes few applications of biological haloperoxidases and halogenases, but efforts are being worked on to understand their catalytic mechanism, so that their catalytic function can be upscaled. In this review, we summarize experimental and computational studies on the catalytic mechanism of a range of haloperoxidases and halogenases with structurally very different catalytic features and cofactors. This chapter gives an overview of heme-dependent haloperoxidases, nonheme vanadium-dependent haloperoxidases, and flavin adenine dinucleotide-dependent haloperoxidases. In addition, we discuss the S-adenosyl-l-methionine fluoridase and nonheme iron/α-ketoglutarate-dependent halogenases. In particular, computational efforts have been applied extensively for several of these haloperoxidases and halogenases and have given insight into the essential structural features that enable these enzymes to perform the unusual halogen atom transfer to substrates. PMID:26415843

  17. Gastric flow and mixing studied using computer simulation.

    PubMed

    Pal, Anupam; Indireshkumar, Keshavamurthy; Schwizer, Werner; Abrahamsson, Bertil; Fried, Michael; Brasseur, James G

    2004-12-22

    The fed human stomach displays regular peristaltic contraction waves that originate in the proximal antrum and propagate to the pylorus. High-resolution concurrent manometry and magnetic resonance imaging (MRI) studies of the stomach suggest a primary function of antral contraction wave (ACW) activity unrelated to gastric emptying. Detailed evaluation is difficult, however, in vivo. Here we analyse the role of ACW activity on intragastric fluid motions, pressure, and mixing with computer simulation. A two-dimensional computer model of the stomach was developed with the 'lattice-Boltzmann' numerical method from the laws of physics, and stomach geometry modelled from MRI. Time changes in gastric volume were specified to match global physiological rates of nutrient liquid emptying. The simulations predicted two basic fluid motions: retrograde 'jets' through ACWs, and circulatory flow between ACWs, both of which contribute to mixing. A well-defined 'zone of mixing', confined to the antrum, was created by the ACWs, with mixing motions enhanced by multiple and narrower ACWs. The simulations also predicted contraction-induced peristaltic pressure waves in the distal antrum consistent with manometric measurements, but with a much lower pressure amplitude than manometric data, indicating that manometric pressure amplitudes reflect direct contact of the catheter with the gastric wall. We conclude that the ACWs are central to gastric mixing, and may also play an indirect role in gastric emptying through local alterations in common cavity pressure. PMID:15615685

  18. Enzymatic Halogenases and Haloperoxidases: Computational Studies on Mechanism and Function.

    PubMed

    Timmins, Amy; de Visser, Sam P

    2015-01-01

    Despite the fact that halogenated compounds are rare in biology, a number of organisms have developed processes to utilize halogens and in recent years, a string of enzymes have been identified that selectively insert halogen atoms into, for instance, a CH aliphatic bond. Thus, a number of natural products, including antibiotics, contain halogenated functional groups. This unusual process has great relevance to the chemical industry for stereoselective and regiospecific synthesis of haloalkanes. Currently, however, industry utilizes few applications of biological haloperoxidases and halogenases, but efforts are being worked on to understand their catalytic mechanism, so that their catalytic function can be upscaled. In this review, we summarize experimental and computational studies on the catalytic mechanism of a range of haloperoxidases and halogenases with structurally very different catalytic features and cofactors. This chapter gives an overview of heme-dependent haloperoxidases, nonheme vanadium-dependent haloperoxidases, and flavin adenine dinucleotide-dependent haloperoxidases. In addition, we discuss the S-adenosyl-l-methionine fluoridase and nonheme iron/α-ketoglutarate-dependent halogenases. In particular, computational efforts have been applied extensively for several of these haloperoxidases and halogenases and have given insight into the essential structural features that enable these enzymes to perform the unusual halogen atom transfer to substrates.

  19. Volcano Monitoring: A Case Study in Pervasive Computing

    NASA Astrophysics Data System (ADS)

    Peterson, Nina; Anusuya-Rangappa, Lohith; Shirazi, Behrooz A.; Song, Wenzhan; Huang, Renjie; Tran, Daniel; Chien, Steve; Lahusen, Rick

    Recent advances in wireless sensor network technology have provided robust and reliable solutions for sophisticated pervasive computing applications such as inhospitable terrain environmental monitoring. We present a case study for developing a real-time pervasive computing system, called OASIS for optimized autonomous space in situ sensor-web, which combines ground assets (a sensor network) and space assets (NASA’s earth observing (EO-1) satellite) to monitor volcanic activities at Mount St. Helens. OASIS’s primary goals are: to integrate complementary space and in situ ground sensors into an interactive and autonomous sensorweb, to optimize power and communication resource management of the sensorweb and to provide mechanisms for seamless and scalable fusion of future space and in situ components. The OASIS in situ ground sensor network development addresses issues related to power management, bandwidth management, quality of service management, topology and routing management, and test-bed design. The space segment development consists of EO-1 architectural enhancements, feedback of EO-1 data into the in situ component, command and control integration, data ingestion and dissemination and field demonstrations.

  20. Does contrast-enhanced ultrasound reveal tumor angiogenesis in pancreatic ductal carcinoma? A prospective study.

    PubMed

    Nishida, Mutsumi; Koito, Kazumitsu; Hirokawa, Naoki; Hori, Masakazu; Satoh, Taishi; Hareyama, Masato

    2009-02-01

    The purpose of this study is to evaluate tumor vascularity of pancreatic carcinoma noninvasively by contrast-enhanced ultrasound (US) and clarify the diagnostic value of tumor vascularity in subjects with nonresectable advanced pancreatic carcinoma. The study was approved by our institutional review board and written informed consent was obtained from all subjects. Twenty-seven subjects with advanced pancreatic ductal carcinoma were treated by chemoradiotherapy. Contrast-enhanced US, US guided biopsies and dynamic computed tomography (CT) were performed before and after the therapy. We assigned the intratumoral enhancement pattern of US as an enhanced ultrasound (EU) score, from 1 to 4, according to the degree of enhancement area. Intratumoral microvessel density (IMD) and average vessel diameter (AVD) were calculated by means of CD 34 immunostaining. Vascular endothelial growth factor (VEGF) staining was graded on a scale of 1 to 3. EU scores before chemoradiotherapy were compared with IMD, AVD, VEGF, histological grading and hepatic metastasis. After the therapy, local treatment response was evaluated by dynamic CT calculating the maximum area of the tumor, by comparing it with its size in pre- therapy. Subjects who had at least a 50% or more decrease of tumor size lasting more than 4 wk were estimated as partial response (PR), more than a 50% of increase progressive disease (PD) and if neither PR nor PD criteria were met, they were classified as stabled disease (SD). Next, EU scores were compared with IMD, AVD, VEGF and treatment response. Statistically significant differences were evaluated by Pearson's correlation, post-hoc, Spearman's rank correlation, Wilcoxon rank sum and Student's t-test. A p < 0.05 was defined as being statistically significant. Before the therapy, the EU score and IMD were significantly correlated (r = 0.50, p < 0.02), as was VEGF (r = 0.45, p < 0.05). The EU score and AVD were negatively correlated (r = - 0.56, p < 0.02). Significant

  1. Revealing the binding modes and the unbinding of 14-3-3σ proteins and inhibitors by computational methods.

    PubMed

    Hu, Guodong; Cao, Zanxia; Xu, Shicai; Wang, Wei; Wang, Jihua

    2015-01-01

    The 14-3-3σ proteins are a family of ubiquitous conserved eukaryotic regulatory molecules involved in the regulation of mitogenic signal transduction, apoptotic cell death, and cell cycle control. A lot of small-molecule inhibitors have been identified for 14-3-3 protein-protein interactions (PPIs). In this work, we carried out molecular dynamics (MD) simulations combined with molecular mechanics generalized Born surface area (MM-GBSA) method to study the binding mechanism between a 14-3-3σ protein and its eight inhibitors. The ranking order of our calculated binding free energies is in agreement with the experimental results. We found that the binding free energies are mainly from interactions between the phosphate group of the inhibitors and the hydrophilic residues. To improve the binding free energy of Rx group, we designed the inhibitor R9 with group R9 = 4-hydroxypheny. However, we also found that the binding free energy of inhibitor R9 is smaller than that of inhibitor R1. By further using the steer molecular dynamics (SMD) simulations, we identified a new hydrogen bond between the inhibitor R8 and residue Arg64 in the pulling paths. The information obtained from this study may be valuable for future rational design of novel inhibitors, and provide better structural understanding of inhibitor binding to 14-3-3σ proteins. PMID:26568041

  2. Steady crack growth through ductile metals: Computational studies

    NASA Astrophysics Data System (ADS)

    Sobotka, James C.

    This thesis examines the crack-front response during sustained ductile tearing in structural metals at quasistatic rates using high resolution finite element computations. At load levels approaching the steady-growth regime, well-established computational methods that model material damage break down numerically as vanishingly small load increments produce increasingly large amounts of crack extension. The computational model adopted here determines the deformation history of a steadily advancing crack directly without the need for a priori (transient) analysis that considers blunting of the pre-existing stationary crack and subsequent growth through the associated initial plastic zone. Crack extension occurs at the remotely applied, fixed loading without the need for a local growth criteria. This numerical scheme utilizes a streamline integration technique to determine the elastic-plastic fields, generalized from a two-dimensional to a fully three-dimensional setting and implemented within mixed Matlab/C++/F-90 based software. Modifications of the conventional finite element formulation lead to an efficient procedure -- readily parallelized -- and determine the invariant near-front fields, representative of steady-state growth, on a fixed mesh in a boundary-layer framework. In the small-scale yielding regime, the crack front does not sense the existence of remote boundaries, and computational results retain a strong transferability among various geometric configurations where near-front, plastic deformation remains entirely enclosed by the surrounding linear-elastic material. The global stress intensity factor (KI ) and imposed T-stress fully specify displacement constraints along the far-field boundary, and in a three-dimensional setting, the panel thickness reflects the only natural length scale. The initial studies in this work consider steady crack advance within the small-scale yielding context under plane-strain conditions and mode I loading. These analyses

  3. Computational and Experimental Approaches to Reveal the Effects of Single Nucleotide Polymorphisms with Respect to Disease Diagnostics

    PubMed Central

    Kucukkal, Tugba G.; Yang, Ye; Chapman, Susan C.; Cao, Weiguo; Alexov, Emil

    2014-01-01

    DNA mutations are the cause of many human diseases and they are the reason for natural differences among individuals by affecting the structure, function, interactions, and other properties of DNA and expressed proteins. The ability to predict whether a given mutation is disease-causing or harmless is of great importance for the early detection of patients with a high risk of developing a particular disease and would pave the way for personalized medicine and diagnostics. Here we review existing methods and techniques to study and predict the effects of DNA mutations from three different perspectives: in silico, in vitro and in vivo. It is emphasized that the problem is complicated and successful detection of a pathogenic mutation frequently requires a combination of several methods and a knowledge of the biological phenomena associated with the corresponding macromolecules. PMID:24886813

  4. Computational sequence analysis of predicted long dsRNA transcriptomes of major crops reveals sequence complementarity with human genes.

    PubMed

    Jensen, Peter D; Zhang, Yuanji; Wiggins, B Elizabeth; Petrick, Jay S; Zhu, Jin; Kerstetter, Randall A; Heck, Gregory R; Ivashuta, Sergey I

    2013-01-01

    Long double-stranded RNAs (long dsRNAs) are precursors for the effector molecules of sequence-specific RNA-based gene silencing in eukaryotes. Plant cells can contain numerous endogenous long dsRNAs. This study demonstrates that such endogenous long dsRNAs in plants have sequence complementarity to human genes. Many of these complementary long dsRNAs have perfect sequence complementarity of at least 21 nucleotides to human genes; enough complementarity to potentially trigger gene silencing in targeted human cells if delivered in functional form. However, the number and diversity of long dsRNA molecules in plant tissue from crops such as lettuce, tomato, corn, soy and rice with complementarity to human genes that have a long history of safe consumption supports a conclusion that long dsRNAs do not present a significant dietary risk.

  5. Computational study of electro-convection effects on dendrite growth in batteries

    NASA Astrophysics Data System (ADS)

    Tan, Jinwang; Ryan, Emily M.

    2016-08-01

    Dendrite formation on the anode surface of a battery is closely related to the safety and capacity of high energy density batteries, thus suppressing dendrite growth will significantly improve the performance of batteries. Many experimental reports reveal that convection near the dendrite nucleation site can change the local mass transport, and ultimately affect dendrite growth. Investigation of the convection effect in batteries will guide the development of strategies to suppress dendrite growth in a convective electrolyte. Most of the existing electro-convection computational models for dendrite growth studies are based on Eulerian frameworks. These methods have difficulty modeling the moving boundaries associated with dendrite growth and are less computationally efficient in simulating convective fluid motion. In this paper we adopt a mesh-free particle based Lagrangian method to address the challenges of previous grid based Eulerian electro-convection models. The developed model is verified by comparison to analytical solutions, including verification of ion migration and the electric potential. Simulation results show that the predicted dendrite growth and electro-convective flow patterns compare well with experimental results during early dendrite growth stages. Parametric studies reveal that low viscosity electrolytes suppress the dendrite growth by increasing the mass transport of ions near the anode/electrolyte interface.

  6. Integrated Omics and Computational Glycobiology Reveal Structural Basis for Influenza A Virus Glycan Microheterogeneity and Host Interactions*

    PubMed Central

    Khatri, Kshitij; Klein, Joshua A.; White, Mitchell R.; Grant, Oliver C.; Leymarie, Nancy; Woods, Robert J.; Zaia, Joseph

    2016-01-01

    Despite sustained biomedical research effort, influenza A virus remains an imminent threat to the world population and a major healthcare burden. The challenge in developing vaccines against influenza is the ability of the virus to mutate rapidly in response to selective immune pressure. Hemagglutinin is the predominant surface glycoprotein and the primary determinant of antigenicity, virulence and zoonotic potential. Mutations leading to changes in the number of HA glycosylation sites are often reported. Such genetic sequencing studies predict at best the disruption or creation of sequons for N-linked glycosylation; they do not reflect actual phenotypic changes in HA structure. Therefore, combined analysis of glycan micro and macro-heterogeneity and bioassays will better define the relationships among glycosylation, viral bioactivity and evolution. We present a study that integrates proteomics, glycomics and glycoproteomics of HA before and after adaptation to innate immune system pressure. We combined this information with glycan array and immune lectin binding data to correlate the phenotypic changes with biological activity. Underprocessed glycoforms predominated at the glycosylation sites found to be involved in viral evolution in response to selection pressures and interactions with innate immune-lectins. To understand the structural basis for site-specific glycan microheterogeneity at these sites, we performed structural modeling and molecular dynamics simulations. We observed that the presence of immature, high-mannose type glycans at a particular site correlated with reduced accessibility to glycan remodeling enzymes. Further, the high mannose glycans at sites implicated in immune lectin recognition were predicted to be capable of forming trimeric interactions with the immune-lectin surfactant protein-D. PMID:26984886

  7. Experimental and Computational Study of Beta-Galactosidase Inhibition

    NASA Astrophysics Data System (ADS)

    Cooper, Anthony; Larini, Luca

    In this study, we combine experiments and simulations to design novel inhibitors of enzymes. We aim to characterize the inhibition mechanism which we show to be dependent on the aggregation of inhibitor peptides. As a model system we chose to use β-galactosidase. We selected four peptides out of 10,000 initially screened using microarrays and that show the greatest Michaelis-Menten constant and highest solubility. Molecular dynamics simulations were performed to identify the exact mechanism of action of these peptides. We show that the positive residues, like arginine and lysine, are crucial for inhibiting enzyme activity. According to simulations, these residues are also responsible for the conformations adopted by the peptide in solution. Dynamic light scattering study revealed that the aggregation of peptides with the enzyme takes place and is responsible for inhibiting enzyme activity.

  8. A Review of Evaluative Studies of Computer-based Learning in Nursing Education.

    ERIC Educational Resources Information Center

    Lewis, Michael J.; Davies, Rebecca; Jenkins, David; Tait, Michael I.

    2001-01-01

    Analysis of the methods used in 25 reports of the evaluation of nursing computer-based learning packages revealed significant research design flaws invalidating many conclusions. Ways to improve evaluation research on the effectiveness of computer-assisted instruction were recommended. (Contains 49 references.) (SK)

  9. Case Study: Creation of a Degree Program in Computer Security. White Paper.

    ERIC Educational Resources Information Center

    Belon, Barbara; Wright, Marie

    This paper reports on research into the field of computer security, and undergraduate degrees offered in that field. Research described in the paper reveals only one computer security program at the associate's degree level in the entire country. That program, at Texas State Technical College in Waco, is a 71-credit-hour program leading to an…

  10. An integrated multi-omics study revealed metabolic alterations underlying the effects of coffee consumption.

    PubMed

    Takahashi, Shoko; Saito, Kenji; Jia, Huijuan; Kato, Hisanori

    2014-01-01

    Many epidemiological studies have indicated that coffee consumption may reduce the risks of developing obesity and diabetes, but the underlying mechanisms of these effects are poorly understood. Our previous study revealed the changes on gene expression profiles in the livers of C57BL/6J mice fed a high-fat diet containing three types of coffee (caffeinated, decaffeinated and green unroasted coffee), using DNA microarrays. The results revealed remarkable alterations in lipid metabolism-related molecules which may be involved in the anti-obesity effects of coffee. We conducted the present study to further elucidate the metabolic alterations underlying the effects of coffee consumption through comprehensive proteomic and metabolomic analyses. Proteomics revealed an up-regulation of isocitrate dehydrogenase (a key enzyme in the TCA cycle) and its related proteins, suggesting increased energy generation. The metabolomics showed an up-regulation of metabolites involved in the urea cycle, with which the transcriptome data were highly consistent, indicating accelerated energy expenditure. The TCA cycle and the urea cycle are likely be accelerated in a concerted manner, since they are directly connected by mutually providing each other's intermediates. The up-regulation of these pathways might result in a metabolic shift causing increased ATP turnover, which is related to the alterations of lipid metabolism. This mechanism may play an important part in the suppressive effects of coffee consumption on obesity, inflammation, and hepatosteatosis. This study newly revealed global metabolic alterations induced by coffee intake, providing significant insights into the association between coffee intake and the prevention of type 2 diabetes, utilizing the benefits of multi-omics analyses. PMID:24618914

  11. An Integrated Multi-Omics Study Revealed Metabolic Alterations Underlying the Effects of Coffee Consumption

    PubMed Central

    Takahashi, Shoko; Saito, Kenji; Jia, Huijuan; Kato, Hisanori

    2014-01-01

    Many epidemiological studies have indicated that coffee consumption may reduce the risks of developing obesity and diabetes, but the underlying mechanisms of these effects are poorly understood. Our previous study revealed the changes on gene expression profiles in the livers of C57BL/6J mice fed a high-fat diet containing three types of coffee (caffeinated, decaffeinated and green unroasted coffee), using DNA microarrays. The results revealed remarkable alterations in lipid metabolism-related molecules which may be involved in the anti-obesity effects of coffee. We conducted the present study to further elucidate the metabolic alterations underlying the effects of coffee consumption through comprehensive proteomic and metabolomic analyses. Proteomics revealed an up-regulation of isocitrate dehydrogenase (a key enzyme in the TCA cycle) and its related proteins, suggesting increased energy generation. The metabolomics showed an up-regulation of metabolites involved in the urea cycle, with which the transcriptome data were highly consistent, indicating accelerated energy expenditure. The TCA cycle and the urea cycle are likely be accelerated in a concerted manner, since they are directly connected by mutually providing each other's intermediates. The up-regulation of these pathways might result in a metabolic shift causing increased ATP turnover, which is related to the alterations of lipid metabolism. This mechanism may play an important part in the suppressive effects of coffee consumption on obesity, inflammation, and hepatosteatosis. This study newly revealed global metabolic alterations induced by coffee intake, providing significant insights into the association between coffee intake and the prevention of type 2 diabetes, utilizing the benefits of multi-omics analyses. PMID:24618914

  12. Single-molecule studies reveal the function of a third polymerase in the replisome

    PubMed Central

    Georgescu, Roxana E; Kurth, Isabel; O'Donnell, Mike E

    2013-01-01

    The Escherichia coli replisome contains three polymerases, one more than necessary to duplicate the two parental strands. Using single-molecule studies, we reveal two advantages conferred by the third polymerase. First, dipolymerase replisomes are inefficient at synthesizing lagging strands, leaving single-strand gaps, whereas tripolymerase replisomes fill strands almost to completion. Second, tripolymerase replisomes are much more processive than dipolymerase replisomes. These features account for the unexpected three-polymerase-structure of bacterial replisomes. PMID:22157955

  13. Computer Simulations Reveal Substrate Specificity of Glycosidic Bond Cleavage in Native and Mutant Human Purine Nucleoside Phosphorylase.

    PubMed

    Isaksen, Geir Villy; Hopmann, Kathrin Helen; Åqvist, Johan; Brandsdal, Bjørn Olav

    2016-04-12

    Purine nucleoside phosphorylase (PNP) catalyzes the reversible phosphorolysis of purine ribonucleosides and 2'-deoxyribonucleosides, yielding the purine base and (2'-deoxy)ribose 1-phosphate as products. While this enzyme has been extensively studied, several questions with respect to the catalytic mechanism have remained largely unanswered. The role of the phosphate and key amino acid residues in the catalytic reaction as well as the purine ring protonation state is elucidated using density functional theory calculations and extensive empirical valence bond (EVB) simulations. Free energy surfaces for adenosine, inosine, and guanosine are fitted to ab initio data and yield quantitative agreement with experimental data when the surfaces are used to model the corresponding enzymatic reactions. The cognate substrates 6-aminopurines (inosine and guanosine) interact with PNP through extensive hydrogen bonding, but the substrate specificity is found to be a direct result of the electrostatic preorganization energy along the reaction coordinate. Asn243 has previously been identified as a key residue providing substrate specificity. Mutation of Asn243 to Asp has dramatic effects on the substrate specificity, making 6-amino- and 6-oxopurines equally good as substrates. The principal effect of this particular mutation is the change in the electrostatic preorganization energy between the native enzyme and the Asn243Asp mutant, clearly favoring adenosine over inosine and guanosine. Thus, the EVB simulations show that this particular mutation affects the electrostatic preorganization of the active site, which in turn can explain the substrate specificity. PMID:26985580

  14. Catalytic, Enantioselective Sulfenofunctionalisation of Alkenes: Mechanistic, Crystallographic, and Computational Studies

    PubMed Central

    Denmark, Scott E.; Hartmann, Eduard; Kornfilt, David J. P.; Wang, Hao

    2015-01-01

    The stereocontrolled introduction of vicinal heteroatomic substituents into organic molecules is one of the most powerful ways of adding value and function. Whereas many methods exist for the introduction of oxygen- and nitrogen-containing substituents, the number stereocontrolled methods for the introduction of sulfur-containing substituents pales by comparison. Previous reports from these laboratories have described the sulfenofunctionalization of alkenes that construct vicinal carbon-sulfur and carbon-oxygen, carbon-nitrogen as well as carbon-carbon bonds with high levels of diastereospecificity and enantioselectivity. This process is enabled by the concept of Lewis base activation of Lewis acids that provides activation of Group 16 electrophiles. To provide a foundation for expansion of substrate scope and improved selectivities, we have undertaken a comprehensive study of the catalytically active species. Insights gleaned from kinetic, crystallographic and computational methods have led to the introduction of a new family of sulfenylating agents that provide significantly enhanced selectivities. PMID:25411883

  15. Malignant uveal melanoma and similar lesions studied by computed tomography

    SciTech Connect

    Mafee, M.F.; Peyman, G.A.; McKusick, M.A.

    1985-08-01

    Forty-four patients with intraocular disease were studied by computed tomography (CT); in 19 cases malignant uveal melanoma was considered the likely diagnosis. CT proved to be accurate in determining the location and size of uveal melanomas, demonstrating scleral invasion, and differentiating melanoma from choroidal detachment or angioma, toxocariasis, and senile macular degeneration. On CT, uveal melanomas appeared as hyperdense lesions with slight to moderate contrast enhancement. Tumors thinner than 2 mm could not be seen. Using dynamic CT, the authors noted moderate peak amplitude, normal or delayed tissue transit time, and persistently elevated washout phase (downslope), indicating increased permeability as the result of an impaired tumor blood barrier. Histological types of uveal melanoma could not be differentiated on the basis of circulatory patterns. Dynamic CT may be useful in distinguishing uveal melanoma from choroidal hemangioma or hematoma.

  16. How common standards can diminish collective intelligence: a computational study.

    PubMed

    Morreau, Michael; Lyon, Aidan

    2016-08-01

    Making good decisions depends on having accurate information - quickly, and in a form in which it can be readily communicated and acted upon. Two features of medical practice can help: deliberation in groups and the use of scores and grades in evaluation. We study the contributions of these features using a multi-agent computer simulation of groups of physicians. One might expect individual differences in members' grading standards to reduce the capacity of the group to discover the facts on which well-informed decisions depend. Observations of the simulated groups suggest on the contrary that this kind of diversity can in fact be conducive to epistemic performance. Sometimes, it is adopting common standards that may be expected to result in poor decisions. PMID:27338114

  17. It pays to compare: an experimental study on computational estimation.

    PubMed

    Star, Jon R; Rittle-Johnson, Bethany

    2009-04-01

    Comparing and contrasting examples is a core cognitive process that supports learning in children and adults across a variety of topics. In this experimental study, we evaluated the benefits of supporting comparison in a classroom context for children learning about computational estimation. Fifth- and sixth-grade students (N=157) learned about estimation either by comparing alternative solution strategies or by reflecting on the strategies one at a time. At posttest and retention test, students who compared were more flexible problem solvers on a variety of measures. Comparison also supported greater conceptual knowledge, but only for students who already knew some estimation strategies. These findings indicate that comparison is an effective learning and instructional practice in a domain with multiple acceptable answers.

  18. Anethole-Water a Combined Jet, Matrix, and Computational Study

    NASA Astrophysics Data System (ADS)

    Newby, Josh; Nesheiwat, Jackleen

    2016-06-01

    Anethole [(E)-1-methoxy-4-(1-propenyl)benzene] is a natural product molecule that is commonly recognized as the flavor component of anise, fennel, and licorice. Previously, we reported the jet-cooled, laser-induced fluorescence (LIF) and single vibronic level fluorescence (SVLF) spectra of anethole. In this work, several weak bands were observed and were tentatively assigned as van der Waals clusters of anethole with water. We have since confirmed this assignment and have conducted a more detailed study to determine the geometry of these clusters. Results from LIF, SVLF, and matrix isolation FTIR spectroscopy, as well as computational results will be presented in this talk. J. Phys. Chem. A, 2013, 117 (48), 12831-12841 Newly built system at Hobart and William Smith Colleges

  19. Cogeneration technology alternatives study. Volume 6: Computer data

    NASA Technical Reports Server (NTRS)

    1980-01-01

    The potential technical capabilities of energy conversion systems in the 1985 - 2000 time period were defined with emphasis on systems using coal, coal-derived fuels or alternate fuels. Industrial process data developed for the large energy consuming industries serve as a framework for the cogeneration applications. Ground rules for the study were established and other necessary equipment (balance-of-plant) was defined. This combination of technical information, energy conversion system data ground rules, industrial process information and balance-of-plant characteristics was analyzed to evaluate energy consumption, capital and operating costs and emissions. Data in the form of computer printouts developed for 3000 energy conversion system-industrial process combinations are presented.

  20. Evidence for Homodimerization of the c-Fos Transcription Factor in Live Cells Revealed by Fluorescence Microscopy and Computer Modeling

    PubMed Central

    Szalóki, Nikoletta; Krieger, Jan Wolfgang; Komáromi, István; Tóth, Katalin

    2015-01-01

    The c-Fos and c-Jun transcription factors, members of the activator protein 1 (AP-1) complex, form heterodimers and bind to DNA via a basic leucine zipper and regulate the cell cycle, apoptosis, differentiation, etc. Purified c-Jun leucine zipper fragments could also form stable homodimers, whereas c-Fos leucine zipper homodimers were found to be much less stable in earlier in vitro studies. The importance of c-Fos overexpression in tumors and the controversy in the literature concerning c-Fos homodimerization prompted us to investigate Fos homodimerization. Förster resonance energy transfer (FRET) and molecular brightness analysis of fluorescence correlation spectroscopy data from live HeLa cells transfected with fluorescent-protein-tagged c-Fos indicated that c-Fos formed homodimers. We developed a method to determine the absolute concentrations of transfected and endogenous c-Fos and c-Jun, which allowed us to determine dissociation constants of c-Fos homodimers (Kd = 6.7 ± 1.7 μM) and c-Fos–c-Jun heterodimers (on the order of 10 to 100 nM) from FRET titrations. Imaging fluorescence cross-correlation spectroscopy (SPIM-FCCS) and molecular dynamics modeling confirmed that c-Fos homodimers were stably associated and could bind to the chromatin. Our results establish c-Fos homodimers as a novel form of the AP-1 complex that may be an autonomous transcription factor in c-Fos-overexpressing tissues and could contribute to tumor development. PMID:26303532

  1. Unique Aspects of the Structure and Dynamics of Elementary Iβ Cellulose Microfibrils Revealed by Computational Simulations1[OPEN

    PubMed Central

    Oehme, Daniel P.; Downton, Matthew T.; Doblin, Monika S.; Wagner, John; Gidley, Michael J.; Bacic, Antony

    2015-01-01

    The question of how many chains an elementary cellulose microfibril contains is critical to understanding the molecular mechanism(s) of cellulose biosynthesis and regulation. Given the hexagonal nature of the cellulose synthase rosette, it is assumed that the number of chains must be a multiple of six. We present molecular dynamics simulations on three different models of Iβ cellulose microfibrils, 18, 24, and 36 chains, to investigate their structure and dynamics in a hydrated environment. The 36-chain model stays in a conformational space that is very similar to the initial crystalline phase, while the 18- and 24-chain models sample a conformational space different from the crystalline structure yet similar to conformations observed in recent high-temperature molecular dynamics simulations. Major differences in the conformations sampled between the different models result from changes to the tilt of chains in different layers, specifically a second stage of tilt, increased rotation about the O2-C2 dihedral, and a greater sampling of non-TG exocyclic conformations, particularly the GG conformation in center layers and GT conformation in solvent-exposed exocyclic groups. With a reinterpretation of nuclear magnetic resonance data, specifically for contributions made to the C6 peak, data from the simulations suggest that the 18- and 24-chain structures are more viable models for an elementary cellulose microfibril, which also correlates with recent scattering and diffraction experimental data. These data inform biochemical and molecular studies that must explain how a six-particle cellulose synthase complex rosette synthesizes microfibrils likely comprised of either 18 or 24 chains. PMID:25786828

  2. Computational Studies on Cinchona Alkaloid-Catalyzed Asymmetric Organic Reactions.

    PubMed

    Tanriver, Gamze; Dedeoglu, Burcu; Catak, Saron; Aviyente, Viktorya

    2016-06-21

    Remarkable progress in the area of asymmetric organocatalysis has been achieved in the last decades. Cinchona alkaloids and their derivatives have emerged as powerful organocatalysts owing to their reactivities leading to high enantioselectivities. The widespread usage of cinchona alkaloids has been attributed to their nontoxicity, ease of use, stability, cost effectiveness, recyclability, and practical utilization in industry. The presence of tunable functional groups enables cinchona alkaloids to catalyze a broad range of reactions. Excellent experimental studies have extensively contributed to this field, and highly selective reactions were catalyzed by cinchona alkaloids and their derivatives. Computational modeling has helped elucidate the mechanistic aspects of cinchona alkaloid catalyzed reactions as well as the origins of the selectivity they induce. These studies have complemented experimental work for the design of more efficient catalysts. This Account presents recent computational studies on cinchona alkaloid catalyzed organic reactions and the theoretical rationalizations behind their effectiveness and ability to induce selectivity. Valuable efforts to investigate the mechanisms of reactions catalyzed by cinchona alkaloids and the key aspects of the catalytic activity of cinchona alkaloids in reactions ranging from pharmaceutical to industrial applications are summarized. Quantum mechanics, particularly density functional theory (DFT), and molecular mechanics, including ONIOM, were used to rationalize experimental findings by providing mechanistic insights into reaction mechanisms. B3LYP with modest basis sets has been used in most of the studies; nonetheless, the energetics have been corrected with higher basis sets as well as functionals parametrized to include dispersion M05-2X, M06-2X, and M06-L and functionals with dispersion corrections. Since cinchona alkaloids catalyze reactions by forming complexes with substrates via hydrogen bonds and long

  3. Computational Studies on Cinchona Alkaloid-Catalyzed Asymmetric Organic Reactions.

    PubMed

    Tanriver, Gamze; Dedeoglu, Burcu; Catak, Saron; Aviyente, Viktorya

    2016-06-21

    Remarkable progress in the area of asymmetric organocatalysis has been achieved in the last decades. Cinchona alkaloids and their derivatives have emerged as powerful organocatalysts owing to their reactivities leading to high enantioselectivities. The widespread usage of cinchona alkaloids has been attributed to their nontoxicity, ease of use, stability, cost effectiveness, recyclability, and practical utilization in industry. The presence of tunable functional groups enables cinchona alkaloids to catalyze a broad range of reactions. Excellent experimental studies have extensively contributed to this field, and highly selective reactions were catalyzed by cinchona alkaloids and their derivatives. Computational modeling has helped elucidate the mechanistic aspects of cinchona alkaloid catalyzed reactions as well as the origins of the selectivity they induce. These studies have complemented experimental work for the design of more efficient catalysts. This Account presents recent computational studies on cinchona alkaloid catalyzed organic reactions and the theoretical rationalizations behind their effectiveness and ability to induce selectivity. Valuable efforts to investigate the mechanisms of reactions catalyzed by cinchona alkaloids and the key aspects of the catalytic activity of cinchona alkaloids in reactions ranging from pharmaceutical to industrial applications are summarized. Quantum mechanics, particularly density functional theory (DFT), and molecular mechanics, including ONIOM, were used to rationalize experimental findings by providing mechanistic insights into reaction mechanisms. B3LYP with modest basis sets has been used in most of the studies; nonetheless, the energetics have been corrected with higher basis sets as well as functionals parametrized to include dispersion M05-2X, M06-2X, and M06-L and functionals with dispersion corrections. Since cinchona alkaloids catalyze reactions by forming complexes with substrates via hydrogen bonds and long

  4. Towards New Directions in Black Studies: Black Studies, the Computer Age.

    ERIC Educational Resources Information Center

    Bryant, Henry A.

    The importance of utilizing computer-age technology in various aspects of Black Studies instruction is discussed in this paper. After stressing the continued need for Black Studies programs, the paper describes the evolution of an idea to videotape Ethnic Studies course material in order to improve instruction and make material available to…

  5. Behavioral, computational, and neuroimaging studies of acquired apraxia of speech.

    PubMed

    Ballard, Kirrie J; Tourville, Jason A; Robin, Donald A

    2014-01-01

    A critical examination of speech motor control depends on an in-depth understanding of network connectivity associated with Brodmann areas 44 and 45 and surrounding cortices. Damage to these areas has been associated with two conditions-the speech motor programming disorder apraxia of speech (AOS) and the linguistic/grammatical disorder of Broca's aphasia. Here we focus on AOS, which is most commonly associated with damage to posterior Broca's area (BA) and adjacent cortex. We provide an overview of our own studies into the nature of AOS, including behavioral and neuroimaging methods, to explore components of the speech motor network that are associated with normal and disordered speech motor programming in AOS. Behavioral, neuroimaging, and computational modeling studies are indicating that AOS is associated with impairment in learning feedforward models and/or implementing feedback mechanisms and with the functional contribution of BA6. While functional connectivity methods are not yet routinely applied to the study of AOS, we highlight the need for focusing on the functional impact of localized lesions throughout the speech network, as well as larger scale comparative studies to distinguish the unique behavioral and neurological signature of AOS. By coupling these methods with neural network models, we have a powerful set of tools to improve our understanding of the neural mechanisms that underlie AOS, and speech production generally. PMID:25404911

  6. Behavioral, computational, and neuroimaging studies of acquired apraxia of speech

    PubMed Central

    Ballard, Kirrie J.; Tourville, Jason A.; Robin, Donald A.

    2014-01-01

    A critical examination of speech motor control depends on an in-depth understanding of network connectivity associated with Brodmann areas 44 and 45 and surrounding cortices. Damage to these areas has been associated with two conditions—the speech motor programming disorder apraxia of speech (AOS) and the linguistic/grammatical disorder of Broca’s aphasia. Here we focus on AOS, which is most commonly associated with damage to posterior Broca’s area (BA) and adjacent cortex. We provide an overview of our own studies into the nature of AOS, including behavioral and neuroimaging methods, to explore components of the speech motor network that are associated with normal and disordered speech motor programming in AOS. Behavioral, neuroimaging, and computational modeling studies are indicating that AOS is associated with impairment in learning feedforward models and/or implementing feedback mechanisms and with the functional contribution of BA6. While functional connectivity methods are not yet routinely applied to the study of AOS, we highlight the need for focusing on the functional impact of localized lesions throughout the speech network, as well as larger scale comparative studies to distinguish the unique behavioral and neurological signature of AOS. By coupling these methods with neural network models, we have a powerful set of tools to improve our understanding of the neural mechanisms that underlie AOS, and speech production generally. PMID:25404911

  7. Computers and the Writing Process: A Comparative Protocol Study. CDC Technical Report No. 34.

    ERIC Educational Resources Information Center

    Haas, Christina

    A study examined the extent to which computers affect the writing process. In order to test several hypotheses about writing with a computer 15 experienced writers wrote persuasive letters under four conditions--using pen and paper once and a computer the other three times. All of the subjects were experienced with computers having worked daily or…

  8. Radiation epidemiology and recent paediatric computed tomography studies.

    PubMed

    Boice, J D

    2015-06-01

    Recent record-linkage studies of cancer risk following computed tomography (CT) procedures among children and adolescents under 21 years of age must be interpreted with caution. The reasons why the examinations were performed were not known, and the dosimetric approaches did not include individual dose reconstructions or account for the possibility for missed examinations. The recent report (2013) on children by the United Nations Scientific Committee on the Effects of Atomic Radiation concluded that the associations may have resulted from confounding by indication (also called 'reverse causation'), and not radiation exposure. The reported cancer associations may very well have been related to the patients' underlying health conditions that prompted the examinations. Reverse causation has been observed in other epidemiological investigations, such as a Swedish study of thyroid cancer risk following I-131 scintillation imaging scans, and in studies of brain cancer risk following Thorotrast for cerebral angiography. Epidemiological patterns reported in the CT studies were also inconsistent with the world's literature. For example, in a UK study, teenagers had a higher risk of brain tumour than young children; in an Australian study, cancers not previously linked to radiation were significantly elevated; and in a Taiwanese study, the risk of benign tumours decreased with age at the time of CT examination. In all studies, solid tumours appeared much earlier than previously reported. Remarkably, in the Australian study, brain cancer excesses were seen regardless of whether or not the CT was to the head, i.e. a significant excess was reported for CT examinations of the abdomen and extremities, which involved no radiation exposure to the brain. In the UK study, the significance of the 'leukaemia' finding was only because myelodysplastic syndrome was added to the category, and there was no significance for leukaemia alone. Without knowledge of why CT examinations were

  9. Input to the NSF Study on Computational Requirements in Geosciences

    SciTech Connect

    Antoun, T; Lomov, I; Morris, J

    2004-12-13

    The Computational Physics Group of the Earth Sciences Division focuses much of its effort on improving current understanding of the response of geologic media to strong shock waves, and on the interaction of those waves with underground structures. Two codes have been developed and used to achieve these objectives: LDEC and GEODYN. Both codes are three-dimensional and massively parallel, and they have both been used on LLNLs high performance computing platforms to advance the state of the art in computational geophysics.

  10. Computational/experimental studies of isolated, single component droplet combustion

    NASA Technical Reports Server (NTRS)

    Dryer, Frederick L.

    1993-01-01

    Isolated droplet combustion processes have been the subject of extensive experimental and theoretical investigations for nearly 40 years. The gross features of droplet burning are qualitatively embodied by simple theories and are relatively well understood. However, there remain significant aspects of droplet burning, particularly its dynamics, for which additional basic knowledge is needed for thorough interpretations and quantitative explanations of transient phenomena. Spherically-symmetric droplet combustion, which can only be approximated under conditions of both low Reynolds and Grashof numbers, represents the simplest geometrical configuration in which to study the coupled chemical/transport processes inherent within non-premixed flames. The research summarized here, concerns recent results on isolated, single component, droplet combustion under microgravity conditions, a program pursued jointly with F.A. Williams of the University of California, San Diego. The overall program involves developing and applying experimental methods to study the burning of isolated, single component droplets, in various atmospheres, primarily at atmospheric pressure and below, in both drop towers and aboard space-based platforms such as the Space Shuttle or Space Station. Both computational methods and asymptotic methods, the latter pursued mainly at UCSD, are used in developing the experimental test matrix, in analyzing results, and for extending theoretical understanding. Methanol, and the normal alkanes, n-heptane, and n-decane, have been selected as test fuels to study time-dependent droplet burning phenomena. The following sections summarizes the Princeton efforts on this program, describe work in progress, and briefly delineate future research directions.

  11. Combined computational and experimental analysis reveals mitogen-activated protein kinase-mediated feedback phosphorylation as a mechanism for signaling specificity.

    PubMed

    Hao, Nan; Yildirim, Necmettin; Nagiec, Michal J; Parnell, Stephen C; Errede, Beverly; Dohlman, Henrik G; Elston, Timothy C

    2012-10-01

    Different environmental stimuli often use the same set of signaling proteins to achieve very different physiological outcomes. The mating and invasive growth pathways in yeast each employ a mitogen-activated protein (MAP) kinase cascade that includes Ste20, Ste11, and Ste7. Whereas proper mating requires Ste7 activation of the MAP kinase Fus3, invasive growth requires activation of the alternate MAP kinase Kss1. To determine how MAP kinase specificity is achieved, we used a series of mathematical models to quantitatively characterize pheromone-stimulated kinase activation. In accordance with the computational analysis, MAP kinase feedback phosphorylation of Ste7 results in diminished activation of Kss1, but not Fus3. These findings reveal how feedback phosphorylation of a common pathway component can limit the activity of a competing MAP kinase through feedback phosphorylation of a common activator, and thereby promote signal fidelity. PMID:22875986

  12. A computational study of spatially evolving turbulent plane jets

    NASA Astrophysics Data System (ADS)

    Stanley, Scott Alan

    1998-09-01

    Turbulent plane jets are prototypical free shear flows of practical interest in propulsion, combustion and environmental flows. While considerable experimental research has been performed on planar jets, very few computational studies exist. To the author's knowledge, this is the first computational study of planar turbulent jets utilizing direct numerical simulation. Non-uniform, fourth-order compact derivatives in space and a low storage fourth-order Runge-Kutta integration scheme in time are used to numerically solve the compressible Navier-Stokes equations. Characteristic 'nonreflecting' boundary conditions are coupled with characteristic inflow boundary conditions to allow forcing at the inflow. Up to 2.3 million grid points are used. Two-dimensional simulations are initially performed in order to evaluate their relevance to turbulent jets. It is found that they behave in a fashion fundamentally different than is observed experimentally for planar jets. This difference is due to a two-dimensional vortex dipole instability which unrealistically dominates these simulations. A detailed study of the spatial development of a three- dimensional turbulent jet has been performed. Profiles of the mean velocity field and Reynolds stresses achieve self-similarity rapidly and compare very well with experimental data. The self-similar jet growth rate, K1u = 0.094, and centerline velocity decay rate, C1u = 0.208, are in good agreement with the typical experimental values, K1u = 0.100 and C1u = 0.189, of Gutmark and Wygnanski. The downstream growth of the centerline fluctuation intensities match the experimental evolution, although there are small differences due to the sensitivity of jets to the upstream conditions. The development of the initial shear layer instability as well as the downstream transition to the jet column mode at the end of the potential core is captured well. The evolution of the mixing process in turbulent planar jets is studied through analysis of the

  13. Computational Study of the Genomic and Epigenomic Phenomena

    NASA Astrophysics Data System (ADS)

    Yang, Wenjing

    Biological systems are perhaps the ultimate complex systems, uniquely capable of processing and communicating information, reproducing in their lifetimes, and adapting in evolutionary time scales. My dissertation research focuses on using computational approaches to understand the biocomplexity manifested in the multitude of length scales and time scales. At the molecular and cellular level, central to the complex behavior of a biological system is the regulatory network. My research study focused on epigenetics, which is essential for multicellular organisms to establish cellular identity during development or in response to intracellular and environmental stimuli. My computational study of epigenomics is greatly facilitated by recent advances in high-throughput sequencing technology, which enables high-resolution snapshots of epigenomes and transcriptomes. Using human CD4+ T cell as a model system, the dynamical changes in epigenome and transcriptome pertinent to T cell activation were investigated at the genome scale. Going beyond traditional focus on transcriptional regulation, I provided evidences that post-transcriptional regulation may serve as a major component of the regulatory network. In addition, I explored alternative polyadenylation, another novel aspect of gene regulation, and how it cross-talks with the local chromatin structure. As the renowned theoretical biologist Theodosius Dobzhansky said eloquently, "Nothing in biology makes sense except in the light of evolution''. To better understand this ubiquitous driving force in the biological world, I went beyond molecular events in a single organism, and investigated the dynamical changes of population structure along the evolutionary time scale. To this end, we used HIV virus population dynamics in the host immune system as a model system. The evolution of HIV viral population plays a key role in AIDS immunopathogenesis with its exceptionally high mutation rate. However, the theoretical studies of

  14. A computational study of [2.2]cyclophanes.

    PubMed

    Caramori, Giovanni F; Galembeck, Sérgio E; Laali, Kenneth K

    2005-04-15

    A computational study of isomeric [2.2]cyclophanes, namely [2.2]paracyclophane 1, [2.2]metacyclophane 2, and [2.2]metaparacyclophane 3, has been carried out. For 1, geometry optimizations performed by various methods at different basis sets showed that MP2/6-31+G(d,p) and B3PW91/6-31+G(d,p) provide the best results in comparison to the X-ray data. Compound 1 has D(2) symmetry with distorted bridges. A conformational search was performed for [2.2]cyclophanes 2 and 3. Each cyclophane exists in two conformations which have different energies in the case of 3 but are degenerate in the case of 2. Relative energies and strain energies at the bridges follow the same order, indicating that the relief of bridge tension and repulsion between pi clouds are determining factors for the stability of [2.2]cyclophanes. Through a decomposition of strain energy, it can be concluded that both the rings or the bridges can absorb strain, but it depends on the conformer of butane that is considered in the calculation of SE(br). Changes in aromaticity of these compounds were evaluated by NICS and HOMA and were compared with benzene and xylenes dimers as models. Despite distortions from planarity and shortening and lengthening of the C-C bonds relative to the mean, the phenyl rings are aromatic. NICS suggests a concentration of electronic density between the rings as a result of bridging process. Computed MK, NPA, and GAPT charges were compared for the isomeric cyclophanes. The GIAO chemical shifts were calculated and indicate that 1 has a larger diamagnetic anisotropy than the other isomers.

  15. Outcomes from a pilot study using computer-based rehabilitative tools in a military population.

    PubMed

    Sullivan, Katherine W; Quinn, Julia E; Pramuka, Michael; Sharkey, Laura A; French, Louis M

    2012-01-01

    Novel therapeutic approaches and outcome data are needed for cognitive rehabilitation for patients with a traumatic brain injury; computer-based programs may play a critical role in filling existing knowledge gaps. Brain-fitness computer programs can complement existing therapies, maximize neuroplasticity, provide treatment beyond the clinic, and deliver objective efficacy data. However, these approaches have not been extensively studied in the military and traumatic brain injury population. Walter Reed National Military Medical Center established its Brain Fitness Center (BFC) in 2008 as an adjunct to traditional cognitive therapies for wounded warriors. The BFC offers commercially available "brain-training" products for military Service Members to use in a supportive, structured environment. Over 250 Service Members have utilized this therapeutic intervention. Each patient receives subjective assessments pre and post BFC participation including the Mayo-Portland Adaptability Inventory-4 (MPAI-4), the Neurobehavioral Symptom Inventory (NBSI), and the Satisfaction with Life Scale (SWLS). A review of the first 29 BFC participants, who finished initial and repeat measures, was completed to determine the effectiveness of the BFC program. Two of the three questionnaires of self-reported symptom change completed before and after participation in the BFC revealed a statistically significant reduction in symptom severity based on MPAI and NBSI total scores (p < .05). There were no significant differences in the SWLS score. Despite the typical limitations of a retrospective chart review, such as variation in treatment procedures, preliminary results reveal a trend towards improved self-reported cognitive and functional symptoms.

  16. Combining experimental and computational studies to understand and predict reactivities of relevance to homogeneous catalysis.

    PubMed

    Tsang, Althea S-K; Sanhueza, Italo A; Schoenebeck, Franziska

    2014-12-01

    This article showcases three major uses of computational chemistry in reactivity studies: the application after, in combination with, and before experiment. Following a brief introduction of suitable computational tools, challenges and opportunities in the implementation of computational chemistry in reactivity studies are discussed, exemplified with selected case studies from our and other laboratories.

  17. Case Study: Audio-Guided Learning, with Computer Graphics.

    ERIC Educational Resources Information Center

    Koumi, Jack; Daniels, Judith

    1994-01-01

    Describes teaching packages which involve the use of audiotape recordings with personal computers in Open University (United Kingdom) mathematics courses. Topics addressed include software development; computer graphics; pedagogic principles for distance education; feedback, including course evaluations and student surveys; and future plans.…

  18. High School Computer Science Education: A Five-State Study.

    ERIC Educational Resources Information Center

    Stephenson, Chris

    2002-01-01

    Discusses the place of computer science education in the high school curriculum and reports on a survey of schools in five states that investigated computer science teaching responsibilities, hardware and software use, programming languages, how teachers rank instructional resources, and how teachers rank opportunities for their own skill…

  19. A Study of Work Values of Computer Education in Accounting.

    ERIC Educational Resources Information Center

    Ahadiat, Nasrollah

    1992-01-01

    Describes a survey of students at a large university and a random sample of faculty at accounting accredited schools that investigated the use of microcomputers in accounting curricula. Topics discussed include work values and computer education, student and teacher attitudes toward computers, and differences between upper division and lower…

  20. Computer-aided simulation study of photomultiplier tubes

    NASA Technical Reports Server (NTRS)

    Zaghloul, Mona E.; Rhee, Do Jun

    1989-01-01

    A computer model that simulates the response of photomultiplier tubes (PMTs) and the associated voltage divider circuit is developed. An equivalent circuit that approximates the operation of the device is derived and then used to develop a computer simulation of the PMT. Simulation results are presented and discussed.

  1. Promoting High-Performance Computing and Communications. A CBO Study.

    ERIC Educational Resources Information Center

    Webre, Philip

    In 1991 the Federal Government initiated the multiagency High Performance Computing and Communications program (HPCC) to further the development of U.S. supercomputer technology and high-speed computer network technology. This overview by the Congressional Budget Office (CBO) concentrates on obstacles that might prevent the growth of the…

  2. Exploring Computer Science: A Case Study of School Reform

    ERIC Educational Resources Information Center

    Goode, Joanna; Margolis, Jane

    2011-01-01

    This article will detail efforts to broaden participation in computing in urban schools through a comprehensive reform effort of curricular development, teacher professional development, and policy changes. Beginning with an account of the curricular development of "Exploring Computer Science", we will describe the inquiry-based research that…

  3. Case Studies of Liberal Arts Computer Science Programs

    ERIC Educational Resources Information Center

    Baldwin, D.; Brady, A.; Danyluk, A.; Adams, J.; Lawrence, A.

    2010-01-01

    Many undergraduate liberal arts institutions offer computer science majors. This article illustrates how quality computer science programs can be realized in a wide variety of liberal arts settings by describing and contrasting the actual programs at five liberal arts colleges: Williams College, Kalamazoo College, the State University of New York…

  4. Brain-computer interfacing under distraction: an evaluation study

    NASA Astrophysics Data System (ADS)

    Brandl, Stephanie; Frølich, Laura; Höhne, Johannes; Müller, Klaus-Robert; Samek, Wojciech

    2016-10-01

    Objective. While motor-imagery based brain-computer interfaces (BCIs) have been studied over many years by now, most of these studies have taken place in controlled lab settings. Bringing BCI technology into everyday life is still one of the main challenges in this field of research. Approach. This paper systematically investigates BCI performance under 6 types of distractions that mimic out-of-lab environments. Main results. We report results of 16 participants and show that the performance of the standard common spatial patterns (CSP) + regularized linear discriminant analysis classification pipeline drops significantly in this ‘simulated’ out-of-lab setting. We then investigate three methods for improving the performance: (1) artifact removal, (2) ensemble classification, and (3) a 2-step classification approach. While artifact removal does not enhance the BCI performance significantly, both ensemble classification and the 2-step classification combined with CSP significantly improve the performance compared to the standard procedure. Significance. Systematically analyzing out-of-lab scenarios is crucial when bringing BCI into everyday life. Algorithms must be adapted to overcome nonstationary environments in order to tackle real-world challenges.

  5. Curcumin Binding to Beta Amyloid: A Computational Study.

    PubMed

    Rao, Praveen P N; Mohamed, Tarek; Teckwani, Karan; Tin, Gary

    2015-10-01

    Curcumin, a chemical constituent present in the spice turmeric, is known to prevent the aggregation of amyloid peptide implicated in the pathophysiology of Alzheimer's disease. While curcumin is known to bind directly to various amyloid aggregates, no systematic investigations have been carried out to understand its ability to bind to the amyloid aggregates including oligomers and fibrils. In this study, we constructed computational models of (i) Aβ hexapeptide (16) KLVFFA(21) octamer steric-zipper β-sheet assembly and (ii) full-length Aβ fibril β-sheet assembly. Curcumin binding in these models was evaluated by molecular docking and molecular dynamics (MD) simulation studies. In both the models, curcumin was oriented in a linear extended conformation parallel to fiber axis and exhibited better stability in the Aβ hexapeptide (16) KLVFFA(21) octamer steric-zipper model (Ebinding  = -10.05 kcal/mol) compared to full-length Aβ fibril model (Ebinding  = -3.47 kcal/mol). Analysis of MD trajectories of curcumin bound to full-length Aβ fibril shows good stability with minimum Cα-atom RMSD shifts. Interestingly, curcumin binding led to marked fluctuations in the (14) HQKLVFFA(21) region that constitute the fibril spine with RMSF values ranging from 1.4 to 3.6 Å. These results show that curcumin binding to Aβ shifts the equilibrium in the aggregation pathway by promoting the formation of non-toxic aggregates.

  6. Computed tomography study of pineal calcification in schizophrenia.

    PubMed

    Bersani, G; Garavini, A; Taddei, I; Tanfani, G; Nordio, M; Pancheri, P

    1999-06-01

    Computed tomography studies concerning pineal calcification (PC) in schizophrenia have been conducted mainly by one author who correlated this calcification with several aspects of the illness. On the basis of these findings the aim of the present study was to analyze size and incidence of pineal gland calcification by CT in schizophrenics and healthy controls, and to verify the relationship between pineal calcification and age, and the possible correlation with psychopathologic variables. Pineal calcification was measured on CT scans of 87 schizophrenics and 46 controls divided into seven age subgroups of five years each. No significant differences in PC incidence and mean size between patients and controls were observed as far as the entire group was considered. PC size correlated with age both in schizophrenics and controls. We found a higher incidence of PC in schizophrenics in the age subgroup of 21-25 years, and a negative correlation with positive symptoms of schizophrenia in the overall group. These findings could suggest a premature calcific process in schizophrenics and a probable association with 'non-paranoid' aspects of the illness. Nevertheless the potential role of this process possibly related to some aspects of the altered neurodevelopment in schizophrenia is still unclear. PMID:10572342

  7. A computational study of flashover voltage of iced insulators

    SciTech Connect

    Sundarajan, R.

    1996-11-01

    In cold or mountainous regions, snow or ice, superimposed with contaminants covered on insulators cause flashover of insulators at nominal operating voltage. Laboratory simulation of icing performance of a set of insulators takes elaborate preparation. Additionally, there is a wide scattering of data due to the difference in the nature and quantity of ice and snow. Hence, it is desirable to develop a valid, realistic computer aided technique to study icing flashover. Presented in this paper are the results of an investigation of the flashover voltage of porcelain insulators under iced conditions using a contamination flashover model. The ice or snow is treated as a contaminant, the severity of which is represented in terms of the conductivity of the water melted from the ice or snow, and the thickness and the degree of the ice covering. Model results in good agreement with experimental data have been obtained. Both AC and DC insulators have been considered for this study. The results demonstrate the use of the model as a complement to experimental techniques to rank the icing performance of various HV outdoor insulators.

  8. Computational Study of Intramolecular Heterocyclic Ring Formation with Cyclic Phosphazenes

    PubMed Central

    Miller, Whelton A.; Moore, Preston B.

    2015-01-01

    Polyphosphazenes, because of their unique properties, have generated many opportunities to explore a variety of applications. These applications include areas such as biomedical research (e.g. drug delivery) and material science (e.g. fire-resistant polymers). Phosphazenes potentially have more variations then benzene analogues because of different substitution patterns. Here we present A computational study of the chemical modifications to a group of cyclic phosphazenes mainly hexachlorophosphazene (PNCl2)3. This study focuses on the relative energies of reactivity of hexachlorophosphazene to understand their geometry and the complexes they likely form. We compare diols, amino alcohols, and diamines with a carbon linker of 1-7 atoms. These heteroatom chains are attached to a single phosphorus atom or adjoining phosphorus atoms to form ring structures of geminal, vicinal (cis), and vicinal (trans) moieties. We find that the reactivities of “heteroatom caps” are predicted to be O,O (diol) > N,O (amino alcohol) > N,N (diamine). These results can be used to predict energetics and thus the stability of new compounds for biomedical and industrial applications. PMID:26702403

  9. Automated CFD Parameter Studies on Distributed Parallel Computers

    NASA Technical Reports Server (NTRS)

    Rogers, Stuart E.; Aftosmis, Michael; Pandya, Shishir; Tejnil, Edward; Ahmad, Jasim; Kwak, Dochan (Technical Monitor)

    2002-01-01

    The objective of the current work is to build a prototype software system which will automated the process of running CFD jobs on Information Power Grid (IPG) resources. This system should remove the need for user monitoring and intervention of every single CFD job. It should enable the use of many different computers to populate a massive run matrix in the shortest time possible. Such a software system has been developed, and is known as the AeroDB script system. The approach taken for the development of AeroDB was to build several discrete modules. These include a database, a job-launcher module, a run-manager module to monitor each individual job, and a web-based user portal for monitoring of the progress of the parameter study. The details of the design of AeroDB are presented in the following section. The following section provides the results of a parameter study which was performed using AeroDB for the analysis of a reusable launch vehicle (RLV). The paper concludes with a section on the lessons learned in this effort, and ideas for future work in this area.

  10. A Case Study on the Use of Blended Learning to Encourage Computer Science Students to Study

    NASA Astrophysics Data System (ADS)

    Pérez-Marín, Diana; Pascual-Nieto, Ismael

    2012-02-01

    Students tend to procrastinate. In particular, Computer Science students tend to reduce the number of hours devoted to study concepts after class. In this paper, a case study on the use of Blended Learning to encourage Computer Science students to study is described. Furthermore, an experiment in which the reaction of 131 Computer Science university students to the proposal is analyzed. The material for the preparation of an exam was produced both in electronic and paper formats. 64 students were asked to study using a free-text scoring system, and 67 students were asked to study with printed documentation in the same class. The students' reactions, the results of a pre-post-test and the answers to a voluntary and anonymous satisfaction questionnaire were registered. After that, students were given the option to keep studying with the scoring system or with the printed documentation. 99% of the students chose to study with the computer, and a higher frequency of study was registered during the previous month to the exam.

  11. Computational study of porous materials for gas separations

    NASA Astrophysics Data System (ADS)

    Lin, Li-Chiang

    Nanoporous materials such as zeolites, zeolitic imidazolate frameworks (ZIFs), and metal-organic frameworks (MOFs) are used as sorbents or membranes for gas separations such as carbon dioxide capture, methane capture, paraffin/olefin separations, etc. The total number of nanoporous materials is large; by changing the chemical composition and/or the structural topologies we can envision an infinite number of possible materials. In practice one can synthesize and fully characterize only a small subset of these materials. Hence, computational study can play an important role by utilizing various techniques in molecular simulations as well as quantum chemical calculations to accelerate the search for optimal materials for various energy-related separations. Accordingly, several large-scale computational screenings of over one hundred thousand materials have been performed to find the best materials for carbon capture, methane capture, and ethane/ethene separation. These large-scale screenings identified a number of promising materials for different applications. Moreover, the analysis of these screening studies yielded insights into those molecular characteristics of a material that contribute to an optimal performance for a given application. These insights provided useful guidelines for future structural design and synthesis. For instance, one of the screening studies indicated that some zeolite structures can potentially reduce the energy penalty imposed on a coal-fired power plant by as much as 35% compared to the near-term MEA technology for carbon capture application. These optimal structures have topologies with a maximized density of pockets and they capture and release CO2 molecules with an optimal energy. These screening studies also pointed to some systems, for which conventional force fields were unable to make sufficiently reliable predictions of the adsorption isotherms of different gasses, e.g., CO2 in MOFs with open-metal sites. For these systems, we

  12. Insights into antiviral innate immunity revealed by studying hepatitis C virus

    PubMed Central

    Horner, Stacy M.

    2015-01-01

    Experimental studies on the interactions of the positive strand RNA virus hepatitis C virus (HCV) with the host have contributed to several discoveries in the field of antiviral innate immunity. These include revealing the antiviral sensing pathways that lead to the induction of type I interferon (IFN) during HCV infection and also the importance of type III IFNs in the antiviral immune response to HCV. These studies on HCV/host interactions have contributed to our overall understanding of viral sensing and viral evasion of the antiviral intracellular innate immune response. In this review, I will highlight how these studies of HCV/host interactions have led to new insights into antiviral innate immunity. Overall, I hope to emphasize that studying antiviral immunity in the context of virus infection is necessary to fully understand antiviral immunity and how it controls the outcome of viral infection. PMID:25819428

  13. Validation studies of a computational model for molten material freezing

    SciTech Connect

    Sawada, Tetsuo; Ninokata, Hisashi; Shimizu, Akinao

    1996-02-01

    Validation studies are described of a computational model for the freezing of molten core materials under core disruptive accident conditions of fast breeder reactors. A series of out-of-pile experiments named SIMBATH, performed at Forschungszentrum Karlsruhe in Germany, has already been analyzed with the SIMMER-II code. In the current study, TRAN simulation tests in the SIMBATH facility are analyzed by SIMMER-II for its modeling validation of molten material freezing. The original TRAN experiments were performed at Sandia National laboratories to examine the freezing behavior of molten UO{sub 2} injected into an annular channels. In the TAN simulation experiments of the SIMBATH series, similar freezing phenomena are investigated for molten thermite, a mixture of Al{sub 2}O{sub 3} and iron, instead of UO{sub 2}. Two typical TRAN simulation tests are analyzed that aim at clarification of the applicability of the code to the freezing process during the experiments. The distribution of molten materials that are deposited in the test section according to the experimental measurements and in calculations by SIMMER-II is compared. These studies confirm that the conduction-limited freezing model combined with the rudimentary bulk freezing (particle-jamming) model of SIMMER-II is compared. These studies confirm that the conduction-limited freezing model combined with the rudimentary bulk freezing (particle-jamming) model of SIMMER-II could be used to reproduce the TRAN simulation experiments satisfactorily. This finding encourages the extrapolation of the results of previous validation research for SIMMER-II based on other SIMBATH tests to reactor case analyses. The calculation by SIMMER-II suggest that further improvements of the model, such as freezing on a convex surface of pin cladding and the scraping of crusts, make possible more accurate simulation of freezing phenomena.

  14. Virtual Computing Laboratories: A Case Study with Comparisons to Physical Computing Laboratories

    ERIC Educational Resources Information Center

    Burd, Stephen D.; Seazzu, Alessandro F.; Conway, Christopher

    2009-01-01

    Current technology enables schools to provide remote or virtual computing labs that can be implemented in multiple ways ranging from remote access to banks of dedicated workstations to sophisticated access to large-scale servers hosting virtualized workstations. This paper reports on the implementation of a specific lab using remote access to…

  15. Space station Simulation Computer System (SCS) study for NASA/MSFC. Volume 6: Study issues report

    NASA Technical Reports Server (NTRS)

    1989-01-01

    The Simulation Computer System (SCS) is the computer hardware, software, and workstations that will support the Payload Training Complex (PTC) at the Marshall Space Flight Center (MSFC). The PTC will train the space station payload specialists and mission specialists to operate the wide variety of experiments that will be on-board the Freedom Space Station. This simulation Computer System (SCS) study issues report summarizes the analysis and study done as task 1-identify and analyze the CSC study issues- of the SCS study contract.This work was performed over the first three months of the SCS study which began in August of 1988. First issues were identified from all sources. These included the NASA SOW, the TRW proposal, and working groups which focused the experience of NASA and the contractor team performing the study-TRW, Essex, and Grumman. The final list is organized into training related issues, and SCS associated development issues. To begin the analysis of the issues, a list of all the functions for which the SCS could be used was created, i.e., when the computer is turned on, what will it be doing. Analysis was continued by creating an operational functions matrix of SCS users vs. SCS functions to insure all the functions considered were valid, and to aid in identification of users as the analysis progressed. The functions will form the basis for the requirements, which are currently being developed under task 3 of the SCS study.

  16. A computational study of liposome logic: towards cellular computing from the bottom up

    PubMed Central

    Smaldon, James; Romero-Campero, Francisco J.; Fernández Trillo, Francisco; Gheorghe, Marian; Alexander, Cameron

    2010-01-01

    In this paper we propose a new bottom-up approach to cellular computing, in which computational chemical processes are encapsulated within liposomes. This “liposome logic” approach (also called vesicle computing) makes use of supra-molecular chemistry constructs, e.g. protocells, chells, etc. as minimal cellular platforms to which logical functionality can be added. Modeling and simulations feature prominently in “top-down” synthetic biology, particularly in the specification, design and implementation of logic circuits through bacterial genome reengineering. The second contribution in this paper is the demonstration of a novel set of tools for the specification, modelling and analysis of “bottom-up” liposome logic. In particular, simulation and modelling techniques are used to analyse some example liposome logic designs, ranging from relatively simple NOT gates and NAND gates to SR-Latches, D Flip-Flops all the way to 3 bit ripple counters. The approach we propose consists of specifying, by means of P systems, gene regulatory network-like systems operating inside proto-membranes. This P systems specification can be automatically translated and executed through a multiscaled pipeline composed of dissipative particle dynamics (DPD) simulator and Gillespie’s stochastic simulation algorithm (SSA). Finally, model selection and analysis can be performed through a model checking phase. This is the first paper we are aware of that brings to bear formal specifications, DPD, SSA and model checking to the problem of modeling target computational functionality in protocells. Potential chemical routes for the laboratory implementation of these simulations are also discussed thus for the first time suggesting a potentially realistic physiochemical implementation for membrane computing from the bottom-up. PMID:21886681

  17. Computational study of lean premixed turbulent flames using RANSPDF and LESPDF methods

    NASA Astrophysics Data System (ADS)

    Rowinski, David H.; Pope, Stephen B.

    2013-08-01

    A computational study is performed on a series of four piloted, lean, premixed turbulent jet flames. These flames use the Sydney Piloted Premixed Jet Burner (PPJB), and with jet velocities of 50, 100, 150 and 200 m/s are denoted PM150, PM1100, PM1150 and PM1200, respectively. Calculations are performed using the RANSPDF and LESPDF methodologies, with different treatments of molecular diffusion, with detailed chemistry and flamelet-based chemistry modelling, and using different imposed boundary conditions. The sensitivities of the calculations to these different aspects of the modelling are compared and discussed. Comparisons are made to experimental data and to previously-performed calculations. It is found that, given suitable boundary conditions and treatment of molecular diffusion, excellent agreement between the calculations and experimental measurements of the mean and variance fields can be achieved for PM150 and PM1100. The application of a recently developed implementation of molecular diffusion results in a large improvement in the computed variance fields in the LESPDF calculations. The inclusion of differential diffusion in the LESPDF calculations provides insight on the behaviour in the near-field region of the jet, but its effects are found to be confined to this region and to the species CO, OH and H2. A major discrepancy observed in many previous calculations of these flames is an overprediction of reaction progress in PM1150 and PM1200, and this discrepancy is also observed in the LESPDF calculations; however, a parametric study of the LESPDF mixing model reveals that, with a sufficiently large mixing frequency, calculations of these two flames are capable of yielding improved reaction progress in good qualitative agreement with the mean and RMS scalar measurements up to an x/D of 30. Lastly, the merits of each computational methodology are discussed in light of their computational costs.

  18. Infections Revealing Complement Deficiency in Adults: A French Nationwide Study Enrolling 41 Patients.

    PubMed

    Audemard-Verger, A; Descloux, E; Ponard, D; Deroux, A; Fantin, B; Fieschi, C; John, M; Bouldouyre, A; Karkowsi, L; Moulis, G; Auvinet, H; Valla, F; Lechiche, C; Davido, B; Martinot, M; Biron, C; Lucht, F; Asseray, N; Froissart, A; Buzelé, R; Perlat, A; Boutboul, D; Fremeaux-Bacchi, V; Isnard, S; Bienvenu, B

    2016-05-01

    Complement system is a part of innate immunity, its main function is to protect human from bacterial infection. As genetic disorders, complement deficiencies are often diagnosed in pediatric population. However, complement deficiencies can also be revealed in adults but have been poorly investigated. Herein, we describe a case series of infections revealing complement deficiency in adults to study clinical spectrum and management of complement deficiencies.A nationwide retrospective study was conducted in French university and general hospitals in departments of internal medicine, infectious diseases enrolling patients older than 15 years old who had presented at least one infection leading to a complement deficiency diagnosis.Forty-one patients included between 2002 and 2015 in 19 different departments were enrolled in this study. The male-to-female ratio was 1.3 and the mean age at diagnosis was 28 ± 14 (15-67) years. The main clinical feature was Neisseria meningitidis meningitis 75% (n = 31/41) often involving rare serotype: Y (n = 9) and W 135 (n = 7). The main complement deficiency observed was the common final pathway deficiency 83% (n = 34/41). Half of the cohort displayed severe sepsis or septic shock at diagnosis (n = 22/41) but no patient died. No patient had family history of complement deficiency. The mean follow-up was 1.15 ± 1.95 (0.1-10) years. Half of the patients had already suffered from at least one infection before diagnosis of complement deficiency: meningitis (n = 13), pneumonia (n = 4), fulminans purpura (n = 1), or recurrent otitis (n = 1). Near one-third (n = 10/39) had received prophylactic antibiotics (cotrimoxazole or penicillin) after diagnosis of complement deficiency. The vaccination coverage rate, at the end of the follow-up, for N meningitidis, Streptococcus pneumonia, and Haemophilius influenzae were, respectively, 90% (n = 33/37), 47% (n = 17/36), and 35% (n = 14

  19. Oxidation Induced Doping of Nanoparticles Revealed by in Situ X-ray Absorption Studies.

    PubMed

    Kwon, Soon Gu; Chattopadhyay, Soma; Koo, Bonil; Dos Santos Claro, Paula Cecilia; Shibata, Tomohiro; Requejo, Félix G; Giovanetti, Lisandro J; Liu, Yuzi; Johnson, Christopher; Prakapenka, Vitali; Lee, Byeongdu; Shevchenko, Elena V

    2016-06-01

    Doping is a well-known approach to modulate the electronic and optical properties of nanoparticles (NPs). However, doping at nanoscale is still very challenging, and the reasons for that are not well understood. We studied the formation and doping process of iron and iron oxide NPs in real time by in situ synchrotron X-ray absorption spectroscopy. Our study revealed that the mass flow of the iron triggered by oxidation is responsible for the internalization of the dopant (molybdenum) adsorbed at the surface of the host iron NPs. The oxidation induced doping allows controlling the doping levels by varying the amount of dopant precursor. Our in situ studies also revealed that the dopant precursor substantially changes the reaction kinetics of formation of iron and iron oxide NPs. Thus, in the presence of dopant precursor we observed significantly faster decomposition rate of iron precursors and substantially higher stability of iron NPs against oxidation. The same doping mechanism and higher stability of host metal NPs against oxidation was observed for cobalt-based systems. Since the internalization of the adsorbed dopant at the surface of the host NPs is driven by the mass transport of the host, this mechanism can be potentially applied to introduce dopants into different oxidized forms of metal and metal alloy NPs providing the extra degree of compositional control in material design. PMID:27152970

  20. Computer algebra methods in the study of nonlinear differential systems

    NASA Astrophysics Data System (ADS)

    Irtegov, V. D.; Titorenko, T. N.

    2013-06-01

    Some issues concerning computer algebra methods as applied to the qualitative analysis of differential equations with first integrals are discussed. The problems of finding stationary sets and analyzing their stability and bifurcations are considered. Special attention is given to algorithms for finding and analyzing peculiar stationary sets. It is shown that computer algebra tools, combined with qualitative analysis methods for differential equations, make it possible not only to enhance the computational efficiency of classical algorithms, but also to implement new approaches to the solution of well-known problems and, in this way, to obtain new results.

  1. [Diagnosis. Radiological study. Ultrasound, computed tomography and magnetic resonance imaging].

    PubMed

    Gallo Vallejo, Francisco Javier; Giner Ruiz, Vicente

    2014-01-01

    Because of its low cost, availability in primary care and ease of interpretation, simple X-ray should be the first-line imaging technique used by family physicians for the diagnosis and/or follow-up of patients with osteoarthritis. Nevertheless, this technique should only be used if there are sound indications and if the results will influence decision-making. Despite the increase of indications in patients with rheumatological disease, the role of ultrasound in patients with osteoarthritis continues to be limited. Computed tomography (CT) is of some -although limited- use in osteoarthritis, especially in the study of complex joints (such as the sacroiliac joint and facet joints). Magnetic resonance imaging (MRI) has represented a major advance in the evaluation of joint cartilage and subchondral bone in patients with osteoarthritis but, because of its high cost and diagnostic-prognostic yield, this technique should only be used in highly selected patients. The indications for ultrasound, CT and MRI in patients with osteoarthritis continue to be limited in primary care and often coincide with situations in which the patient may require hospital referral. Patient safety should be bourne in mind. Patients should be protected from excessive ionizing radiation due to unnecessary repeat X-rays or inadequate views or to requests for tests such as CT, when not indicated.

  2. Computational and Experimental Study of Neuroglobin and Mutants

    NASA Astrophysics Data System (ADS)

    Nelson, Lauren; Cho, Samuel; Kim-Shaprio, Daniel

    Neuroglobin (Ngb) is a hexacoordinated heme protein that is closely related to hemoglobin and myoglobin and normally found in the brain and nervous systems. It is involved in cellular oxygen homeostasis and reversibly binds to oxygen with a higher binding affinity than hemoglobin. To protect the brain tissue from hypoxic or ischemic conditions, Ngb increases oxygen availability. We have previously shown that a mutant form of Ngb reduces nitrite to nitric oxide 50x faster than myoglobin and 500x faster than hemoglobin. It also tightly binds to carbon monoxide (CO) with an association rate that is 500x faster than hemoglobin. To analyze the structure of neuroglobin and the characteristics causing these phenomena, we performed 3 sets of 1 microsecond molecular dynamic (MD) simulations of wild-type oxidized and reduced human Ngb and their C46A, C55A, H64L, and H64Q mutants. We also directly compare our MD simulations with time-resolved absorption spectroscopy. These studies will help identify treatments for diseases involving low nitric oxide availability and carbon monoxide poisoning. This research was supported by an NIH NSRA predoctoral fellowship in the Structural and Computational Biophysics Program training Grant (T32GM095440-05).

  3. Stereoselectivity of chalcone isomerase with chalcone derivatives: a computational study.

    PubMed

    Yao, Yuan; Zhang, Hui; Li, Ze-Sheng

    2013-11-01

    Chalcone isomerase (CHI) catalyzes the intramolecular cyclization of chalcones into flavonoids. The activity of CHI is essential for the biosynthesis of flavonoids precursors of floral pigments and phenylpropanoid plant defense compounds. In the present study, we explored the detailed binding structures and binding free energies for two different active site conformations of CHI with s-cis/s-trans conformers of three chalcone compounds by performing molecular dynamics (MD) simulations and binding free energy calculations. The computational results indicate that s-cis/s-trans conformers of chalcone compounds are orientated in the similar binding position in the active site of CHI and stabilized by the different first hydrogen bond network and the same second hydrogen bond network. The first hydrogen bond network results in much lower binding affinity of s-trans conformer of chalcone compound with CHI than that of s-cis conformer. The conformational change of the active site residue T48 from indirectly interacting with the substrate via the second hydrogen bond network to directly forming the hydrogen bond with the substrates cannot affect the binding mode of both conformers of chalcone compounds, but remarkably improves the binding affinity. These results show that CHI has a strong stereoselectivity. The calculated binding free energies for three chalcone compounds with CHI are consistent with the experimental activity data. In addition, several valuable insights are suggested for future rational design and discovery of high-efficiency mutants of CHI. PMID:23989772

  4. Computational Study of Ventilation and Disease Spread in Poultry Houses

    NASA Astrophysics Data System (ADS)

    Cimbala, John; Pawar, Sourabh; Wheeler, Eileen; Lindberg, Darla

    2006-11-01

    The air flow in and around poultry houses has been studied numerically with the goal of determining disease spread characteristics and comparing ventilation schemes. A typical manure-belt layer egg production facility is considered. The continuity, momentum, and energy equations are solved for flow both inside and outside poultry houses using the commercial computational fluid dynamics (CFD) code FLUENT. Both simplified two-dimensional and fully three-dimensional geometries are modeled. The spread of virus particles is considered to be analogous to diffusion of a tracer contaminant gas, in this case ammonia. The effect of thermal plumes produced by the hens in the poultry house is also considered. Two ventilation schemes with opposite flow directions are compared. Contours of temperature and ammonia mass fraction for both cases are obtained and compared. The analysis shows that ventilation and air quality characteristics are much better for the case in which the air flow is from bottom to top (enhancing the thermal plume) instead of from top to bottom (fighting the thermal plume) as in most poultry houses. This has implications in air quality control in the event of epidemic outbreaks of avian flu or other infectious diseases.

  5. Computational and Experimental Studies of Fluidized Beds for Biomass Gasification

    NASA Astrophysics Data System (ADS)

    Battaglia, Francine; Deza, Mirka; Franka, Nathan; Heindel, Theodore

    2007-11-01

    Fluidized bed gasifiers can convert feedstocks with low-carbon content into valuable products such as ethanol. Understanding fluidized bed hydrodynamics is important for reactor design and avoiding issues such as agglomeration or defluidization of the bed. In particular, biomass gasification is not well characterized and is the focus of this work. Glass beads or sand particles are typically used as bed materials due to their high sphericity and uniform properties. X-ray imaging will be used to visualize these complex flows and alternative bed materials will be considered to increase X-ray penetration and resolution to enhance flow visualization. Furthermore, computational modeling of fluidized beds can be used to predict operation of biomass gasifiers after extensive validation with experimental data. The hydrodynamics will be modeled assuming each phase behaves as interpenetrating continua using an Eulerian model and each solid phase is characterized by a particle diameter and density so that segregation and elutriation can be described. The simulations will model the cold-flow fluidized bed experiment, and consider factors such as sphericity of the particles, and calibration of drag coefficients. Hydrodynamic results from the simulations will be qualitatively and quantitatively compared to X-ray flow visualization studies of a similar bed.

  6. Primary cilia mechanics affects cell mechanosensation: A computational study.

    PubMed

    Khayyeri, Hanifeh; Barreto, Sara; Lacroix, Damien

    2015-08-21

    Primary cilia (PC) are mechanical cell structures linked to the cytoskeleton and are central to how cells sense biomechanical signals from their environment. However, it is unclear exactly how PC mechanics influences cell mechanosensation. In this study we investigate how the PC mechanical characteristics are involved in the mechanotransduction process whereby cilium deflection under fluid flow induces strains on the internal cell components that regulate the cell׳s mechanosensitive response. Our investigation employs a computational approach in which a finite element model of a cell consisting of a nucleus, cytoplasm, cortex, microtubules, actin bundles and a primary cilium was used together with a finite element representation of a flow chamber. Fluid-structure interaction analysis was performed by simulating perfusion flow of 1mm/s on the cell model. Simulations of cells with different PC mechanical characteristics, showed that the length and the stiffness of PC are responsible for the transmission of mechanical stimuli to the cytoskeleton. Fluid flow deflects the cilium, with the highest strains found at the base of the PC and in the cytoplasm. The PC deflection created further strains on the cell nucleus but did not influence microtubules and actin bundles significantly. Our results indicate that PC deflection under fluid flow stimulation transmits mechanical strain primarily to other essential organelles in the cytoplasm, such as the Golgi complex, that regulate cells' mechanoresponse. The simulations further suggest that cell mechanosensitivity can be altered by targeting PC length and rigidity.

  7. Molecular energetics of alkyl pyrrolecarboxylates: calorimetric and computational study.

    PubMed

    Santos, Ana Filipa L O M; Ribeiro da Silva, Manuel A V

    2013-06-20

    ), whose study was not performed experimentally. The computational analysis, at the B3LYP/6-31G(d) level of theory, of the six molecules allowed a detailed inspection and a better knowledge about their molecular structure and geometrical parameters. PMID:23682652

  8. Molecular energetics of alkyl pyrrolecarboxylates: calorimetric and computational study.

    PubMed

    Santos, Ana Filipa L O M; Ribeiro da Silva, Manuel A V

    2013-06-20

    ), whose study was not performed experimentally. The computational analysis, at the B3LYP/6-31G(d) level of theory, of the six molecules allowed a detailed inspection and a better knowledge about their molecular structure and geometrical parameters.

  9. Computational studies of model disordered and strongly correlated electronic systems

    NASA Astrophysics Data System (ADS)

    Johri, Sonika

    cannot be achieved perfectly in experiments. A chapter of this thesis is devoted to studying signatures of incomplete localization in a disordered system with interacting particles which is coupled to a bath. . Strongly interacting particles can also give rise to topological phases of matter that have exotic emergent properties, such as quasiparticles with fractional charges and anyonic, or perhaps even non-Abelian statistics. In addition to their intrinsic novelty, these particles (e.g. Majorana fermions) may be the building blocks of future quantum computers. The third part of my thesis focuses on the best experimentally known realizations of such systems - the fractional quantum Hall effect (FQHE) which occurs in two-dimensional electron gases in a strong perpendicular magnetic field. It has been observed in systems such as semiconductor heterostructures and, more recently, graphene. I have developed software for exact diagonalization of the many-body FQHE problem on the surface of a cylinder, a hitherto unstudied type of geometry. This geometry turns out to be optimal for the DMRG algorithm. Using this new geometry, I have studied properties of various fractionally-filled states, computing the overlap between exact ground states and model wavefunctions, their edge excitations, and entanglement spectra. I have calculated the sizes and tunneling amplitudes of quasiparticles, information which is needed to design the interferometers used to experimentally measure their Aharanov-Bohm phase. I have also designed numerical probes of the recently discovered geometric degree of freedom of FQHE states.

  10. Computational Kinetic Study for the Unimolecular Decomposition Pathways of Cyclohexanone.

    PubMed

    Zaras, Aristotelis M; Dagaut, Philippe; Serinyel, Zeynep

    2015-07-16

    There has been evidence lately that several endophytic fungi can convert lignocellulosic biomass into ketones among other oxygenated compounds. Such compounds could prove useful as biofuels for internal combustion engines. Therefore, their combustion properties are of high interest. Cyclohexanone was identified as an interesting second-generation biofuel ( Boot , M. ; et al. Cyclic Oxygenates: A New Class of Second-Generation Biofuels for Diesel Engines? Energy Fuels 2009 , 23 , 1808 - 1817 ; Klein-Douwel , R. J. H. ; et al. Soot and Chemiluminescence in Diesel Combustion of Bio-Derived, Oxygenated and Reference Fuels . Proc. Combust. Inst. 2009 , 32 , 2817 - 2825 ). However, until recently ( Serinyel , Z. ; et al. Kinetics of Oxidation of Cyclohexanone in a Jet- Stirred Reactor: Experimental and Modeling . Proc. Combust. Inst. 2014 ; DOI: 10.1016/j.proci.2014.06.150 ), no previous studies on the kinetics of oxidation of that fuel could be found in the literature. In this work, we present the first theoretical kinetic study of the unimolecular decomposition pathways of cyclohexanone, a cyclic ketone that could demonstrate important fuel potential. Using the quantum composite G3B3 method, we identified six different decomposition pathways for cyclohexanone and computed the corresponding rate constants. The rate constants were calculated using the G3B3 method coupled with Rice-Ramsperger-Kassel-Marcus theory in the temperature range of 800-2000 K. Our calculations show that the kinetically more favorable channel for thermal decomposition is pathway 2 that produces 1,3-butadien-2-ol, which in turn can isomerize easily to methyl vinyl ketone through a small barrier. The results presented here can be used in a future kinetic combustion mechanism.

  11. Dopaminergic Contributions to Hippocampal Pathophysiology in Schizophrenia: A Computational Study

    PubMed Central

    Siekmeier, Peter J; vanMaanen, David P

    2014-01-01

    Since the original formulation of the dopamine hypothesis, a number of other cellular-level abnormalities—eg, NMDA receptor hypofunction, GABA system dysfunction, neural connectivity disturbances—have been identified in schizophrenia, but the manner in which these potentially interact with hyperdopaminergia to lead to schizophrenic symptomatology remains uncertain. Previously, we created a neuroanatomically detailed, biophysically realistic computational model of hippocampus in the control (unaffected) and schizophrenic conditions, implemented on a 72-processor supercomputer platform. In the current study, we apply the effects of dopamine (DA), dose-dependently, to both models on the basis of an exhaustive review of the neurophysiologic literature on DA's ion channel and synaptic level effects. To index schizophrenic behavior, we use the specific inability of the model to attune to the 40 Hz (gamma band) frequency, a finding that has been well replicated in the clinical electroencephalography (EEG) and magnetoencephalography literature. In trials using 20 ‘simulated patients', we find that DA applied to the control model produces modest increases in 40 Hz activity, similar to experimental studies. However, in the schizophrenic model, increasing DA induces a decrement in 40 Hz resonance. This modeling work is significant in that it suggests that DA's effects may vary based on the neural substrate on which it acts, and—via simulated EEG recordings—points to the neurophysiologic mechanisms by which this may occur. We also feel that it makes a methodological contribution, as it exhibits a process by which a large amount of neurobiological data can be integrated to run pharmacologically relevant in silico experiments, using a systems biology approach. PMID:24469592

  12. A computed tomography phantom study of foam earplugs

    PubMed Central

    Hsu, Li-Sheng; Yen, Ju-Bei; Wang, Shie-Shan; Liao, Chien-Lin

    2016-01-01

    Abstract Ingestion of a foreign body is common among children. However, ingestion of foam earplugs (FEPs) has not been reported previously. A 7-month-old female infant presented with small bowel obstruction, which was finally proved to be a case of FEP ingestion. Computed tomography (CT) phantom study was performed to examine the imaging features of FEPs. We studied the following dry and fully wet FEPs, FEPs squeezed in pure water to varying degrees, and FEPs with different degrees of compression in the dry and wet states from day 0 to 6 and all scanned with a CT scanner. The density of a dry FEP is −843.5 ± 4.5 Hounsfield units (HU) and it increases to 0.76 ± 9.3 HU when fully wet. The densities of FEPs ranged from −844.2 to 1.0 HU with different water/air ratios, and some showed a heterogeneous geographic pattern. The densities of FEPs increase due to compression and gradual water absorption. FEPs can be potentially hazardous objects to children. Owing to the special foam structure of the FEP, it can mimic a fatty lesion if the density ranges from −100 to −50 HU; moreover, it can hide in the water if fully wet. However, it should not be mistaken as air, as the density of a dry FEP is −843.5 HU, and the contour can be observed if the window level is set appropriately. Because of its soft texture, the surgeon should be careful not to miss an FEP during the operation. Moreover, radiologists should be familiar with the CT features of FEPs so that they can be identified before surgery. PMID:27583901

  13. Computational Kinetic Study for the Unimolecular Decomposition Pathways of Cyclohexanone.

    PubMed

    Zaras, Aristotelis M; Dagaut, Philippe; Serinyel, Zeynep

    2015-07-16

    There has been evidence lately that several endophytic fungi can convert lignocellulosic biomass into ketones among other oxygenated compounds. Such compounds could prove useful as biofuels for internal combustion engines. Therefore, their combustion properties are of high interest. Cyclohexanone was identified as an interesting second-generation biofuel ( Boot , M. ; et al. Cyclic Oxygenates: A New Class of Second-Generation Biofuels for Diesel Engines? Energy Fuels 2009 , 23 , 1808 - 1817 ; Klein-Douwel , R. J. H. ; et al. Soot and Chemiluminescence in Diesel Combustion of Bio-Derived, Oxygenated and Reference Fuels . Proc. Combust. Inst. 2009 , 32 , 2817 - 2825 ). However, until recently ( Serinyel , Z. ; et al. Kinetics of Oxidation of Cyclohexanone in a Jet- Stirred Reactor: Experimental and Modeling . Proc. Combust. Inst. 2014 ; DOI: 10.1016/j.proci.2014.06.150 ), no previous studies on the kinetics of oxidation of that fuel could be found in the literature. In this work, we present the first theoretical kinetic study of the unimolecular decomposition pathways of cyclohexanone, a cyclic ketone that could demonstrate important fuel potential. Using the quantum composite G3B3 method, we identified six different decomposition pathways for cyclohexanone and computed the corresponding rate constants. The rate constants were calculated using the G3B3 method coupled with Rice-Ramsperger-Kassel-Marcus theory in the temperature range of 800-2000 K. Our calculations show that the kinetically more favorable channel for thermal decomposition is pathway 2 that produces 1,3-butadien-2-ol, which in turn can isomerize easily to methyl vinyl ketone through a small barrier. The results presented here can be used in a future kinetic combustion mechanism. PMID:25354027

  14. Life cycle assessment study of a Chinese desktop personal computer.

    PubMed

    Duan, Huabo; Eugster, Martin; Hischier, Roland; Streicher-Porte, Martin; Li, Jinhui

    2009-02-15

    Associated with the tremendous prosperity in world electronic information and telecommunication industry, there continues to be an increasing awareness of the environmental impacts related to the accelerating mass production, electricity use, and waste management of electronic and electric products (e-products). China's importance as both a consumer and supplier of e-products has grown at an unprecedented pace in recent decade. Hence, this paper aims to describe the application of life cycle assessment (LCA) to investigate the environmental performance of Chinese e-products from a global level. A desktop personal computer system has been selected to carry out a detailed and modular LCA which follows the ISO 14040 series. The LCA is constructed by SimaPro software version 7.0 and expressed with the Eco-indicator'99 life cycle impact assessment method. For a sensitivity analysis of the overall LCA results, the so-called CML method is used in order to estimate the influence of the choice of the assessment method on the result. Life cycle inventory information is complied by ecoinvent 1.3 databases, combined with literature and field investigations on the present Chinese situation. The established LCA study shows that that the manufacturing and the use of such devices are of the highest environmental importance. In the manufacturing of such devices, the integrated circuits (ICs) and the Liquid Crystal Display (LCD) are those parts contributing most to the impact. As no other aspects are taken into account during the use phase, the impact is due to the way how the electricity is produced. The final process steps--i.e. the end of life phase--lead to a clear environmental benefit if a formal and modern, up-to-date technical system is assumed, like here in this study. PMID:19070352

  15. Phylogenetic and Molecular Variability Studies Reveal a New Genetic Clade of Citrus leprosis virus C.

    PubMed

    Ramos-González, Pedro Luis; Chabi-Jesus, Camila; Guerra-Peraza, Orlene; Breton, Michèle Claire; Arena, Gabriella Dias; Nunes, Maria Andreia; Kitajima, Elliot Watanabe; Machado, Marcos Antonio; Freitas-Astúa, Juliana

    2016-01-01

    Citrus leprosis virus C (CiLV-C) causes a severe disease affecting citrus orchards in the Western hemisphere. This study reveals the molecular variability of the virus by analyzing four genomic regions (p29, p15, MP and RNA2-intergenic region) distributed over its two RNAs. Nucleotide diversity (π) values were relatively low but statistically different over the analyzed genes and subpopulations, indicating their distinct evolutionary history. Values of πp29 and πMP were higher than those of πp15 and πRNA2-IR, whereas πMP was increased due to novel discovered isolates phylogenetically clustered in a divergent clade that we called SJP. Isolate BR_SP_SJP_01 RNA1 and RNA2 sequences, clade SJP, showed an identity of 85.6% and 88.4%, respectively, with those corresponding to CiLV-C, the type member of the genus Cilevirus, and its RNA2 5'-proximal region was revealed as a minor donor in a putative inter-clade recombination event. In addition to citrus, BR_SP_SJP_01 naturally infects the weed Commelina benghalensis and is efficiently transmitted by Brevipalpus yothersi mites. Our data demonstrated that negative selection was the major force operating in the evaluated viral coding regions and defined amino acids putatively relevant for the biological function of cilevirus proteins. This work provides molecular tools and sets up a framework for further epidemiological studies. PMID:27275832

  16. Proteomics study revealed altered proteome of Dichogaster curgensis upon exposure to fly ash.

    PubMed

    Markad, Vijaykumar L; Adav, Sunil S; Ghole, Vikram S; Sze, Siu Kwan; Kodam, Kisan M

    2016-10-01

    Fly ash is toxic and its escalating use as a soil amendment and disposal by dumping into environment is receiving alarming attention due to its impact on environment. Proteomics technology is being used for environmental studies since proteins respond rapidly when an organism is exposed to a toxicant, and hence soil engineers such as earthworms are used as model organisms to assess the toxic effects of soil toxicants. This study adopted proteomics technology and profiled proteome of earthworm Dichogaster curgensis that was exposed to fly ash, with main aim to elucidate fly ash effects on cellular and metabolic pathways. The functional classification of identified proteins revealed carbohydrate metabolism (14.36%), genetic information processing (15.02%), folding, sorting and degradation (10.83%), replication and repair (3.95%); environmental information processing (2.19%), signal transduction (9.61%), transport and catabolism (17.27%), energy metabolism (6.69%), etc. in the proteome. Proteomics data and functional assays revealed that the exposure of earthworm to fly ash induced protein synthesis, up-regulation of gluconeogenesis, disturbed energy metabolism, oxidative and cellular stress, and mis-folding of proteins. The regulation of ubiquitination, proteasome and modified alkaline comet assay in earthworm coelomocytes suggested DNA-protein cross link affecting chromatin remodeling and protein folding. PMID:27371791

  17. Phylogenetic and Molecular Variability Studies Reveal a New Genetic Clade of Citrus leprosis virus C

    PubMed Central

    Ramos-González, Pedro Luis; Chabi-Jesus, Camila; Guerra-Peraza, Orlene; Breton, Michèle Claire; Arena, Gabriella Dias; Nunes, Maria Andreia; Kitajima, Elliot Watanabe; Machado, Marcos Antonio; Freitas-Astúa, Juliana

    2016-01-01

    Citrus leprosis virus C (CiLV-C) causes a severe disease affecting citrus orchards in the Western hemisphere. This study reveals the molecular variability of the virus by analyzing four genomic regions (p29, p15, MP and RNA2-intergenic region) distributed over its two RNAs. Nucleotide diversity (π) values were relatively low but statistically different over the analyzed genes and subpopulations, indicating their distinct evolutionary history. Values of πp29 and πMP were higher than those of πp15 and πRNA2–IR, whereas πMP was increased due to novel discovered isolates phylogenetically clustered in a divergent clade that we called SJP. Isolate BR_SP_SJP_01 RNA1 and RNA2 sequences, clade SJP, showed an identity of 85.6% and 88.4%, respectively, with those corresponding to CiLV-C, the type member of the genus Cilevirus, and its RNA2 5′-proximal region was revealed as a minor donor in a putative inter-clade recombination event. In addition to citrus, BR_SP_SJP_01 naturally infects the weed Commelina benghalensis and is efficiently transmitted by Brevipalpus yothersi mites. Our data demonstrated that negative selection was the major force operating in the evaluated viral coding regions and defined amino acids putatively relevant for the biological function of cilevirus proteins. This work provides molecular tools and sets up a framework for further epidemiological studies. PMID:27275832

  18. Revealing pathologies in the liquid crystalline structures of the brain by polarimetric studies (Presentation Recording)

    NASA Astrophysics Data System (ADS)

    Bakhshetyan, Karen; Melkonyan, Gurgen G.; Galstian, Tigran V.; Saghatelyan, Armen

    2015-10-01

    Natural or "self" alignment of molecular complexes in living tissue represents many similarities with liquid crystals (LC), which are anisotropic liquids. The orientational characteristics of those complexes may be related to many important functional parameters and their study may reveal important pathologies. The know-how, accumulated thanks to the study of LC materials, may thus be used to this end. One of the traditionally used methods, to characterize those materials, is the polarized light imaging (PLI) that allows for label-free analysis of anisotropic structures in the brain tissue and can be used, for example, for the analysis of myelinated fiber bundles. In the current work, we first attempted to apply the PLI on the mouse histological brain sections to create a map of anisotropic structures using cross-polarizer transmission light. Then we implemented the PLI for comparative study of histological sections of human postmortem brain samples under normal and pathological conditions, such as Parkinson's disease (PD). Imaging the coronal, sagittal and horizontal sections of mouse brain allowed us to create a false color-coded fiber orientation map under polarized light. In human brain datasets for both control and PD groups we measured the pixel intensities in myelin-rich subregions of internal capsule and normalized these to non-myelinated background signal from putamen and caudate nucleus. Quantification of intensities revealed a statistically significant reduction of fiber intensity of PD compared to control subjects (2.801 +/- 0.303 and 3.724 +/- 0.07 respectively; *p < 0.05). Our study confirms the validity of PLI method for visualizing myelinated axonal fibers. This relatively simple technique can become a promising tool for study of neurodegenerative diseases where labeling-free imaging is an important benefit.

  19. Water properties inside nanoscopic hydrophobic pocket studied by computer simulations

    NASA Astrophysics Data System (ADS)

    Setny, Piotr; Geller, Maciej

    2006-10-01

    The structure and dynamics of water in the vicinity of the hemispherical hydrophobic pocket of 8Å radius were examined via molecular dynamics simulations in NVT ensemble. Density, hydrogen bonding properties, and residence times of water molecules were projected on two-dimensional planes providing a spatial description of water behavior. We found that the average water density is significantly depleted relative to bulk value. A detailed analysis of pocket occupancy revealed fluctuations between states of completely empty pocket and a pocket filled with a bulklike fluid, which seem to result from collective behavior of water molecules. Free energy differences accompanying these fluctuations are rather small, suggesting that the given pocket radius is close to the critical one for transition between gas and liquid phases in the considered system. We show that the situation is different in the case of a simple Lennard-Jones fluid. These results indicate that changing the surface curvature from flat to concave may lead to qualitative difference in water behavior in its vicinity. We think that our studies may also put some light on binding site desolvation process which is necessary to understand to make correct predictions of binding energies.

  20. Computational Studies of Physical Properties of Boron Carbide

    SciTech Connect

    Lizhi Ouyang

    2011-09-30

    The overall goal is to provide valuable insight in to the mechanisms and processes that could lead to better engineering the widely used boron carbide which could play an important role in current plight towards greener energy. Carbon distribution in boron carbide, which has been difficult to retrieve from experimental methods, is critical to our understanding of its structure-properties relation. For modeling disorders in boron carbide, we implemented a first principles method based on supercell approach within our G(P,T) package. The supercell approach was applied to boron carbide to determine its carbon distribution. Our results reveal that carbon prefers to occupy the end sites of the 3-atom chain in boron carbide and further carbon atoms will distribute mainly on the equatorial sites with a small percentage on the 3-atom chains and the apex sites. Supercell approach was also applied to study mechanical properties of boron carbide under uniaxial load. We found that uniaxial load can lead to amorphization. Other physical properties of boron carbide were calculated using the G(P,T) package.

  1. Using 4D Cardiovascular Magnetic Resonance Imaging to Validate Computational Fluid Dynamics: A Case Study

    PubMed Central

    Biglino, Giovanni; Cosentino, Daria; Steeden, Jennifer A.; De Nova, Lorenzo; Castelli, Matteo; Ntsinjana, Hopewell; Pennati, Giancarlo; Taylor, Andrew M.; Schievano, Silvia

    2015-01-01

    Computational fluid dynamics (CFD) can have a complementary predictive role alongside the exquisite visualization capabilities of 4D cardiovascular magnetic resonance (CMR) imaging. In order to exploit these capabilities (e.g., for decision-making), it is necessary to validate computational models against real world data. In this study, we sought to acquire 4D CMR flow data in a controllable, experimental setup and use these data to validate a corresponding computational model. We applied this paradigm to a case of congenital heart disease, namely, transposition of the great arteries (TGA) repaired with arterial switch operation. For this purpose, a mock circulatory loop compatible with the CMR environment was constructed and two detailed aortic 3D models (i.e., one TGA case and one normal aortic anatomy) were tested under realistic hemodynamic conditions, acquiring 4D CMR flow. The same 3D domains were used for multi-scale CFD simulations, whereby the remainder of the mock circulatory system was appropriately summarized with a lumped parameter network. Boundary conditions of the simulations mirrored those measured in vitro. Results showed a very good quantitative agreement between experimental and computational models in terms of pressure (overall maximum % error = 4.4% aortic pressure in the control anatomy) and flow distribution data (overall maximum % error = 3.6% at the subclavian artery outlet of the TGA model). Very good qualitative agreement could also be appreciated in terms of streamlines, throughout the cardiac cycle. Additionally, velocity vectors in the ascending aorta revealed less symmetrical flow in the TGA model, which also exhibited higher wall shear stress in the anterior ascending aorta. PMID:26697416

  2. Rotating Detonation Combustion: A Computational Study for Stationary Power Generation

    NASA Astrophysics Data System (ADS)

    Escobar, Sergio

    The increased availability of gaseous fossil fuels in The US has led to the substantial growth of stationary Gas Turbine (GT) usage for electrical power generation. In fact, from 2013 to 2104, out of the 11 Tera Watts-hour per day produced from fossil fuels, approximately 27% was generated through the combustion of natural gas in stationary GT. The thermodynamic efficiency for simple-cycle GT has increased from 20% to 40% during the last six decades, mainly due to research and development in the fields of combustion science, material science and machine design. However, additional improvements have become more costly and more difficult to obtain as technology is further refined. An alternative to improve GT thermal efficiency is the implementation of a combustion regime leading to pressure-gain; rather than pressure loss across the combustor. One concept being considered for such purpose is Rotating Detonation Combustion (RDC). RDC refers to a combustion regime in which a detonation wave propagates continuously in the azimuthal direction of a cylindrical annular chamber. In RDC, the fuel and oxidizer, injected from separated streams, are mixed near the injection plane and are then consumed by the detonation front traveling inside the annular gap of the combustion chamber. The detonation products then expand in the azimuthal and axial direction away from the detonation front and exit through the combustion chamber outlet. In the present study Computational Fluid Dynamics (CFD) is used to predict the performance of Rotating Detonation Combustion (RDC) at operating conditions relevant to GT applications. As part of this study, a modeling strategy for RDC simulations was developed. The validation of the model was performed using benchmark cases with different levels of complexity. First, 2D simulations of non-reactive shock tube and detonation tubes were performed. The numerical predictions that were obtained using different modeling parameters were compared with

  3. An experimental and computational study of pulse detonation engines

    NASA Astrophysics Data System (ADS)

    Allgood, Daniel C.

    Research studies investigating the performance optimization and fundamental physics of pulse detonation engines (PDE) were performed. Experimental and computational methods were developed and used in these studies. Four primary research tasks were established. The first research task was to obtain detailed measurements of a PDE exhaust plume for a variety of operating conditions and engine geometries. Shadowgraph visualizations in conjunction with OH* and CH* chemiluminescence imaging were performed. The PDE plume visualizations provided a means of studying the flowfield behavior associated with PDE ejectors and exhaust nozzles as well as providing explanations for the observed acoustic behavior of the PDE. The second research task was to quantify the thrust augmentation of PDE-ejectors. Significant losses in the ejector entrainment were observed when the ejector inlet was not of an aerodynamic shape. Performance measurements of axisymmetric PDE-ejector systems showed the thrust augmentation to be a strong function of the ejector length-to-diameter ratio, ejector axial placement and PDE fill-fraction. Peak thrust augmentation levels were recorded to be approximately 20% for a straight-ejector and 65% for a diverging-ejector. An increase in thrust augmentation was obtained with a reduction in fill-fraction. Performance measurements of PDE converging and diverging exhaust nozzles were also obtained at various operating conditions of the engine. At low fill-fractions, both converging and diverging exhaust nozzles were observed to adversely affect the PDE performance. At fill-fractions close to and greater than 1, the converging nozzles showed the best performance due to increased PDE blow-down time (maintaining PDE chamber pressure) and acceleration of the primarily subsonic exhaust flow. The fourth research task was to perform a detailed far-field study of PDE acoustics. The acoustic energy of the PDE blast-wave was observed to be highly directional. Very good

  4. A computational study of an atomizing liquid sheet

    SciTech Connect

    Deshpande, Suraj S.; Gurjar, Soumil R.; Trujillo, Mario F.

    2015-08-15

    Linear instability predictions of liquid sheets injected into a gas medium are well established in the literature. These analyses are often used in Lagrangian-Eulerian spray simulations, a prominent simulation method, to model the dynamics occurring in the near-nozzle region. In the present work, these instability predictions are re-examined by first generalizing the treatment of interfacial conditions and related assumptions with a two-phase Orr-Sommerfeld (OS) system, and second, by employing highly resolved-Volume-of-Fluid (VoF) simulations. After presenting some validation exercises for both the VoF and OS solvers, the OS predictions are compared to earlier studies from the literature leading to reasonable agreement in the limit as the boundary layer thickness tends to zero. Results from VoF simulations of liquid sheet injection are used to characterize the range of scales of the liquid structures immediately before atomization. The mean value in this range is found to be approximately two to three orders of magnitude larger than the corresponding predictions from previous studies. A two-phase mixing layer under the same physical conditions is used to examine this disparity, revealing that within the linear regime, relatively good agreement exists between the VoF and OS predicted instability mechanisms. However, the most unstable mode in the linear regime is too small to cause a fracture or atomization of the liquid sheet and hence cannot be directly responsible for the atomization. The generation of a much larger mode, which emerges well beyond the linear regime, is the one causing breakup.

  5. Polarization of poly(vinylidene fluoride) and poly(vinylidene fluoride-trifluoroethylene) thin films revealed by emission spectroscopy with computational simulation during phase transition

    NASA Astrophysics Data System (ADS)

    Bystrov, Vladimir S.; Paramonova, Ekaterina V.; Dekhtyar, Yuri; Pullar, Robert C.; Katashev, Aleksey; Polyaka, Natalie; Bystrova, Anna V.; Sapronova, Alla V.; Fridkin, Vladimir M.; Kliem, Herbert; Kholkin, Andrei L.

    2012-05-01

    The electronic structure and self-polarization of P(VDF-TrFE) Langmuir-Blodgett nanofilms were analyzed under temperature-driven phase transitions, according to their thickness, composition, and structural conformation. Both thermo-stimulated exoelectron emission (TSEE) spectroscopy and computational simulation, including quantum-chemical calculations from first principles, were carried out. PVDF and composite P(VDF-TrFE) (70:30) molecular chains as Trans and Gauche conformers, as well as crystal cells, were modeled for these TSEE analyses. The quantum-chemical calculations and the computational simulation were based on the density functional theory (DFT) as well as semi-empirical (PM3) methods. It was demonstrated that the energy of electron states, as well as the total energies of the studied P(VDF-TrFE) molecular clusters during phase transformation, is influenced by electron work function and electron affinity. Analysis was performed by combining TSEE experimental data with the computational data of the molecular models, demonstrating the effectiveness of this joint approach. For the first time, TSEE was used for contactless measurements of nanofilm polarization, and characterization of the phase transition. The proposed new method can be widely applied in nanobiomedicine, particularly in development of new bone bio-implants, including built-in sensors (new smart nanotechnology).

  6. Time-dependent computational studies of flames in microgravity

    NASA Technical Reports Server (NTRS)

    Oran, Elaine S.; Kailasanath, K.

    1989-01-01

    The research performed at the Center for Reactive Flow and Dynamical Systems in the Laboratory for Computational Physics and Fluid Dynamics, at the Naval Research Laboratory, in support of the NASA Microgravity Science and Applications Program is described. The primary focus was on investigating fundamental questions concerning the propagation and extinction of premixed flames in Earth gravity and in microgravity environments. The approach was to use detailed time-dependent, multispecies, numerical models as tools to simulate flames in different gravity environments. The models include a detailed chemical kinetics mechanism consisting of elementary reactions among the eight reactive species involved in hydrogen combustion, coupled to algorithms for convection, thermal conduction, viscosity, molecular and thermal diffusion, and external forces. The external force, gravity, can be put in any direction relative to flame propagation and can have a range of values. A combination of one-dimensional and two-dimensional simulations was used to investigate the effects of curvature and dilution on ignition and propagation of flames, to help resolve fundamental questions on the existence of flammability limits when there are no external losses or buoyancy forces in the system, to understand the mechanism leading to cellular instability, and to study the effects of gravity on the transition to cellular structure. A flame in a microgravity environment can be extinguished without external losses, and the mechanism leading to cellular structure is not preferential diffusion but a thermo-diffusive instability. The simulations have also lead to a better understanding of the interactions between buoyancy forces and the processes leading to thermo-diffusive instability.

  7. Computational studies of bioceramic crystals and related materials

    NASA Astrophysics Data System (ADS)

    Rulis, Paul Michael

    Ongoing research to improve the foundations of knowledge concerning the human body requires a detailed understanding of the effects derived from atomic interactions. The details of these fundamental interactions will pave the way to the effective manipulation of macroscopic tissue. As a small step towards the realization of that goal the Orthogonalized Linear Combination of Atomic Orbitals (OLCAO) program suite has been applied to complex bioceramic crystals and other prototypes of hard tissue biological nanostructures. In addition, the OLCAO program suite has been further developed and extended in terms of efficiency, features, ease of use, and ease of maintenance such that even more complex systems and effects can be treated in the future. Through extensive OLCAO ab initio calculations on a collection of prototype bioceramic crystals the differences between them in terms of bonding, charge transfer, electronic structure, and spectroscopic properties have been detailed in an effort to lay the foundations of further research where interfaces, dopants, and defects are considered. In addition, inactive silicon defects that can be considered as prototypes for the complex environment in which bioceramic apatites exist have also been studied with the OLCAO program suite in an effort to expand the detection limit of small structures through spectroscopic means. With much effort, the OLCAO program suite has undergone a detailed conversion to a more modern programming language and programming style. A thorough review of the source code has accounted for many inaccuracies, corrected some programming errors, and removed various inefficient algorithmic bottlenecks. The generation of OLCAO input files, the execution of the components of the OLCAO suite, and the analysis of resultant data has been automated with numerous control scripts. Various external library packages have been instrumented for the benefit of profiling and resource efficiency in a high performance computing

  8. Time-dependent Computational Studies of Premixed Flames in Microgravity

    NASA Technical Reports Server (NTRS)

    Kailasanath, K.; Patnaik, Gopal; Oran, Elaine S.

    1993-01-01

    This report describes the research performed at the Center for Reactive Flow and Dynamical Systems in the Laboratory for Computational Physics and Fluid Dynamics, at the Naval Research Laboratory, in support of NASA Microgravity Science and Applications Program. The primary focus of this research is on investigating fundamental questions concerning the propagation and extinction of premixed flames in earth gravity and in microgravity environments. Our approach is to use detailed time-dependent, multispecies, numerical models as tools to simulate flames in different gravity environments. The models include a detailed chemical kinetics mechanism consisting of elementary reactions among the eight reactive species involved in hydrogen combustion, coupled to algorithms for convection, thermal conduction, viscosity, molecular and thermal diffusion, and external forces. The external force, gravity, can be put in any direction relative to flame propagation and can have a range of values. Recently more advanced wall boundary conditions such as isothermal and no-slip have been added to the model. This enables the simulation of flames propagating in more practical systems than before. We have used the numerical simulations to investigate the effects of heat losses and buoyancy forces on the structure and stability of flames, to help resolve fundamental questions on the existence of flammability limits when there are no external losses or buoyancy forces in the system, to understand the interaction between the various processes leading to flame instabilities and extinguishment, and to study the dynamics of cell formation and splitting. Our studies have been able to bring out the differences between upward- and downward-propagating flames and predict the zero-gravity behavior of these flames. The simulations have also highlighted the dominant role of wall heat losses in the case of downward-propagating flames. The simulations have been able to qualitatively predict the

  9. Computer analysis of lighting style in fine art: steps towards inter-artist studies

    NASA Astrophysics Data System (ADS)

    Stork, David G.

    2011-03-01

    Stylometry in visual art-the mathematical description of artists' styles - has been based on a number of properties of works, such as color, brush stroke shape, visual texture, and measures of contours' curvatures. We introduce the concept of quantitative measures of lighting, such as statistical descriptions of spatial coherence, diuseness, and so forth, as properties of artistic style. Some artists of the high Renaissance, such as Leonardo, worked from nature and strove to render illumination "faithfully" photorealists, such as Richard Estes, worked from photographs and duplicated the "physics based" lighting accurately. As such, each had dierent motivations, methodologies, stagings, and "accuracies" in rendering lighting clues. Perceptual studies show that observers are poor judges of properties of lighting in photographs such as consistency (and thus by extension in paintings as well); computer methods such as rigorous cast-shadow analysis, occluding-contour analysis and spherical harmonic based estimation of light fields can be quite accurate. For this reasons, computer lighting analysis can provide a new tools for art historical studies. We review lighting analysis in paintings such as Vermeer's Girl with a pearl earring, de la Tour's Christ in the carpenter's studio, Caravaggio's Magdalen with the smoking flame and Calling of St. Matthew) and extend our corpus to works where lighting coherence is of interest to art historians, such as Caravaggio's Adoration of the Shepherds or Nativity (1609) in the Capuchin church of Santa Maria degli Angeli. Our measure of lighting coherence may help reveal the working methods of some artists and in diachronic studies of individual artists. We speculate on artists and art historical questions that may ultimately profit from future renements to these new computational tools.

  10. Transcription closed and open complex dynamics studies reveal balance between genetic determinants and co-factors.

    PubMed

    Sala, Adrien; Shoaib, Muhammad; Anufrieva, Olga; Mutharasu, Gnanavel; Jahan Hoque, Rawnak; Yli-Harja, Olli; Kandhavelu, Meenakshisundaram

    2015-05-19

    In E. coli, promoter closed and open complexes are key steps in transcription initiation, where magnesium-dependent RNA polymerase catalyzes RNA synthesis. However, the exact mechanism of initiation remains to be fully elucidated. Here, using single mRNA detection and dual reporter studies, we show that increased intracellular magnesium concentration affects Plac initiation complex formation resulting in a highly dynamic process over the cell growth phases. Mg2+ regulates transcription transition, which modulates bimodality of mRNA distribution in the exponential phase. We reveal that Mg2+ regulates the size and frequency of the mRNA burst by changing the open complex duration. Moreover, increasing magnesium concentration leads to higher intrinsic and extrinsic noise in the exponential phase. RNAP-Mg2+ interaction simulation reveals critical movements creating a shorter contact distance between aspartic acid residues and Nucleotide Triphosphate residues and increasing electrostatic charges in the active site. Our findings provide unique biophysical insights into the balanced mechanism of genetic determinants and magnesium ion in transcription initiation regulation during cell growth.

  11. Transcription closed and open complex dynamics studies reveal balance between genetic determinants and co-factors

    NASA Astrophysics Data System (ADS)

    Sala, Adrien; Shoaib, Muhammad; Anufrieva, Olga; Mutharasu, Gnanavel; Jahan Hoque, Rawnak; Yli-Harja, Olli; Kandhavelu, Meenakshisundaram

    2015-05-01

    In E. coli, promoter closed and open complexes are key steps in transcription initiation, where magnesium-dependent RNA polymerase catalyzes RNA synthesis. However, the exact mechanism of initiation remains to be fully elucidated. Here, using single mRNA detection and dual reporter studies, we show that increased intracellular magnesium concentration affects Plac initiation complex formation resulting in a highly dynamic process over the cell growth phases. Mg2+ regulates transcription transition, which modulates bimodality of mRNA distribution in the exponential phase. We reveal that Mg2+ regulates the size and frequency of the mRNA burst by changing the open complex duration. Moreover, increasing magnesium concentration leads to higher intrinsic and extrinsic noise in the exponential phase. RNAP-Mg2+ interaction simulation reveals critical movements creating a shorter contact distance between aspartic acid residues and Nucleotide Triphosphate residues and increasing electrostatic charges in the active site. Our findings provide unique biophysical insights into the balanced mechanism of genetic determinants and magnesium ion in transcription initiation regulation during cell growth.

  12. Mind the gap: an attempt to bridge computational and neuroscientific approaches to study creativity

    PubMed Central

    Wiggins, Geraint A.; Bhattacharya, Joydeep

    2014-01-01

    Creativity is the hallmark of human cognition and is behind every innovation, scientific discovery, piece of music, artwork, and idea that have shaped our lives, from ancient times till today. Yet scientific understanding of creative processes is quite limited, mostly due to the traditional belief that considers creativity as a mysterious puzzle, a paradox, defying empirical enquiry. Recently, there has been an increasing interest in revealing the neural correlates of human creativity. Though many of these studies, pioneering in nature, help demystification of creativity, but the field is still dominated by popular beliefs in associating creativity with “right brain thinking”, “divergent thinking”, “altered states” and so on (Dietrich and Kanso, 2010). In this article, we discuss a computational framework for creativity based on Baars’ Global Workspace Theory (GWT; Baars, 1988) enhanced with mechanisms based on information theory. Next we propose a neurocognitive architecture of creativity with a strong focus on various facets (i.e., unconscious thought theory, mind wandering, spontaneous brain states) of un/pre-conscious brain responses. Our principal argument is that pre-conscious creativity happens prior to conscious creativity and the proposed computational model may provide a mechanism by which this transition is managed. This integrative approach, albeit unconventional, will hopefully stimulate future neuroscientific studies of the inscrutable phenomenon of creativity. PMID:25104930

  13. Mind the gap: an attempt to bridge computational and neuroscientific approaches to study creativity.

    PubMed

    Wiggins, Geraint A; Bhattacharya, Joydeep

    2014-01-01

    Creativity is the hallmark of human cognition and is behind every innovation, scientific discovery, piece of music, artwork, and idea that have shaped our lives, from ancient times till today. Yet scientific understanding of creative processes is quite limited, mostly due to the traditional belief that considers creativity as a mysterious puzzle, a paradox, defying empirical enquiry. Recently, there has been an increasing interest in revealing the neural correlates of human creativity. Though many of these studies, pioneering in nature, help demystification of creativity, but the field is still dominated by popular beliefs in associating creativity with "right brain thinking", "divergent thinking", "altered states" and so on (Dietrich and Kanso, 2010). In this article, we discuss a computational framework for creativity based on Baars' Global Workspace Theory (GWT; Baars, 1988) enhanced with mechanisms based on information theory. Next we propose a neurocognitive architecture of creativity with a strong focus on various facets (i.e., unconscious thought theory, mind wandering, spontaneous brain states) of un/pre-conscious brain responses. Our principal argument is that pre-conscious creativity happens prior to conscious creativity and the proposed computational model may provide a mechanism by which this transition is managed. This integrative approach, albeit unconventional, will hopefully stimulate future neuroscientific studies of the inscrutable phenomenon of creativity.

  14. Mind the gap: an attempt to bridge computational and neuroscientific approaches to study creativity.

    PubMed

    Wiggins, Geraint A; Bhattacharya, Joydeep

    2014-01-01

    Creativity is the hallmark of human cognition and is behind every innovation, scientific discovery, piece of music, artwork, and idea that have shaped our lives, from ancient times till today. Yet scientific understanding of creative processes is quite limited, mostly due to the traditional belief that considers creativity as a mysterious puzzle, a paradox, defying empirical enquiry. Recently, there has been an increasing interest in revealing the neural correlates of human creativity. Though many of these studies, pioneering in nature, help demystification of creativity, but the field is still dominated by popular beliefs in associating creativity with "right brain thinking", "divergent thinking", "altered states" and so on (Dietrich and Kanso, 2010). In this article, we discuss a computational framework for creativity based on Baars' Global Workspace Theory (GWT; Baars, 1988) enhanced with mechanisms based on information theory. Next we propose a neurocognitive architecture of creativity with a strong focus on various facets (i.e., unconscious thought theory, mind wandering, spontaneous brain states) of un/pre-conscious brain responses. Our principal argument is that pre-conscious creativity happens prior to conscious creativity and the proposed computational model may provide a mechanism by which this transition is managed. This integrative approach, albeit unconventional, will hopefully stimulate future neuroscientific studies of the inscrutable phenomenon of creativity. PMID:25104930

  15. Active Site, Catalytic Cycle, and Iodination Reactions of Vanadium Iodoperoxidase: A Computational Study.

    PubMed

    Pacios, Luis F; Gálvez, Oscar

    2010-05-11

    A combined computational study using molecular surfaces and Poisson-Boltzmann electrostatic potentials for proteins and quantum calculations on complexes representing the vanadate cofactor throughout the catalytic cycle is employed to study the activity of vanadium iodoperoxidase (VIPO) from alga Laminaria digitata . A model structure of VIPO is compared with available crystal structures of chloroperoxidases (VClPOs) and bromoperoxidases (VBrPOs) focusing on properties of the active site that concern halogen specificity. It is found that VIPO displays distinctive features regarding electrostatic potentials at the site cavity and the local topography of the cavity entrance. Quantum calculations on cofactor stages throughout the catalytic cycle reveal that, while steps involving binding of hydrogen peroxide and halide oxidization agree with available data on VBrPO, final formation and subsequent release of hypohalous acid could follow a different pathway consisting of His476-assisted protonation of bonded hypoiodite and further displacement by a water molecule. Ab initio free energies of reaction computed to explore iodination of organic substrates predict strongly exoergonic reactions with HOI, whereas other possible iodination reagents give thermodynamically disfavored reactions.

  16. A computational study of the TiO2 molecule

    NASA Technical Reports Server (NTRS)

    Ramana, M. V.; Phillips, D. H.

    1988-01-01

    A computational investigation of the ground 1A1 and lowest energy B2 states of the titanium dioxide molecule has been carried out. The treatment utilized SCF calculations in an extended basis followed by a CI treatment for each geometry. The ground state geometry agrees well with experiment, while the agreement between the computed vibrational frequency nu1 and the experimental value for a matrix isolated TiO2 is less satisfactory. Population analysis for the ground state indicates less than one excess electron on each oxygen atom. The first excited state has a linear geometry and the singlet and triplet are essentially degenerate.

  17. Challenges in computational studies of enzyme structure, function and dynamics.

    PubMed

    Carvalho, Alexandra T P; Barrozo, Alexandre; Doron, Dvir; Kilshtain, Alexandra Vardi; Major, Dan Thomas; Kamerlin, Shina Caroline Lynn

    2014-11-01

    In this review we give an overview of the field of Computational enzymology. We start by describing the birth of the field, with emphasis on the work of the 2013 chemistry Nobel Laureates. We then present key features of the state-of-the-art in the field, showing what theory, accompanied by experiments, has taught us so far about enzymes. We also briefly describe computational methods, such as quantum mechanics-molecular mechanics approaches, reaction coordinate treatment, and free energy simulation approaches. We finalize by discussing open questions and challenges.

  18. Report of the Computer Study Committee; Submitted to the Board of Regents, State of Kansas.

    ERIC Educational Resources Information Center

    Kansas State Board of Regents, Topeka.

    The Computer Study Committee was formed under the Board of Regents in Kansas to determine the presence and use of computers in the seven state institutions. To collect data, the Committee sent out questionnaires, made campus visits and conducted interviews. The bulk of the report discusses (1) funding and accounting procedures for computer use and…

  19. Educational Computer Use in Leisure Contexts: A Phenomenological Study of Adolescents' Experiences at Internet Cafes

    ERIC Educational Resources Information Center

    Cilesiz, Sebnem

    2009-01-01

    Computer use is a widespread leisure activity for adolescents. Leisure contexts, such as Internet cafes, constitute specific social environments for computer use and may hold significant educational potential. This article reports a phenomenological study of adolescents' experiences of educational computer use at Internet cafes in Turkey. The…

  20. The Study of Surface Computer Supported Cooperative Work and Its Design, Efficiency, and Challenges

    ERIC Educational Resources Information Center

    Hwang, Wu-Yuin; Su, Jia-Han

    2012-01-01

    In this study, a Surface Computer Supported Cooperative Work paradigm is proposed. Recently, multitouch technology has become widely available for human-computer interaction. We found it has great potential to facilitate more awareness of human-to-human interaction than personal computers (PCs) in colocated collaborative work. However, other…

  1. Case Studies of Auditing in a Computer-Based Systems Environment.

    ERIC Educational Resources Information Center

    General Accounting Office, Washington, DC.

    In response to a growing need for effective and efficient means for auditing computer-based systems, a number of studies dealing primarily with batch-processing type computer operations have been conducted to explore the impact of computers on auditing activities in the Federal Government. This report first presents some statistical data on…

  2. The Effects of Integrating Service Learning into Computer Science: An Inter-Institutional Longitudinal Study

    ERIC Educational Resources Information Center

    Payton, Jamie; Barnes, Tiffany; Buch, Kim; Rorrer, Audrey; Zuo, Huifang

    2015-01-01

    This study is a follow-up to one published in computer science education in 2010 that reported preliminary results showing a positive impact of service learning on student attitudes associated with success and retention in computer science. That paper described how service learning was incorporated into a computer science course in the context of…

  3. Revealing Nature’s Synthetic Potential Through the Study of Ribosomal Natural Product Biosynthesis

    PubMed Central

    Dunbar, Kyle L.; Mitchell, Douglas A.

    2013-01-01

    Ribosomally synthesized posttranslationally modified peptides (RiPPs) are a rapidly growing class of natural products with diverse structures and activities. In recent years, a great deal of progress has been made in elucidating the biosynthesis of various RiPP family members. As with the study of nonribosomal peptide and polyketide biosynthetic enzymes, these investigations have led to the discovery of entirely new biological chemistry. With each unique enzyme investigated, a more complex picture of Nature’s synthetic potential is revealed. This review focuses on recent reports (since 2008) that have changed the way that we think about ribosomal natural product biosynthesis and the enzymology of complex bond-forming reactions. PMID:23286465

  4. Arguing on the Computer: A Microgenetic Study of Developing Argument Skills in a Computer-Supported Environment

    ERIC Educational Resources Information Center

    Kuhn, Deanna; Goh, Wendy; Iordanou, Kalypso; Shaenfield, David

    2008-01-01

    We report a study of a class of 28 sixth graders engaged in an extended computer-supported argumentive discourse activity. Participants collaborated with a same-side peer in arguing against successive pairs of peers on the opposing side of an issue. Meta-level awareness was facilitated by conducting the dialogs via instant messaging software,…

  5. A Qualitative Study of Students' Computational Thinking Skills in a Data-Driven Computing Class

    ERIC Educational Resources Information Center

    Yuen, Timothy T.; Robbins, Kay A.

    2014-01-01

    Critical thinking, problem solving, the use of tools, and the ability to consume and analyze information are important skills for the 21st century workforce. This article presents a qualitative case study that follows five undergraduate biology majors in a computer science course (CS0). This CS0 course teaches programming within a data-driven…

  6. Seed metabolomic study reveals significant metabolite variations and correlations among different soybean cultivars.

    PubMed

    Lin, Hong; Rao, Jun; Shi, Jianxin; Hu, Chaoyang; Cheng, Fang; Wilson, Zoe A; Zhang, Dabing; Quan, Sheng

    2014-09-01

    Soybean [Glycine max (L.) Merr.] is one of the world's major crops, and soybean seeds are a rich and important resource for proteins and oils. While "omics" studies, such as genomics, transcriptomics, and proteomics, have been widely applied in soybean molecular research, fewer metabolomic studies have been conducted for large-scale detection of low molecular weight metabolites, especially in soybean seeds. In this study, we investigated the seed metabolomes of 29 common soybean cultivars through combined gas chromatography-mass spectrometry and ultra-performance liquid chromatography-tandem mass spectrometry. One hundred sixty-nine named metabolites were identified and subsequently used to construct a metabolic network of mature soybean seed. Among the 169 detected metabolites, 104 were found to be significantly variable in their levels across tested cultivars. Metabolite markers that could be used to distinguish genetically related soybean cultivars were also identified, and metabolite-metabolite correlation analysis revealed some significant associations within the same or among different metabolite groups. Findings from this work may potentially provide the basis for further studies on both soybean seed metabolism and metabolic engineering to improve soybean seed quality and yield.

  7. Neurobiology of mood, anxiety, and emotions as revealed by studies of a unique antidepressant: tianeptine.

    PubMed

    McEwen, B S; Olié, J P

    2005-06-01

    Recent studies have provided evidence that structural remodeling of certain brain regions is a feature of depressive illness, and the postulated underlying mechanisms contribute to the idea that there is more to antidepressant actions that can be explained exclusively by a monoaminergic hypothesis. This review summarizes recent neurobiological studies on the antidepressant, tianeptine (S-1574, [3-chloro-6-methyl-5,5-dioxo-6,11-dihydro-(c,f)-dibenzo-(1,2-thiazepine)-11-yl) amino]-7 heptanoic acid, sodium salt), a compound with structural similarities to the tricyclic antidepressant agents, the efficacy and good tolerance of which have been clearly established. These studies have revealed that the neurobiological properties of tianeptine involve the dynamic interplay between numerous neurotransmitter systems, as well as a critical role of structural and functional plasticity in the brain regions that permit the full expression of emotional learning. Although the story is far from complete, the schema underlying the effect of tianeptine on central plasticity is the most thoroughly studied of any antidepressants. Effects of tianeptine on neuronal excitability, neuroprotection, anxiety, and memory have also been found. Together with clinical data on the efficacy of tianeptine as an antidepressant, these actions offer insights into how compounds like tianeptine may be useful in the treatment of neurobiological features of depressive disorders.

  8. Evolution- and structure-based computational strategy reveals the impact of deleterious missense mutations on MODY 2 (maturity-onset diabetes of the young, type 2).

    PubMed

    George, Doss C Priya; Chakraborty, Chiranjib; Haneef, S A Syed; Nagasundaram, Nagarajan; Chen, Luonan; Zhu, Hailong

    2014-01-01

    Heterozygous mutations in the central glycolytic enzyme glucokinase (GCK) can result in an autosomal dominant inherited disease, namely maturity-onset diabetes of the young, type 2 (MODY 2). MODY 2 is characterised by early onset: it usually appears before 25 years of age and presents as a mild form of hyperglycaemia. In recent years, the number of known GCK mutations has markedly increased. As a result, interpreting which mutations cause a disease or confer susceptibility to a disease and characterising these deleterious mutations can be a difficult task in large-scale analyses and may be impossible when using a structural perspective. The laborious and time-consuming nature of the experimental analysis led us to attempt to develop a cost-effective computational pipeline for diabetic research that is based on the fundamentals of protein biophysics and that facilitates our understanding of the relationship between phenotypic effects and evolutionary processes. In this study, we investigate missense mutations in the GCK gene by using a wide array of evolution- and structure-based computational methods, such as SIFT, PolyPhen2, PhD-SNP, SNAP, SNPs&GO, fathmm, and Align GVGD. Based on the computational prediction scores obtained using these methods, three mutations, namely E70K, A188T, and W257R, were identified as highly deleterious on the basis of their effects on protein structure and function. Using the evolutionary conservation predictors Consurf and Scorecons, we further demonstrated that most of the predicted deleterious mutations, including E70K, A188T, and W257R, occur in highly conserved regions of GCK. The effects of the mutations on protein stability were computed using PoPMusic 2.1, I-mutant 3.0, and Dmutant. We also conducted molecular dynamics (MD) simulation analysis through in silico modelling to investigate the conformational differences between the native and the mutant proteins and found that the identified deleterious mutations alter the stability

  9. Structural Studies of FlaA1 from Helicobacter Pylori Reveal the Mechanism for Inverting 4,6-dehydratase Activity

    SciTech Connect

    Ishiyama,N.; Creuzenet, C.; Miller, W.; Demendi, M.; Anderson, E.; Harauz, G.; Lam, J.; Berghuis, A.

    2006-01-01

    FlaA1 from the human pathogen Helicobacter pylori is an enzyme involved in saccharide biosynthesis that has been shown to be essential for pathogenicity. Here we present five crystal structures of FlaA1 in the presence of substrate, inhibitors, and bound cofactor, with resolutions ranging from 2.8 to 1.9 {angstrom}. These structures reveal that the enzyme is a novel member of the short-chain dehydrogenase/reductase superfamily. Additional electron microscopy studies show the enzyme to possess a hexameric doughnut-shaped quaternary structure. NMR analyses of 'real time' enzyme-substrate reactions indicate that FlaA1 is a UDP-GlcNAc-inverting 4,6-dehydratase, suggesting that the enzyme catalyzes the first step in the biosynthetic pathway of a pseudaminic acid derivative, which is implicated in protein glycosylation. Guided by evidence from site-directed mutagenesis and computational simulations, a three-step reaction mechanism is proposed that involves Lys-133 functioning as both a catalytic acid and base.

  10. Computer-Integrated Instruction Inservice Notebook: Secondary School Social Studies.

    ERIC Educational Resources Information Center

    Franklin, Sharon, Ed.; Strudler, Neal, Ed.

    The purpose of this notebook is to assist educators who are designing and implementing inservice education programs to facilitate the effective use of computer integrated instruction (CII) in schools. It is divided into the following five sections: (1) Effective Inservice (a brief summary of inservice literature focused on inservice dimensions and…

  11. "It's Boring": Female Students' Experience of Studying ICT and Computing

    ERIC Educational Resources Information Center

    Pau, Reena; Hall, Wendy; Grace, Marcus

    2011-01-01

    The declining number of women in computing is a cause for concern for those in education and the IT industry. A diverse workforce is necessary for there to be a creative balance in the IT industry. The reasons for this decline are varied and can be attributed to factors such as schooling, parental influences and the media. This article focuses on…

  12. Studying Collective Human Decision Making and Creativity with Evolutionary Computation.

    PubMed

    Sayama, Hiroki; Dionne, Shelley D

    2015-01-01

    We report a summary of our interdisciplinary research project "Evolutionary Perspective on Collective Decision Making" that was conducted through close collaboration between computational, organizational, and social scientists at Binghamton University. We redefined collective human decision making and creativity as evolution of ecologies of ideas, where populations of ideas evolve via continual applications of evolutionary operators such as reproduction, recombination, mutation, selection, and migration of ideas, each conducted by participating humans. Based on this evolutionary perspective, we generated hypotheses about collective human decision making, using agent-based computer simulations. The hypotheses were then tested through several experiments with real human subjects. Throughout this project, we utilized evolutionary computation (EC) in non-traditional ways-(1) as a theoretical framework for reinterpreting the dynamics of idea generation and selection, (2) as a computational simulation model of collective human decision-making processes, and (3) as a research tool for collecting high-resolution experimental data on actual collaborative design and decision making from human subjects. We believe our work demonstrates untapped potential of EC for interdisciplinary research involving human and social dynamics.

  13. A Successful Course of Study in Computer Programming

    ERIC Educational Resources Information Center

    Seeger, David H.

    1977-01-01

    Three keys to the successful development of the program of the computer programming department of the Technical Institute of Oklahoma State University are discussed: Community involvement, faculty/administration commitment to the basic principles of technical career education, and availability of appropriate equipment for student use. (HD)

  14. Computational study on Kerr constants of neutral and ionized gases

    NASA Astrophysics Data System (ADS)

    Sato, M.; Kumada, A.; Hidaka, K.

    2015-08-01

    In order to quantitatively examine the measurement capability of Poisson's field using electro-optic Kerr-effect (EOKE), Kerr constants of neutral molecules and ions are examined by means of first principle calculations. We have systematically computed Kerr constants of neutral molecules and ions of several molecular symmetry groups, with consistent theory level and basis sets. Computed Kerr constants of neutral molecules (N2, CO2, SF6, and CF3I) ranging across two orders of magnitudes are within 50% error of the experimental values, which are comparable to the scattering between experimental values itself. The results show that SF6 has smaller Kerr constant due to its high molecular symmetry compared to those of N2 and CO2. In contrast, CF3I has large Kerr constant due to its permanent dipole. Computed Kerr constants for anions are larger by two orders of magnitude than those of neutral molecules, probably due to the shielding effect. For cations, the opposite holds true; however, due to anisotropic polarizability, computed Kerr constants for some cations are comparable to neutral molecules, while others show smaller values. The ratio of Kerr constants of ions to those of neutral molecules are at most 102; EOKE is valid for measuring electric field in weakly ionized gas whose ionization degree is smaller than 10-3.

  15. Computational Study of Axisymmetric Off-Design Nozzle Flows

    NASA Technical Reports Server (NTRS)

    DalBello, Teryn; Georgiadis, Nicholas; Yoder, Dennis; Keith, Theo

    2003-01-01

    Computational Fluid Dynamics (CFD) analyses of axisymmetric circular-arc boattail nozzles operating off-design at transonic Mach numbers have been completed. These computations span the very difficult transonic flight regime with shock-induced separations and strong adverse pressure gradients. External afterbody and internal nozzle pressure distributions computed with the Wind code are compared with experimental data. A range of turbulence models were examined, including the Explicit Algebraic Stress model. Computations have been completed at freestream Mach numbers of 0.9 and 1.2, and nozzle pressure ratios (NPR) of 4 and 6. Calculations completed with variable time-stepping (steady-state) did not converge to a true steady-state solution. Calculations obtained using constant timestepping (timeaccurate) indicate less variations in flow properties compared with steady-state solutions. This failure to converge to a steady-state solution was the result of using variable time-stepping with large-scale separations present in the flow. Nevertheless, time-averaged boattail surface pressure coefficient and internal nozzle pressures show reasonable agreement with experimental data. The SST turbulence model demonstrates the best overall agreement with experimental data.

  16. A Diagnostic Study of Computer Application of Structural Communication Grid

    ERIC Educational Resources Information Center

    Bahar, Mehmet; Aydin, Fatih; Karakirik, Erol

    2009-01-01

    In this article, Structural communication grid (SCG), an alternative measurement and evaluation technique, has been firstly summarised and the design, development and implementation of a computer based SCG system have been introduced. The system is then tested on a sample of 154 participants consisting of candidate students, science teachers and…

  17. Framework for Computer Assisted Instruction Courseware: A Case Study.

    ERIC Educational Resources Information Center

    Betlach, Judith A.

    1987-01-01

    Systematically investigates, defines, and organizes variables related to production of internally designed and implemented computer assisted instruction (CAI) courseware: special needs of users; costs; identification and definition of realistic training needs; CAI definition and design methodology; hardware and software requirements; and general…

  18. A study of standard building blocks for the design of fault-tolerant distributed computer systems

    NASA Technical Reports Server (NTRS)

    Rennels, D. A.; Avizienis, A.; Ercegovac, M.

    1978-01-01

    This paper presents the results of a study that has established a standard set of four semiconductor VLSI building-block circuits. These circuits can be assembled with off-the-shelf microprocessors and semiconductor memory modules into fault-tolerant distributed computer configurations. The resulting multi-computer architecture uses self-checking computer modules backed up by a limited number of spares. A redundant bus system is employed for communication between computer modules.

  19. Computational studies of competing phases in model Hamiltonians

    NASA Astrophysics Data System (ADS)

    Jiang, Mi

    Model Hamiltonians play an important role in our understanding of both quantum and classical systems, such as strongly correlated unconventional superconductivity, quantum magnetism, non-fermi liquid heavy fermion materials and classical magnetic phase transitions. The central problem is how models with many degrees of freedom choose between competing ground states, e.g. magnetic, superconducting, metallic, insulating as the degree of thermal and quantum fluctuations is varied. This dissertation focuses on the numerical investigation of several important model Hamiltonians. Specifically, we used the determinant Quantum Monte Carlo (DQMC) to study three Hubbard-like models: the Fermi-Hubbard model with two regions of different interaction strength, the Fermi-Hubbard model with a spin-dependent band structure, and the related periodic Anderson model (PAM). The first model used was to explore inter-penetration of metallic and Mott insulator physics across a Metal-Mott Insulator interface by computing the magnetic properties and spectral functions. As a minimal model of a half metallic magnet, the second model was used to explore the impact of on-site Hubbard interaction U, finite temperature, and an external (Zeeman) magnetic field on a bilayer tight-binding model with spin-dependent hybridization. We use PAM to study the Knight shift anomaly in heavy fermion materials found in Nuclear magnetic resonance (NMR) experiments and confirm several predictions of the two-fluid theory accounting for the anomaly. Another application of the Hubbard model described in this dissertation is the investigation on the effects of spin-dependent disorder on s-wave superconductors based on the attractive Hubbard model. Here we used the Bogoliubov-de Gennes (BdG) self-consistent approach instead of quantum simulations. The spin-dependent random potential was shown to induce distinct transitions at which the energy gap and average order parameter vanish, generating an intermediate gapless

  20. HIGH-PERFORMANCE COMPUTING FOR THE STUDY OF EARTH AND ENVIRONMENTAL SCIENCE MATERIALS USING SYNCHROTRON X-RAY COMPUTED MICROTOMOGRAPHY.

    SciTech Connect

    FENG,H.; JONES,K.W.; MCGUIGAN,M.; SMITH,G.J.; SPILETIC,J.

    2001-10-12

    Synchrotron x-ray computed microtomography (CMT) is a non-destructive method for examination of rock, soil, and other types of samples studied in the earth and environmental sciences. The high x-ray intensities of the synchrotron source make possible the acquisition of tomographic volumes at a high rate that requires the application of high-performance computing techniques for data reconstruction to produce the three-dimensional volumes, for their visualization, and for data analysis. These problems are exacerbated by the need to share information between collaborators at widely separated locations over both local and tide-area networks. A summary of the CMT technique and examples of applications are given here together with a discussion of the applications of high-performance computing methods to improve the experimental techniques and analysis of the data.

  1. Computer Simulation Studies of Ion Channels at High Temperatures

    NASA Astrophysics Data System (ADS)

    Song, Hyun Deok

    The gramicidin channel is the smallest known biological ion channel, and it exhibits cation selectivity. Recently, Dr. John Cuppoletti's group at the University of Cincinnati showed that the gramicidin channel can function at high temperatures (360 ˜ 380K) with significant currents. This finding may have significant implications for fuel cell technology. In this thesis, we have examined the gramicidin channel at 300K, 330K, and 360K by computer simulation. We have investigated how the temperature affects the current and differences in magnitude of free energy between the two gramicidin forms, the helical dimer (HD) and the double helix (DH). A slight decrease of the free energy barrier inside the gramicidin channel and increased diffusion at high temperatures result in an increase of current. An applied external field of 0.2V/nm along the membrane normal results in directly observable ion transport across the channels at high temperatures for both HD and DH forms. We found that higher temperatures also affect the probability distribution of hydrogen bonds, the bending angle, the distance between dimers, and the size of the pore radius for the helical dimer structure. These findings may be related to the gating of the gramicidin channel. Methanococcus jannaschii (MJ) is a methane-producing thermophile, which was discovered at a depth of 2600m in a Pacific Ocean vent in 1983. It has the ability to thrive at high temperatures and high pressures, which are unfavorable for most life forms. There have been some experiments to study its stability under extreme conditions, but still the origin of the stability of MJ is not exactly known. MJ0305 is the chloride channel protein from the thermophile MJ. After generating a structure of MJ0305 by homology modeling based on the Ecoli ClC templates, we examined the thermal stability, and the network stability from the change of network entropy calculated from the adjacency matrices of the protein. High temperatures increase the

  2. Communication maps computed for homodimeric hemoglobin: computational study of water-mediated energy transport in proteins.

    PubMed

    Gnanasekaran, Ramachandran; Agbo, Johnson K; Leitner, David M

    2011-08-14

    Frequency-resolved communication maps provide a coarse-grained picture of energy transport in nanoscale systems. We calculate communication maps for homodimeric hemoglobin from Scapharca inaequivalvis and sample them to elucidate energy transfer pathways between the binding sites and other parts of the protein with focus on the role of the cluster of water molecules at the interface between the globules. We complement analysis of communication maps with molecular simulations of energy flow. Both approaches reveal that excess energy in one heme flows mainly to regions of the interface where early hydrogen bond rearrangements occur in the allosteric transition. In particular, energy is carried disproportionately by the water molecules, consistent with the larger thermal conductivity of water compared to proteins.

  3. A study revealing the key aroma compounds of steamed bread made by Chinese traditional sourdough*

    PubMed Central

    Zhang, Guo-hua; Wu, Tao; Sadiq, Faizan A.; Yang, Huan-yi; Liu, Tong-jie; Ruan, Hui; He, Guo-qing

    2016-01-01

    Aroma of Chinese steamed bread (CSB) is one of the important parameters that determines the overall quality attributes and consumer acceptance. However, the aroma profile of CSB still remains poorly understood, mainly because of relying on only a single method for aroma extraction in previous studies. Therefore, the objective of this study was to determine the volatile aroma compounds of five different samples of CSB using three different aroma extraction methods, namely solid-phase microextraction (SPME), simultaneous distillation–extraction (SDE), and purge and trap (P&T). All samples showed a unique aroma profile, which could be attributed to their unique microbial consortia. (E)-2-Nonenal and (E,E)-2,4-decadienal were the most prevalent aromatic compounds revealed by SDE, which have not been reported previously, while ethanol and acetic acid proved to be the most dominant compounds by both SPME and P&T. Our approach of combining three different aroma extraction methods provided better insights into the aroma profile of CSB, which had remained largely unknown in previous studies. PMID:27704748

  4. Markov models of the apo-MDM2 lid region reveal diffuse yet two-state binding dynamics and receptor poses for computational docking

    NASA Astrophysics Data System (ADS)

    Mukherjee, Sudipto; Pantelopulos, George A.; Voelz, Vincent A.

    2016-08-01

    MDM2 is a negative regulator of p53 activity and an important target for cancer therapeutics. The N-terminal lid region of MDM2 modulates interactions with p53 via competition for its binding cleft, exchanging slowly between docked and undocked conformations in the absence of p53. To better understand these dynamics, we constructed Markov State Models (MSMs) from large collections of unbiased simulation trajectories of apo-MDM2, and find strong evidence for diffuse, yet two-state folding and binding of the N-terminal region to the p53 receptor site. The MSM also identifies holo-like receptor conformations highly suitable for computational docking, despite initiating trajectories from closed-cleft receptor structures unsuitable for docking. Fixed-anchor docking studies using a test set of high-affinity small molecules and peptides show simulated receptor ensembles achieve docking successes comparable to cross-docking studies using crystal structures of receptors bound by alternative ligands. For p53, the best-scoring receptor structures have the N-terminal region lid region bound in a helical conformation mimicking the bound structure of p53, suggesting lid region association induces receptor conformations suitable for binding. These results suggest that MD + MSM approaches can sample binding-competent receptor conformations suitable for computational peptidomimetic design, and that inclusion of disordered regions may be essential to capturing the correct receptor dynamics.

  5. Markov models of the apo-MDM2 lid region reveal diffuse yet two-state binding dynamics and receptor poses for computational docking

    PubMed Central

    Mukherjee, Sudipto; Pantelopulos, George A.; Voelz, Vincent A.

    2016-01-01

    MDM2 is a negative regulator of p53 activity and an important target for cancer therapeutics. The N-terminal lid region of MDM2 modulates interactions with p53 via competition for its binding cleft, exchanging slowly between docked and undocked conformations in the absence of p53. To better understand these dynamics, we constructed Markov State Models (MSMs) from large collections of unbiased simulation trajectories of apo-MDM2, and find strong evidence for diffuse, yet two-state folding and binding of the N-terminal region to the p53 receptor site. The MSM also identifies holo-like receptor conformations highly suitable for computational docking, despite initiating trajectories from closed-cleft receptor structures unsuitable for docking. Fixed-anchor docking studies using a test set of high-affinity small molecules and peptides show simulated receptor ensembles achieve docking successes comparable to cross-docking studies using crystal structures of receptors bound by alternative ligands. For p53, the best-scoring receptor structures have the N-terminal region lid region bound in a helical conformation mimicking the bound structure of p53, suggesting lid region association induces receptor conformations suitable for binding. These results suggest that MD + MSM approaches can sample binding-competent receptor conformations suitable for computational peptidomimetic design, and that inclusion of disordered regions may be essential to capturing the correct receptor dynamics. PMID:27538695

  6. Markov models of the apo-MDM2 lid region reveal diffuse yet two-state binding dynamics and receptor poses for computational docking.

    PubMed

    Mukherjee, Sudipto; Pantelopulos, George A; Voelz, Vincent A

    2016-01-01

    MDM2 is a negative regulator of p53 activity and an important target for cancer therapeutics. The N-terminal lid region of MDM2 modulates interactions with p53 via competition for its binding cleft, exchanging slowly between docked and undocked conformations in the absence of p53. To better understand these dynamics, we constructed Markov State Models (MSMs) from large collections of unbiased simulation trajectories of apo-MDM2, and find strong evidence for diffuse, yet two-state folding and binding of the N-terminal region to the p53 receptor site. The MSM also identifies holo-like receptor conformations highly suitable for computational docking, despite initiating trajectories from closed-cleft receptor structures unsuitable for docking. Fixed-anchor docking studies using a test set of high-affinity small molecules and peptides show simulated receptor ensembles achieve docking successes comparable to cross-docking studies using crystal structures of receptors bound by alternative ligands. For p53, the best-scoring receptor structures have the N-terminal region lid region bound in a helical conformation mimicking the bound structure of p53, suggesting lid region association induces receptor conformations suitable for binding. These results suggest that MD + MSM approaches can sample binding-competent receptor conformations suitable for computational peptidomimetic design, and that inclusion of disordered regions may be essential to capturing the correct receptor dynamics. PMID:27538695

  7. Revealed social preference for potable groundwater: An Eastern Iowa case study

    NASA Astrophysics Data System (ADS)

    Raunikar, R. P.; Bernknopf, R. L.; Forney, W.; Mishra, S.

    2011-12-01

    The spatially explicit land use and land cover information provided by Landsat moderate-resolution land imagery (MRLI) is needed to more efficiently balance the production of goods and services over landscapes. For example, economic trade-offs are needed to provide both clean groundwater resources and other non-environmental goods and services produced by activities that affect the vadose zone and thus contribute to contamination of groundwater. These trade-off choices are made by numerous economic agents and are constrained by many social institutions including governmental regulations at many levels, contractual obligations and traditions. In effect, on a social level, society acts as if it values groundwater by foregoing other goods to protect these resources. The result of the protection afforded to groundwater resources is observable by measuring contamination in well samples. This observed level of groundwater contamination risk is the revealed preference of society as a whole for clean groundwater. We observed the risk of groundwater contamination in a sampling of well data from our study area (35 counties of Eastern Iowa.) We used a proportional hazard model to quantify the nitrate contamination survival implied by the panel of 19,873 well data, where remaining below a 10 mg/ml maximum contamination level (MCL) is defined as survival. We tested the data for evidence that the levels of protection provided to these resources is correlated with aquifer and vadose zone characteristics and geographic location and whether it changed over time and with economic and other conditions. We demonstrate the use of a nitrate conditioned hazard function for projecting the survival of wells based on nitrate exposure information over the 1940 to 2010 time period. We discuss results of simulations of the survival process that demonstrate the economic significance of this approach. We find that aquifer survival has been significantly improving over time. The principle of

  8. Computer-Assisted Cognitive Remediation for Schizophrenia: A Randomized Single-Blind Pilot Study

    PubMed Central

    Rass, Olga; Forsyth, Jennifer K.; Bolbecker, Amanda R; Hetrick, William P.; Breier, Alan; Lysaker, Paul H.; O’Donnell, Brian F.

    2012-01-01

    Cognitive impairment is a core symptom in schizophrenia that has a significant impact on psychosocial function, but shows a weak response to pharmacological treatment. Consequently, a variety of cognitive remediation strategies have been evaluated to improve cognitive function in schizophrenia. The efficacy of computer-based cognitive remediation as a stand-alone intervention on general measures of neuropsychological function remains unclear. We tested the effectiveness of biweekly training using computerized cognitive remediation programs on neuropsychological and event-related potential outcome measures. Schizophrenia patients were randomly assigned to cognitive remediation training (N=17), active control (TV-watching; N=17), or treatment as usual (N=10) groups for ten weeks and run in parallel. Functional, cognitive, and ERP measures revealed no differential improvement over time in the cognitive remediation group. Practice effects might explain change over time on several cognitive measures for all groups, consistent with studies indicating task-specific improvement. Computer-assisted cognitive remediation alone may not be sufficient for robust or generalized effects on cognitive and electrophysiological measures in schizophrenia patients. PMID:22682988

  9. Computational study of the acid dissociation of esters and lactones. A case study of diketene.

    PubMed

    Gómez-Bombarelli, Rafael; González-Pérez, Marina; Pérez-Prior, María Teresa; Calle, Emilio; Casado, Julio

    2009-07-17

    A computational study of the aqueous pK(a) of some saturated and unsaturated cyclic and linear esters and ketones was carried out at the DFT-B3LYP 6-31++G(2df,2pd), CBS-Q, and G2 levels, with the integral equation formalism polarizable continuum model for solvation, using a proton exchange mechanism. The influence of unsaturation, position of the double bond, and cyclization were studied. The computational results show that (a) in all cases studied except that of diketene (4-methylene-2-oxetanone), the alpha-beta unsaturated isomer is 20-30 kJ mol(-1) lower in energy that the beta-gamma unsaturated one; (b) alpha-beta unsaturation lowers the pK(a) of an ester approximately 6 units, whereas beta-gamma unsaturation lowers it by approximately 10 units, and cyclization lowers the pK(a) by approximately 3 units. In order to check the predictive power of the methodology, the acid dissociation constant of diketene in water was measured via kinetic study of its base-catalyzed hydrolysis. The pK(a) value obtained (15.2 +/- 0.3) is in keeping with the expected value for a beta-gamma unsaturated beta-lactone. This low value also suggests that deprotonated diketene does not interconvert to a more stable, less acidic alpha-beta unsaturated isomer, which is also consistent with computational results. PMID:19459649

  10. Computational study on the internal layer in a diffuser

    NASA Astrophysics Data System (ADS)

    Wu, Xiaohua; Schlüter, Jörg; Moin, Parviz; Pitsch, Heinz; Iaccarino, Gianluca; Ham, Frank

    2006-03-01

    reveals a string of well-defined spanwise vortices outside the internal layer. The internal layer discovered from this study provides qualified support for a conjecture advanced by Azad & Kassab some years ago (Phys. Fluids A, vol. 1, 1989, p. 564).

  11. The effects of integrating service learning into computer science: an inter-institutional longitudinal study

    NASA Astrophysics Data System (ADS)

    Payton, Jamie; Barnes, Tiffany; Buch, Kim; Rorrer, Audrey; Zuo, Huifang

    2015-07-01

    This study is a follow-up to one published in computer science education in 2010 that reported preliminary results showing a positive impact of service learning on student attitudes associated with success and retention in computer science. That paper described how service learning was incorporated into a computer science course in the context of the Students & Technology in Academia, Research, and Service (STARS) Alliance, an NSF-supported broadening participation in computing initiative that aims to diversify the computer science pipeline through innovative pedagogy and inter-institutional partnerships. The current paper describes how the STARS Alliance has expanded to diverse institutions, all using service learning as a vehicle for broadening participation in computing and enhancing attitudes and behaviors associated with student success. Results supported the STARS model of service learning for enhancing computing efficacy and computing commitment and for providing diverse students with many personal and professional development benefits.

  12. Computational study of developing high-quality decision trees

    NASA Astrophysics Data System (ADS)

    Fu, Zhiwei

    2002-03-01

    Recently, decision tree algorithms have been widely used in dealing with data mining problems to find out valuable rules and patterns. However, scalability, accuracy and efficiency are significant concerns regarding how to effectively deal with large and complex data sets in the implementation. In this paper, we propose an innovative machine learning approach (we call our approach GAIT), combining genetic algorithm, statistical sampling, and decision tree, to develop intelligent decision trees that can alleviate some of these problems. We design our computational experiments and run GAIT on three different data sets (namely Socio- Olympic data, Westinghouse data, and FAA data) to test its performance against standard decision tree algorithm, neural network classifier, and statistical discriminant technique, respectively. The computational results show that our approach outperforms standard decision tree algorithm profoundly at lower sampling levels, and achieves significantly better results with less effort than both neural network and discriminant classifiers.

  13. Computational Study of Flow Interactions in Coaxial Rotors

    NASA Technical Reports Server (NTRS)

    Yoon, Seokkwan; Lee, Henry C.; Pulliam, Thomas H.

    2016-01-01

    account for multiple real-world constraints up front in design nor possible to know what performance is possible with a given design. Since unmanned vehicles are sized and optimized for the particular mission, a modern low-fidelity conceptual design and sizing tool that has been used for the design of large helicopters can be used for design of small coaxial rotorcraft. However, unlike most helicopters with single main rotor, the interactions between the upper and lower rotors emerge as an important factor to consider in design because an increase in performance of a multi-rotor system is not proportional to the number of rotors. Interference losses and differences in thrusts between the upper and lower rotors were investigated by theoretical methods as well as a computational fluid dynamics (CFD) method using the Reynolds-Averaged Navier-Stokes (RANS) equations. In this work, hybrid turbulence models are used to investigate the physics of interactions between coaxial rotors and a fuselage that are not well understood. Present study covers not only small-scale drones but also large-scale coaxial rotors for heavy-lifting missions. Considering the recently proposed FAA drone rules that require the flight only in visual line-of-sight, a large multirotor might be used as an airborne carrier for launch and recovery of unmanned aircraft systems with a human operator onboard. For applications to civil operations, their aerodynamic performance and noise levels need to be assessed. Noise is one of the largest limiting factors to rotorcraft operations in urban area. Since the high-frequency noise of multi-rotors may increase the annoyance, noise may turn out to be a key issue that must be addressed for market acceptability. One of the objectives of the present work is to study the effects of inter-rotor spacing and collectives on the performance, efficiency, and acoustics of coaxial rotor systems.

  14. Dose spread functions in computed tomography: A Monte Carlo study

    PubMed Central

    Boone, John M.

    2009-01-01

    Purpose: Current CT dosimetry employing CTDI methodology has come under fire in recent years, partially in response to the increasing width of collimated x-ray fields in modern CT scanners. This study was conducted to provide a better understanding of the radiation dose distributions in CT. Methods: Monte Carlo simulations were used to evaluate radiation dose distributions along the z axis arising from CT imaging in cylindrical phantoms. Mathematical cylinders were simulated with compositions of water, polymethyl methacrylate (PMMA), and polyethylene. Cylinder diameters from 10 to 50 cm were studied. X-ray spectra typical of several CT manufacturers (80, 100, 120, and 140 kVp) were used. In addition to no bow tie filter, the head and body bow tie filters from modern General Electric and Siemens CT scanners were evaluated. Each cylinder was divided into three concentric regions of equal volume such that the energy deposited is proportional to dose for each region. Two additional dose assessment regions, central and edge locations 10 mm in diameter, were included for comparisons to CTDI100 measurements. Dose spread functions (DSFs) were computed for a wide number of imaging parameters. Results: DSFs generally exhibit a biexponential falloff from the z=0 position. For a very narrow primary beam input (⪡1 mm), DSFs demonstrated significant low amplitude long range scatter dose tails. For body imaging conditions (30 cm diameter in water), the DSF at the center showed ∼160 mm at full width at tenth maximum (FWTM), while at the edge the FWTM was ∼80 mm. Polyethylene phantoms exhibited wider DSFs than PMMA or water, as did higher tube voltages in any material. The FWTM were 80, 180, and 250 mm for 10, 30, and 50 cm phantom diameters, respectively, at the center in water at 120 kVp with a typical body bow tie filter. Scatter to primary dose ratios (SPRs) increased with phantom diameter from 4 at the center (1 cm diameter) for a 16 cm diameter cylinder to ∼12.5 for a

  15. Using Wearable Computers in Shuttle Processing: A Feasibility Study

    NASA Technical Reports Server (NTRS)

    Centeno, Martha A.; Correa, Daisy; Groh-Hammond, Marcia

    2001-01-01

    Shuttle processing operations are performed following prescribed instructions compiled in a Work Authorization Document (WAD). Until very recently, WADs were printed so that they could be properly executed, including the buy off of each and every step by the appropriate authorizing agent. However, with the development of EPICs, Maximo, and PeopleSoft applications, some of these documents are now available in electronic format; hence, it is possible for technicians and engineers to access them on line and buy off the steps electronically. To take full advantage of these developments, technicians need access to such documents at the point of job execution. Body wearable computers present an opportunity to develop a WAD delivery system that enables access while preserving technician's mobility, safety levels, and quality of work done. The primary objectives of this project were to determine if body wearable computers are a feasible delivery system for WADs. More specifically, identify and recommend specific brands of body wearable computers readily available on the market. Thus, this effort has field-tested this technology in two areas of shuttle processing, and it has examined the usability of the technology. Results of two field tests and a Human Factors Usability Test are presented. Section 2 provides a description of the body wearable computer technology. Section 3 presents the test at the Space Shuttle Main Engine (SSME) Shop. Section 4 presents the results of the integration test at the Solid Rocket Boosters Assembly and Refurbishing Facility (SRBARF). Section 5 presents the results of the usability test done at the Operations Support Building (OSB).

  16. Cogeneration computer model assessment: Advanced cogeneration research study

    NASA Technical Reports Server (NTRS)

    Rosenberg, L.

    1983-01-01

    Cogeneration computer simulation models to recommend the most desirable models or their components for use by the Southern California Edison Company (SCE) in evaluating potential cogeneration projects was assessed. Existing cogeneration modeling capabilities are described, preferred models are identified, and an approach to the development of a code which will best satisfy SCE requirements is recommended. Five models (CELCAP, COGEN 2, CPA, DEUS, and OASIS) are recommended for further consideration.

  17. A Study on Strategic Provisioning of Cloud Computing Services

    PubMed Central

    Rejaul Karim Chowdhury, Md

    2014-01-01

    Cloud computing is currently emerging as an ever-changing, growing paradigm that models “everything-as-a-service.” Virtualised physical resources, infrastructure, and applications are supplied by service provisioning in the cloud. The evolution in the adoption of cloud computing is driven by clear and distinct promising features for both cloud users and cloud providers. However, the increasing number of cloud providers and the variety of service offerings have made it difficult for the customers to choose the best services. By employing successful service provisioning, the essential services required by customers, such as agility and availability, pricing, security and trust, and user metrics can be guaranteed by service provisioning. Hence, continuous service provisioning that satisfies the user requirements is a mandatory feature for the cloud user and vitally important in cloud computing service offerings. Therefore, we aim to review the state-of-the-art service provisioning objectives, essential services, topologies, user requirements, necessary metrics, and pricing mechanisms. We synthesize and summarize different provision techniques, approaches, and models through a comprehensive literature review. A thematic taxonomy of cloud service provisioning is presented after the systematic review. Finally, future research directions and open research issues are identified. PMID:25032243

  18. A study on strategic provisioning of cloud computing services.

    PubMed

    Whaiduzzaman, Md; Haque, Mohammad Nazmul; Rejaul Karim Chowdhury, Md; Gani, Abdullah

    2014-01-01

    Cloud computing is currently emerging as an ever-changing, growing paradigm that models "everything-as-a-service." Virtualised physical resources, infrastructure, and applications are supplied by service provisioning in the cloud. The evolution in the adoption of cloud computing is driven by clear and distinct promising features for both cloud users and cloud providers. However, the increasing number of cloud providers and the variety of service offerings have made it difficult for the customers to choose the best services. By employing successful service provisioning, the essential services required by customers, such as agility and availability, pricing, security and trust, and user metrics can be guaranteed by service provisioning. Hence, continuous service provisioning that satisfies the user requirements is a mandatory feature for the cloud user and vitally important in cloud computing service offerings. Therefore, we aim to review the state-of-the-art service provisioning objectives, essential services, topologies, user requirements, necessary metrics, and pricing mechanisms. We synthesize and summarize different provision techniques, approaches, and models through a comprehensive literature review. A thematic taxonomy of cloud service provisioning is presented after the systematic review. Finally, future research directions and open research issues are identified.

  19. Assessment of the role of sutures in a lizard skull: a computer modelling study

    PubMed Central

    Moazen, Mehran; Curtis, Neil; O'Higgins, Paul; Jones, Marc E.H; Evans, Susan E; Fagan, Michael J

    2008-01-01

    Sutures form an integral part of the functioning skull, but their role has long been debated among vertebrate morphologists and palaeontologists. Furthermore, the relationship between typical skull sutures, and those involved in cranial kinesis, is poorly understood. In a series of computational modelling studies, complex loading conditions obtained through multibody dynamics analysis were imposed on a finite element model of the skull of Uromastyx hardwickii, an akinetic herbivorous lizard. A finite element analysis (FEA) of a skull with no sutures revealed higher patterns of strain in regions where cranial sutures are located in the skull. From these findings, FEAs were performed on skulls with sutures (individual and groups of sutures) to investigate their role and function more thoroughly. Our results showed that individual sutures relieved strain locally, but only at the expense of elevated strain in other regions of the skull. These findings provide an insight into the behaviour of sutures and show how they are adapted to work together to distribute strain around the skull. Premature fusion of one suture could therefore lead to increased abnormal loading on other regions of the skull causing irregular bone growth and deformities. This detailed investigation also revealed that the frontal–parietal suture of the Uromastyx skull played a substantial role in relieving strain compared with the other sutures. This raises questions about the original role of mesokinesis in squamate evolution. PMID:18765341

  20. Assessment of the role of sutures in a lizard skull: a computer modelling study.

    PubMed

    Moazen, Mehran; Curtis, Neil; O'Higgins, Paul; Jones, Marc E H; Evans, Susan E; Fagan, Michael J

    2009-01-01

    Sutures form an integral part of the functioning skull, but their role has long been debated among vertebrate morphologists and palaeontologists. Furthermore, the relationship between typical skull sutures, and those involved in cranial kinesis, is poorly understood. In a series of computational modelling studies, complex loading conditions obtained through multibody dynamics analysis were imposed on a finite element model of the skull of Uromastyx hardwickii, an akinetic herbivorous lizard. A finite element analysis (FEA) of a skull with no sutures revealed higher patterns of strain in regions where cranial sutures are located in the skull. From these findings, FEAs were performed on skulls with sutures (individual and groups of sutures) to investigate their role and function more thoroughly. Our results showed that individual sutures relieved strain locally, but only at the expense of elevated strain in other regions of the skull. These findings provide an insight into the behaviour of sutures and show how they are adapted to work together to distribute strain around the skull. Premature fusion of one suture could therefore lead to increased abnormal loading on other regions of the skull causing irregular bone growth and deformities. This detailed investigation also revealed that the frontal-parietal suture of the Uromastyx skull played a substantial role in relieving strain compared with the other sutures. This raises questions about the original role of mesokinesis in squamate evolution.

  1. Mixed valence Creutz-Taube ion analogues incorporating thiacrowns: synthesis, structure, physical properties, and computational studies.

    PubMed

    Adams, Harry; Costa, Paulo J; Newell, Mike; Vickers, Steven J; Ward, Michael D; Félix, Vítor; Thomas, Jim A

    2008-12-15

    A series of nine new complexes incorporating [Ru(II)Cl([n]aneS(3))] (n = 12, 14, 16) metal centers bridged by three ditopic ligands containing two monodentate sites (pyrazine, 4,4'-bipyridine, and 3,6-bis(4-pyridyl)-1,2,4,5-tetrazine) have been synthesized and fully characterized. The solid-state structures of three of the complexes have been further characterized by X-ray crystallography studies. Intermetallic interactions within the new systems have been probed using electrochemistry and optical spectroscopy. Cyclic voltammetry reveals that the three pyrazine bridged systems display two separate Ru(III)/(II) redox couples. Using spectroelectrochemistry, we have investigated the optical properties of these mixed valence, Creutz-Taube ion analogues. An analysis of the intervalence charge transfer bands for the complexes revealed that, despite possessing the same donor sets, the electronic delocalization within these systems is modulated by the nature of the coordinated thiacrown. Computational modeling using density function theory offers further evidence of interaction between metal centers and provides insights into how these interactions are mediated. PMID:19012395

  2. Single exosome study reveals subpopulations distributed among cell lines with variability related to membrane content

    PubMed Central

    Smith, Zachary J.; Lee, Changwon; Rojalin, Tatu; Carney, Randy P.; Hazari, Sidhartha; Knudson, Alisha; Lam, Kit; Saari, Heikki; Ibañez, Elisa Lazaro; Viitala, Tapani; Laaksonen, Timo; Yliperttula, Marjo; Wachsmann-Hogiu, Sebastian

    2015-01-01

    Current analysis of exosomes focuses primarily on bulk analysis, where exosome-to-exosome variability cannot be assessed. In this study, we used Raman spectroscopy to study the chemical composition of single exosomes. We measured spectra of individual exosomes from 8 cell lines. Cell-line-averaged spectra varied considerably, reflecting the variation in total exosomal protein, lipid, genetic, and cytosolic content. Unexpectedly, single exosomes isolated from the same cell type also exhibited high spectral variability. Subsequent spectral analysis revealed clustering of single exosomes into 4 distinct groups that were not cell-line specific. Each group contained exosomes from multiple cell lines, and most cell lines had exosomes in multiple groups. The differences between these groups are related to chemical differences primarily due to differing membrane composition. Through a principal components analysis, we identified that the major sources of spectral variation among the exosomes were in cholesterol content, relative expression of phospholipids to cholesterol, and surface protein expression. For example, exosomes derived from cancerous versus non-cancerous cell lines can be largely separated based on their relative expression of cholesterol and phospholipids. We are the first to indicate that exosome subpopulations are shared among cell types, suggesting distributed exosome functionality. The origins of these differences are likely related to the specific role of extracellular vesicle subpopulations in both normal cell function and carcinogenesis, and they may provide diagnostic potential at the single exosome level. PMID:26649679

  3. A HUPO test sample study reveals common problems in mass spectrometry-based proteomics

    PubMed Central

    Bell, Alexander W.; Deutsch, Eric W.; Au, Catherine E.; Kearney, Robert E.; Beavis, Ron; Sechi, Salvatore; Nilsson, Tommy; Bergeron, John J.M.

    2009-01-01

    We carried out a test sample study to try to identify errors leading to irreproducibility, including incompleteness of peptide sampling, in LC-MS-based proteomics. We distributed a test sample consisting of an equimolar mix of 20 highly purified recombinant human proteins, to 27 laboratories for identification. Each protein contained one or more unique tryptic peptides of 1250 Da to also test for ion selection and sampling in the mass spectrometer. Of the 27 labs, initially only 7 labs reported all 20 proteins correctly, and only 1 lab reported all the tryptic peptides of 1250 Da. Nevertheless, a subsequent centralized analysis of the raw data revealed that all 20 proteins and most of the 1250 Da peptides had in fact been detected by all 27 labs. The centralized analysis allowed us to determine sources of problems encountered in the study, which include missed identifications (false negatives), environmental contamination, database matching, and curation of protein identifications. Improved search engines and databases are likely to increase the fidelity of mass spectrometry-based proteomics. PMID:19448641

  4. A comprehensive immunoinformatics and target site study revealed the corner-stone toward Chikungunya virus treatment.

    PubMed

    Hasan, Md Anayet; Khan, Md Arif; Datta, Amit; Mazumder, Md Habibul Hasan; Hossain, Mohammad Uzzal

    2015-05-01

    Recent concerning facts of Chikungunya virus (CHIKV); a Togaviridae family alphavirus has proved this as a worldwide emerging threat which causes Chikungunya fever and devitalizing arthritis. Despite severe outbreaks and lack of antiviral drug, a mere progress has been made regarding to an epitope-based vaccine designed for CHIKV. In this study, we aimed to design an epitope-based vaccine that can trigger a significant immune response as well as to prognosticate inhibitor that can bind with potential drug target sites by using various immunoinformatics and docking simulation tools. Initially, whole proteome of CHIKV was retrieved from database and perused to identify the most immunogenic protein. Structural properties of the selected protein were analyzed. The capacity to induce both humoral and cell-mediated immunity by T cell and B cell were checked for the selected protein. The peptide region spanning 9 amino acids from 397 to 405 and the sequence YYYELYPTM were found as the most potential B cell and T cell epitopes respectively. This peptide could interact with as many as 19 HLAs and showed high population coverage ranging from 69.50% to 84.94%. By using in silico docking techniques the epitope was further assessed for binding against HLA molecules to verify the binding cleft interaction. In addition with this, the allergenicity of the epitopes was also evaluated. In the post therapeutic strategy, three dimensional structure was predicted along with validation and verification that resulted in molecular docking study to identify the potential drug binding sites and suitable therapeutic inhibitor against targeted protein. Finally, pharmacophore study was also performed in quest of seeing potent drug activity. However, this computational epitope-based peptide vaccine designing and target site prediction against CHIKV opens up a new horizon which may be the prospective way in Chikungunya virus research; the results require validation by in vitro and in vivo

  5. Space station Simulation Computer System (SCS) study for NASA/MSFC. Volume 5: Study analysis report

    NASA Technical Reports Server (NTRS)

    1989-01-01

    The Simulation Computer System (SCS) is the computer hardware, software, and workstations that will support the Payload Training Complex (PTC) at the Marshall Space Flight Center (MSFC). The PTC will train the space station payload scientists, station scientists, and ground controllers to operate the wide variety of experiments that will be on-board the Freedom Space Station. The further analysis performed on the SCS study as part of task 2-Perform Studies and Parametric Analysis-of the SCS study contract is summarized. These analyses were performed to resolve open issues remaining after the completion of task 1, and the publishing of the SCS study issues report. The results of these studies provide inputs into SCS task 3-Develop and present SCS requirements, and SCS task 4-develop SCS conceptual designs. The purpose of these studies is to resolve the issues into usable requirements given the best available information at the time of the study. A list of all the SCS study issues is given.

  6. Academic Computing at the Community College of Baltimore: A Case Study.

    ERIC Educational Resources Information Center

    Hunter, Beverly; Kearsley, Greg

    Part of a series of case studies on successful academic computing programs at minority institutions, this monograph focuses on the Community College of Baltimore (CCB). Sections I and II outline the purpose and background of the case study project, focusing on the 11 computing activities the case studies are designed to facilitate, the need for…

  7. Computer Game Theories for Designing Motivating Educational Software: A Survey Study

    ERIC Educational Resources Information Center

    Ang, Chee Siang; Rao, G. S. V. Radha Krishna

    2008-01-01

    The purpose of this study is to evaluate computer game theories for educational software. We propose a framework for designing engaging educational games based on contemporary game studies which includes ludology and narratology. Ludology focuses on the study of computer games as play and game activities, while narratology revolves around the…

  8. An Exploratory Study of the Implementation of Computer Technology in an American Islamic Private School

    ERIC Educational Resources Information Center

    Saleem, Mohammed M.

    2009-01-01

    This exploratory study of the implementation of computer technology in an American Islamic private school leveraged the case study methodology and ethnographic methods informed by symbolic interactionism and the framework of the Muslim Diaspora. The study focused on describing the implementation of computer technology and identifying the…

  9. A Computer-Assisted 3D Model for Analyzing the Aggregation of Tumorigenic Cells Reveals Specialized Behaviors and Unique Cell Types that Facilitate Aggregate Coalescence

    PubMed Central

    Scherer, Amanda; Kuhl, Spencer; Wessels, Deborah; Lusche, Daniel F.; Hanson, Brett; Ambrose, Joseph; Voss, Edward; Fletcher, Emily; Goldman, Charles; Soll, David R.

    2015-01-01

    We have developed a 4D computer-assisted reconstruction and motion analysis system, J3D-DIAS 4.1, and applied it to the reconstruction and motion analysis of tumorigenic cells in a 3D matrix. The system is unique in that it is fast, high-resolution, acquires optical sections using DIC microscopy (hence there is no associated photoxicity), and is capable of long-term 4D reconstruction. Specifically, a z-series at 5 μm increments can be acquired in less than a minute on tissue samples embedded in a 1.5 mm thick 3D Matrigel matrix. Reconstruction can be repeated at intervals as short as every minute and continued for 30 days or longer. Images are converted to mathematical representations from which quantitative parameters can be derived. Application of this system to cancer cells from established lines and fresh tumor tissue has revealed unique behaviors and cell types not present in non-tumorigenic lines. We report here that cells from tumorigenic lines and tumors undergo rapid coalescence in 3D, mediated by specific cell types that we have named “facilitators” and “probes.” A third cell type, the “dervish”, is capable of rapid movement through the gel and does not adhere to it. These cell types have never before been described. Our data suggest that tumorigenesis in vitro is a developmental process involving coalescence facilitated by specialized cells that culminates in large hollow spheres with complex architecture. The unique effects of select monoclonal antibodies on these processes demonstrate the usefulness of the model for analyzing the mechanisms of anti-cancer drugs. PMID:25790299

  10. Computer Simulation Study of Human Locomotion with a Three-Dimensional Entire-Body Neuro-Musculo-Skeletal Model

    NASA Astrophysics Data System (ADS)

    Hase, Kazunori; Obinata, Goro

    It is essential for the biomechanical study of human walking motion to consider not only in vivo mechanical load and energy efficiency but also aspects of motor control such as walking stability. In this study, walking stability was investigated using a three-dimensional entire-body neuro-musculo-skeletal model in the computer simulation. In the computational experiments, imaginary constraints, such as no muscular system, were set in the neuro-musculo-skeletal model to investigate their influence on walking stability. The neuronal parameters were adjusted using numerical search techniques in order to adapt walking patterns to constraints on the neuro-musculo-skeletal system. Simulation results revealed that the model of the normal neuro-musculo-skeletal system yielded a higher stability than the imaginary models. Unstable walking by a model with a time delay in the neuronal system suggested significant unknown mechanisms which stabilized walking patterns that have been neglected in previous studies.

  11. Computational approach to the study of thermal spin crossover phenomena

    SciTech Connect

    Rudavskyi, Andrii; Broer, Ria; Sousa, Carmen

    2014-05-14

    The key parameters associated to the thermally induced spin crossover process have been calculated for a series of Fe(II) complexes with mono-, bi-, and tridentate ligands. Combination of density functional theory calculations for the geometries and for normal vibrational modes, and highly correlated wave function methods for the energies, allows us to accurately compute the entropy variation associated to the spin transition and the zero-point corrected energy difference between the low- and high-spin states. From these values, the transition temperature, T{sub 1/2}, is estimated for different compounds.

  12. Computer studies of multiple-quantum spin dynamics

    SciTech Connect

    Murdoch, J.B.

    1982-11-01

    The excitation and detection of multiple-quantum (MQ) transitions in Fourier transform NMR spectroscopy is an interesting problem in the quantum mechanical dynamics of spin systems as well as an important new technique for investigation of molecular structure. In particular, multiple-quantum spectroscopy can be used to simplify overly complex spectra or to separate the various interactions between a nucleus and its environment. The emphasis of this work is on computer simulation of spin-system evolution to better relate theory and experiment.

  13. Computer-based study strategies for students with learning disabilities: individual differences associated with adoption level.

    PubMed

    Anderson-Inman, L; Knox-Quinn, C; Horney, M A

    1996-09-01

    This article reports results from a study of the use of technology to support students with learning disabilities in the use of effective study strategies. Thirty secondary students were given laptop computers and taught a variety of computer-based study strategies designed to facilitate information recording, organization, and manipulation. Results suggest that students adopted this innovation at three levels: (a) Power Users (skilled, independent users, integrating the computer into their schoolwork); (b) Prompted Users (skilled computer users, but requiring prompting); and (c) Reluctant Users (having limited knowledge and working only under supervision). Intelligence and reading test scores were associated with adoption levels in a statistically significant way.

  14. Associations among temporomandibular disorders, chronic neck pain and neck pain disability in computer office workers: a pilot study.

    PubMed

    Bragatto, M M; Bevilaqua-Grossi, D; Regalo, S C H; Sousa, J D; Chaves, T C

    2016-05-01

    Neck pain is the most common musculoskeletal complaint among computer office workers. There are several reports about the coexistence of neck pain and temporomandibular disorders (TMD). However, there are no studies investigating this association in the context of work involving computers. The purpose of this study was to verify the association between TMD and neck pain in computer office workers. Fifty-two female computer workers who were divided into two groups: (i) those with self-reported chronic neck pain and disability (WNP) (n = 26) and (ii) those without self-reported neck pain (WONP) (n = 26), and a control group (CG) consisting of 26 women who did not work with computers participated in this study. Clinical assessments were performed to establish a diagnosis of TMD, and craniocervical mechanical pain was assessed using manual palpation and pressure pain threshold (PPT). The results of this study showed that the WNP group had a higher percentage of participants with TMD than the WONP group (42·30% vs. 23·07%, χ(2) = 5·70, P = 0·02). PPTs in all cervical sites were significantly lower in the groups WNP and WONP compared to the CG. Regression analysis revealed TMD, neck pain and work-related factors to be good predictors of disability (R(2) = 0·93, P < 0·001). These results highlighted the importance of considering the work conditions of patients with TMD, as neck disability in computer workers is explained by the association among neck pain, TMD and unfavourable workplace conditions. Consequently, this study attempted to emphasise the importance of considering work activity for minimising neck pain-related disability. PMID:26732204

  15. Scanning electron microscopic study of flowing erythrocytes in hepatic sinusoids as revealed by 'in vivo cryotechnique'.

    PubMed

    Terada, N; Kato, Y; Fuji, Y; Ueda, H; Baba, T; Ohno, S

    1998-01-01

    The purpose of this study is to develop a method for stabilizing erythrocytes under flowing condition in living livers, as revealed by scanning electron microscopy (SEM). After the procedure of the 'in vivo cryotechnique', both freeze-substitution and subsequent t-butyl alcohol freeze-drying methods were used for preparing SEM specimens. By freeze-fracturing with a scalpel in liquid nitrogen before the freeze-substitution, better preserved surface tissues were obtained for examination. Erythrocytes in hepatic sinusoids were clearly detected without plasma components by the freeze-substitution method, and well preserved in parts where they were flowing with their original shapes. Some were accumulated in sinusoids, especially injunctioning areas of sinusoidal networks, as compared with those in narrow lumens between hepatocyte plates. Shapes of such erythrocytes were various, locating along endothelial cells. After stopping the blood supply into livers by artificial cardiac arrest, their shapes were dramatically changed into biconcaves and they became aggregated side by side to be packed in the sinusoids. The three-dimensional shapes of flowing erythrocytes in hepatic sinusoids were demonstrated for the first time by the 'in vivo cryotechnique' combined with SEM. PMID:9602528

  16. Metagenomic study of red biofilms from Diamante Lake reveals ancient arsenic bioenergetics in haloarchaea.

    PubMed

    Rascovan, Nicolás; Maldonado, Javier; Vazquez, Martín P; Eugenia Farías, María

    2016-02-01

    Arsenic metabolism is proposed to be an ancient mechanism in microbial life. Different bacteria and archaea use detoxification processes to grow under high arsenic concentration. Some of them are also able to use arsenic as a bioenergetic substrate in either anaerobic arsenate respiration or chemolithotrophic growth on arsenite. However, among the archaea, bioenergetic arsenic metabolism has only been found in the Crenarchaeota phylum. Here we report the discovery of haloarchaea (Euryarchaeota phylum) biofilms forming under the extreme environmental conditions such as high salinity, pH and arsenic concentration at 4589 m above sea level inside a volcano crater in Diamante Lake, Argentina. Metagenomic analyses revealed a surprisingly high abundance of genes used for arsenite oxidation (aioBA) and respiratory arsenate reduction (arrCBA) suggesting that these haloarchaea use arsenic compounds as bioenergetics substrates. We showed that several haloarchaea species, not only from this study, have all genes required for these bioenergetic processes. The phylogenetic analysis of aioA showed that haloarchaea sequences cluster in a novel and monophyletic group, suggesting that the origin of arsenic metabolism in haloarchaea is ancient. Our results also suggest that arsenite chemolithotrophy likely emerged within the archaeal lineage. Our results give a broad new perspective on the haloarchaea metabolism and shed light on the evolutionary history of arsenic bioenergetics. PMID:26140530

  17. Phylogenetic analyses and expression studies reveal two distinct groups of calreticulin isoforms in higher plants.

    PubMed

    Persson, Staffan; Rosenquist, Magnus; Svensson, Karin; Galvão, Rafaelo; Boss, Wendy F; Sommarin, Marianne

    2003-11-01

    Calreticulin (CRT) is a multifunctional protein mainly localized to the endoplasmic reticulum in eukaryotic cells. Here, we present the first analysis, to our knowledge, of evolutionary diversity and expression profiling among different plant CRT isoforms. Phylogenetic studies and expression analysis show that higher plants contain two distinct groups of CRTs: a CRT1/CRT2 group and a CRT3 group. To corroborate the existence of these isoform groups, we cloned a putative CRT3 ortholog from Brassica rapa. The CRT3 gene appears to be most closely related to the ancestral CRT gene in higher plants. Distinct tissue-dependent expression patterns and stress-related regulation were observed for the isoform groups. Furthermore, analysis of posttranslational modifications revealed differences in the glycosylation status among members within the CRT1/CRT2 isoform group. Based on evolutionary relationship, a new nomenclature for plant CRTs is suggested. The presence of two distinct CRT isoform groups, with distinct expression patterns and posttranslational modifications, supports functional specificity among plant CRTs and could account for the multiple functional roles assigned to CRTs.

  18. Structural Studies of a Bacterial Condensin Complex Reveal ATP-Dependent Disruption of Intersubunit Interactions

    SciTech Connect

    Woo, J.; Lim, J; Shin, H; Suh, M; Ku, B; Lee, H; Joo, K; Robinson, H; Lee, J; et. al.

    2009-01-01

    Condensins are key mediators of chromosome condensation across organisms. Like other condensins, the bacterial MukBEF condensin complex consists of an SMC family protein dimer containing two ATPase head domains, MukB, and two interacting subunits, MukE and MukF. We report complete structural views of the intersubunit interactions of this condensin along with ensuing studies that reveal a role for the ATPase activity of MukB. MukE and MukF together form an elongated dimeric frame, and MukF's C-terminal winged-helix domains (C-WHDs) bind MukB heads to constitute closed ring-like structures. Surprisingly, one of the two bound C-WHDs is forced to detach upon ATP-mediated engagement of MukB heads. This detachment reaction depends on the linker segment preceding the C-WHD, and mutations on the linker restrict cell growth. Thus ATP-dependent transient disruption of the MukB-MukF interaction, which creates openings in condensin ring structures, is likely to be a critical feature of the functional mechanism of condensins.

  19. Solid-State NMR Studies Reveal Native-like β-Sheet Structures in Transthyretin Amyloid.

    PubMed

    Lim, Kwang Hun; Dasari, Anvesh K R; Hung, Ivan; Gan, Zhehong; Kelly, Jeffery W; Wright, Peter E; Wemmer, David E

    2016-09-20

    Structural characterization of amyloid rich in cross-β structures is crucial for unraveling the molecular basis of protein misfolding and amyloid formation associated with a wide range of human disorders. Elucidation of the β-sheet structure in noncrystalline amyloid has, however, remained an enormous challenge. Here we report structural analyses of the β-sheet structure in a full-length transthyretin amyloid using solid-state NMR spectroscopy. Magic-angle-spinning (MAS) solid-state NMR was employed to investigate native-like β-sheet structures in the amyloid state using selective labeling schemes for more efficient solid-state NMR studies. Analyses of extensive long-range (13)C-(13)C correlation MAS spectra obtained with selectively (13)CO- and (13)Cα-labeled TTR reveal that the two main β-structures in the native state, the CBEF and DAGH β-sheets, remain intact after amyloid formation. The tertiary structural information would be of great use for examining the quaternary structure of TTR amyloid. PMID:27589034

  20. Metagenomic study of red biofilms from Diamante Lake reveals ancient arsenic bioenergetics in haloarchaea.

    PubMed

    Rascovan, Nicolás; Maldonado, Javier; Vazquez, Martín P; Eugenia Farías, María

    2016-02-01

    Arsenic metabolism is proposed to be an ancient mechanism in microbial life. Different bacteria and archaea use detoxification processes to grow under high arsenic concentration. Some of them are also able to use arsenic as a bioenergetic substrate in either anaerobic arsenate respiration or chemolithotrophic growth on arsenite. However, among the archaea, bioenergetic arsenic metabolism has only been found in the Crenarchaeota phylum. Here we report the discovery of haloarchaea (Euryarchaeota phylum) biofilms forming under the extreme environmental conditions such as high salinity, pH and arsenic concentration at 4589 m above sea level inside a volcano crater in Diamante Lake, Argentina. Metagenomic analyses revealed a surprisingly high abundance of genes used for arsenite oxidation (aioBA) and respiratory arsenate reduction (arrCBA) suggesting that these haloarchaea use arsenic compounds as bioenergetics substrates. We showed that several haloarchaea species, not only from this study, have all genes required for these bioenergetic processes. The phylogenetic analysis of aioA showed that haloarchaea sequences cluster in a novel and monophyletic group, suggesting that the origin of arsenic metabolism in haloarchaea is ancient. Our results also suggest that arsenite chemolithotrophy likely emerged within the archaeal lineage. Our results give a broad new perspective on the haloarchaea metabolism and shed light on the evolutionary history of arsenic bioenergetics.

  1. Abnormal affective decision making revealed in adolescent binge drinkers using a functional magnetic resonance imaging study.

    PubMed

    Xiao, Lin; Bechara, Antoine; Gong, Qiyong; Huang, Xiaoqi; Li, Xiangrui; Xue, Gui; Wong, Savio; Lu, Zhong-Lin; Palmer, Paula; Wei, Yonglan; Jia, Yong; Johnson, C Anderson

    2013-06-01

    The goal of this study was to investigate the neural correlates of affective decision making, as measured by the Iowa Gambling Task (IGT), which are associated with adolescent binge drinking. Fourteen adolescent binge drinkers (16-18 years of age) and 14 age-matched adolescents who had never consumed alcohol--never drinkers--were recruited from local high schools in Chengdu, China. Questionnaires were used to assess academic performance, drinking experience, and urgency. Brain regions activated by the IGT performance were identified with functional magnetic resonance imaging. Results showed that, compared to never drinkers, binge drinkers performed worse on the IGT and showed higher activity in the subcomponents of the decision-making neural circuitry implicated in the execution of emotional and incentive-related behaviors, namely, the left amygdala and insula bilaterally. Moreover, measures of the severity of drinking problems in real life, as well as high urgency scores, were associated with increased activity within the insula, combined with decreased activity within the orbitofrontal cortex. These results suggest that hyperreactivity of a neural system implicated in the execution of emotional and incentive-related behaviors can be associated with socially undesirable behaviors, such as binge drinking, among adolescents. These findings have social implications because they potentially reveal underlying neural mechanisms for making poor decisions, which may increase an individual's risk and vulnerability for alcoholism.

  2. Glycoproteomic Study Reveals Altered Plasma Proteins Associated with HIV Elite Suppressors

    PubMed Central

    Yang, Weiming; Laeyendecker, Oliver; Wendel, Sarah K.; Zhang, Bai; Sun, Shisheng; Zhou, Jian-Ying; Ao, Minghui; Moore, Richard D.; Jackson, J. Brooks; Zhang, Hui

    2014-01-01

    HIV elite suppressors (ES) or controllers are individuals achieving control of viremia by their natural immunological mechanisms without highly active antiretroviral therapy (HAART). Study of the mechanisms responsible for the immunological suppression of viremia in ES may lead to the detection of individuals with ES and the effective control of HIV infection. We hypothesize that plasma glycoproteins play essential roles in the immune system of ES since plasma proteins are critical and highly relevant in anti-viral immunity and most plasma proteins are glycoproteins. To examine glycoproteins associated with ES, plasma samples from ES individuals (n=20), and from individuals on HAART (n=20), with AIDS (n=20), and no HIV infection (n=10) were analyzed by quantitative glycoproteomics. We found that a number of glycoproteins changed between ES versus HAART, AIDS and HIV- individuals. In sharp contrast, the level of plasma glycoproteins in the HAART cohort showed fewer changes compared with AIDS and HIV- individuals. These results showed that although both ES and HAART effectively suppress viremia, ES appeared to profoundly affect immunologically relevant glycoproteins in plasma as consequence of or support for anti-viral immunity. Bioinformatic analysis revealed that altered proteins in ES plasma were mainly associated with inflammation. This analysis suggests that overlapping, while distinguishable, glycoprotein profiles for inflammation and immune activation appeared to be present between ES and non-ES (HAART+AIDS) cohorts, indicating different triggers for inflammation and immune activation between natural and treatment-related viral suppression. PMID:25285165

  3. A resurrection study reveals rapid adaptive evolution within populations of an invasive plant.

    PubMed

    Sultan, Sonia E; Horgan-Kobelski, Tim; Nichols, Lauren M; Riggs, Charlotte E; Waples, Ryan K

    2013-02-01

    The future spread and impact of an introduced species will depend on how it adapts to the abiotic and biotic conditions encountered in its new range, so the potential for rapid evolution subsequent to species introduction is a critical, evolutionary dimension of invasion biology. Using a resurrection approach, we provide a direct test for change over time within populations in a species' introduced range, in the Asian shade annual Polygonum cespitosum. We document, over an 11-year period, the evolution of increased reproductive output as well as greater physiological and root-allocational plasticity in response to the more open, sunny conditions found in the North American range in which the species has become invasive. These findings show that extremely rapid adaptive modifications to ecologically-important traits and plastic expression patterns can evolve subsequent to a species' introduction, within populations established in its introduced range. This study is one of the first to directly document evolutionary change in adaptive plasticity. Such rapid evolutionary changes can facilitate the spread of introduced species into novel habitats and hence contribute to their invasive success in a new range. The data also reveal how evolutionary trajectories can differ among populations in ways that can influence invasion dynamics.

  4. Meta-analysis of Dense Genecentric Association Studies Reveals Common and Uncommon Variants Associated with Height

    PubMed Central

    Lanktree, Matthew B.; Guo, Yiran; Murtaza, Muhammed; Glessner, Joseph T.; Bailey, Swneke D.; Onland-Moret, N. Charlotte; Lettre, Guillaume; Ongen, Halit; Rajagopalan, Ramakrishnan; Johnson, Toby; Shen, Haiqing; Nelson, Christopher P.; Klopp, Norman; Baumert, Jens; Padmanabhan, Sandosh; Pankratz, Nathan; Pankow, James S.; Shah, Sonia; Taylor, Kira; Barnard, John; Peters, Bas J.; M. Maloney, Cliona; Lobmeyer, Maximilian T.; Stanton, Alice; Zafarmand, M. Hadi; Romaine, Simon P.R.; Mehta, Amar; van Iperen, Erik P.A.; Gong, Yan; Price, Tom S.; Smith, Erin N.; Kim, Cecilia E.; Li, Yun R.; Asselbergs, Folkert W.; Atwood, Larry D.; Bailey, Kristian M.; Bhatt, Deepak; Bauer, Florianne; Behr, Elijah R.; Bhangale, Tushar; Boer, Jolanda M.A.; Boehm, Bernhard O.; Bradfield, Jonathan P.; Brown, Morris; Braund, Peter S.; Burton, Paul R.; Carty, Cara; Chandrupatla, Hareesh R.; Chen, Wei; Connell, John; Dalgeorgou, Chrysoula; Boer, Anthonius de; Drenos, Fotios; Elbers, Clara C.; Fang, James C.; Fox, Caroline S.; Frackelton, Edward C.; Fuchs, Barry; Furlong, Clement E.; Gibson, Quince; Gieger, Christian; Goel, Anuj; Grobbee, Diederik E.; Hastie, Claire; Howard, Philip J.; Huang, Guan-Hua; Johnson, W. Craig; Li, Qing; Kleber, Marcus E.; Klein, Barbara E.K.; Klein, Ronald; Kooperberg, Charles; Ky, Bonnie; LaCroix, Andrea; Lanken, Paul; Lathrop, Mark; Li, Mingyao; Marshall, Vanessa; Melander, Olle; Mentch, Frank D.; J. Meyer, Nuala; Monda, Keri L.; Montpetit, Alexandre; Murugesan, Gurunathan; Nakayama, Karen; Nondahl, Dave; Onipinla, Abiodun; Rafelt, Suzanne; Newhouse, Stephen J.; Otieno, F. George; Patel, Sanjey R.; Putt, Mary E.; Rodriguez, Santiago; Safa, Radwan N.; Sawyer, Douglas B.; Schreiner, Pamela J.; Simpson, Claire; Sivapalaratnam, Suthesh; Srinivasan, Sathanur R.; Suver, Christine; Swergold, Gary; Sweitzer, Nancy K.; Thomas, Kelly A.; Thorand, Barbara; Timpson, Nicholas J.; Tischfield, Sam; Tobin, Martin; Tomaszweski, Maciej; Verschuren, W.M. Monique; Wallace, Chris; Winkelmann, Bernhard; Zhang, Haitao; Zheng, Dongling; Zhang, Li; Zmuda, Joseph M.; Clarke, Robert; Balmforth, Anthony J.; Danesh, John; Day, Ian N.; Schork, Nicholas J.; de Bakker, Paul I.W.; Delles, Christian; Duggan, David; Hingorani, Aroon D.; Hirschhorn, Joel N.; Hofker, Marten H.; Humphries, Steve E.; Kivimaki, Mika; Lawlor, Debbie A.; Kottke-Marchant, Kandice; Mega, Jessica L.; Mitchell, Braxton D.; Morrow, David A.; Palmen, Jutta; Redline, Susan; Shields, Denis C.; Shuldiner, Alan R.; Sleiman, Patrick M.; Smith, George Davey; Farrall, Martin; Jamshidi, Yalda; Christiani, David C.; Casas, Juan P.; Hall, Alistair S.; Doevendans, Pieter A.; D. Christie, Jason; Berenson, Gerald S.; Murray, Sarah S.; Illig, Thomas; Dorn, Gerald W.; Cappola, Thomas P.; Boerwinkle, Eric; Sever, Peter; Rader, Daniel J.; Reilly, Muredach P.; Caulfield, Mark; Talmud, Philippa J.; Topol, Eric; Engert, James C.; Wang, Kai; Dominiczak, Anna; Hamsten, Anders; Curtis, Sean P.; Silverstein, Roy L.; Lange, Leslie A.; Sabatine, Marc S.; Trip, Mieke; Saleheen, Danish; Peden, John F.; Cruickshanks, Karen J.; März, Winfried; O'Connell, Jeffrey R.; Klungel, Olaf H.; Wijmenga, Cisca; Maitland-van der Zee, Anke Hilse; Schadt, Eric E.; Johnson, Julie A.; Jarvik, Gail P.; Papanicolaou, George J.; Grant, Struan F.A.; Munroe, Patricia B.; North, Kari E.; Samani, Nilesh J.; Koenig, Wolfgang; Gaunt, Tom R.; Anand, Sonia S.; van der Schouw, Yvonne T.; Soranzo, Nicole; FitzGerald, Garret A.; Reiner, Alex; Hegele, Robert A.; Hakonarson, Hakon; Keating, Brendan J.

    2011-01-01

    Height is a classic complex trait with common variants in a growing list of genes known to contribute to the phenotype. Using a genecentric genotyping array targeted toward cardiovascular-related loci, comprising 49,320 SNPs across approximately 2000 loci, we evaluated the association of common and uncommon SNPs with adult height in 114,223 individuals from 47 studies and six ethnicities. A total of 64 loci contained a SNP associated with height at array-wide significance (p < 2.4 × 10−6), with 42 loci surpassing the conventional genome-wide significance threshold (p < 5 × 10−8). Common variants with minor allele frequencies greater than 5% were observed to be associated with height in 37 previously reported loci. In individuals of European ancestry, uncommon SNPs in IL11 and SMAD3, which would not be genotyped with the use of standard genome-wide genotyping arrays, were strongly associated with height (p < 3 × 10−11). Conditional analysis within associated regions revealed five additional variants associated with height independent of lead SNPs within the locus, suggesting allelic heterogeneity. Although underpowered to replicate findings from individuals of European ancestry, the direction of effect of associated variants was largely consistent in African American, South Asian, and Hispanic populations. Overall, we show that dense coverage of genes for uncommon SNPs, coupled with large-scale meta-analysis, can successfully identify additional variants associated with a common complex trait. PMID:21194676

  5. Vibrational spectroscopic studies and computational study of ethyl methyl ketone thiosemicarbazone

    NASA Astrophysics Data System (ADS)

    Anoop, M. R.; Binil, P. S.; Suma, S.; Sudarsanakumar, M. R.; Y, Sheena Mary.; Varghese, Hema Tresa; Panicker, C. Yohannan

    2010-04-01

    FT-IR and FT-Raman spectra of ethyl methyl ketone thiosemicarbazone were recorded and analyzed. The crystal structure is also described. The vibrational wavenumbers were computed using HF/6-31G(d) and B3LYP/6-31G(d) basis sets and are assigned with the aid of MOLEKEL program. The first hyperpolarizability, infrared intensities and Raman activities are also reported. The calculated first hyperpolarizability is comparable with the reported values of similar derivatives and is an attractive molecule for future applications in non-linear optics. The geometrical parameters of the title compound obtained from XRD studies are in agreement with the calculated values. The red shift of the NH stretching wavenumber in the infrared spectrum compared to the computed wavenumber indicates the weakening of the N-H bond resulting in proton transfer to the neighbouring sulfur atom.

  6. Computation and Experiment Reveal that the Ring-Rearrangement Metathesis of Himbert Cycloadducts Can Be Subject to Kinetic or Thermodynamic Control

    PubMed Central

    Lam, Jonathan K.; Pham, Hung V.; Houk, K. N.; Vanderwal, Christopher D.

    2013-01-01

    Unusual observations in the ring-rearrangement metathesis (RRM) of Himbert arene/allene cycloadducts to form fused polycylic lactams led to a more in-depth experimental study that yielded conflicting results. Differences in reactivity within related systems and unexpected changes in diastereoselectivity among other similar substrates were not readily explained on the basis of the experimental results. Computational investigations demonstrated substrate-dependent changes in reaction pathways (ring-opening metathesis/ring-closing metathesis [ROM/RCM] cascade vs. ring-closing metathesis/ring-opening metathesis [RCM/ROM] cascade). Furthermore, some reactions were judged to be under thermodynamic control, and others under kinetic control. The greater understanding of the most likely reaction pathways and their energetics provided a reasonable explanation for the previously irreconcilable results. PMID:24111571

  7. AN IMAGING AND SPECTROSCOPIC STUDY OF FOUR STRONG Mg II ABSORBERS REVEALED BY GRB 060418

    SciTech Connect

    Pollack, L. K.; Prochaska, J. X.; Chen, H.-W.; Bloom, J. S.

    2009-08-20

    We present results from an imaging and spectroscopic study of four strong Mg II absorbers of W(2796) {approx}> 1 A revealed by the afterglow of GRB 060418 at z{sub GRB} = 1.491. These absorbers, at z = 0.603, 0.656, 1.107, and z {sub GRB}, exhibit large ion abundances that suggest neutral gas columns characteristic of damped Ly{alpha} systems. The imaging data include optical images obtained using Low-Resolution Imaging Spectrometer (LRIS) on the Keck I telescope and using Advanced Camera for Surveys on board Hubble Space Telescope, and near-infrared H-band images obtained using Persson's Auxiliary Nasmyth Infrared Camera on the Magellan Baade Telescope and K'-band images obtained using NIRC2 with laser guide star adaptive optics on the Keck II telescope. These images reveal six distinct objects at {delta} {theta} {approx}< 3.''5 of the afterglow's position, two of which exhibit well-resolved mature disk morphology, one shows red colors, and three are blue compact sources. Follow-up spectroscopic observations using LRIS confirm that one of the disk galaxies coincides with the Mg II absorber at z = 0.656. The observed broadband spectral energy distributions of the second disk galaxy and the red source indicate that they are associated with the absorbers at z = 0.603 and z = 1.107, respectively. These results show that strong Mg II absorbers identified in gamma-ray burst (GRB) afterglow spectra are associated with typical galaxies of luminosity {approx}0.1 - 1 L{sub *} at impact parameter of {rho} {approx}< 10 h {sup -1} kpc. The close angular separation would preclude easy detections toward a bright quasar. Finally, we associate the remaining three blue compact sources with the GRB host galaxy, noting that they are likely star-forming knots located at projected distances of {rho} = 2 - 12 h {sup -1} kpc from the afterglow. At the afterglow's position, we derive a 2{sigma} upper limit to the underlying star-formation rate intensity of 0.0074 M{sub sun} yr{sup -1} kpc

  8. Synthesis, characterization, and computational studies of cycloparaphenylene dimers.

    PubMed

    Xia, Jianlong; Golder, Matthew R; Foster, Michael E; Wong, Bryan M; Jasti, Ramesh

    2012-12-01

    Two novel arene-bridged cycloparaphenylene dimers (1 and 2) were prepared using a functionalized precursor, bromo-substituted macrocycle 7. The preferred conformations of these dimeric structures were evaluated computationally in the solid state, as well as in the gas and solution phases. In the solid state, the trans configuration of 1 is preferred by 34 kcal/mol due to the denser crystal packing structure that is achieved. In contrast, in the gas phase and in solution, the cis conformation is favored by 7 kcal/mol (dimer 1) and 10 kcal/mol (dimer 2), with a cis to trans activation barrier of 20 kcal/mol. The stabilization seen in the cis conformations is attributed to the increased van der Waals interactions between the two cycloparaphenylene rings. These calculations indicate that the cis conformation is accessible in solution, which is promising for future efforts toward the synthesis of short carbon nanotubes (CNTs) via cycloparaphenylene monomers. In addition, the optoelectronic properties of these dimeric cycloparaphenylenes were characterized both experimentally and computationally for the first time. PMID:23130993

  9. Computational meta'omics for microbial community studies

    PubMed Central

    Segata, Nicola; Boernigen, Daniela; Tickle, Timothy L; Morgan, Xochitl C; Garrett, Wendy S; Huttenhower, Curtis

    2013-01-01

    Complex microbial communities are an integral part of the Earth's ecosystem and of our bodies in health and disease. In the last two decades, culture-independent approaches have provided new insights into their structure and function, with the exponentially decreasing cost of high-throughput sequencing resulting in broadly available tools for microbial surveys. However, the field remains far from reaching a technological plateau, as both computational techniques and nucleotide sequencing platforms for microbial genomic and transcriptional content continue to improve. Current microbiome analyses are thus starting to adopt multiple and complementary meta'omic approaches, leading to unprecedented opportunities to comprehensively and accurately characterize microbial communities and their interactions with their environments and hosts. This diversity of available assays, analysis methods, and public data is in turn beginning to enable microbiome-based predictive and modeling tools. We thus review here the technological and computational meta'omics approaches that are already available, those that are under active development, their success in biological discovery, and several outstanding challenges. PMID:23670539

  10. A Computational Study of Systemic Hydration in Vocal Fold Collision

    PubMed Central

    Bhattacharya, Pinaki; Siegmund, Thomas

    2013-01-01

    Mechanical stresses develop within vocal fold (VF) soft tissues, due to phonation-associated vibration and collision. These stresses in turn affect the hydration of VF tissue and thus influence voice health. In this paper, high-fidelty numerical computations are described taking into account fully three-dimensional geometry, realistic tissue and air properties, and high-amplitude vibration and collision. A segregated solver approach is employed, using sophisticated commercial solvers for both the VF tissue and glottal airflow domains. The tissue viscoelastic properties were derived from a biphasic formulation. Two cases were considered, whereby the tissue viscoelastic properties corresponded to two different volume fractions of the fluid phase of the VF tissue. For each case, hydrostatic stresses occurring as a result of vibration and collision were investigated. Assuming the VF tissue to be poroelastic, interstitial fluid movement within VF tissue was estimated from the hydrostatic stress gradient. Computed measures of overall VF dynamics (peak air-flow velocity, magnitude of VF deformation, frequency of vibration and contact pressure) were well within the range of experimentally observed values. The VF motion leading to mechanical stresses within the VFs and their effect on the interstitial fluid flux is detailed. It is found that average deformation and vibration of VFs tends to increase the state of hydration of the VF tissue whereas VF collision works to reduce hydration. PMID:23531170

  11. Multifactoriality in Psychiatric Disorders: A Computational Study of Schizophrenia.

    PubMed

    Pavão, Rodrigo; Tort, Adriano B L; Amaral, Olavo B

    2015-07-01

    The search for biological causes of mental disorders has up to now met with limited success, leading to growing dissatisfaction with diagnostic classifications. However, it is questionable whether most clinical syndromes should be expected to correspond to specific microscale brain alterations, as multiple low-level causes could lead to similar symptoms in different individuals. In order to evaluate the potential multifactoriality of alterations related to psychiatric illness, we performed a parametric exploration of published computational models of schizophrenia. By varying multiple parameters simultaneously, such as receptor conductances, connectivity patterns, and background excitation, we generated 5625 different versions of an attractor-based network model of schizophrenia symptoms. Among networks presenting activity within valid ranges, 154 parameter combinations out of 3002 (5.1%) presented a phenotype reminiscent of schizophrenia symptoms as defined in the original publication. We repeated this analysis in a model of schizophrenia-related deficits in spatial working memory, building 3125 different networks, and found that 41 (4.9%) out of 834 networks with valid activity presented schizophrenia-like alterations. In isolation, none of the parameters in either model showed adequate sensitivity or specificity to identify schizophrenia-like networks. Thus, in computational models of schizophrenia, even simple network phenotypes related to the disorder can be produced by a myriad of causes at the molecular and circuit levels. This suggests that unified explanations for either the full syndrome or its behavioral and network endophenotypes are unlikely to be expected at the genetic and molecular levels.

  12. Computer Studies Of The Isleworth And Louvre Mona Lisas

    NASA Astrophysics Data System (ADS)

    Asmus, John F.

    1989-07-01

    One of the most pervasive problems in the scholarship of classical paintings is that of authenticity. Traditionally, the attribution of a work of art rests on the subjective opinion of an art historian bolstered by scientific data pertaining to the types and possibly the ages of the materials of the artwork. To expand the range of technical information that may be applied to the painting authentication problem, the methods of computer image processing (IP) have been employed to compare the techniques in two paintings. One is the Mona Lisa del Gioconda by Leonardo da Vinci. The other is known as the Isleworth Mona Lisa and has also been attributed to Leonardo by a few scholars. Computer IP was used to compare statistical and geometrical features of the two paintings. It emerged that the Isleworth work is not a copy of the Louvre painting but does have numerous similarities in composition and execution. These findings lend support to the theory that the Louvre Mona Lisa may be a portrait of Costanza by Leonardo that had been thought lost.

  13. Multifactoriality in Psychiatric Disorders: A Computational Study of Schizophrenia

    PubMed Central

    Pavão, Rodrigo; Tort, Adriano B. L.; Amaral, Olavo B.

    2015-01-01

    The search for biological causes of mental disorders has up to now met with limited success, leading to growing dissatisfaction with diagnostic classifications. However, it is questionable whether most clinical syndromes should be expected to correspond to specific microscale brain alterations, as multiple low-level causes could lead to similar symptoms in different individuals. In order to evaluate the potential multifactoriality of alterations related to psychiatric illness, we performed a parametric exploration of published computational models of schizophrenia. By varying multiple parameters simultaneously, such as receptor conductances, connectivity patterns, and background excitation, we generated 5625 different versions of an attractor-based network model of schizophrenia symptoms. Among networks presenting activity within valid ranges, 154 parameter combinations out of 3002 (5.1%) presented a phenotype reminiscent of schizophrenia symptoms as defined in the original publication. We repeated this analysis in a model of schizophrenia-related deficits in spatial working memory, building 3125 different networks, and found that 41 (4.9%) out of 834 networks with valid activity presented schizophrenia-like alterations. In isolation, none of the parameters in either model showed adequate sensitivity or specificity to identify schizophrenia-like networks. Thus, in computational models of schizophrenia, even simple network phenotypes related to the disorder can be produced by a myriad of causes at the molecular and circuit levels. This suggests that unified explanations for either the full syndrome or its behavioral and network endophenotypes are unlikely to be expected at the genetic and molecular levels. PMID:25332409

  14. Computational meta'omics for microbial community studies.

    PubMed

    Segata, Nicola; Boernigen, Daniela; Tickle, Timothy L; Morgan, Xochitl C; Garrett, Wendy S; Huttenhower, Curtis

    2013-01-01

    Complex microbial communities are an integral part of the Earth's ecosystem and of our bodies in health and disease. In the last two decades, culture-independent approaches have provided new insights into their structure and function, with the exponentially decreasing cost of high-throughput sequencing resulting in broadly available tools for microbial surveys. However, the field remains far from reaching a technological plateau, as both computational techniques and nucleotide sequencing platforms for microbial genomic and transcriptional content continue to improve. Current microbiome analyses are thus starting to adopt multiple and complementary meta'omic approaches, leading to unprecedented opportunities to comprehensively and accurately characterize microbial communities and their interactions with their environments and hosts. This diversity of available assays, analysis methods, and public data is in turn beginning to enable microbiome-based predictive and modeling tools. We thus review here the technological and computational meta'omics approaches that are already available, those that are under active development, their success in biological discovery, and several outstanding challenges.

  15. Interaction studies reveal specific recognition of an anti-inflammatory polyphosphorhydrazone dendrimer by human monocytes

    NASA Astrophysics Data System (ADS)

    Ledall, Jérémy; Fruchon, Séverine; Garzoni, Matteo; Pavan, Giovanni M.; Caminade, Anne-Marie; Turrin, Cédric-Olivier; Blanzat, Muriel; Poupot, Rémy

    2015-10-01

    Dendrimers are nano-materials with perfectly defined structure and size, and multivalency properties that confer substantial advantages for biomedical applications. Previous work has shown that phosphorus-based polyphosphorhydrazone (PPH) dendrimers capped with azabisphosphonate (ABP) end groups have immuno-modulatory and anti-inflammatory properties leading to efficient therapeutic control of inflammatory diseases in animal models. These properties are mainly prompted through activation of monocytes. Here, we disclose new insights into the molecular mechanisms underlying the anti-inflammatory activation of human monocytes by ABP-capped PPH dendrimers. Following an interdisciplinary approach, we have characterized the physicochemical and biological behavior of the lead ABP dendrimer with model and cell membranes, and compared this experimental set of data to predictive computational modelling studies. The behavior of the ABP dendrimer was compared to the one of an isosteric analog dendrimer capped with twelve azabiscarboxylate (ABC) end groups instead of twelve ABP end groups. The ABC dendrimer displayed no biological activity on human monocytes, therefore it was considered as a negative control. In detail, we show that the ABP dendrimer can bind both non-specifically and specifically to the membrane of human monocytes. The specific binding leads to the internalization of the ABP dendrimer by human monocytes. On the contrary, the ABC dendrimer only interacts non-specifically with human monocytes and is not internalized. These data indicate that the bioactive ABP dendrimer is recognized by specific receptor(s) at the surface of human monocytes.Dendrimers are nano-materials with perfectly defined structure and size, and multivalency properties that confer substantial advantages for biomedical applications. Previous work has shown that phosphorus-based polyphosphorhydrazone (PPH) dendrimers capped with azabisphosphonate (ABP) end groups have immuno-modulatory and anti

  16. Computer-aided assessment of head computed tomography (CT) studies in patients with suspected traumatic brain injury.

    PubMed

    Yuh, Esther L; Gean, Alisa D; Manley, Geoffrey T; Callen, Andrew L; Wintermark, Max

    2008-10-01

    In this study, we sought to determine the accuracy of a computer algorithm that automatically assesses head computed tomography (CT) studies in patients with suspected traumatic brain injury (TBI) for features of intracranial hemorrhage and mass effect, employing a neuroradiologist's interpretation as the gold standard. To this end, we designed a suite of computer algorithms that evaluates in a fully automated fashion the presence of intracranial blood and/or mass effect based on the following CT findings: (1) presence or absence of a subdural or epidural hematoma, (2) presence or absence of subarachnoid hemorrhage, (3) presence or absence of an intraparenchymal hematoma, (4) presence or absence of clinically significant midline shift (>or=5 mm), and (5) normal, partly effaced, or completely effaced basal cisterns. The algorithm displays abnormal findings as color overlays on the original head CT images, and calculates the volume of each type of blood collection, the midline shift, and the volume of the basal cisterns, based on the above-described features. Thresholds and parameters yielding optimal accuracy of the computer algorithm were determined using a development sample of 33 selected, nonconsecutive patients. The software was then applied to a validation sample of 250 consecutive patients evaluated for suspicion of acute TBI at our institution in 2006-2007. Software detection of the presence of at least one noncontrast CT (NCT) feature of acute TBI demonstrated high sensitivity of 98% and high negative predictive value (NPV) of 99%. There was actually only one false negative case, where a very subtle subdural hematoma, extending exclusively along the falx, was diagnosed by the neuroradiologist, while the case was considered as normal by the computer algorithm. The software was excellent at detecting the presence of mass effect and intracranial hemorrhage, but showed some disagreements with the neuroradiologist in quantifying the degree of mass effect and

  17. Dropping Out of Computer Science: A Phenomenological Study of Student Lived Experiences in Community College Computer Science

    NASA Astrophysics Data System (ADS)

    Gilbert-Valencia, Daniel H.

    California community colleges contribute alarmingly few computer science degree or certificate earners. While the literature shows clear K-12 impediments to CS matriculation in higher education, very little is known about the experiences of those who overcome initial impediments to CS yet do not persist through to program completion. This phenomenological study explores insights into that specific experience by interviewing underrepresented, low income, first-generation college students who began community college intending to transfer to 4-year institutions majoring in CS but switched to another field and remain enrolled or graduated. This study explores the lived experiences of students facing barriers, their avenues for developing interest in CS, and the persistence support systems they encountered, specifically looking at how students constructed their academic choice from these experiences. The growing diversity within California's population necessitates that experiences specific to underrepresented students be considered as part of this exploration. Ten semi-structured interviews and observations were conducted, transcribed and coded. Artifacts supporting student experiences were also collected. Data was analyzed through a social-constructivist lens to provide insight into experiences and how they can be navigated to create actionable strategies for community college computer science departments wishing to increase student success. Three major themes emerged from this research: (1) students shared pre-college characteristics; (2) faced similar challenges in college CS courses; and (3) shared similar reactions to the "work" of computer science. Results of the study included (1) CS interest development hinged on computer ownership in the home; (2) participants shared characteristics that were ideal for college success but not CS success; and (3) encounters in CS departments produced unique challenges for participants. Though CS interest was and remains

  18. A Study of Effectiveness of Computer Assisted Instruction (CAI) over Classroom Lecture (CRL) at ICS Level

    ERIC Educational Resources Information Center

    Kaousar, Tayyeba; Choudhry, Bushra Naoreen; Gujjar, Aijaz Ahmed

    2008-01-01

    This study was aimed to evaluate the effectiveness of CAI vs. classroom lecture for computer science at ICS level. The objectives were to compare the learning effects of two groups with classroom lecture and computer-assisted instruction studying the same curriculum and the effects of CAI and CRL in terms of cognitive development. Hypotheses of…

  19. Short Stories via Computers in EFL Classrooms: An Empirical Study for Reading and Writing Skills

    ERIC Educational Resources Information Center

    Yilmaz, Adnan

    2015-01-01

    The present empirical study scrutinizes the use of short stories via computer technologies in teaching and learning English language. The objective of the study is two-fold: to examine how short stories could be used through computer programs in teaching and learning English and to collect data about students' perceptions of this technique via…

  20. CBSS Outreach Project: Computer-Based Study Strategies for Students with Learning Disabilities. Final Report.

    ERIC Educational Resources Information Center

    Anderson-Inman, Lynne; Ditson, Mary

    This final report describes activities and accomplishments of the four-year Computer-Based Study Strategies (CBSS) Outreach Project at the University of Oregon. This project disseminated information about using computer-based study strategies as an intervention for students with learning disabilities and provided teachers in participating outreach…

  1. Effectiveness of Computer-Assisted Mathematics Education (CAME) over Academic Achievement: A Meta-Analysis Study

    ERIC Educational Resources Information Center

    Demir, Seda; Basol, Gülsah

    2014-01-01

    The aim of the current study is to determine the overall effects of Computer-Assisted Mathematics Education (CAME) on academic achievement. After an extensive review of the literature, studies using Turkish samples and observing the effects of Computer-Assisted Education (CAE) on mathematics achievement were examined. As a result of this…

  2. Effect of Computer-Based Video Games on Children: An Experimental Study

    ERIC Educational Resources Information Center

    Chuang, Tsung-Yen; Chen, Wei-Fan

    2009-01-01

    This experimental study investigated whether computer-based video games facilitate children's cognitive learning. In comparison to traditional computer-assisted instruction (CAI), this study explored the impact of the varied types of instructional delivery strategies on children's learning achievement. One major research null hypothesis was…

  3. International Computer and Information Literacy Study: ICILS 2013 User Guide for the International Database

    ERIC Educational Resources Information Center

    Jung, Michael, Ed.; Carstens, Ralph, Ed.

    2015-01-01

    The International Computer and Information Literacy Study (ICILS) 2013, conducted by the International Association for the Evaluation of Educational Achievement (IEA), studied how students in different countries develop the knowledge, understanding, attitudes, dispositions, and skills that comprise computer and information literacy (CIL). The aim…

  4. Using Computer Assisted Instruction in a Reading and Study Skills Course.

    ERIC Educational Resources Information Center

    Rauch, Margaret

    Test wiseness programs and computer assisted study skills instruction (CASSI) were found to be valuable resources for college reading and study skills instructors and students at St. Cloud State University (Minnesota). Two booklets on test wiseness cues were reorganized and used as computer programs to allow the information to be presented outside…

  5. Study of USGS/NASA land use classification system. [computer analysis from LANDSAT data

    NASA Technical Reports Server (NTRS)

    Spann, G. W.

    1975-01-01

    The results of a computer mapping project using LANDSAT data and the USGS/NASA land use classification system are summarized. During the computer mapping portion of the project, accuracies of 67 percent to 79 percent were achieved using Level II of the classification system and a 4,000 acre test site centered on Douglasville, Georgia. Analysis of response to a questionaire circulated to actual and potential LANDSAT data users reveals several important findings: (1) there is a substantial desire for additional information related to LANDSAT capabilities; (2) a majority of the respondents feel computer mapping from LANDSAT data could aid present or future projects; and (3) the costs of computer mapping are substantially less than those of other methods.

  6. Computational studies of the purine-functionalized graphene sheets

    NASA Astrophysics Data System (ADS)

    Mirzaei, Mahmoud; Yousefi, Mohammad

    2012-10-01

    We performed a computational work to investigate the properties of functionalized graphene sheets (S) by adenine (A) and guanine (G) purine nucleobases. To achieve the purpose of this work, we examined the functionalization of armchair and zigzag tips of the S model by each of the A and G purines. The results indicated that the optimized properties for the investigated hybrid structures are different depending on the tip of functionalization and the used purine nucleobase. Moreover, the atomic level properties of the investigated structures were investigated by evaluating quadrupole coupling constants (CQ) for the atoms of the optimized structures. The remarkable trend of the CQ parameters is that the changes of atomic properties are many more significant for the functionalization of the zigzag-tip by the G nucleobase, which is in agreement with the results of the optimized properties.

  7. Computational Study of Growth and Remodeling in the Aortic Arch

    PubMed Central

    Alford, Patrick W.; Taber, Larry A.

    2009-01-01

    Opening angles (OAs) are associated with growth and remodeling in arteries. One curiosity has been the relatively large OAs found in the aortic arch of some animals. Here, we use computational models to explore the reasons behind this phenomenon. The artery is assumed to contain a smooth muscle/collagen phase and an elastin phase. In the models, growth and remodeling of smooth muscle/collagen depends on wall stress and fluid shear stress. Remodeling of elastin, which normally turns over very slowly, is neglected. The results indicate that OAs generally increase with longitudinal curvature (torus model), earlier elastin production during development, and decreased wall stiffness. Correlating these results with available experimental data suggests that all of these effects may contribute to the large OAs in the aortic arch. The models also suggest that the slow turnover rate of elastin limits longitudinal growth. These results should promote increased understanding of the causes of residual stress in arteries. PMID:18792831

  8. Computer programs for eddy-current defect studies

    SciTech Connect

    Pate, J. R.; Dodd, C. V.

    1990-06-01

    Several computer programs to aid in the design of eddy-current tests and probes have been written. The programs, written in Fortran, deal in various ways with the response to defects exhibited by four types of probes: the pancake probe, the reflection probe, the circumferential boreside probe, and the circumferential encircling probe. Programs are included which calculate the impedance or voltage change in a coil due to a defect, which calculate and plot the defect sensitivity factor of a coil, and which invert calculated or experimental readings to obtain the size of a defect. The theory upon which the programs are based is the Burrows point defect theory, and thus the calculations of the programs will be more accurate for small defects. 6 refs., 21 figs.

  9. Computational anatomy for studying use-dependant brain plasticity

    PubMed Central

    Draganski, Bogdan; Kherif, Ferath; Lutti, Antoine

    2014-01-01

    In this article we provide a comprehensive literature review on the in vivo assessment of use-dependant brain structure changes in humans using magnetic resonance imaging (MRI) and computational anatomy. We highlight the recent findings in this field that allow the uncovering of the basic principles behind brain plasticity in light of the existing theoretical models at various scales of observation. Given the current lack of in-depth understanding of the neurobiological basis of brain structure changes we emphasize the necessity of a paradigm shift in the investigation and interpretation of use-dependent brain plasticity. Novel quantitative MRI acquisition techniques provide access to brain tissue microstructural properties (e.g., myelin, iron, and water content) in-vivo, thereby allowing unprecedented specific insights into the mechanisms underlying brain plasticity. These quantitative MRI techniques require novel methods for image processing and analysis of longitudinal data allowing for straightforward interpretation and causality inferences. PMID:25018716

  10. Hybrid Epidemics—A Case Study on Computer Worm Conficker

    PubMed Central

    Zhang, Changwang; Zhou, Shi; Chain, Benjamin M.

    2015-01-01

    Conficker is a computer worm that erupted on the Internet in 2008. It is unique in combining three different spreading strategies: local probing, neighbourhood probing, and global probing. We propose a mathematical model that combines three modes of spreading: local, neighbourhood, and global, to capture the worm’s spreading behaviour. The parameters of the model are inferred directly from network data obtained during the first day of the Conficker epidemic. The model is then used to explore the tradeoff between spreading modes in determining the worm’s effectiveness. Our results show that the Conficker epidemic is an example of a critically hybrid epidemic, in which the different modes of spreading in isolation do not lead to successful epidemics. Such hybrid spreading strategies may be used beneficially to provide the most effective strategies for promulgating information across a large population. When used maliciously, however, they can present a dangerous challenge to current internet security protocols. PMID:25978309

  11. Computational study of ion beam extraction phenomena through multiple apertures

    SciTech Connect

    Hu, Wanpeng; Sang, Chaofeng; Tang, Tengfei; Wang, Dezhen; Li, Ming; Jin, Dazhi; Tan, Xiaohua

    2014-03-15

    The process of ion extraction through multiple apertures is investigated using a two-dimensional particle-in-cell code. We consider apertures with a fixed diameter with a hydrogen plasma background, and the trajectories of electrons, H{sup +} and H{sub 2}{sup +} ions in the self-consistently calculated electric field are traced. The focus of this work is the fundamental physics of the ion extraction, and not particular to a specific device. The computed convergence and divergence of the extracted ion beam are analyzed. We find that the extracted ion flux reaching the extraction electrode is non-uniform, and the peak flux positions change according to operational parameters, and do not necessarily match the positions of the apertures in the y-direction. The profile of the ion flux reaching the electrode is mainly affected by the bias voltage and the distance between grid wall and extraction electrode.

  12. Computational approaches to study the effects of small genomic variations.

    PubMed

    Khafizov, Kamil; Ivanov, Maxim V; Glazova, Olga V; Kovalenko, Sergei P

    2015-10-01

    Advances in DNA sequencing technologies have led to an avalanche-like increase in the number of gene sequences deposited in public databases over the last decade as well as the detection of an enormous number of previously unseen nucleotide variants therein. Given the size and complex nature of the genome-wide sequence variation data, as well as the rate of data generation, experimental characterization of the disease association of each of these variations or their effects on protein structure/function would be costly, laborious, time-consuming, and essentially impossible. Thus, in silico methods to predict the functional effects of sequence variations are constantly being developed. In this review, we summarize the major computational approaches and tools that are aimed at the prediction of the functional effect of mutations, and describe the state-of-the-art databases that can be used to obtain information about mutation significance. We also discuss future directions in this highly competitive field.

  13. Carbonyl mediated conductance through metal bound peptides: a computational study

    NASA Astrophysics Data System (ADS)

    Perrine, Trilisa M.; Dunietz, Barry D.

    2007-10-01

    Large increases in the conductance of peptides upon binding to metal ions have recently been reported experimentally. The mechanism of the conductance switching is examined computationally. It is suggested that oxidation of the metal ion occurs after binding to the peptide. This is caused by the bias potential placed across the metal-peptide complex. A combination of configurational changes, metal ion involvement and interactions between carbonyl group oxygen atoms and the gold leads are all shown to be necessary for the large improvement in the conductance seen experimentally. Differences in the molecular orbitals of the nickel and copper complexes are noted and serve to explain the variation of the improvement in conductance upon binding to either a nickel or copper ion.

  14. A computational study of highly viscous impinging jets

    SciTech Connect

    Silva, M.W.

    1998-11-01

    Two commercially-available computational fluid dynamics codes, FIDAP (Fluent, Inc., Lebanon, NH) and FLOW-3D (Flow Science, Inc., Los Alamos, NM), were used to simulate the landing region of jets of highly viscous fluids impinging on flat surfaces. The volume-of-fluid method was combined with finite difference and finite element approaches to predict the jet behavior. Several computational models with varying degrees of physical realism were developed, and the results were compared with experimental observations. In experiments, the jet exhibited several complex behaviors. As soon as it exited the nozzle, the jet began to neck down and become narrower. When it impacted the solid surface, the jet developed an instability near the impact point and buckled to the side. This buckling became a spiraling motion, and the jet spiraled about the impact point. As the jet spiraled around, a cone-shaped pile was build up which eventually became unstable and slumped to the side. While all of these behaviors were occurring, air bubbles, or voids, were being entrapped in the fluid pool. The results obtained from the FLOW-3D models more closely matched the behavior of real jets than the results obtained from /the FIDAP models. Most of the FLOW-3D models predicted all of the significant jet behaviors observed in experiments: necking, buckling, spiraling, slumping, and void entrapment. All of the FIDAP models predicted that the jet would buckle relatively far from the point of impact, whereas the experimentally observed jet behavior indicates that the jets buckle much nearer the impact point. Furthermore, it was shown that FIDAP is incapable of incorporating heat transfer effects into the model, making it unsuitable for this work.

  15. Attitudes of dental students towards using computers in education--a mixed design study.

    PubMed

    El Tantawi, M M A; Saleh, S M

    2008-01-01

    This mixed design study explored attitudes of dental students towards use of computers. It employed quantitative analyses of a questionnaire answered by 979 students and qualitative analysis of suggestions by a subgroup of 339. Positive attitudes towards computers were predicted by "computer use for > 1 year" and "year of study". Qualitative analysis of students' suggestions confirmed these findings and brought up new issues such as the need for establishing a website for the faculty. The results indicate that careful planning is needed to improve students' skills and incorporate computer applications in educational curricula.

  16. A 3-D Computational Study of a Variable Camber Continuous Trailing Edge Flap (VCCTEF) Spanwise Segment

    NASA Technical Reports Server (NTRS)

    Kaul, Upender K.; Nguyen, Nhan T.

    2015-01-01

    Results of a computational study carried out to explore the effects of various elastomer configurations joining spanwise contiguous Variable Camber Continuous Trailing Edge Flap (VCCTEF) segments are reported here. This research is carried out as a proof-of-concept study that will seek to push the flight envelope in cruise with drag optimization as the objective. The cruise conditions can be well off design such as caused by environmental conditions, maneuvering, etc. To handle these off-design conditions, flap deflection is used so when the flap is deflected in a given direction, the aircraft angle of attack changes accordingly to maintain a given lift. The angle of attack is also a design parameter along with the flap deflection. In a previous 2D study,1 the effect of camber was investigated and the results revealed some insight into the relative merit of various camber settings of the VCCTEF. The present state of the art has not advanced sufficiently to do a full 3-D viscous analysis of the whole NASA Generic Transport Model (GTM) wing with VCCTEF deployed with elastomers. Therefore, this study seeks to explore the local effects of three contiguous flap segments on lift and drag of a model devised here to determine possible trades among various flap deflections to achieve desired lift and drag results. Although this approach is an approximation, it provides new insights into the "local" effects of the relative deflections of the contiguous spanwise flap systems and various elastomer segment configurations. The present study is a natural extension of the 2-D study to assess these local 3-D effects. Design cruise condition at 36,000 feet at free stream Mach number of 0.797 and a mean aerodynamic chord (MAC) based Reynolds number of 30.734x10(exp 6) is simulated for an angle of attack (AoA) range of 0 to 6 deg. In the previous 2-D study, the calculations revealed that the parabolic arc camber (1x2x3) and circular arc camber (VCCTEF222) offered the best L

  17. Revealing fibrinogen monolayer conformations at different pHs: electrokinetic and colloid deposition studies.

    PubMed

    Nattich-Rak, Małgorzata; Adamczyk, Zbigniew; Wasilewska, Monika; Sadowska, Marta

    2015-07-01

    Adsorption mechanism of human fibrinogen on mica at different pHs is studied using the streaming potential and colloid deposition measurements. The fibrinogen monolayers are produced by a controlled adsorption under diffusion transport at pH of 3.5 and 7.4. Initially, the electrokinetic properties of these monolayers and their stability for various ionic strength are determined. It is shown that at pH 3.5 fibrinogen adsorbs irreversibly on mica for ionic strength range of 4×10(-4) to 0.15 M. At pH 7.4, a partial desorption is observed for ionic strength below 10(-2) M. This is attributed to the desorption of the end-on oriented molecules whereas the side-on adsorbed molecules remain irreversibly bound at all ionic strengths. The orientation of molecules and monolayer structure is evaluated by the colloid deposition measurements involving negatively charged polystyrene latex microspheres, 820 nm in diameter. An anomalous deposition of negative latex particles on substrates exhibiting a negative zeta potential is observed. At pH 3.5 measurable deposition of latex is observed even at low ionic strength where the approach distance of latex particles exceeded 70 nm. At pH 7.4 this critical distance is 23 nm. This confirms that fibrinogen monolayers formed at both pHs are characterized by the presence of the side-on and end-on oriented molecules that prevail at higher coverage range. It is also shown that positive charge is located at the end parts of the αA chains of the adsorbed fibrinogen molecules. Therefore, it is concluded that the colloid deposition method is an efficient tool for revealing protein adsorption mechanisms at solid/electrolyte interfaces.

  18. Genome-wide association study of toxic metals and trace elements reveals novel associations

    PubMed Central

    Ng, Esther; Lind, P. Monica; Lindgren, Cecilia; Ingelsson, Erik; Mahajan, Anubha; Morris, Andrew; Lind, Lars

    2015-01-01

    The accumulation of toxic metals in the human body is influenced by exposure and mechanisms involved in metabolism, some of which may be under genetic control. This is the first genome-wide association study to investigate variants associated with whole blood levels of a range of toxic metals. Eleven toxic metals and trace elements (aluminium, cadmium, cobalt, copper, chromium, mercury, manganese, molybdenum, nickel, lead and zinc) were assayed in a cohort of 949 individuals using mass spectrometry. DNA samples were genotyped on the Infinium Omni Express bead microarray and imputed up to reference panels from the 1000 Genomes Project. Analyses revealed two regions associated with manganese level at genome-wide significance, mapping to 4q24 and 1q41. The lead single nucleotide polymorphism (SNP) in the 4q24 locus was rs13107325 (P-value = 5.1 × 10−11, β = −0.77), located in an exon of SLC39A8, which encodes a protein involved in manganese and zinc transport. The lead SNP in the 1q41 locus is rs1776029 (P-value = 2.2 × 10−14, β = −0.46). The SNP lies within the intronic region of SLC30A10, another transporter protein. Among other metals, the loci 6q14.1 and 3q26.32 were associated with cadmium and mercury levels (P = 1.4 × 10−10, β = −1.2 and P = 1.8 × 10−9, β = −1.8, respectively). Whole blood measurements of toxic metals are associated with genetic variants in metal transporter genes and others. This is relevant in inferring metabolic pathways of metals and identifying subsets of individuals who may be more susceptible to metal toxicity. PMID:26025379

  19. Genome-wide association study of toxic metals and trace elements reveals novel associations.

    PubMed

    Ng, Esther; Lind, P Monica; Lindgren, Cecilia; Ingelsson, Erik; Mahajan, Anubha; Morris, Andrew; Lind, Lars

    2015-08-15

    The accumulation of toxic metals in the human body is influenced by exposure and mechanisms involved in metabolism, some of which may be under genetic control. This is the first genome-wide association study to investigate variants associated with whole blood levels of a range of toxic metals. Eleven toxic metals and trace elements (aluminium, cadmium, cobalt, copper, chromium, mercury, manganese, molybdenum, nickel, lead and zinc) were assayed in a cohort of 949 individuals using mass spectrometry. DNA samples were genotyped on the Infinium Omni Express bead microarray and imputed up to reference panels from the 1000 Genomes Project. Analyses revealed two regions associated with manganese level at genome-wide significance, mapping to 4q24 and 1q41. The lead single nucleotide polymorphism (SNP) in the 4q24 locus was rs13107325 (P-value = 5.1 × 10(-11), β = -0.77), located in an exon of SLC39A8, which encodes a protein involved in manganese and zinc transport. The lead SNP in the 1q41 locus is rs1776029 (P-value = 2.2 × 10(-14), β = -0.46). The SNP lies within the intronic region of SLC30A10, another transporter protein. Among other metals, the loci 6q14.1 and 3q26.32 were associated with cadmium and mercury levels (P = 1.4 × 10(-10), β = -1.2 and P = 1.8 × 10(-9), β = -1.8, respectively). Whole blood measurements of toxic metals are associated with genetic variants in metal transporter genes and others. This is relevant in inferring metabolic pathways of metals and identifying subsets of individuals who may be more susceptible to metal toxicity.

  20. MuRF1-dependent regulation of systemic carbohydrate metabolism as revealed from transgenic mouse studies.

    PubMed

    Hirner, Stephanie; Krohne, Christian; Schuster, Alexander; Hoffmann, Sigrid; Witt, Stephanie; Erber, Ralf; Sticht, Carsten; Gasch, Alexander; Labeit, Siegfried; Labeit, Dittmar

    2008-06-13

    Under various pathophysiological muscle-wasting conditions, such as diabetes and starvation, a family of ubiquitin ligases, including muscle-specific RING-finger protein 1 (MuRF1), are induced to target muscle proteins for degradation via ubiquitination. We have generated transgenic mouse lines over-expressing MuRF1 in a skeletal muscle-specific fashion (MuRF1-TG mice) in an attempt to identify the in vivo targets of MuRF1. MuRF1-TG lines were viable, had normal fertility and normal muscle weights at eight weeks of age. Comparison of quadriceps from MuRF1-TG and wild type mice did not reveal elevated multi-ubiquitination of myosin as observed in human patients with muscle wasting. Instead, MuRF1-TG mice expressed lower levels of pyruvate dehydrogenase (PDH), a mitochondrial key enzyme in charge of glycolysis, and of its regulator PDK2. Furthermore, yeast two-hybrid interaction studies demonstrated the interaction of MuRF1 with PDH, PDK2, PDK4, PKM2 (all participating in glycolysis) and with phosphorylase beta (PYGM) and glycogenin (both regulating glycogen metabolism). Consistent with the idea that MuRF1 may regulate carbohydrate metabolism, MuRF1-TG mice had twofold elevated insulin blood levels and lower hepatic glycogen contents. To further examine MuRF1's role for systemic carbohydrate regulation, we performed glucose tolerance tests (GTT) in wild type and MuRF1-TG mice. During GTT, MuRF1-TG mice developed striking hyperinsulinaemia and hepatic glycogen stores, that were depleted at basal levels, became rapidly replenished. Taken together, our data demonstrate that MuRF1 expression in skeletal muscle re-directs glycogen synthesis to the liver and stimulates pancreatic insulin secretion, thereby providing a regulatory feedback loop that connects skeletal muscle metabolism with the liver and the pancreas during metabolic stress. PMID:18468620

  1. Numerous risk factors for Helicobacter pylori antibiotic resistance revealed by extended anamnesis: a Bulgarian study.

    PubMed

    Boyanova, Lyudmila; Ilieva, Juliana; Gergova, Galina; Davidkov, Lubomir; Spassova, Zoya; Kamburov, Victor; Katsarov, Nikolai; Mitov, Ivan

    2012-01-01

    The aim of this study was to assess risk factors for primary Helicobacter pylori antibiotic resistance by an extended anamnesis. In total, 519 H. pylori strains from untreated symptomatic adults who answered a questionnaire were evaluated. Strain susceptibility was assessed by a breakpoint susceptibility test. Primary resistance rates were 29.5 % for metronidazole, 17.9 % for clarithromycin, 7.3 % for metronidazole+clarithromycin, 4.0 % for tetracycline and 10.8 % for ciprofloxacin. On multivariate analysis, younger (≤65 years) age was an independent predictor for metronidazole resistance. To our knowledge, for the first time, being a member of the health-care profession was revealed as a risk factor for H. pylori resistance to metronidazole and both metronidazole and clarithromycin. Respiratory and urinary tract infections were independent predictors of clarithromycin and ciprofloxacin resistance, respectively. The presence of co-infections was an independent risk factor for clarithromycin, metronidazole and ciprofloxacin resistance. Surprisingly, female sex was the only predictor for tetracycline resistance. The antibiotic resistance rates were not associated with disease type, place of residence, birthplace, educational level, non-steroidal anti-inflammatory drug or proton pump inhibitor use, smoking or dietary factors, such as consumption of coffee, yogurt, green tea, raw garlic, raw onion, honey or meat. There was a trend for higher metronidazole resistance in strains from diabetic patients. In conclusion, the extended anamnesis of H. pylori-positive patients should include data on patient age, sex, whether they are in the health-care profession, co-infections and possibly diabetes to improve the choice of empiric therapy. Tailored treatment based on the extended anamnesis is suggested, and susceptibility testing of the strains is recommended for patients at risk for antibiotic resistance, especially to clarithromycin, fluoroquinolones or both metronidazole

  2. Computational Studies of Molecular Permeation through Connexin26 Channels.

    PubMed

    Luo, Yun; Rossi, Angelo R; Harris, Andrew L

    2016-02-01

    A signal property of connexin channels is the ability to mediate selective diffusive movement of molecules through plasma membrane(s), but the energetics and determinants of molecular movement through these channels have yet to be understood. Different connexin channels have distinct molecular selectivities that cannot be explained simply on the basis of size or charge of the permeants. To gain insight into the forces and interactions that underlie selective molecular permeation, we investigated the energetics of two uncharged derivatized sugars, one permeable and one impermeable, through a validated connexin26 (Cx26) channel structural model, using molecular dynamics and associated analytic tools. The system is a Cx26 channel equilibrated in explicit membrane/solvent, shown by Brownian dynamics to reproduce key conductance characteristics of the native channel. The results are consistent with the known difference in permeability to each molecule. The energetic barriers extend through most of the pore length, rather than being highly localized as in ion-specific channels. There is little evidence for binding within the pore. Force decomposition reveals how, for each tested molecule, interactions with water and the Cx26 protein vary over the length of the pore and reveals a significant contribution from hydrogen bonding and interaction with K(+). The flexibility of the pore width varies along its length, and the tested molecules have differential effects on pore width as they pass through. Potential sites of interaction within the pore are defined for each molecule. The results suggest that for the tested molecules, differences in hydrogen bonding and entropic factors arising from permeant flexibility substantially contribute to the energetics of permeation. This work highlights factors involved in selective molecular permeation that differ from those that define selectivity among atomic ions. PMID:26840724

  3. Mt. Etna plumbing system revealed by combined textural, compositional, and thermobarometric studies in clinopyroxenes

    NASA Astrophysics Data System (ADS)

    Giacomoni, P. P.; Coltorti, M.; Bryce, J. G.; Fahnestock, M. F.; Guitreau, M.

    2016-04-01

    Coupled textural and in situ geochemical studies of clinopyroxene (cpx) phenocrysts, from both historical and recent eruptions of Mt. Etna volcano, provide a means to investigate the processes occurring in the deepest portion of the feeding system (>10 km depth). Five distinct textures were recognized: (1) normal oscillatory zoning, (2) normal zoning with Fe-rich rim, (3) sieve-textured core, (4) reverse oscillatory zoning, and (5) dusty rim. Electron microprobe analyses indicate an almost constant diopside-augite composition, with a slight enrichment in the enstatite for more recent erupted cpx. Core-to-rim compositional profiles, performed along the cpx, reveal distinct compositional characteristics. Normal oscillatory zoning is often characterized by a sharp increase in FeO (Δ ~ 2 wt%) accompanied by a drop in Al2O3 on the outermost 30 μm. Reverse oscillatory zoning, by contrast, exhibits a drop in FeO, Al2O3 (Δ ~ 2 wt%), and a remarkable crystal rim increase in MgO (up to 5 wt%). Similar compositional changes are evident in dusty-textured rims, which are characterized by dissolution edges and overgrowth containing glass pockets and channels. No significant compositional variations have been observed across crystals with sieve-textured cores. Trace element concentrations show enrichments in Sr, La, Zr, and REE, together with a decreasing La/Yb ratio (from ~7 to ~4) in rims of normally zoned crystals. Cpx with reverse zoning and dusty rims has low Sr, La, Zr, and REE contents toward crystal rims. Thermometers and barometers, based on equilibrium cpx-melt pairs, suggest that cpx cores start nucleating at 720 MPa, with the majority of them forming between 600 and 400 MPa but continuing to crystallize until very shallow depths (<100 MPa). Normal oscillatory-zoned phenocrysts surrounded by rims form at pressures shallower than 400 MPa, while reverse zoning and dusty rims occur between 400 and 500 MPa. Coupled petrologic and thermobarometric studies on both

  4. Transepithelial Na+ transport and the intracellular fluids: a computer study.

    PubMed

    Civan, M M; Bookman, R J

    1982-01-01

    Computer simulations of tight epithelia under three experimental conditions have been carried out, using the rheogenic nonlinear model of Lew, Ferreira and Moura (Proc. Roy. Soc. London. B 206:53-83, 1979) based largely on the formulation of Koefoed-Johnsen and Ussing (Acta Physiol. Scand. 42: 298-308. 1958). First, analysis of the transition between the short-circuited and open-circuited states has indicated that (i) apical Cl- permeability is a critical parameter requiring experimental definition in order to analyze cell volume regulation, and (ii) contrary to certain experimental reports, intracellular Na+ concentration (ccNa) is expected to be a strong function of transepithelial clamping voltage. Second, analysis of the effects of lowering serosal K+ concentration (csK) indicates that the basic model cannot simulate several well-documented observations; these defects can be overcome, at least qualitatively, by modifying the model to take account of the negative feedback interaction likely to exist between the apical Na+ permeability and ccNa. Third, analysis of the strongly supports the concept that osmotically induced permeability changes in the apical intercellular junctions play a physiological role in conserving the body's stores of NaCl. The analyses also demonstrate that the importance of Na+ entry across the basolateral membrane is strongly dependent upon transepithelial potential, cmNa and csK; under certain conditions, net Na+ entry could be appreciably greater across the basolateral than across the apical membrane.

  5. Serial computed tomography scanning in acute pancreatitis: a prospective study.

    PubMed Central

    London, N J; Neoptolemos, J P; Lavelle, J; Bailey, I; James, D

    1989-01-01

    One hundred and two patients with acute pancreatitis had abdominal computed tomography (CT) scans within 72 hours of admission, at one week and at six weeks. Twenty eight attacks were clinically severe, 74 clinically mild. Ninety three (91%) admission scans, 85 (84%) one week scans, and 52 (51%) six week scans were abnormal. The aetiology of the pancreatitis could be inferred from 28 (27%) of admission scans, the CT sign of fatty liver having a sensitivity of 21% and specificity of 100% for alcoholic aetiology. The sensitivity of CT for gall stone aetiology was 34%, specificity 100%. The pancreatic size indices (max anteroposterior measurement of head x max anteroposterior measurement of body) of those patients with severe attacks were significantly greater than those with mild attacks on admission, at one week and at six weeks (p less than 0.004). Fourteen pseudocysts were detected by CT, five (36%) of which were clinically apparent. The pseudocyst size indices (max anteroposterior x max transverse measurement) of the pseudocysts which were clinically apparent were significantly greater than those which were not apparent (p less than 0.01) and only those pseudocysts with a size index greater than or equal to 15 cm2 required treatment. PMID:2651228

  6. A Landing Gear Noise Reduction Study Based on Computational Simulations

    NASA Technical Reports Server (NTRS)

    Khorrami, Mehdi R.; Lockard, David P.

    2006-01-01

    Landing gear is one of the more prominent airframe noise sources. Techniques that diminish gear noise and suppress its radiation to the ground are highly desirable. Using a hybrid computational approach, this paper investigates the noise reduction potential of devices added to a simplified main landing gear model without small scale geometric details. The Ffowcs Williams and Hawkings equation is used to predict the noise at far-field observer locations from surface pressure data provided by unsteady CFD calculations. Because of the simplified nature of the model, most of the flow unsteadiness is restricted to low frequencies. The wheels, gear boxes, and oleo appear to be the primary sources of unsteadiness at these frequencies. The addition of fairings around the gear boxes and wheels, and the attachment of a splitter plate on the downstream side of the oleo significantly reduces the noise over a wide range of frequencies, but a dramatic increase in noise is observed at one frequency. The increased flow velocities, a consequence of the more streamlined bodies, appear to generate extra unsteadiness around other parts giving rise to the additional noise. Nonetheless, the calculations demonstrate the capability of the devices to improve overall landing gear noise.

  7. Computational studies of steering nanoparticles with magnetic gradients

    NASA Astrophysics Data System (ADS)

    Aylak, Sultan Suleyman

    Magnetic Resonance Imaging (MRI) guided nanorobotic systems that could perform diagnostic, curative, and reconstructive treatments in the human body at the cellular and subcellular level in a controllable manner have recently been proposed. The concept of a MRI-guided nanorobotic system is based on the use of a MRI scanner to induce the required external driving forces to guide magnetic nanocapsules to a specific target. However, the maximum magnetic gradient specifications of existing clinical MRI systems are not capable of driving magnetic nanocapsules against the blood flow. This thesis presents the visualization of nanoparticles inside blood vessel, Graphical User Interface (GUI) for updating file including initial parameters and demonstrating the simulation of particles and C++ code for computing magnetic forces and fluidic forces. The visualization and GUI were designed using Virtual Reality Modeling Language (VRML), MATLAB and C#. The addition of software for MRI-guided nanorobotic system provides simulation results. Preliminary simulation results demonstrate that external magnetic field causes aggregation of nanoparticles while they flow in the vessel. This is a promising result --in accordance with similar experimental results- and encourages further investigation on the nanoparticle-based self-assembly structures for use in nanorobotic drug delivery.

  8. Computational and experimental study of spin coater air flow

    NASA Astrophysics Data System (ADS)

    Zhu, Xiaoguang; Liang, Faqiu; Haji-Sheikh, A.; Ghariban, N.

    1998-06-01

    An extensive 2- and 3-D analysis of air flow in a POLARISTM 2200 Microlithography Cluster spin coater was conducted using FLUENTTM Computational Fluid Dynamics (CFD) software. To supplement this analysis, direct measurement of air flow velocity was also performed using a DantecTM Hot Wire Anemometer. Velocity measurements were made along two major planes across the entire flow field in the spin coater at various operating conditions. It was found that the flow velocity at the spin coater inlet is much lower than previously assumed and quite nonuniform. Based on this observation, a pressure boundary condition rather than a velocity boundary condition was used for subsequent CFD analysis. A comparison between calculated results and experimental data shows that the 3D model accurately predicts the air flow field in the spin coater. An added advantage of this approach is that the CFD model can be easily generated from the mechanical design database and used to analyze the effect of design changes. The modeled and measured results show that the flow pattern in the spin bowl is affected by interactions between the spinning wafer, exhaust flow, and the gap between the spin head and surrounding baffle. Different operating conditions such as spin speed, inlet pressure, and exhaust pressure were found to generate substantially different flow patterns. It was also found that backflow of air could be generated under certain conditions.

  9. Specificity in lipases: A computational study of transesterification of sucrose

    PubMed Central

    Fuentes, Gloria; Ballesteros, Anthonio; Verma, Chandra S.

    2004-01-01

    Computational conformational searches of putative transition states of the reaction of sucrose with vinyl laurate catalyzed by lipases from Candida antarctica B and Thermomyces lanuginosus have been carried out. The dielectric of the media have been varied to understand the role of protein plasticity in modulating the observed regioselective transesterification. The binding pocket of lipase from Candida adapts to the conformational variability of the various substates of the substrates by small, local adjustments within the binding pocket. In contrast, the more constrained pocket of the lipase from Thermomyces adapts by adjusting through concerted global motions between subdomains. This leads to the identification of one large pocket in Candida that accommodates both the sucrose and the lauroyl moieties of the transition state, whereas in Thermomyces the binding pocket is smaller, leading to the localization of the two moieties in two distinct pockets; this partly rationalizes the broader specificity of the former relative to the latter. Mutations have been suggested to exploit the differences towards changing the observed selectivities. PMID:15557256

  10. Genome-Wide Influence of Indel Substitutions on Evolution of Bacteria of the PVC Superphylum, Revealed Using a Novel Computational Method

    PubMed Central

    Kamneva, Olga K.; Liberles, David A.; Ward, Naomi L.

    2010-01-01

    Whole-genome scans for positive Darwinian selection are widely used to detect evolution of genome novelty. Most approaches are based on evaluation of nonsynonymous to synonymous substitution rate ratio across evolutionary lineages. These methods are sensitive to saturation of synonymous sites and thus cannot be used to study evolution of distantly related organisms. In contrast, indels occur less frequently than amino acid replacements, accumulate more slowly, and can be employed to characterize evolution of diverged organisms. As indels are also subject to the forces of natural selection, they can generate functional changes through positive selection. Here, we present a new computational approach to detect selective constraints on indel substitutions at the whole-genome level for distantly related organisms. Our method is based on ancestral sequence reconstruction, takes into account the varying susceptibility of different types of secondary structure to indels, and according to simulation studies is conservative. We applied this newly developed framework to characterize the evolution of organisms of the Planctomycetes, Verrucomicrobia, Chlamydiae (PVC) bacterial superphylum. The superphylum contains organisms with unique cell biology, physiology, and diverse lifestyles. It includes bacteria with simple cell organization and more complex eukaryote-like compartmentalization. Lifestyles range from free-living organisms to obligate pathogens. In this study, we conduct a whole-genome level analysis of indel substitutions specific to evolutionary lineages of the PVC superphylum and found that indels evolved under positive selection on up to 12% of gene tree branches. We also analyzed possible functional consequences for several case studies of predicted indel events. PMID:21048002

  11. Characteristics of the interaction of azulene with water and hydrogen sulfide: A computational study.

    PubMed

    Cabaleiro-Lago, Enrique M; Rodríguez-Otero, Jesús; Peña-Gallego, Angeles

    2008-08-28

    A computational study was carried out for studying the characteristics of the interaction between azulene and water or hydrogen sulfide. In azulene...water complex the water molecule is located with both hydrogen atoms pointing toward the aromatic cloud but displaced to the five-membered ring. Hydrogen sulfide adopts a similar arrangement but located roughly over the central C-C bond of azulene. Calculations show that hydrogen sulfide interacts with azulene more strongly (-4.19 kcal/mol) than water (-3.76 kcal/mol), although this is only revealed at the highest levels of calculation. The nature of the interaction is electrostatic and dispersive in the same percentage for water cluster, whereas for hydrogen sulfide dispersion is the dominant contribution. Clusters containing two water molecules are controlled by the possibility of establishing an O-H...O hydrogen bond. As a consequence, the most stable structure corresponds to the interaction between a water dimer and azulene, with an interaction energy amounting to -11.77 kcal/mol. Hydrogen sulfide interaction is stronger with azulene than with itself, so structures with S-H...S contact and others, where H(2)S only interacts with azulene, present similar interaction energies (-8.02 kcal/mol for the most stable one).

  12. Demonstrating the synergy of synthetic, mechanistic, and computational studies in a regioselective aniline synthesis.

    PubMed

    Davies, Ian W; Marcoux, Jean-François; Kuethe, Jeffery T; Lankshear, Michael D; Taylor, Jeremy D O; Tsou, Nancy; Dormer, Peter G; Hughes, David L; Houk, K N; Guner, Vildan

    2004-02-20

    Tri- and tetrasubstituted anilines are formed in good to excellent yields by the addition of ketones to vinamidinium salts (up to 98%). The reaction proceeds via the formation of dienone intermediates, which react to form an enamine with the liberated amine. In the case of a nitro, or dimethylaminomethylene substituent, the enamines undergo a facile electrocyclic ring closure to form a cyclohexadiene, which goes on to form anilines with a high degree of selectivity (up to 50:1) with a minor competing pathway proceeding via the enol providing phenols. Competition experiments using isotopic substitution reveal that the rate determining step en route to dienone is enol/enolate addition to the vinamidinium salt, which is characterized by an inverse secondary isotope effect (k(H/D) 0.7-0.9). Computational studies have been used to provide a framework for understanding the reaction pathway. The original proposal for a [1,5]-H shift was ruled out on the basis of the calculations, which did not locate a thermally accessible transition state. The minimum energy conformation of the enamine is such that a facile electrocyclic ring closure is ensured, which is corroborated by the experimental studies. A framework for understanding the reaction pathway is presented. PMID:14961684

  13. Synthesis, photophysical, photochemical, and computational studies of coumarin-labeled nicotinamide derivatives.

    PubMed

    Bourbon, Pauline; Peng, Qian; Ferraudi, Guillermo; Stauffacher, Cynthia; Wiest, Olaf; Helquist, Paul

    2012-03-16

    The syntheses and photophysical/photochemical properties of two amide-tethered coumarin-labeled nicotinamides are described. Photochemical studies of 6-bromo-7-hydroxycoumarin-4-ylmethylnicotinamide (BHC-nicotinamide) revealed an unexpected solvent effect. This result is rationalized by computational studies of the different protonation states using TD-DFT with the M06L/6-311+G** method with implicit and explicit solvation models. Molecular orbital energies responsible for the λ(max) excitation show that the functionalization of the coumarin ring results in a strong red-shift from 330 to 370 nm when the pH of solution is increased from 3.06 to 8.07. From this MO analysis, a model for solvent interactions has been proposed. The BHC-nicotinamide proved to be photochemically stable, which is also interpreted in terms of NBO calculations. The results provide a set of principles for the rational design of either photostable labeling reagents or photolabile cage compounds.

  14. Computational Study and Analysis of Structural Imperfections in 1D and 2D Photonic Crystals

    SciTech Connect

    Maskaly, Karlene Rosera

    2005-06-01

    increasing RMS roughness. Again, the homogenization approximation is able to predict these results. The problem of surface scratches on 1D photonic crystals is also addressed. Although the reflectivity decreases are lower in this study, up to a 15% change in reflectivity is observed in certain scratched photonic crystal structures. However, this reflectivity change can be significantly decreased by adding a low index protective coating to the surface of the photonic crystal. Again, application of homogenization theory to these structures confirms its predictive power for this type of imperfection as well. Additionally, the problem of a circular pores in 2D photonic crystals is investigated, showing that almost a 50% change in reflectivity can occur for some structures. Furthermore, this study reveals trends that are consistent with the 1D simulations: parameter changes that increase the absolute reflectivity of the photonic crystal will also increase its tolerance to structural imperfections. Finally, experimental reflectance spectra from roughened 1D photonic crystals are compared to the results predicted computationally in this thesis. Both the computed and experimental spectra correlate favorably, validating the findings presented herein.

  15. Comparative micro computed tomography study of a vertebral body

    NASA Astrophysics Data System (ADS)

    Drews, Susanne; Beckmann, Felix; Herzen, Julia; Brunke, Oliver; Salmon, Phil; Friess, Sebastian; Laib, Andres; Koller, Bruno; Hemberger, Thomas; Müller-Gerbl, Magdalena; Müller, Bert

    2008-08-01

    Investigations of bony tissues are often performed using micro computed tomography based on X-rays, since the calcium distribution leads to superior contrast. Osteoporotic bone, for example, can be well compared with healthy one with respect to density and morphology. Degenerative and rheumatoid diseases usually start, however, at the bone-cartilage-interface, which is hardly accessible. The direct influence on the bone itself becomes only visible at later stage. For the development of suitable therapies against degenerative cartilage damages the exact three-dimensional description of the bone-cartilage interface is vital, as demonstrated for transplanted cartilage-cells or bone-cartilage-constructs in animal models. So far, the morphological characterization was restricted to magnetic resonance imaging (MRI) with poor spatial resolution or to time-consuming histological sectioning with appropriate spatial resolution only in two rather arbitrarily chosen directions. Therefore, one should develop μCT to extract the features of low absorbing cartilage. The morphology and the volume of the inter-vertebral cartilage disc of lumbar motion segments have been determined for one PMMA embedded specimen. Tomograms were recorded using nanotom® (Phoenix|x-ray, Wunstorf, Germany), μCT 35TM (Scanco Medical, Brütisellen, Switzerland), 1172TM and 1174TM (both Skyscan, Kontich, Belgium), as well as using the SRμCT at HASYLAB/DESY. Conventional and SRμCT can provide the morphology and the volume of cartilage between bones. Increasing the acquisition time, the signal-to-noise ratio becomes better and better but the prominent artifacts in conventional μCT as the result of inhomogeneously distributed bony tissue prevents the exact segmentation of cartilage. SRμCT allows segmenting the cartilage but requires long periods of expensive beam-time to obtain reasonable contrast.

  16. Studies in computational geometry motivated by mesh generation

    SciTech Connect

    Smith, W.D.

    1989-01-01

    This thesis sprawls over most of discrete and computational geometry. There are four loose bodies of theory developed. (1) A quantitative and algorithmic theory of crossing number and crossing-free line segment graphs in the plane. As five applications of this theory: the author disproves two long - standing conjectures on the crossing number of the complete and complete bipartite graphs, he presents the first exponential algorithm for planar minimum Steiner tree, and the first subexponential algorithms for planar traveling salesman tour and optimum triangulation, and he presents an algorithm for generating all non-isomorphic V-vertex planar graphs, in O(V{sup 3)}time per graph, using O(V) total workspace. (2) Mesh generation, and the triangulation of polytopes: He has the strongest bounds on the number of d-simplices required to triangulate the d-cube, and new triangulation methods in the plane. A quantitative and qualitative - and practical - theory of finite element mesh quality suggest a new, simple strategy for generating good meshes. (3) The theory of geometrical graphs on N point sites in d-space. This subsumes many new results in: geometrical probability, sphere packing, and extremal configurations. An array of new multidimensional search date structures are used to devise fast algorithms for construction many geometrical graphs. (4) Useful new results concerning the mensuration and structure of d-polytopes. In particular he extensively generalizes the famous formula of Heron and Alexandria (75 AD), for the area of a triangle, and he presents the first linear time congruence algorithm for 3 -dimensional polyhedra. He closes with the largest bibliography of the field, containing over 3000 references.

  17. Small-scale studies of roasted ore waste reveal extreme ranges of stable mercury isotope signatures

    NASA Astrophysics Data System (ADS)

    Smith, Robin S.; Wiederhold, Jan G.; Jew, Adam D.; Brown, Gordon E.; Bourdon, Bernard; Kretzschmar, Ruben

    2014-07-01

    Active and closed Hg mines are significant sources of Hg contamination to the environment, mainly due to large volumes of mine waste material disposed of on-site. The application of Hg isotopes as source tracer from such contaminated sites requires knowledge of the Hg isotope signatures of different materials potentially released to the environment. Previous work has shown that calcine, the waste residue of the on-site ore roasting process, can exhibit distinct Hg isotope signatures compared with the primary ore. Here, we report results from a detailed small-scale study of Hg isotope variations in calcine collected from the closed New Idria Hg mine, San Benito County, CA, USA. The calcine samples exhibited different internal layering features which were investigated using optical microscopy, micro X-ray fluorescence, micro X-ray absorption spectroscopy (μ-XAS), and stable Hg isotope analysis. Significant Fe, S, and Hg concentration gradients were found across the different internal layers. Isotopic analyses revealed an extreme variation with pronounced isotopic gradients across the internal layered features. Overall, δ202Hg (±0.10‰, 2 SD) describing mass-dependent fractionation (MDF) ranged from -5.96 to 14.49‰, which is by far the largest range of δ202Hg values reported for any environmental sample. In addition, Δ199Hg (±0.06‰, 2 SD) describing mass-independent fractionation (MIF) ranged from -0.17 to 0.21‰. The μ-XAS analyses suggested that cinnabar and metacinnabar are the dominant Hg-bearing phases in the calcine. Our results demonstrate that the incomplete roasting of HgS ores in Hg mines can cause extreme mass-dependent Hg isotope fractionations at the scale of individual calcine pieces with enrichments in both light and heavy Hg isotopes relative to the primary ore signatures. This finding has important implications for the application of Hg isotopes as potential source tracers for Hg released to the environment from closed Hg mines and

  18. Detailed computational analysis revealed mutation V210I on PrP induced conformational conversion on β2-α2 loop and α2-α3.

    PubMed

    Chandrasekaran, P; Rajasekaran, R

    2016-10-20

    The development of fatal transmissible spongiform encephalopathies (TSE) is associated with the conformational conversion of the normal cellular prion protein, PrP(C), into its pathogenic isoform, PrP(Sc). The present study revealed the structural consequences that induce the conversion of PrP(C)→ PrP(Sc) upon mutation V210I linked with genetic Creutzfeldt-Jakob disease (CJD) using the classical molecular dynamics (MD) approach. Similar to the experimental results, the mutant showed biased disruption in the local folding of α2 and the complete distortion of α3. In addition, substitution of bulkier Ile at position 210 induced reorientations of several residues that were the constituent of hydrophobic cores, thereby influencing α2-α3 inter-helical interactions. In addition, the β2-α2 loop was greatly altered due to the loss of π-π interactions of the residue Tyr(169) with Phe(175), Tye(163), Tyr(162), and Tyr(218), facilitating more conformational flexibility, which may be involved in the conversion of PrP(C)→ PrP(Sc). This study afforded a detailed structure and dynamic properties of the mutant, which were consistent with the experimental results, providing an insight into the molecular basis for the conversion of PrP(C)→ PrP(Sc), which could be used for the development of antiprion drugs. PMID:27523988

  19. Hemodynamic study of the elliptic St. Jude Medical valve: A computational study.

    PubMed

    Jahandardoost, Mehdi; Fradet, Guy; Mohammadi, Hadi

    2016-02-01

    Despite successful implantation of St. Jude Medical bileaflet mechanical heart valves, red blood cell lysis and thrombogenic complications associated with these types of valves are yet to be addressed. In our previous study, we proposed an elliptic housing where 10% ovality was applied to the housing of St. Jude Medical valves. Our preliminary results suggested that the overall hemodynamic performance of St. Jude Medical valves improved in both the closing and opening phases. In this study, we evaluated the hemodynamics around the leaflets in the opening phase using a more sophisticated computational platform, computational fluid dynamics. Results suggested both lower shear stress and wall shear stress values and an overall improved hemodynamic performance in the proposed design. This improvement is characterized by lower values of shear stress and wall shear stress in the regions downstream of the leaflets, lower pressure drop across the valve and smaller recirculation zones in the sinuses areas. The proposed design may open a new chapter in the concept of design and hemodynamic improvement of the next generation of mechanical heart valves. PMID:26783246

  20. The Impact of Learner's Prior Knowledge on Their Use of Chemistry Computer Simulations: A Case Study

    NASA Astrophysics Data System (ADS)

    Liu, Han-Chin; Andre, Thomas; Greenbowe, Thomas

    2008-10-01

    It is complicated to design a computer simulation that adapts to students with different characteristics. This study documented cases that show how college students' prior chemistry knowledge level affected their interaction with peers and their approach to solving problems with the use of computer simulations that were designed to learn electrochemistry. Students with different prior knowledge levels were found to use different approaches to solving problems with the use of computer simulations. In particular, the cases showed that students with a high level of prior knowledge tended to use the equations and formulas to accomplish the learning tasks and then use the computer simulations to confirm their predictions. Students with a low level of prior chemistry knowledge used the computer simulations as the main resources to accomplish their tasks. Considerations of individual differences and the integration of learning materials were suggested for further research on instructional use of computer simulations.