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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. PMID:26682934

  2. Computational studies reveal phosphorylation-dependent changes in the unstructured R domain of CFTR.

    PubMed

    Hegedus, Tamás; Serohijos, Adrian W R; Dokholyan, Nikolay V; He, Lihua; Riordan, John R

    2008-05-16

    The cystic fibrosis transmembrane conductance regulator (CFTR) is a cAMP-dependent chloride channel that is mutated in cystic fibrosis, an inherited disease of high morbidity and mortality. The phosphorylation of its approximately 200 amino acid R domain by protein kinase A is obligatory for channel gating under normal conditions. The R domain contains more than ten PKA phosphorylation sites. No individual site is essential but phosphorylation of increasing numbers of sites enables progressively greater channel activity. In spite of numerous studies of the role of the R domain in CFTR regulation, its mechanism of action remains largely unknown. This is because neither its structure nor its interactions with other parts of CFTR have been completely elucidated. Studies have shown that the R domain lacks well-defined secondary structural elements and is an intrinsically disordered region of the channel protein. Here, we have analyzed the disorder pattern and employed computational methods to explore low-energy conformations of the R domain. The specific disorder and secondary structure patterns detected suggest the presence of molecular recognition elements (MoREs) that may mediate phosphorylation-regulated intra- and inter-domain interactions. Simulations were performed to generate an ensemble of accessible R domain conformations. Although the calculated structures may represent more compact conformers than occur in vivo, their secondary structure propensities are consistent with predictions and published experimental data. Equilibrium simulations of a mimic of a phosphorylated R domain showed that it exhibited an increased radius of gyration. In one possible interpretation of these findings, by changing its size, the globally unstructured R domain may act as an entropic spring to perturb the packing of membrane-spanning sequences that constitute the ion permeability pathway and thereby activate channel gating. PMID:18423665

  3. Computational studies reveal phosphorylation dependent changes in the unstructured R domain of CFTR

    PubMed Central

    Hegedűs, Tamás; Serohijos, Adrian W.R.; Dokholyan, Nikolay V.; He, Lihua; Riordan, John R.

    2008-01-01

    The Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) is a cAMP dependent chloride channel that is mutated in cystic fibrosis, an inherited disease of high morbidity and mortality. The phosphorylation of its ∼200 amino acid R domain by protein kinase A is obligatory for channel gating under normal conditions. The R domain contains more than ten PKA phosphorylation sites. No individual site is essential but phosphorylation of increasing numbers of sites enables progressively greater channel activity. In spite of numerous studies of the role of the R domain in CFTR regulation, its mechanism of action remains largely unknown. This is because neither its structure nor its interactions with other parts of CFTR have been completely elucidated. Studies have shown that the R domain lacks well-defined secondary structural elements and is an intrinsically disordered region of the channel protein. Here, we have analyzed the disorder pattern and employed computational methods to explore low energy conformations of the R domain. Specific disorder and secondary structure patterns detected suggest the presence of Molecular Recognition Elements (MoREs) that may mediate phosphorylation regulated intra- and inter-domain interactions. Simulations were performed to generate an ensemble of accessible R domain conformations. Although the calculated structures may represent more compact conformers than occur in vivo, their secondary structure propensities are consistent with predictions and published experimental data. Equilibrium simulations of a mimic of a phosphorylated R domain showed that it exhibited an increased radius of gyration. In one possible interpretation of these findings, by changing its size, the globally unstructured R domain may act as an entropic spring to perturb the packing of membrane-spanning sequences that constitute the ion permeability pathway and thereby activate channel gating. PMID:18423665

  4. Experimental and Computational Studies Reveal An Alternative Supramolecular Structure for Fmocdipeptide Self-assembly

    PubMed Central

    Mu, Xiaojia; Eckes, Kevin M.; Nguyen, Mary M.; Suggs, Laura J.; Ren, Pengyu

    2012-01-01

    We have investigated the self-assembly of fluorenylmethoxycarbonyl-conjugated dialanine (Fmoc-AA) molecules using combined computational and experimental approaches. Fmoc-AA gels were characterized using TEM, circular dichroism, FTIR, and WAXS. Computationally, we simulated the assembly of Fmoc-AA using molecular dynamics techniques. All simulations converged to a condensed fibril structure in which the Fmoc groups stack mostly within in the center of the fibril. However, the Fmoc groups are partially exposed to water, creating an amphiphilic surface, which may be responsible for aggregation of fibrils into nano-scale fibers observed in TEM. From the fibril models, radial distribution calculations agree with d-spacings observed in WAXS for the fibril diameter and π-stacking interactions. Our analyses show that dialanine, despite its short length, adopts a mainly extended polyproline II conformation. In contrast to previous hypotheses, these results indicate that β-sheet-like hydrogen bonding is not prevalent. Rather, stacking of Fmoc groups, inter-residue hydrogen bonding and hydrogen bonding with water play the important roles in stabilizing the fibril structure of supramolecular assemblies of short conjugated peptides. PMID:23020140

  5. Integration of computational modeling with membrane transport studies reveals new insights into amino acid exchange transport mechanisms

    PubMed Central

    Widdows, Kate L.; Panitchob, Nuttanont; Crocker, Ian P.; Please, Colin P.; Hanson, Mark A.; Sibley, Colin P.; Johnstone, Edward D.; Sengers, Bram G.; Lewis, Rohan M.; Glazier, Jocelyn D.

    2015-01-01

    Uptake of system L amino acid substrates into isolated placental plasma membrane vesicles in the absence of opposing side amino acid (zero-trans uptake) is incompatible with the concept of obligatory exchange, where influx of amino acid is coupled to efflux. We therefore hypothesized that system L amino acid exchange transporters are not fully obligatory and/or that amino acids are initially present inside the vesicles. To address this, we combined computational modeling with vesicle transport assays and transporter localization studies to investigate the mechanisms mediating [14C]l-serine (a system L substrate) transport into human placental microvillous plasma membrane (MVM) vesicles. The carrier model provided a quantitative framework to test the 2 hypotheses that l-serine transport occurs by either obligate exchange or nonobligate exchange coupled with facilitated transport (mixed transport model). The computational model could only account for experimental [14C]l-serine uptake data when the transporter was not exclusively in exchange mode, best described by the mixed transport model. MVM vesicle isolates contained endogenous amino acids allowing for potential contribution to zero-trans uptake. Both L-type amino acid transporter (LAT)1 and LAT2 subtypes of system L were distributed to MVM, with l-serine transport attributed to LAT2. These findings suggest that exchange transporters do not function exclusively as obligate exchangers.—Widdows, K. L., Panitchob, N., Crocker, I. P., Please, C. P., Hanson, M. A., Sibley, C. P., Johnstone, E. D., Sengers, B. G., Lewis, R. M., Glazier, J. D. Integration of computational modeling with membrane transport studies reveals new insights into amino acid exchange transport mechanisms. PMID:25761365

  6. Structural and Computational Studies of the Staphylococcus aureus Sortase B-Substrate Complex Reveal a Substrate-stabilized Oxyanion Hole*

    PubMed Central

    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.

    2014-01-01

    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 Glu224 and the side chain of Arg233 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. PMID:24519933

  7. Structural determinants of species-selective substrate recognition in human and Drosophila serotonin transporters revealed through computational docking studies.

    PubMed

    Kaufmann, Kristian W; Dawson, Eric S; Henry, L Keith; Field, Julie R; Blakely, Randy D; Meiler, Jens

    2009-02-15

    To identify potential determinants of substrate selectivity in serotonin (5-HT) transporters (SERT), models of human and Drosophila serotonin transporters (hSERT, dSERT) were built based on the leucine transporter (LeuT(Aa)) structure reported by Yamashita et al. (Nature 2005;437:215-223), PBDID 2A65. Although the overall amino acid identity between SERTs and the LeuT(Aa) is only 17%, it increases to above 50% in the first shell of the putative 5-HT binding site, allowing de novo computational docking of tryptamine derivatives in atomic detail. Comparison of hSERT and dSERT complexed with substrates pinpoints likely structural determinants for substrate binding. Forgoing the use of experimental transport and binding data of tryptamine derivatives for construction of these models enables us to critically assess and validate their predictive power: A single 5-HT binding mode was identified that retains the amine placement observed in the LeuT(Aa) structure, matches site-directed mutagenesis and substituted cysteine accessibility method (SCAM) data, complies with support vector machine derived relations activity relations, and predicts computational binding energies for 5-HT analogs with a significant correlation coefficient (R = 0.72). This binding mode places 5-HT deep in the binding pocket of the SERT with the 5-position near residue hSERT A169/dSERT D164 in transmembrane helix 3, the indole nitrogen next to residue Y176/Y171, and the ethylamine tail under residues F335/F327 and S336/S328 within 4 A of residue D98. Our studies identify a number of potential contacts whose contribution to substrate binding and transport was previously unsuspected. PMID:18704946

  8. Structural determinants of species-selective substrate recognition in human and Drosophila serotonin transporters revealed through computational docking studies

    PubMed Central

    Kaufmann, Kristian W.; Dawson, Eric S.; Henry, L. Keith; Field, Julie R.; Blakely, Randy D.; Meiler, Jens

    2009-01-01

    To identify potential determinants of substrate selectivity in serotonin (5-HT) transporters (SERT), models of human and Drosophila serotonin transporters (hSERT, dSERT) were built based on the leucine transporter (LeuTAa) structure reported by Yamashita et al. (Nature 2005;437:215–223), PBDID 2A65. Although the overall amino acid identity between SERTs and the LeuTAa is only 17%, it increases to above 50% in the first shell of the putative 5-HT binding site, allowing de novo computational docking of tryptamine derivatives in atomic detail. Comparison of hSERT and dSERT complexed with substrates pinpoints likely structural determinants for substrate binding. Forgoing the use of experimental transport and binding data of tryptamine derivatives for construction of these models enables us to cHitically assess and validate their predictive power: A single 5-HT binding mode was identified that retains the amine placement observed in the LeuTAa structure, matches site-directed mutagenesis and substituted cysteine accessibility method (SCAM) data, complies with support vector machine derived relations activity relations, and predicts computational binding energies for 5-HT analogs with a significant correlation coefficient (R = 0.72). This binding mode places 5-HT deep in the binding pocket of the SERT with the 5-position near residue hSERT A169/dSERT D164 in transmembrane helix 3, the indole nitrogen next to residue Y176/Y171, and the ethylamine tail under residues F335/F327 and S336/S328 within 4 Å of residue D98. Our studies identify a number of potential contacts whose contribution to substrate binding and transport was previously unsuspected. PMID:18704946

  9. Revealing the structure-property relationship of covalent organic frameworks for CO₂ capture from postcombustion gas: a multi-scale computational study.

    PubMed

    Tong, Minman; Yang, Qingyuan; Xiao, Yuanlong; Zhong, Chongli

    2014-08-01

    With the aid of multi-scale computational methods, a diverse set of 46 covalent organic frameworks (COFs), covering the most typical COFs synthesized to date, were collected to study the structure-property relationship of COFs for CO2 capture. For this purpose, CO2 capture from postcombustion gas (CO2-N2 mixture) under industrial vacuum swing adsorption (VSA) conditions was considered as an example. This work shows that adsorption selectivity, CO2 working capacity and the sorbent selection parameter of COFs all exhibit strong correlation with the difference in the adsorbility of adsorbates (ΔAD), highlighting that realization of large ΔAD can be regarded as an important starting point for designing COFs with improved separation performance. Furthermore, it was revealed that the separation performance of 2D-layered COFs can be greatly enhanced by generating "splint effects", which can be achieved through structural realignment to form slit-like pores with suitable size in the structures. Such "splint effects" in 2D-COFs can find their similar counterpart of "catenation effects" in 3D-COFs or MOFs. On the basis of these observations, a new design strategy was proposed to strengthen the separation performance of COFs. It could be expected that the information obtained in this work not only will enrich the knowledge of the structure-property relationship of COFs for separation, but also will largely facilitate their future applications to the fields related to energy and environmental science, such as natural gas purification, CO2, NO(x) and SO(x) capture, etc. PMID:24936781

  10. Computational Assembly of Polymorphic Amyloid Fibrils Reveals Stable Aggregates

    PubMed Central

    Smaoui, Mohamed Raef; Poitevin, Frédéric; Delarue, Marc; Koehl, Patrice; Orland, Henri; Waldispühl, Jérôme

    2013-01-01

    Amyloid proteins aggregate into polymorphic fibrils that damage tissues of the brain, nerves, and heart. Experimental and computational studies have examined the structural basis and the nucleation of short fibrils, but the ability to predict and precisely quantify the stability of larger aggregates has remained elusive. We established a complete classification of fibril shapes and developed a tool called CreateFibril to build such complex, polymorphic, modular structures automatically. We applied stability landscapes, a technique we developed to reveal reliable fibril structural parameters, to assess fibril stability. CreateFibril constructed HET-s, Aβ, and amylin fibrils up to 17 nm in length, and utilized a novel dipolar solvent model that captured the effect of dipole-dipole interactions between water and very large molecular systems to assess their aqueous stability. Our results validate experimental data for HET-s and Aβ, and suggest novel (to our knowledge) findings for amylin. In particular, we predicted the correct structural parameters (rotation angles, packing distances, hydrogen bond lengths, and helical pitches) for the one and three predominant HET-s protofilaments. We reveal and structurally characterize all known Aβ polymorphic fibrils, including structures recently classified as wrapped fibrils. Finally, we elucidate the predominant amylin fibrils and assert that native amylin is more stable than its amyloid form. CreateFibril and a database of all stable polymorphic fibril models we tested, along with their structural energy landscapes, are available at http://amyloid.cs.mcgill.ca. PMID:23442919

  11. 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…

  12. 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

  13. Melanoma Cell Colony Expansion Parameters Revealed by Approximate Bayesian Computation

    PubMed Central

    Vo, Brenda N.; Drovandi, Christopher C.; Pettitt, Anthony N.; Pettet, Graeme J.

    2015-01-01

    In vitro studies and mathematical models are now being widely used to study the underlying mechanisms driving the expansion of cell colonies. This can improve our understanding of cancer formation and progression. Although much progress has been made in terms of developing and analysing mathematical models, far less progress has been made in terms of understanding how to estimate model parameters using experimental in vitro image-based data. To address this issue, a new approximate Bayesian computation (ABC) algorithm is proposed to estimate key parameters governing the expansion of melanoma cell (MM127) colonies, including cell diffusivity, D, cell proliferation rate, λ, and cell-to-cell adhesion, q, in two experimental scenarios, namely with and without a chemical treatment to suppress cell proliferation. Even when little prior biological knowledge about the parameters is assumed, all parameters are precisely inferred with a small posterior coefficient of variation, approximately 2–12%. The ABC analyses reveal that the posterior distributions of D and q depend on the experimental elapsed time, whereas the posterior distribution of λ does not. The posterior mean values of D and q are in the ranges 226–268 µm2h−1, 311–351 µm2h−1 and 0.23–0.39, 0.32–0.61 for the experimental periods of 0–24 h and 24–48 h, respectively. Furthermore, we found that the posterior distribution of q also depends on the initial cell density, whereas the posterior distributions of D and λ do not. The ABC approach also enables information from the two experiments to be combined, resulting in greater precision for all estimates of D and λ. PMID:26642072

  14. Melanoma Cell Colony Expansion Parameters Revealed by Approximate Bayesian Computation.

    PubMed

    Vo, Brenda N; Drovandi, Christopher C; Pettitt, Anthony N; Pettet, Graeme J

    2015-12-01

    In vitro studies and mathematical models are now being widely used to study the underlying mechanisms driving the expansion of cell colonies. This can improve our understanding of cancer formation and progression. Although much progress has been made in terms of developing and analysing mathematical models, far less progress has been made in terms of understanding how to estimate model parameters using experimental in vitro image-based data. To address this issue, a new approximate Bayesian computation (ABC) algorithm is proposed to estimate key parameters governing the expansion of melanoma cell (MM127) colonies, including cell diffusivity, D, cell proliferation rate, λ, and cell-to-cell adhesion, q, in two experimental scenarios, namely with and without a chemical treatment to suppress cell proliferation. Even when little prior biological knowledge about the parameters is assumed, all parameters are precisely inferred with a small posterior coefficient of variation, approximately 2-12%. The ABC analyses reveal that the posterior distributions of D and q depend on the experimental elapsed time, whereas the posterior distribution of λ does not. The posterior mean values of D and q are in the ranges 226-268 µm2h-1, 311-351 µm2h-1 and 0.23-0.39, 0.32-0.61 for the experimental periods of 0-24 h and 24-48 h, respectively. Furthermore, we found that the posterior distribution of q also depends on the initial cell density, whereas the posterior distributions of D and λ do not. The ABC approach also enables information from the two experiments to be combined, resulting in greater precision for all estimates of D and λ. PMID:26642072

  15. 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

  16. 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. PMID:24712982

  17. Instructional Computing: Ten Case Studies.

    ERIC Educational Resources Information Center

    Hargan, Carol; Hunter, Beverly

    These case studies are written for educational institutions that wish to plan, extend, or improve their use of computers for learning and teaching. Each case study includes a brief description of each of the following: profile of the institution, history of the development of instructional computing, organization and management, student access to…

  18. 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.

  19. 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

  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. A Qualitative Study of Computers and Printouts in the Classroom.

    ERIC Educational Resources Information Center

    Eastman, Susan Tyler

    1986-01-01

    This study of microcomputer use to access an online encyclopedia revealed attitudes of eighth-graders towards computer technology and videotex. Electronic searching is compared to searching with traditional library print materials for a science course, the role of computer printouts is discussed, and research methods including observation and…

  5. A Study in Computer Abuse.

    ERIC Educational Resources Information Center

    Caulfield Inst. of Technology (Australia).

    Computer abuse is examined as both a general issue and as a specific problem. A statistical profile of computer crime lists distribution by country of reported cases, by industry of occurrence, and by amount of monetary loss. The characteristics of computer abuse are described along with the important categories of such crimes. Factors inhibiting…

  6. 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

  7. Computing in the Social Studies Classroom.

    ERIC Educational Resources Information Center

    Glenn, Allen; Rawitsch, Don

    This manual for social studies teachers examines the current status of computer use in social studies classrooms, suggests reasons to use the computer, and discusses five ways computers can be used in social studies; i.e., as a method of delivering content, as a tool for retrieving and analyzing information, as an example of technology use in…

  8. Computational analysis reveals increased blood deposition following repeated mild traumatic brain injury☆

    PubMed Central

    Donovan, Virginia; Bianchi, Anthony; Hartman, Richard; Bhanu, Bir; Carson, Monica J.; Obenaus, Andre

    2012-01-01

    Mild traumatic brain injury (mTBI) has become an increasing public health concern as subsequent injuries can exacerbate existing neuropathology and result in neurological deficits. This study investigated the temporal development of cortical lesions using magnetic resonance imaging (MRI) to assess two mTBIs delivered to opposite cortical hemispheres. The controlled cortical impact model was used to produce an initial mTBI on the right cortex followed by a second injury induced on the left cortex at 3 (rmTBI 3d) or 7 (rmTBI 7d) days later. Histogram analysis was combined with a novel semi-automated computational approach to perform a voxel-wise examination of extravascular blood and edema volumes within the lesion. Examination of lesion volume 1d post last injury revealed increased tissue abnormalities within rmTBI 7d animals compared to other groups, particularly at the site of the second impact. Histogram analysis of lesion T2 values suggested increased edematous tissue within the rmTBI 3d group and elevated blood deposition in the rm TBI 7d animals. Further quantification of lesion composition for blood and edema containing voxels supported our histogram findings, with increased edema at the site of second impact in rmTBI 3d animals and elevated blood deposition in the rmTBI 7d group at the site of the first injury. Histological measurements revealed spatial overlap of regions containing blood deposition and microglial activation within the cortices of all animals. In conclusion, our findings suggest that there is a window of tissue vulnerability where a second distant mTBI, induced 7d after an initial injury, exacerbates tissue abnormalities consistent with hemorrhagic progression. PMID:24179733

  9. Computer-Assisted International Studies.

    ERIC Educational Resources Information Center

    Wilkenfeld, Jonathan

    1983-01-01

    Describes an interdisciplinary college level program which uses computer simulation exercises to teach about foreign policy and global issues. In the foreign policy simulation, political science and foreign language students role play national decision makers. In the international futures simulation, students debate demographic, economic, energy,…

  10. Computer Usage and Reading in Elementary Schools: A Cross-Cultural Study

    ERIC Educational Resources Information Center

    Lai, Shu-Ling; Chang, Tai-Shent; Ye, Renmin

    2006-01-01

    This study uses international data to investigate computer use situations in elementary school reading classes and the impacts of computer usage on students' reading performance across 15 countries. The study compares and reveals computer use levels in reading classes, frequencies of teachers having students use computers, times and places of…

  11. 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.

  12. Reveal genes functionally associated with ACADS by a network study.

    PubMed

    Chen, Yulong; Su, Zhiguang

    2015-09-15

    Establishing a systematic network is aimed at finding essential human gene-gene/gene-disease pathway by means of network inter-connecting patterns and functional annotation analysis. In the present study, we have analyzed functional gene interactions of short-chain acyl-coenzyme A dehydrogenase gene (ACADS). ACADS plays a vital role in free fatty acid β-oxidation and regulates energy homeostasis. Modules of highly inter-connected genes in disease-specific ACADS network are derived by integrating gene function and protein interaction data. Among the 8 genes in ACADS web retrieved from both STRING and GeneMANIA, ACADS is effectively conjoined with 4 genes including HAHDA, HADHB, ECHS1 and ACAT1. The functional analysis is done via ontological briefing and candidate disease identification. We observed that the highly efficient-interlinked genes connected with ACADS are HAHDA, HADHB, ECHS1 and ACAT1. Interestingly, the ontological aspect of genes in the ACADS network reveals that ACADS, HAHDA and HADHB play equally vital roles in fatty acid metabolism. The gene ACAT1 together with ACADS indulges in ketone metabolism. Our computational gene web analysis also predicts potential candidate disease recognition, thus indicating the involvement of ACADS, HAHDA, HADHB, ECHS1 and ACAT1 not only with lipid metabolism but also with infant death syndrome, skeletal myopathy, acute hepatic encephalopathy, Reye-like syndrome, episodic ketosis, and metabolic acidosis. The current study presents a comprehensible layout of ACADS network, its functional strategies and candidate disease approach associated with ACADS network. PMID:26045367

  13. Developing Computer Literate Social Studies Teachers.

    ERIC Educational Resources Information Center

    Martorella, Peter H.

    Six dimensions of computer literacy for social studies educators to address are discussed. In preparing social studies teachers for the 21st century, educators need to determine which aspects of computer literacy are essential to incorporate into teacher education. First, teachers must have knowledge of the basic sources of information, such as…

  14. Pacific Educational Computer Network Study. Final Report.

    ERIC Educational Resources Information Center

    Hawaii Univ., Honolulu. ALOHA System.

    The Pacific Educational Computer Network Feasibility Study examined technical and non-technical aspects of the formation of an international Pacific Area computer network for higher education. The technical study covered the assessment of the feasibility of a packet-switched satellite and radio ground distribution network for data transmission…

  15. Computational Center for Studies of Plasma Microturbulence

    SciTech Connect

    William Dorland

    2006-10-11

    The Maryland Computational Center for Studies of Microturbulence (CCSM) was one component of a larger, multi-institutional Plasma Microturbulence Project, funded through what eventually became DOE's Scientific Discovery Through Advanced Computing Program. The primary focus of research in CCSM was to develop, deploy, maintain, and utilize kinetic simulation techniques, especially the gyrokinetic code called GS2.

  16. 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…

  17. 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.

  18. 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.

  19. Progress in computational studies of host-pathogen interactions.

    PubMed

    Zhou, Hufeng; Jin, Jingjing; Wong, Limsoon

    2013-04-01

    Host-pathogen interactions are important for understanding infection mechanism and developing better treatment and prevention of infectious diseases. Many computational studies on host-pathogen interactions have been published. Here, we review recent progress and results in this field and provide a systematic summary, comparison and discussion of computational studies on host-pathogen interactions, including prediction and analysis of host-pathogen protein-protein interactions; basic principles revealed from host-pathogen interactions; and database and software tools for host-pathogen interaction data collection, integration and analysis. PMID:23600809

  20. 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…

  1. Computational Study of Low Energy Nuclear Scattering

    NASA Astrophysics Data System (ADS)

    Salazar, Justin; Hira, Ajit; Brownrigg, Clifton; Pacheco, Jose

    2013-04-01

    We continue our interest in the interactions between different nuclear species with a computational study of the scattering of the low-energy nuclei of H through F atoms ( Z<=9 ) from Palladium and other metals. First, a FORTRAN computer program was developed to compute stopping cross sections and scattering angles in Pd and other metals for the small nuclear projectiles, using Monte Carlo calculation. This code allows for different angles of incidence. Next, simulations were done in the energy interval from 10 to 140kev. The computational results thus obtained are compared with relevant experimental data. The data are further analyzed to identify periodic trends in terms of the atomic number of the projectile. Such studies have potential applications in nuclear physics and in nuclear medicine.

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

    PubMed

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

    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

  3. 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

  4. 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.

  5. 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…

  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. 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.

  8. 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

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

    PubMed

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

    2015-10-13

    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

  10. 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

  11. Experimental and computational studies of polar solvation

    SciTech Connect

    Not Available

    1991-01-01

    Many articles and papers were published; a few are still in preparation or will be published. The solvation dynamics studies will be extended to ionic solutions. Computer simulations were also performed. A new line of research was begun on excited-state proton-transfer reactions catalyzed by alcohol solvents. (DLC)

  12. The Use of Computers in Slavonic Studies.

    ERIC Educational Resources Information Center

    Tambovtsev, Yuri A.

    1993-01-01

    Discussion of the use of computers in Slavonic studies in the Ukraine focuses on linguistics. Topics addressed include the Machine Fund of Russian, a Russian language database; the Machine Fund of Non-Russian Languages that includes each republic of the former Soviet Union; natural language processing; and comparing languages. (18 references) (LRW)

  13. Junior High Computer Studies: Teacher Resource Manual.

    ERIC Educational Resources Information Center

    Alberta Dept. of Education, Edmonton. Curriculum Branch.

    This manual is designed to help classroom teachers in Alberta, Canada implement the Junior High Computer Studies Program. The first eight sections cover the following material: (1) introduction to the teacher resource manual; (2) program rationale and philosophy; (3) general learner expectations; (4) program framework and flexibility; (5) program…

  14. Computational analysis reveals a correlation of exon-skipping events with splicing, transcription and epigenetic factors.

    PubMed

    Ye, Zhenqing; Chen, Zhong; Lan, Xun; Hara, Stephen; Sunkel, Benjamin; Huang, Tim H-M; Elnitski, Laura; Wang, Qianben; Jin, Victor X

    2014-03-01

    Alternative splicing (AS), in higher eukaryotes, is one of the mechanisms of post-transcriptional regulation that generate multiple transcripts from the same gene. One particular mode of AS is the skipping event where an exon may be alternatively excluded or constitutively included in the resulting mature mRNA. Both transcript isoforms from this skipping event site, i.e. in which the exon is either included (inclusion isoform) or excluded (skipping isoform), are typically present in one cell, and maintain a subtle balance that is vital to cellular function and dynamics. However, how the prevailing conditions dictate which isoform is expressed and what biological factors might influence the regulation of this process remain areas requiring further exploration. In this study, we have developed a novel computational method, graph-based exon-skipping scanner (GESS), for de novo detection of skipping event sites from raw RNA-seq reads without prior knowledge of gene annotations, as well as for determining the dominant isoform generated from such sites. We have applied our method to publicly available RNA-seq data in GM12878 and K562 cells from the ENCODE consortium and experimentally validated several skipping site predictions by RT-PCR. Furthermore, we integrated other sequencing-based genomic data to investigate the impact of splicing activities, transcription factors (TFs) and epigenetic histone modifications on splicing outcomes. Our computational analysis found that splice sites within the skipping-isoform-dominated group (SIDG) tended to exhibit weaker MaxEntScan-calculated splice site strength around middle, 'skipping', exons compared to those in the inclusion-isoform-dominated group (IIDG). We further showed the positional preference pattern of splicing factors, characterized by enrichment in the intronic splice sites immediately bordering middle exons. Finally, our analysis suggested that different epigenetic factors may introduce a variable obstacle in the

  15. 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

  16. Computers and Problem Solving: An Independent Study Course.

    ERIC Educational Resources Information Center

    Moursund, David

    The first chapter of this text for an independent study course on computers and problem solving provides an overview of computers in education which focuses on the three main instructional uses of computers in schools--learning about computers, the computer-as-tool, and computer-assisted instruction. Using a workshop format, chapter 2 discusses…

  17. Computational studies of molecular machines: the ribosome.

    PubMed

    Sanbonmatsu, Karissa Y

    2012-04-01

    The past decade has produced an avalanche of experimental data on the structure and dynamics of the ribosome. Groundbreaking studies in structural biology and kinetics have placed important constraints on ribosome structural dynamics. However, a gulf remains between static structures and time dependent data. In particular, X-ray crystallography and cryo-EM studies produce static models of the ribosome in various states, but lack dynamic information. Single molecule studies produce information on the rates of transitions between these states but do not have high-resolution spatial information. Computational studies have aided in bridging this gap by providing atomic resolution simulations of structural fluctuations and transitions between configurations. PMID:22336622

  18. Computational studies of molecular machines: the ribosome

    PubMed Central

    Sanbonmatsu, Karissa Y.

    2013-01-01

    The past decade has produced an avalanche of experimental data on the structure and dynamics of the ribosome. Groundbreaking studies in structural biology and kinetics have placed important constraints on ribosome structural dynamics. However, a gulf remains between static structures and time dependent data. In particular, x-ray crystallography and cryo-EM studies produce static models of the ribosome in various states, but lack dynamic information. Single molecule studies produce information on the rates of transitions between these states but do not have high-resolution spatial information. Computational studies have aided in bridging this gap by providing atomic resolution simulations of structural fluctuations and transitions between configurations. PMID:22336622

  19. National Computing Studies Summit: Open Learning Approaches to Computing Studies--An ACCE Discussion Paper

    ERIC Educational Resources Information Center

    Webb, Ian

    2008-01-01

    In 2005 the Australian Council for Computers in Education (ACCE) was successful in obtaining a grant from National Centre of Science, Information and Communication Technology and Mathematics Education for Rural and Regional Australia (SiMERR) to undertake the Computing Studies Teachers Network Rural and Regional Focus Project. The project had five…

  20. Whisker Movements Reveal Spatial Attention: A Unified Computational Model of Active Sensing Control in the Rat

    PubMed Central

    Mitchinson, Ben; Prescott, Tony J.

    2013-01-01

    Spatial attention is most often investigated in the visual modality through measurement of eye movements, with primates, including humans, a widely-studied model. Its study in laboratory rodents, such as mice and rats, requires different techniques, owing to the lack of a visual fovea and the particular ethological relevance of orienting movements of the snout and the whiskers in these animals. In recent years, several reliable relationships have been observed between environmental and behavioural variables and movements of the whiskers, but the function of these responses, as well as how they integrate, remains unclear. Here, we propose a unifying abstract model of whisker movement control that has as its key variable the region of space that is the animal's current focus of attention, and demonstrate, using computer-simulated behavioral experiments, that the model is consistent with a broad range of experimental observations. A core hypothesis is that the rat explicitly decodes the location in space of whisker contacts and that this representation is used to regulate whisker drive signals. This proposition stands in contrast to earlier proposals that the modulation of whisker movement during exploration is mediated primarily by reflex loops. We go on to argue that the superior colliculus is a candidate neural substrate for the siting of a head-centred map guiding whisker movement, in analogy to current models of visual attention. The proposed model has the potential to offer a more complete understanding of whisker control as well as to highlight the potential of the rodent and its whiskers as a tool for the study of mammalian attention. PMID:24086120

  1. 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

  2. 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

  3. Extremely high paw accelerations during paw shake in the cat: A mechanism revealed by computer simulations

    NASA Astrophysics Data System (ADS)

    Klishko, Alexander; Cofer, David; Edwards, Donald; Prilutsky, Boris

    2008-03-01

    Paw shake response is a reflex aimed at removing an irritating stimulus from the paw by imparting to it high periodic accelerations (>10 g). These values seem too high to be produced by distal muscles exclusively. According to Prilutsky et al. (2005), resultant hip moments during paw shake are much greater than distal joint moments, whereas distal joint velocities and accelerations exceed those of the proximal joints. The goal of this study was to examine how proximal hip muscles could contribute to high paw accelerations. Using software AnimatLab, we developed a 2D model of the cat hindlimb consisting of 5 rigid segments with 4 hinge joints and 11 muscles spanning all joints. The muscles were assumed passive except for those crossing the hip. When in simulations the hip muscles were reciprocally activated to periodically flex and extend the hip joint with a typical paw shake frequency of 10 Hz, the hindlimb segments demonstrated motion resembling experimental observations: linear and angular velocities and accelerations of the distal segments exceeded several fold the values of the proximal segments. Simulated paw shake revealed features of a whip-like motion.

  4. 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

  5. Traffic study of a computer system.

    NASA Technical Reports Server (NTRS)

    Cramer, R. L.

    1973-01-01

    A study which may guide the operations of existing computer installations, as well as the design of future networks, is described. Performance data and evaluations are considered with reference to interarrival time, users' habits, waiting time for execution, time spent in a partition, figures of merit, and states of the system. The analysis of the variables proceeds from examination of typical data with appropriate statistical tests to conclusions about the possible state of nature.

  6. Unethical Computer Using Behavior Scale: A Study of Reliability and Validity on Turkish University Students

    ERIC Educational Resources Information Center

    Namlu, Aysen Gurcan; Odabasi, Hatice Ferhan

    2007-01-01

    This study was carried out in a Turkish university with 216 undergraduate students of computer technology as respondents. The study aimed to develop a scale (UECUBS) to determine the unethical computer use behavior. A factor analysis of the related items revealed that the factors were can be divided under five headings; intellectual property,…

  7. 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

  8. 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

  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. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. 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

  16. Computational Study of Metal Hydride Destabilization

    NASA Astrophysics Data System (ADS)

    Johnson, Karl

    2006-03-01

    The safe and efficient on-board storage of hydrogen in fuel cell vehicles is one of the major road-blocks for utilization of hydrogen in transportation. This talk will illustrate the use quantum molecular modeling techniques for investigating atomic- level details of hydrogen storage in new materials. Metal hydrides of period 2 and 3 materials have high volumetric and gravimetric hydrogen storage capacities. However, these materials typically have very high heats of reaction, meaning that high temperatures are required to dissociate the hydrides. Likewise, hydrogenation reactions evolve very large quantities of energy, making thermal management during refueling a impractical. Recent experimental work has focused on chemical destabilization of metal hydrides as a means of decreasing the heats of reaction. We have carried out quantum mechanical calculations, using the electronic density functional theory (DFT) formalism, for various metal hydride systems. The heats of reaction for over 300 different reactions have been computed. We have compared our calculations with experimental and tabulated data where available and find reasonable agreement. Our calculations demonstrate the utility of DFT for screening reactions and for identifying promising materials for further computational and experimental studies. We have also studied the hydration of Mg2Si, a destabilized hydride of MgH2. Experiments have failed to hydrogenate this material in the laboratory under high pressures of H2. We examine adsorption of H2 and dissociation on the Mg2Si(110) surface to see if kinetic limitations are responsible for the failure to observe hydrogenation of this material.

  17. 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.

  18. 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

  19. Computational Models Reveal a Passive Mechanism for Cell Migration in the Crypt

    PubMed Central

    Dunn, Sara-Jane; Näthke, Inke S.; Osborne, James M.

    2013-01-01

    Cell migration in the intestinal crypt is essential for the regular renewal of the epithelium, and the continued upward movement of cells is a key characteristic of healthy crypt dynamics. However, the driving force behind this migration is unknown. Possibilities include mitotic pressure, active movement driven by motility cues, or negative pressure arising from cell loss at the crypt collar. It is possible that a combination of factors together coordinate migration. Here, three different computational models are used to provide insight into the mechanisms that underpin cell movement in the crypt, by examining the consequence of eliminating cell division on cell movement. Computational simulations agree with existing experimental results, confirming that migration can continue in the absence of mitosis. Importantly, however, simulations allow us to infer mechanisms that are sufficient to generate cell movement, which is not possible through experimental observation alone. The results produced by the three models agree and suggest that cell loss due to apoptosis and extrusion at the crypt collar relieves cell compression below, allowing cells to expand and move upwards. This finding suggests that future experiments should focus on the role of apoptosis and cell extrusion in controlling cell migration in the crypt. PMID:24260407

  20. Computational study of hydroxyapatite structures, properties and defects

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  1. 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

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

    PubMed

    Sanchita; Sharma, Ashok

    2016-03-01

    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

  3. 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

  4. 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

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

    PubMed Central

    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.

    2014-01-01

    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. PMID:25079871

  6. 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

  7. 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

  8. 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,…

  9. 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

  10. Computational studies of nonlinear dispersive plasma systems

    NASA Astrophysics Data System (ADS)

    Qian, Xin

    Plasma systems with dispersive waves are ubiquitous. Dispersive waves have the property that their wave velocity depends on the wave number of the wave. These waves show up in weakly as well as strongly coupled plasmas, and play a significant role in the underlying plasma dynamics. Dispersive waves bring new challenges to the computer simulation of nonlinear phenomena. The goal of this thesis is to discuss two computational studies of plasma phenomena, one drawn from strongly coupled complex or dusty plasmas, and the other from weakly coupled hydrogen plasmas. In the realm of dusty plasmas, we focus on the problem of three-dimensional (3D) Mach cones which we study by means of Molecular Dynamics (MD) simulations, assuming that the dust particles interact via a Yukawa potential. While laboratory and MD simulations have explored thoroughly the properties of Mach cones in 2D, elucidating the important role of dispersive waves in the formation of multiple cones, the simulations presented in this thesis represent the first 3D MD studies of Mach cones in strongly coupled dusty plasmas. These results have qualitative similarities with experimental observations on 3D Mach cones from the PK-3 plus project, which studies complex plasmas under microgravity conditions aboard the International Space station. In the realm of weakly coupled plasmas, we present results on the application of non-oscillatory central schemes to Hall MHD reconnection problems, in which the presence of dispersive whistler waves presents a formidable challenge for numerical algorithms that rely on explicit time-stepping schemes. In particular, we focus on the semi-discrete central formulation of Kurganov and Tadmor (2000), which has the advantage that it allow for larger time steps, and with significantly smaller numerical viscosity, than fully discrete schemes. We implement the Hall MHD equations through the CentPACK software package that implements the Kurganov-Tadmor formulation for a wide range of

  11. 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.

  12. Physical Properties of GaN Nanotubes as Revealed by Computer Simulation

    SciTech Connect

    Wang, Zhiguo; Gao, Fei; Zu, Xiaotao; Weber, William J.

    2008-07-25

    Single-crystalline wurtzite GaN nanotubes have been synthesized recently with proposed applications in nanoscale electronics, optoelectronics and the biochemical-sensing field. Molecular dynamics methods with a Stillinger-Weber potential are used to investigate the melting behavior, thermal conductivity and mechanical properties of these wurtzite-type single crystalline GaN nanotubes. Four major topical areas are summarized in this chapter. (1) The melting temperature of the GaN nanotubes increases with the thickness of the nanotubes to a saturation value, which is close to the melting temperature of bulk GaN. The simulations result reveal that the nanotubes begin to melt at the surface, and then the melting rapidly extends to the interior of the nanotubes as the temperature increases. (2) The thermal conductivity of nanotubes is smaller than that of the bulk GaN single crystal. The thermal conductivity is also found to decrease with temperature and increase with increasing wall thickness of the nanotubes. The change of phonon spectrum and surface inelastic scattering may account for the reduction of thermal conductivity in the nanotubes, while thermal softening and high frequency phonon interactions at high temperatures may provide an explanation for its decrease with increasing temperature. (3) At low temperatures, the simulation results show that the nanotubes exhibit brittle properties; whereas at high temperatures, they behave as ductile materials. The brittle to ductile transition temperature generally increases with increasing wall thickness of the nanotubes and increasing strain rate. (4) The simulation temperature, tube length and strain rate affect the buckling behavior of GaN nanotubes. The critical stress decreases with the increase of simulation temperature and tube length. The dependence of buckling on tube length is consistent with the analysis of equivalent continuum structures using Euler buckling theory.

  13. Computer Technology and the Social Studies.

    ERIC Educational Resources Information Center

    Glenn, Allen D.; Klassen, Daniel L.

    1983-01-01

    The citizen of tomorrow needs to understand the role of information in political systems; computer technology and information storage, retrieval, and use; the implications of information systems for individual rights; and the impact of computer crime, databanks, and systems analysis on the social, economic, and political spheres. (QKR)

  14. 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…

  15. Post Graduate Students' Computing Confidence, Computer and Internet Usage at Kuvempu University--An Indian Study

    ERIC Educational Resources Information Center

    Dange, Jagannath K.

    2010-01-01

    There is a common belief that students entering Post Graduation have appropriate computing skills for study purposes and there is no longer a felt need for computer training programmes in tertiary education. First year students of Post Graduation were surveyed in 2009, they were asked about their Education and Computing backgrounds. Further, the…

  16. Environmental studies: Mathematical, computational, and statistical analysis

    SciTech Connect

    Wheeler, M.F.

    1996-12-31

    The Summer Program on Mathematical, Computational, and Statistical Analyses in Environmental Studies held 6--31 July 1992 was designed to provide a much needed interdisciplinary forum for joint exploration of recent advances in the formulation and application of (A) environmental models, (B) environmental data and data assimilation, (C) stochastic modeling and optimization, and (D) global climate modeling. These four conceptual frameworks provided common themes among a broad spectrum of specific technical topics at this workshop. The program brought forth a mix of physical concepts and processes such as chemical kinetics, atmospheric dynamics, cloud physics and dynamics, flow in porous media, remote sensing, climate statistical, stochastic processes, parameter identification, model performance evaluation, aerosol physics and chemistry, and data sampling together with mathematical concepts in stiff differential systems, advective-diffusive-reactive PDEs, inverse scattering theory, time series analysis, particle dynamics, stochastic equations, optimal control, and others. Nineteen papers are presented in this volume. Selected papers are indexed separately for inclusion in the Energy Science and Technology Database.

  17. [Progress in molecular biology study of DNA computer].

    PubMed

    Zhang, Zhi-Zhou; Zhao, Jian; He, Lin

    2003-09-01

    DNA (deoxyribonucleotide acids) computer is an emerging new study area that basically combines molecular biology study of DNA molecules and computational study on how to employ these specific molecules to calculate. In 1994 Adleman described his pioneering research on DNA computing in Science. This is the first experimental report on DNA computer study. In 2001 Benenson et al published a paper in Nature regarding a programmable and autonomous DNA computing device. Because of its Turing-like functions, the device is regarded as another milestone progress for DNA computer study. The main features of DNA computer are massively parallel computing ability and potential enormous data storage capacity. Comparing with conventional electronic computers, DNA molecules provide conceptually a revolution in computing, and more and more implications have been found in various disciplines. DNA computer studies have brought great progress not only in its own computing mechanisms, but also in DNA manipulation technologies especially nano-technology. This article presents the basic principles of DNA computer, its applications, its important relationship with genomic research and our comments on all above issues. PMID:14577383

  18. A study of pipelining in computing arrays

    NASA Technical Reports Server (NTRS)

    Jagadish, H. V.; Mathews, R. G.; Newkirk, J. A.; Kailath, T.

    1986-01-01

    Scheduling considerations in computing arrays are examined. A simple sufficient condition is developed for determining whether a computing array can be pipelined. If the array cannot be pipelined in the form given, the condition also indicates the direction in which to proceed to make it pipelineable. The overall framework and methodology take a good part of the load off the logical architect of the array, and make the translation from the logical to the physical architecture a mechanical process.

  19. Computational analysis reveal inhibitory action of nimbin against dengue viral envelope protein.

    PubMed

    Lavanya, P; Ramaiah, Sudha; Anbarasu, Anand

    2015-12-01

    Dengue has emerged to be global health problem worldwide. Hence there is an immediate need to adopt new strategies in the development of effective anti-dengue drugs. Extracts from the leaves of Azadirachta indica has been traditionally used in folk medicine for viral infections. In the present study we report the anti-viral potency of nimbin, the active compound from the neem leaf extract against the envelope protein of dengue virus. Progression of viral entry into the host cell is facilitated by the envelope protein of dengue virus, suggesting; it as an effective anti-viral target. Nimbin is found to be effective against the envelope protein of all four types of dengue virus (dengue 1-4), which is evident from our in silico analysis. Our findings suggest the clinical importance of nimbin, which can serve as effective lead compound for further analysis. PMID:26645034

  20. Unique aspects of the structure and dynamics of elementary Iβ cellulose microfibrils revealed by computational simulations.

    PubMed

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

    2015-05-01

    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

  1. 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.

  2. 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

  3. 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

  4. 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

  5. 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.

  6. 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

    2015-08-01

    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

  7. Study of Setting in English. [Computer Diskette].

    ERIC Educational Resources Information Center

    Hughes, Tony

    Part of a three-program set, this computer software program is designed to aid teachers in the search for literary meaning by providing questions from different reading positions. The program provides 150 questions in 3 forms--a generic version of each question (without reference to any particular work), an example question (showing how the…

  8. Study of Character in English. [Computer Diskette].

    ERIC Educational Resources Information Center

    Hughes, Tony

    Part of a three-program set, this computer software program is designed to support the teaching of literary criticism in the English classroom through a focus on characterization. It aids teachers in the search for literary meaning by providing questions from different reading positions. The program is easy to operate and requires little prior…

  9. 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…

  10. 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.

  11. 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.

  12. 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…

  13. Study of Plot in English. [Computer Diskette].

    ERIC Educational Resources Information Center

    Hughes, Tony

    Part of a three-program set, this computer software provides a comprehensive range of generic questions on plot in literature. The program is comprised of: 150 questions sorted into 14 categories; supporting ideological commentary classifying question types; and a user-friendly program enabling worksheet production. It is underpinned by a Critical…

  14. Biomedical Visual Computing: Case Studies and Challenges

    PubMed Central

    Johnson, Chris R.

    2012-01-01

    Advances in computational geometric modeling, imaging, and simulation let researchers build and test models of increasing complexity, generating unprecedented amounts of data. As recent research in biomedical applications illustrates, visualization will be critical in making this vast amount of data usable; it’s also fundamental to understanding models of complex phenomena. PMID:22545005

  15. 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…

  16. 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…

  17. 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…

  18. 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…

  19. Distance Learning: A Study of Computer Modem Students.

    ERIC Educational Resources Information Center

    Richards, Irving; And Others

    Since distance learning via computer/modem is a relatively new concept, little is known about the students in computer/modem classes. This paper investigated computer/modem college students' backgrounds, ages, interests, reasons for enrollment, grades, and course completion rates as compared to traditional students. In the study there were 167…

  20. Computational studies of nonstoichiometric sodium auride clusters.

    PubMed

    Lin, Ying-Chan; Sundholm, Dage

    2012-05-31

    The molecular structures of low-lying isomers of anionic and neutral sodium auride clusters have been studied computationally at the second-order Møller-Plesset perturbation theory level using quadruple-ζ basis sets augmented with a double set of polarization functions. The first vertical detachment energies were calculated at the Møller-Plesset level as the energy difference between the cluster anion and the corresponding neutral cluster. The photodetachment energies of higher-lying ionization channels were calculated by adding electronic excitation energies of the neutral clusters to the first vertical detachment energy. The excitation energies were calculated at the linear response approximate coupled-cluster singles and doubles level using the anionic cluster structures. The obtained ionization energies for NaAu(-), NaAu(2)(-), NaAu(3)(-), NaAu(4)(-), Na(2)Au(2)(-), Na(2)Au(3)(-), Na(3)Au(3)(-), and Na(2)Au(4)(-) were compared to values deduced from experimental photoelectron spectra. Comparison of the calculated photoelectron spectra for a few energetically low-lying isomers shows that the energetically lowest cluster structures obtained in the calculations do not always correspond to the clusters produced experimentally. Spin-component-scaled second-order Møller-Plesset perturbation theory calculations shift the order of the isomers such that the observed clusters more often correspond to the energetically lowest structure, whereas the spin-component-scaled approach does not improve the photodetachment energies of the sodium aurides. The potential energy surface of the sodium aurides is very soft, with several low-lying isomers requiring an accurate electron correlation treatment. The calculations show that merely the energetic criterion is not a reliable means to identify the structures of the observed sodium auride clusters; other experimental information is needed to ensure a correct assignment of the cluster structures. The cluster structures of

  1. 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…

  2. 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

  3. 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. PMID:27140158

  4. Mechanical Influences on Morphogenesis of the Knee Joint Revealed through Morphological, Molecular and Computational Analysis of Immobilised Embryos

    PubMed Central

    Roddy, Karen A.; Prendergast, Patrick J.; Murphy, Paula

    2011-01-01

    Very little is known about the regulation of morphogenesis in synovial joints. Mechanical forces generated from muscle contractions are required for normal development of several aspects of normal skeletogenesis. Here we show that biophysical stimuli generated by muscle contractions impact multiple events during chick knee joint morphogenesis influencing differential growth of the skeletal rudiment epiphyses and patterning of the emerging tissues in the joint interzone. Immobilisation of chick embryos was achieved through treatment with the neuromuscular blocking agent Decamethonium Bromide. The effects on development of the knee joint were examined using a combination of computational modelling to predict alterations in biophysical stimuli, detailed morphometric analysis of 3D digital representations, cell proliferation assays and in situ hybridisation to examine the expression of a selected panel of genes known to regulate joint development. This work revealed the precise changes to shape, particularly in the distal femur, that occur in an altered mechanical environment, corresponding to predicted changes in the spatial and dynamic patterns of mechanical stimuli and region specific changes in cell proliferation rates. In addition, we show altered patterning of the emerging tissues of the joint interzone with the loss of clearly defined and organised cell territories revealed by loss of characteristic interzone gene expression and abnormal expression of cartilage markers. This work shows that local dynamic patterns of biophysical stimuli generated from muscle contractions in the embryo act as a source of positional information guiding patterning and morphogenesis of the developing knee joint. PMID:21386908

  5. 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.

  6. 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

  7. Future volcanic lake research: revealing secrets from poorly studied lakes

    NASA Astrophysics Data System (ADS)

    Rouwet, D.; Tassi, F.; Mora-Amador, R. A.

    2012-04-01

    Volcanic lake research boosted after the 1986 Lake Nyos lethal gas burst, a limnic rather than volcanic event. This led to the formation of the IAVCEI-Commission on Volcanic Lakes, which grew out into a multi-disciplinary scientific community since the 1990's. At Lake Nyos, a degassing pipe is functional since 2001, and two additional pipes were added in 2011, aimed to prevent further limnic eruption events. There are between 150 and 200 volcanic lakes on Earth. Some acidic crater lakes topping active magmatic-hydrothermal systems are monitored continuously or discontinuously. Such detailed studies have shown their usefulness in volcanic surveillance (e.g. Ruapehu, Yugama-Kusatsu-Shiran, Poás). Others are "Nyos-type" lakes, with possible gas accumulation in bottom waters and thus potentially hazardous. "Nyos-type" lakes tend to remain stably stratified in tropical and sub-tropical climates (meromictic), leading to long-term gas build-up and thus higher potential risk. In temperate climates, such lakes tend to turn over in winter (monomictic), and thus liberating its gas charge yearly. We line out research strategies for the different types of lakes. We believe a complementary, multi-disciplinary approach (geochemistry, geophysics, limnology, biology, statistics, etc.) will lead to new insights and ideas, which can be the base for future following-up and monitoring. After 25 years of pioneering studies on rather few lakes, the scientific community should be challenged to study the many poorly studied volcanic lakes, in order to better constrain the related hazard, based on probabilistic approaches.

  8. Yeast studies reveal moonlighting functions of the ancient actin cytoskeleton.

    PubMed

    Sattlegger, Evelyn; Chernova, Tatiana A; Gogoi, Neeku M; Pillai, Indu V; Chernoff, Yury O; Munn, Alan L

    2014-08-01

    Classic functions of the actin cytoskeleton include control of cell size and shape and the internal organization of cells. These functions are manifest in cellular processes of fundamental importance throughout biology such as the generation of cell polarity, cell migration, cell adhesion, and cell division. However, studies in the unicellular model eukaryote Saccharomyces cerevisiae (Baker's yeast) are giving insights into other functions in which the actin cytoskeleton plays a critical role. These include endocytosis, control of protein translation, and determination of protein 3-dimensional shape (especially conversion of normal cellular proteins into prions). Here, we present a concise overview of these new "moonlighting" roles for the actin cytoskeleton and how some of these roles might lie at the heart of important molecular switches. This is an exciting time for researchers interested in the actin cytoskeleton. We show here how studies of actin are leading us into many new and exciting realms at the interface of genetics, biochemistry, and cell biology. While many of the pioneering studies have been conducted using yeast, the conservation of the actin cytoskeleton and its component proteins throughout eukaryotes suggests that these new roles for the actin cytoskeleton may not be restricted to yeast cells but rather may reflect new roles for the actin cytoskeleton of all eukaryotes. PMID:25138357

  9. Yeast studies reveal moonlighting functions of the ancient actin cytoskeleton

    PubMed Central

    Sattlegger, Evelyn; Chernova, Tatiana A.; Gogoi, Neeku M.; Pillai, Indu V.; Chernoff, Yury O.; Munn, Alan L.

    2014-01-01

    Classic functions of the actin cytoskeleton include control of cell size and shape and the internal organisation of cells. These functions are manifest in cellular processes of fundamental importance throughout biology such as the generation of cell polarity, cell migration, cell adhesion and cell division. However, studies in the unicellular model eukaryote Saccharomyces cerevisiae (Baker's yeast) are giving insights into other functions in which the actin cytoskeleton plays a critical role. These include endocytosis, control of protein translation and determination of protein 3-dimensional shape (especially conversion of normal cellular proteins into prions). Here we present a concise overview of these new "moonlighting" roles for the actin cytoskeleton and how some of these roles might lie at the heart of important molecular switches. This is an exciting time for researchers interested in the actin cytoskeleton. We show here how studies of actin are leading us into many new and exciting realms at the interface of genetics, biochemistry and cell biology. While many of the pioneering studies have been conducted using yeast, the conservation of the actin cytoskeleton and its component proteins throughout eukaryotes suggests that these new roles for the actin cytoskeleton may not be restricted to yeast cells but rather may reflect new roles for the actin cytoskeleton of all eukaryotes. PMID:25138357

  10. 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

  11. Pubertal control mechanisms as revealed from human studies.

    PubMed

    Chipman, J J

    1980-05-15

    Human puberty is thought to be regulated by a central nervous system (CNS) program. Strong presumptive evidence for this thesis has been drawn from the augmented gonadotropin secretion that occurs synchronously with sleep in early puberty and serves as a biologic index to CNS puberty. In response to wake/sleep gonadotropin patterns, sex steroids are also secreted in circadian-like patterns during puberty. In disorders such as precocious puberty, anorexia nervosa, and gonadal dysgenesis, the physiological mechanisms that control wake/sleep differences in gonadotropin secretion appear to be intact. Studies in such patients suggest that the primary sex hormones have a quantitative but not qualitative modulating effect on the CNS program. Possible additional control mechanisms include adrenal androgen secretion and body composition. PMID:6989643

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

    PubMed

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

    2015-09-01

    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

  13. 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.

  14. 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.

  15. 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

  16. Computational studies of lobed forced mixer flows

    NASA Astrophysics Data System (ADS)

    Hu, H.; Wu, S. S.; Yu, S. C. M.

    1998-03-01

    Full Navier-Stokes Analyses have been conducted for the flows behind the trailing edge of a lobed forced mixer. The governing equations are derived from the time-dependent compressible Navier-Stokes equations and discretized in the finite-difference form. A simple two-layer eddy viscosity model has also been used to account for the turbulence. Computed results are compared with some of the velocity measurements using a laser-Doppler anemometer (Yu and Yip (1997)). In general, good agreement can be obtained in the streamwise mean velocity distribution but the decay of the streamwise circulation is underpredicted. Some suggestions to the discrepancy are proposed.

  17. 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

  18. 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

  19. 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

  20. New study reveals twice as many asteroids as previously believed

    NASA Astrophysics Data System (ADS)

    2002-05-01

    The ISO satellite Credits: ESA ISO An artist's impression of the ISO spacecraft. The ISO Deep Asteroid Search indicates that there are between 1.1 million and 1.9 million 'space rocks' larger than 1 kilometre in diameter in the so-called 'main asteroid belt', about twice as many as previously believed. However, astronomers think it is premature to revise current assessments of the risk of the Earth being hit by an asteroid. Despite being in our own Solar System, asteroids can be more difficult to study than very distant galaxies. With sizes of up to one thousand kilometres in diameter, the brightness of these rocky objects may vary considerably in just a few minutes. They move very quickly with respect to the stars - they have been dubbed 'vermin of the sky' because they often appear as trails on long exposure images. This elusiveness explains why their actual number and size distribution remains uncertain. Most of the almost 40,000 asteroids catalogued so far (1) orbit the Sun forming the 'main asteroid belt', between Mars and Jupiter, too far to pose any threat to Earth. However, space-watchers do keep a closer eye on another category of asteroids, the 'Near Earth Asteroids' or 'NEAs', which are those whose orbits cross, or are likely to cross, that of our planet. The ISO Deep Asteroid Search (IDAS), the first systematic search for these objects performed in infrared light, focused on main belt asteroids. Because it is impossible to simply point the telescope at the whole main belt and count, astronomers choose selected regions of the belt and then use a theoretical model to extrapolate the data to the whole belt. Edward Tedesco (TerraSystems, Inc., New Hampshire, United States) and François-Xavier Desert (Observatoire de Grenoble, France) observed their main belt selected areas in 1996 and 1997 with ESA's ISO. They found that in the middle region of the belt the density of asteroids was 160 asteroids larger than 1 kilometre per square degree - an area of the

  1. Neck after vertical hemilaryngectomy: computed tomographic study

    SciTech Connect

    DiSantis, D.J.; Balfe, D.M.; Hayden, R.; Sessions, D.; Sagel, S.S.

    1984-06-01

    Computed tomographic scans in 22 postoperative vertical hemilaryngectomy patients were analyzed retrospectively to determine the normal postoperative appearance and to evaluate the role of CT in assessing recurrent neoplasm. Twelve patients without clinical evidence of recurrence illustrated the normal postoperative changes. In the six patients with recurrent neoplasm, the CT manifestations included increased width of the remaining true vocal cord, convexity of the surgically formed pseudocord at glottic level, subglottic tumor, and extralaryngeal neck masses. Recurrence was mimicked in four patients by bulky soft tissue at the endolaryngeal operative site at both CT and laryngoscopy. CT supplemented the physical examination and indirect laryngoscopy, providing information regarding the presence and extent of tumor that was useful in planning the mode or scope of subsequent therapy.

  2. 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

  3. 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…

  4. What Do Social Studies Teachers Say about Using Computers?

    ERIC Educational Resources Information Center

    Schug, Mark C.

    1988-01-01

    Describes a study which examined teachers' use of computers in order to understand current teacher practices and to collect ideas on what changes may be necessary. Recommends intensive training in computer software selection and instructional procedures for social studies teachers. (BSR)

  5. 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…

  6. 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…

  7. 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…

  8. 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…

  9. Network-Based Study Reveals Potential Infection Pathways of Hepatitis-C Leading to Various Diseases

    PubMed Central

    Mukhopadhyay, Anirban; Maulik, Ujjwal

    2014-01-01

    Protein-protein interaction network-based study of viral pathogenesis has been gaining popularity among computational biologists in recent days. In the present study we attempt to investigate the possible pathways of hepatitis-C virus (HCV) infection by integrating the HCV-human interaction network, human protein interactome and human genetic disease association network. We have proposed quasi-biclique and quasi-clique mining algorithms to integrate these three networks to identify infection gateway host proteins and possible pathways of HCV pathogenesis leading to various diseases. Integrated study of three networks, namely HCV-human interaction network, human protein interaction network, and human proteins-disease association network reveals potential pathways of infection by the HCV that lead to various diseases including cancers. The gateway proteins have been found to be biologically coherent and have high degrees in human interactome compared to the other virus-targeted proteins. The analyses done in this study provide possible targets for more effective anti-hepatitis-C therapeutic involvement. PMID:24743187

  10. 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.

  11. 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.

  12. 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.'

  13. Disease-Drug Pairs Revealed by Computational Genomic Connectivity Mapping on GBA1 Deficient, Gaucher Disease Mice

    PubMed Central

    Yuen, Tony; Iqbal, Jameel; Zhu, Ling-Ling; Sun, Li; Lin, Aiping; Zhao, Hongyu; Liu, Jun; Mistry, Pramod K.; Zaidi, Mone

    2012-01-01

    We have reported that, in addition to recapitulating the classical human Gaucher disease (GD1) phenotype, deletion of the glucocerebrosidase (GBA1) gene in mice results in the dysfunction of a diverse population of immune cells. Most of immune-related, non-classical features of GD1, including gammopathies and autoimmune diathesis, are resistant to macrophage-directed therapies. This has prompted a search for newer agents for human GD1. Here, we used high-density microarray on splenic and liver cells from affected GBA1−/− mice to establish a gene “signature”, which was then utilized to interrogate the Broad Institute database, CMAP. Computational connectivity mapping of disease and drug pairs through CMAP revealed several highly enriched, non-null, mimic and anti-mimic hits. Most notably, two compounds with anti-helminthic properties, namely albendazole and oxamniquine, were identified; these are particularly relevant for future testing as the expression of chitinases is enhanced in GD1. PMID:22588172

  14. 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. PMID:25369583

  15. Polyelectrolyte complexes and salt: a computational study

    NASA Astrophysics Data System (ADS)

    Antila, Hanne; van Tassel, Paul; Sammalkorpi, Maria

    2014-03-01

    Charged polymers, polyelectrolytes (PEs), are versatile materials with applications ranging from tissue engineering to sensing elements. In aqueous solutions, oppositely charged PEs form complexes which are known to be sensitive to added salt with responses including shrinking, flocculation or swelling, and at higher concentrations loosening and destabilization of the complex. However, the role of electrostatics, charge correlations, hydration, and ion specific interactions remain unclear. In this work, we use all-atom molecular dynamics with explicit water and ions to probe the effect of excess salt to DNA-polylysine complex formation and stability, and demonstrate the mechanism of PE and ion species specific salt-driven dissociation. The dissociation occurs accompanied by charge reversal in which charge correlations and ion binding chemistry play a role. Our results agree with experimental work on complex dissociation but in addition show the underlying microstructural correlations driving the behavior. We expand the full atomic level detail and dynamics results with theoretical and computational work describing the PE complex as oppositely charged rods to provide a more complete understanding of PE interactions in salt.

  16. 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.

  17. Studies in Mathematics, Volume 22. Studies in Computer Science.

    ERIC Educational Resources Information Center

    Pollack, Seymour V., Ed.

    The nine articles in this collection were selected because they represent concerns central to computer science, emphasize topics of particular interest to mathematicians, and underscore the wide range of areas deeply and continually affected by computer science. The contents consist of: "Introduction" (S. V. Pollack), "The Development of Computer…

  18. A community-based study of asthenopia in computer operators

    PubMed Central

    Choudhary, Sushilkumar; Doshi, Vikas G

    2008-01-01

    Context: There is growing body of evidence that use of computers can adversely affect the visual health. Considering the rising number of computer users in India, computer-related asthenopia might take an epidemic form. In view of that, this study was undertaken to find out the magnitude of asthenopia in computer operators and its relationship with various personal and workplace factors. Aims: To study the prevalence of asthenopia among computer operators and its association with various epidemiological factors. Settings and Design: Community-based cross-sectional study of 419 subjects who work on computer for varying period of time. Materials and Methods: Four hundred forty computer operators working in different institutes were selected randomly. Twenty-one did not participate in the study, making the nonresponse rate 4.8%. Rest of the subjects (n = 419) were asked to fill a pre-tested questionnaire, after obtaining their verbal consent. Other relevant information was obtained by personal interview and inspection of workstation. Statistical Analysis Used: Simple proportions and Chi-square test. Results: Among the 419 subjects studied, 194 (46.3%) suffered from asthenopia during or after work on computer. Marginally higher proportion of asthenopia was noted in females compared to males. Occurrence of asthenopia was significantly associated with age of starting use of computer, presence of refractive error, viewing distance, level of top of the computer screen with respect to eyes, use of antiglare screen and adjustment of contrast and brightness of monitor screen. Conclusions: Prevalence of asthenopia was noted to be quite high among computer operators, particularly in those who started its use at an early age. Individual as well as work-related factors were found to be predictive of asthenopia. PMID:18158404

  19. Verification, Validation and Sensitivity Studies in Computational Biomechanics

    PubMed Central

    Anderson, Andrew E.; Ellis, Benjamin J.; Weiss, Jeffrey A.

    2012-01-01

    Computational techniques and software for the analysis of problems in mechanics have naturally moved from their origins in the traditional engineering disciplines to the study of cell, tissue and organ biomechanics. Increasingly complex models have been developed to describe and predict the mechanical behavior of such biological systems. While the availability of advanced computational tools has led to exciting research advances in the field, the utility of these models is often the subject of criticism due to inadequate model verification and validation. The objective of this review is to present the concepts of verification, validation and sensitivity studies with regard to the construction, analysis and interpretation of models in computational biomechanics. Specific examples from the field are discussed. It is hoped that this review will serve as a guide to the use of verification and validation principles in the field of computational biomechanics, thereby improving the peer acceptance of studies that use computational modeling techniques. PMID:17558646

  20. A Computer-Based System for Studies in Learning.

    ERIC Educational Resources Information Center

    Gentner, Donald R.; And Others

    A computer-based system, called the FLOW system, was used in experimental studies of human learning. The student learns a simple computer language from printed instructions and can run his programs interactively on the FLOW system. An automated tutor simulates a human tutor who watches over the student and gives help when the student has…

  1. A Study of Computer-Based Instruction in Nursing Education.

    ERIC Educational Resources Information Center

    Conklin, D. N.

    1983-01-01

    Describes a comparative study of instruction in surgical nursing, which investigates the impact of computer-assisted instruction (CAI) on learning and student attitudes. Flowcharts of the computer-management program and CAI modules are included. Significant improvement was shown by the group using CAI. (EAO)

  2. The Link between Computer Simulations and Social Studies Learning: Debriefing.

    ERIC Educational Resources Information Center

    Chiodo, John J.; Flaim, Mary L.

    1993-01-01

    Asserts that debriefing is the missing link between learning achievement and simulations in social studies. Maintains that teachers who employ computer-assisted instruction must utilize effective debriefing activities. Provides a four-step debriefing model using the computer simulation, Oregon Trail. (CFR)

  3. Academic Computing at Bennett College. A Case Study.

    ERIC Educational Resources Information Center

    Hunter, Beverly; Kearsley, Greg

    Prepared by the Human Resources Research Organization to assist administrators, faculty, and staff at other minority institutions to plan and implement successful computing projects, this book is one of a series of case studies on educational uses of computers. The profile of Bennett College is presented in terms of its mission, location, programs…

  4. How to Incorporate the Computer into the Social Studies Classroom.

    ERIC Educational Resources Information Center

    Dockterman, David; Snyder, Tom

    This brochure offers answers to 13 questions about using computers in the social studies classroom. Written by teachers for teachers, its goal is to provide a foundation to consider whether or not computers have a place in the classroom and how to go about using them if they do. The questions are: "What's in this booklet?""Should I be using…

  5. Factors Affecting Softlifting Intention of Computing Students: An Empirical Study.

    ERIC Educational Resources Information Center

    Rahim, Md. Mahbubur; Seyal, Afzaal H.; Rahman, Mohd. Noah Abd.

    2001-01-01

    Discusses softlifting as a form of software piracy and describes a study that analyzed the softlifting intentions of computing students in Brunei Darussalam. Considers student attitudes; gender; family income; personal computer ownership; experience; faculty remarks; institutional monitoring; and implications for attempts to curb software piracy.…

  6. 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.

  7. 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…

  8. 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…

  9. 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

  10. A computational NMR study on zigzag aluminum nitride nanotubes

    NASA Astrophysics Data System (ADS)

    Bodaghi, Ali; Mirzaei, Mahmoud; Seif, Ahmad; Giahi, Masoud

    2008-12-01

    A computational nuclear magnetic resonance (NMR) study is performed to investigate the electronic structure properties of the single-walled zigzag aluminum nitride nanotubes (AlNNTs). The chemical-shielding (CS) tensors are calculated at the sites of Al-27 and N-15 nuclei in three structural forms of AlNNT including H-saturated, Al-terminated, and N-terminated ones. The structural forms are firstly optimized and then the calculated CS tensors in the optimized structures are converted to chemical-shielding isotropic (CSI) and chemical-shielding anisotropic (CSA) parameters. The calculated parameters reveal that various Al-27 and N-15 nuclei are divided into some layers with equivalent electrostatic properties; furthermore, Al and N can act as Lewis base and acid, respectively. In the Al-terminated and N-terminated forms of AlNNT, in which one mouth of the nanotube is terminated by aluminum and nitrogen nuclei, respectively, just the CS tensors of the nearest nuclei to the mouth of the nanotube are significantly changed due to removal of saturating hydrogen atoms. Density functional theory (DFT) calculations are performed using GAUSSIAN 98 package of program.

  11. Grade One: Math Computation. Case Study #1

    ERIC Educational Resources Information Center

    Powell, Sarah R.; Seethaler, Pamela M.

    2007-01-01

    The purpose of this case study is to highlight the integral role that progress monitoring (PM) plays throughout any Response to Intervention (RTI) process. This example uses a three-level, responsiveness-to-intervention (RTI) method for identifying students with learning difficulties. Using a fictional first-grade classroom as the setting for…

  12. A twin study of computer anxiety in Turkish adolescents.

    PubMed

    Deryakulu, Deniz; Calışkan, Erkan

    2012-04-01

    The present study investigated computer anxiety within a sample of Turkish twins aged 10-18. A total of 185 twin-pairs participated in the study. Of the twins, 64 pairs (34.6 percent) were monozygotic (MZ) and 121 pairs (65.4 percent) were dizygotic (DZ). Of the 121 DZ twins, 54 pairs (44.63 percent) were same-sex twins and 67 pairs (55.37 percent) were opposite-sex twins. Computer anxiety was assessed using Computer Anxiety Rating Scale-Turkish Version (CARS-TV), one of the three main scales of "Measuring Technophobia Instruments" developed by Rosen and Weil. The results of paired t test comparisons showed no significant differences in MZ and same-sex DZ twin-pairs' levels of computer anxiety. On the other hand, a significant difference was found in opposite-sex DZ twin-pairs' level of computer anxiety. Interesting enough, males appeared to be more computer anxious than their female co-twins. In the present study, using Falconer's formula, heritability estimate for computer anxiety was derived from correlations based on MZ and DZ twins' mean scores on CARS-TV. The results showed that 57 percent of the variance in computer anxiety was from genetics and 41.5 percent was from nonshared environmental factors. Shared environmental influence, on the other hand, was very small and negligible. Interpretations of results and potential directions for future research are presented. PMID:22394420

  13. 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

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

    DOE PAGESBeta

    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

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

    SciTech Connect

    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 in 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.

  16. Computational study of wax deposition in pipeline

    NASA Astrophysics Data System (ADS)

    Duan, Jimiao; Gong, Jing; Liu, Huishu

    2013-07-01

    Wax deposition in subsea pipelines is one of the flow assurance problems for oil and gas production. In contrast to many studies about single phase wax deposition, gas-oil wax deposition studies are very limited. The wax deposition mechanism and model prediction are restricted by many factors such as hydrodynamic and thermal when multiphase flow is involved. Wax deposition modeling becomes complicated under multiphase flowing conditions. wax deposition is depended by the flow pattern. The stratified flow is one of the most common flow patterns in the actual subsea gas-oil flowing conditions. In this work, numerical methods are used to study wax deposition in oil-gas stratified flow through a pipe. Based on the flow analysis about stratified flow, the non-isothermal heat and mass transfer is calculated. The temperature profile of the oil and the concentration profile of wax in oil are obtained. The change of the oil-gas interface i.e. the liquid holdup throughout the pipe must be taken into the heat and mass balance. The valid wax deposition surface must be taken into the wax deposition modeling by establishing function of the liquid holdup and the wetted area by oil. The molecular diffusion is as the deposition mechanism. The increase of the wax fraction in the deposit as a function of time depends on the mass flux from the oil deposit interface into the gel and the growth of the deposit thickness depends on the difference between the mass flux from the bulk oil to the oil deposit interface and the mass flux from the interface into the deposit. In addition, the growth of the wax deposit as a function of time along with the effect oil flow rate, gas flow rate and the inlet temperature are discussed. The presence of gas significantly reduces the severity of wax deposition by altering the heat and mass transfer characteristics.

  17. 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..

  18. Semiconducting layered blue phosphorus: a computational study.

    PubMed

    Zhu, Zhen; Tománek, David

    2014-05-01

    We investigate a previously unknown phase of phosphorus that shares its layered structure and high stability with the black phosphorus allotrope. We find the in-plane hexagonal structure and bulk layer stacking of this structure, which we call "blue phosphorus," to be related to graphite. Unlike graphite and black phosphorus, blue phosphorus displays a wide fundamental band gap. Still, it should exfoliate easily to form quasi-two-dimensional structures suitable for electronic applications. We study a likely transformation pathway from black to blue phosphorus and discuss possible ways to synthesize the new structure. PMID:24836265

  19. 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.

  20. 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.

  1. 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.

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

    PubMed

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

    2015-10-01

    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. PMID:25974669

  3. The Choice Not To Use Computers: A Case Study of Community College Faculty Who Do Not Use Computers in Teaching.

    ERIC Educational Resources Information Center

    Stocker, Bradford R.

    This dissertation studies the motives of community college faculty who decide not to use computers in teaching. For the purpose of the study, non-adoption of computers in teaching is defined as not using computers for more than word processing. In spite of the fact that many of the environmental blocks that inhibit the use of computers have been…

  4. 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

  5. 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

  6. Dynamics of Bottlebrush Networks: A Computational Study

    NASA Astrophysics Data System (ADS)

    Dobrynin, Andrey; Cao, Zhen; Sheiko, Sergei

    We study dynamics of deformation of bottlebrush networks using molecular dynamics simulations and theoretical calculations. Analysis of our simulation results show that the dynamics of bottlebrush network deformation can be described by a Rouse model for polydisperse networks with effective Rouse time of the bottlebrush network strand, τR =τ0Ns2 (Nsc + 1) where, Ns is the number-average degree of polymerization of the bottlebrush backbone strands between crosslinks, Nsc is the degree of polymerization of the side chains and τ0is a characteristic monomeric relaxation time. At time scales t smaller than the Rouse time, t <τR , the time dependent network shear modulus decays with time as G (t) ~ ρkB T(τ0 / t) 1 / 2 , where ρis the monomer number density. However, at the time scale t larger than the Rouse time of the bottlebrush strands between crosslinks, the network response is pure elastic with shear modulus G (t) =G0 , where G0 is the equilibrium shear modulus at small deformation. The stress evolution in the bottlebrush networks can be described by a universal function of t /τR . NSF DMR-1409710.

  7. Computational and theoretical studies of globular proteins

    NASA Astrophysics Data System (ADS)

    Pagan, Daniel L.

    Protein crystallization is often achieved in experiment through a trial and error approach. To date, there exists a dearth of theoretical understanding of the initial conditions necessary to promote crystallization. While a better understanding of crystallization will help to create good crystals suitable for structure analysis, it will also allow us to prevent the onset of certain diseases. The core of this thesis is to model and, ultimately, understand the phase behavior of protein particles in solution. Toward this goal, we calculate the fluid-fluid coexistence curve in the vicinity of the metastable critical point of the modified Lennard-Jones potential, where it has been shown that nucleation is increased by many orders of magnitude. We use finite-size scaling techniques and grand canonical Monte Carlo simulation methods. This has allowed us to pinpoint the critical point and subcritical region with high accuracy in spite of the critical fluctuations that hinder sampling using other Monte Carlo techniques. We also attempt to model the phase behavior of the gamma-crystallins, mutations of which have been linked to genetic cataracts. The complete phase behavior of the square well potential at the ranges of attraction lambda = 1.15 and lambda = 1.25 is calculated and compared with that of the gammaII-crystallin. The role of solvent is also important in the crystallization process and affects the phase behavior of proteins in solution. We study a model that accounts for the contribution of the solvent free-energy to the free-energy of globular proteins. This model allows us to model phase behavior that includes solvent.

  8. 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…

  9. 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

  10. 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

  11. Computational Analysis of Full-length cDNAs Reveals Frequent Coupling Between Transcriptional and Splicing Programs

    PubMed Central

    Chern, Tzu-Ming; Paul, Nicodeme; van Nimwegen, Erik; Zavolan, Mihaela

    2008-01-01

    High-throughput sequencing studies revealed that the majority of human and mouse multi-exon genes have multiple splice forms. High-density oligonucleotide array-based measurements have further established that many exons are expressed in a tissue-specific manner. The mechanisms underlying the tissue-dependent expression of most alternative exons remain, however, to be understood. In this study, we focus on one possible mechanism, namely the coupling of (tissue specific) transcription regulation with alternative splicing. We analyzed the FANTOM3 and H-Invitational datasets of full-length mouse and human cDNAs, respectively, and found that in transcription units with multiple start sites, the inclusion of at least 15% and possibly up to 30% of the ‘cassette’ exons correlates with the use of specific transcription start sites (TSS). The vast majority of TSS-associated exons are conserved between human and mouse, yet the conservation is weaker when compared with TSS-independent exons. Additionally, the currently available data only support a weak correlation between the probabilities of TSS association of orthologous exons. Our analysis thus suggests frequent coupling of transcriptional and splicing programs, and provides a large dataset of exons on which the molecular basis of this coupling can be further studied. PMID:18276623

  12. 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…

  13. 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. PMID:24936174

  14. 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

  15. 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…

  16. Computational Study of Low Energy Nuclear Scattering from Metal Nuclei

    NASA Astrophysics Data System (ADS)

    Jaramillo, Danelle; Hira, Ajit; Pacheco, Jose; Salazar, Justin

    2014-03-01

    We continue our interest in the interactions between different nuclear species with a computational study of the scattering of the low-energy nuclei of H through F atoms (Z <= 9) from Palladium, Nickel and other metals. First, a FORTRAN computer program was developed to compute stopping cross sections and scattering angles in Pd and other metals for the small nuclear projectiles, using Monte Carlo calculation. This code allows for different angles of incidence. Next, simulations were done in the energy interval from 10 to 140 keV. The computational results thus obtained are compared with relevant experimental data. The data are further analyzed to identify periodic trends in terms of the atomic number of the projectile. Such studies have potential applications in nuclear physics and in nuclear medicine.

  17. 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

  18. 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

  19. Metabolism and development – integration of micro computed tomography data and metabolite profiling reveals metabolic reprogramming from floral initiation to silique development

    PubMed Central

    Bellaire, Anke; Ischebeck, Till; Staedler, Yannick; Weinhaeuser, Isabell; Mair, Andrea; Parameswaran, Sriram; Ito, Toshiro; Schönenberger, Jürg; Weckwerth, Wolfram

    2014-01-01

    The interrelationship of morphogenesis and metabolism is a poorly studied phenomenon. The main paradigm is that development is controlled by gene expression. The aim of the present study was to correlate metabolism to early and late stages of flower and fruit development in order to provide the basis for the identification of metabolic adjustment and limitations. A highly detailed picture of morphogenesis is achieved using nondestructive micro computed tomography. This technique was used to quantify morphometric parameters of early and late flower development in an Arabidopsis thaliana mutant with synchronized flower initiation. The synchronized flower phenotype made it possible to sample enough early floral tissue otherwise not accessible for metabolomic analysis. The integration of metabolomic and morphometric data enabled the correlation of metabolic signatures with the process of flower morphogenesis. These signatures changed significantly during development, indicating a pronounced metabolic reprogramming in the tissue. Distinct sets of metabolites involved in these processes were identified and were linked to the findings of previous gene expression studies of flower development. High correlations with basic leucine zipper (bZIP) transcription factors and nitrogen metabolism genes involved in the control of metabolic carbon : nitrogen partitioning were revealed. Based on these observations a model for metabolic adjustment during flower development is proposed. PMID:24350948

  20. Mixed Aggregates of the Dilithiated Koga Tetraamine: NMR Spectroscopic and Computational Studies.

    PubMed

    Ma, Yun; Mack, Kyle A; Liang, Jun; Keresztes, Ivan; Collum, David B; Zakarian, Armen

    2016-08-16

    A combination of (1) H, (6) Li, (13) C, and (15) N NMR spectroscopies and density functional theory computations explores the formation of mixed aggregates by a dilithium salt of a C2 -symmetric chiral tetraamine (Koga's base). Lithium halides, acetylides, alkoxides, and monoalkylamides form isostructural trilithiated mixed aggregates with few exceptions. (6) Li-(13) C and (6) Li-(15) N couplings reveal heretofore undetected transannular contacts (laddering) with lithium acetylides and lithium monoalkylamides. Marked temperature-dependent (15) N chemical shifts seem to be associated with this laddering. Computational studies shed light on the general structures of the aggregates, their penchant for laddering, and the stereochemical consequences of aggregation. PMID:27435147

  1. 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.

  2. A Plea for Neutral Comparison Studies in Computational Sciences

    PubMed Central

    Eugster, Manuel J. A.

    2013-01-01

    In computational science literature including, e.g., bioinformatics, computational statistics or machine learning, most published articles are devoted to the development of “new methods”, while comparison studies are generally appreciated by readers but surprisingly given poor consideration by many journals. This paper stresses the importance of neutral comparison studies for the objective evaluation of existing methods and the establishment of standards by drawing parallels with clinical research. The goal of the paper is twofold. Firstly, we present a survey of recent computational papers on supervised classification published in seven high-ranking computational science journals. The aim is to provide an up-to-date picture of current scientific practice with respect to the comparison of methods in both articles presenting new methods and articles focusing on the comparison study itself. Secondly, based on the results of our survey we critically discuss the necessity, impact and limitations of neutral comparison studies in computational sciences. We define three reasonable criteria a comparison study has to fulfill in order to be considered as neutral, and explicate general considerations on the individual components of a “tidy neutral comparison study”. R codes for completely replicating our statistical analyses and figures are available from the companion website http://www.ibe.med.uni-muenchen.de/organisation/mitarbeiter/020_professuren/boulesteix/plea2013. PMID:23637855

  3. The 3D microscopic 'signature' of strain within glacial sediments revealed using X-ray computed microtomography

    NASA Astrophysics Data System (ADS)

    Tarplee, Mark F. V.; van der Meer, Jaap J. M.; Davis, Graham R.

    2011-11-01

    X-ray computed microtomography (μCT), a non-destructive analytical technique, was used to create volumetric three-dimensional (3D) models representing the internal composition and structure of undisturbed pro- and subglacial soft sediment sample plugs for the purposes of identifying and analysing kinematic indicators. The technique is introduced and a methodology is presented addressing specific issues relating to the investigation of unlithified, polymineralic sediments. Six samples were selected based on their proximity to 'type' brittle and ductile deformation structures, or because of their perceived suitability for successful application of the technique. Analysis of a proglacial 'ideal' specimen permitted the 3D geometry of a suite of micro-faults and folds to be investigated and the strain history of the sample reconstructed. The poor contrast achieved in scanning a diamicton of glaciomarine origin is attributable to overconsolidation under normal loading, the sediment demonstrated to have undergone subsequent subglacial deformation. Another overconsolidated diamicton contains an extensive, small scale (<20 μm) network of fractures delineating a 'marble-bed' structure, hitherto unknown at this scale. A volcanic lithic clast contrasts well with the surrounding matrix in a 'lodgement' till sample containing μCT (void) and thin-section evidence of clast ploughing. Initial ductile deformation was followed by dewatering of the matrix, which led to brittle failure and subsequent emplacement. Compelling evidence of clast rotation is located in the top of another sample, μCT analysis revealing that the grain has a proximal décollement surface orientated parallel to the plane of shear. The lenticular morphology of the rotational structure defined suggests an unequal distribution of forces along two of the principal stress axes. The excellent contrast between erratics contained within a sample and the enclosing till highlight the considerable potential of the

  4. Using Computers in Mathematics Teaching. A Collection of Case Studies.

    ERIC Educational Resources Information Center

    Ponte, Joao Pedro; And Others

    This collection of case studies of classroom experiences in middle and secondary schools throughout the European Community describes the use of computers in mathematics education. The 16 studies are organized in four main groups: (1) experience in geometry using educational software and Logo in grades 5-10; (2) arithmetic number concepts,…

  5. 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…

  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. Computational wing design studies relating to natural laminar flow

    NASA Technical Reports Server (NTRS)

    Waggoner, Edgar G.

    1986-01-01

    Two research studies are described which directly relate to the application of natural laminar flow (NLF) technology to transonic transport-type wing planforms. Each involved using state-of-the-art computational methods to design three-dimensional wing contours which generate significant runs of favorable pressure gradients. The first study supported the Variable Sweep Transition Flight Experiment and involves design of a full-span glove which extends from the leading edge to the spoiler hinge line on the upper surface of an F-14 outer wing panel. A wing was designed computationally for a corporate transport aircraft in the second study. The resulting wing design generated favorable pressure gradients from the leading edge aft to the mid-chord on both upper and lower surfaces at the cruise design point. Detailed descriptions of the computational design approach are presented along with the various constraints imposed on each of the designs.

  8. Computational Estimation in the Primary School: A Single Case Study of One Teacher's Involvement in a Professional Learning Intervention

    ERIC Educational Resources Information Center

    Mildenhall, Paula; Hackling, Mark; Swan, Paul

    2010-01-01

    This paper focuses on the initial analysis of a study of a professional learning intervention. Using a case study design it was possible to describe one teacher's involvement in this research. The study revealed how the teacher's beliefs and pedagogical content knowledge of computational estimation was altered as a result of participating in the…

  9. 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

  10. The Computer Aversion, Attitudes, and Familiarity Index (CAAFI): A Measure for the Study of Computer-Related Constructs

    ERIC Educational Resources Information Center

    Schulenberg, Stefan E.; Yutrzenka, Barbara A.; Gohm, Carol L.

    2006-01-01

    The purpose of this study was to systematically develop an instrument to measure computer aversion, computer attitudes, and computer familiarity. The study is an extension of previous research (Schulenberg, 2002). Development involved item generation, pilot testing, and exploratory and confirmatory factor analyses. The measure was administered to…

  11. 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.

  12. Computational studies of Ras and PI3K

    NASA Technical Reports Server (NTRS)

    Ren, Lei; Cucinotta, Francis A.

    2004-01-01

    Until recently, experimental techniques in molecular cell biology have been the primary means to investigate biological risk upon space radiation. However, computational modeling provides an alternative theoretical approach, which utilizes various computational tools to simulate proteins, nucleotides, and their interactions. In this study, we are focused on using molecular mechanics (MM) and molecular dynamics (MD) to study the mechanism of protein-protein binding and to estimate the binding free energy between proteins. Ras is a key element in a variety of cell processes, and its activation of phosphoinositide 3-kinase (PI3K) is important for survival of transformed cells. Different computational approaches for this particular study are presented to calculate the solvation energies and binding free energies of H-Ras and PI3K. The goal of this study is to establish computational methods to investigate the roles of different proteins played in the cellular responses to space radiation, including modification of protein function through gene mutation, and to support the studies in molecular cell biology and theoretical kinetics models for our risk assessment project.

  13. Computational Study of Computed Tomography Contrast Gradients in Models of Stenosed Coronary Arteries.

    PubMed

    Eslami, Parastou; Seo, Jung-Hee; Rahsepar, Amir Ali; George, Richard; Lardo, Albert C; Mittal, Rajat

    2015-09-01

    Recent computed tomography coronary angiography (CCTA) studies have noted higher transluminal contrast agent gradients in arteries with stenotic lesions, but the physical mechanism responsible for these gradients is not clear. We use computational fluid dynamics (CFD) modeling coupled with contrast agent dispersion to investigate the mechanism for these gradients. Simulations of blood flow and contrast agent dispersion in models of coronary artery are carried out for both steady and pulsatile flows, and axisymmetric stenoses of severities varying from 0% (unobstructed) to 80% are considered. Simulations show the presence of measurable gradients with magnitudes that increase monotonically with stenotic severity when other parameters are held fixed. The computational results enable us to examine and validate the hypothesis that transluminal contrast gradients (TCG) are generated due to the advection of the contrast bolus with time-varying contrast concentration that appears at the coronary ostium. Since the advection of the bolus is determined by the flow velocity in the artery, the magnitude of the gradient, therefore, encodes the coronary flow velocity. The correlation between the flow rate estimated from TCG and the actual flow rate in the computational model of a physiologically realistic coronary artery is 96% with a R2 value of 0.98. The mathematical formulae connecting TCG to flow velocity derived here represent a novel and potentially powerful approach for noninvasive estimation of coronary flow velocity from CT angiography. PMID:26102356

  14. 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.

  15. Computer-Supported Study Strategies for Purple People.

    ERIC Educational Resources Information Center

    Tenny, John L.

    1992-01-01

    Describes how the computer can support the study process of students variously described as "multivariate, nonlinear thinkers,""dyslexic,""learning disabled," and "purple people." Describes features of a Macintosh program called "Inspiration" that enables easy test entry and manipulation in a graphic mode, placing emphasis on the considerable…

  16. A Study on the Korean Educational Computer Network.

    ERIC Educational Resources Information Center

    Ahn, Moon-Suk

    Future development and operations of the Korean Educational Computer Network are discussed and possible network layout and cost implications are studied. The Aloha System radio communication, telephone lines and satellite systems are considered as possible alternatives to the present network. The availability of telecommunication facilities and…

  17. A Study To Increase Computer Applications in Social Work Management.

    ERIC Educational Resources Information Center

    Lucero, John A.

    The purpose of this study was to address the use of computers in social work practice and to survey the field for tools, concepts, and trends that could assist social workers in their practice. In addition to a review of the relevant literature, information was requested from the Social Work Service and Ambulatory Care Database Section at Walter…

  18. Computer-Based Concept Mapping: Active Studying for Active Learners.

    ERIC Educational Resources Information Center

    Anderson-Inman, Lynne; Zeitz, Leigh

    1993-01-01

    Describes the use of computer-generated concept maps using a new genre of graphics programs that allows students to create, alter and expand maps as they acquire more subject matter knowledge. Four examples of increasingly complex concept maps developed by a high school student studying cellular biology are discussed and illustrated. (Contains 19…

  19. It Pays to Compare: An Experimental Study on Computational Estimation

    ERIC Educational Resources Information Center

    Star, Jon R.; Rittle-Johnson, Bethany

    2009-01-01

    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…

  20. 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…

  1. 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.

  2. 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.

  3. Computational fluid dynamics studies of nuclear rocket performance

    NASA Technical Reports Server (NTRS)

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

    1991-01-01

    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. 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.

  5. Computer vision for dual spacecraft proximity operations -- A feasibility study

    NASA Astrophysics Data System (ADS)

    Stich, Melanie Katherine

    A computer vision-based navigation feasibility study consisting of two navigation algorithms is presented to determine whether computer vision can be used to safely navigate a small semi-autonomous inspection satellite in proximity to the International Space Station. Using stereoscopic image-sensors and computer vision, the relative attitude determination and the relative distance determination algorithms estimate the inspection satellite's relative position in relation to its host spacecraft. An algorithm needed to calibrate the stereo camera system is presented, and this calibration method is discussed. These relative navigation algorithms are tested in NASA Johnson Space Center's simulation software, Engineering Dynamic On-board Ubiquitous Graphics (DOUG) Graphics for Exploration (EDGE), using a rendered model of the International Space Station to serve as the host spacecraft. Both vision-based algorithms proved to attain successful results, and the recommended future work is discussed.

  6. Optimizing Quantum Simulation for Heterogeneous Computing: a Hadamard Transformation Study

    NASA Astrophysics Data System (ADS)

    de Avila, Anderson B.; Schumalfuss, Murilo F.; Reiser, Renata H. S.; Pilla, Mauricio L.; Maron, Adriano K.

    2015-10-01

    The D-GM execution environment improves distributed simulation of quantum algorithms in heterogeneous computing environments comprising both multi-core CPUs and GPUs. The main contribution of this work consists in the optimization of the environment VirD-GM, conceived in three steps: (i) the theoretical studies and implementation of the abstractions of the Mixed Partial Process defined in the qGM model, focusing on the reduction of the memory consumption regarding multidimensional QTs; (ii) the distributed/parallel implementation of such abstractions allowing its execution on clusters of GPUs; (iii) and optimizations that predict multiplications by zero-value of the quantum states/transformations, implying reduction in the number of computations. The results obtained in this work embrace the distribute/parallel simulation of Hadamard gates up to 21 qubits, showing scalability with the increase in the number of computing nodes.

  7. 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.

  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. Case Study Discussion Experiences of Computer Education and Instructional Technologies Students about Instructional Design on an Asynchronous Environment

    ERIC Educational Resources Information Center

    Baran, Bahar; Keles, Esra

    2011-01-01

    The aim of this study is to reveal opinions and experiences of two Computer Education and Instructional Technologies Departments' students about case study discussion method after they discussed in online asynchronous environment about Instructional Design (ID). Totally, 80 second year students, 40 from Dokuz Eylul University and 40 from Karadeniz…

  11. 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

  12. 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

  13. 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

  14. Bridging the digital divide through the integration of computer and information technology in science education: An action research study

    NASA Astrophysics Data System (ADS)

    Brown, Gail Laverne

    The presence of a digital divide, computer and information technology integration effectiveness, and barriers to continued usage of computer and information technology were investigated. Thirty-four African American and Caucasian American students (17 males and 17 females) in grades 9--11 from 2 Georgia high school science classes were exposed to 30 hours of hands-on computer and information technology skills. The purpose of the exposure was to improve students' computer and information technology skills. Pre-study and post-study skills surveys, and structured interviews were used to compare race, gender, income, grade-level, and age differences with respect to computer usage. A paired t-test and McNemar test determined mean differences between student pre-study and post-study perceived skills levels. The results were consistent with findings of the National Telecommunications and Information Administration (2000) that indicated the presence of a digital divide and digital inclusion. Caucasian American participants were found to have more at-home computer and Internet access than African American participants, indicating that there is a digital divide by ethnicity. Caucasian American females were found to have more computer and Internet access which was an indication of digital inclusion. Sophomores had more at-home computer access and Internet access than other levels indicating digital inclusion. Students receiving regular meals had more computer and Internet access than students receiving free/reduced meals. Older students had more computer and Internet access than younger students. African American males had been using computer and information technology the longest which is an indication of inclusion. The paired t-test and McNemar test revealed significant perceived student increases in all skills levels. Interviews did not reveal any barriers to continued usage of the computer and information technology skills.

  15. Study on the Computational Estimation Performance and Computational Estimation Attitude of Elementary School Fifth Graders in Taiwan

    ERIC Educational Resources Information Center

    Tsao, Yea-Ling; Pan, Ting-Rung

    2011-01-01

    Main purpose of this study is to investigate what level of computational estimation performance is possessed by fifth graders and explore computational estimation attitude towards fifth graders. Two hundred and thirty-five Grade-5 students from four elementary schools in Taipei City were selected for "Computational Estimation Test" and…

  16. FDG positron emission computed tomography in a study of aphasia

    SciTech Connect

    Metter, E.J.; Wasterlain, C.G.; Kuhl, D.E.; Hanson, W.R.; Phelps, M.E.

    1981-08-01

    Positron emission computed tomography (PECT) using 18F-2-fluoro-2-deoxy-D-glucose (FDG) was used to investigate the correlations between clinical status, anatomy (as described by CT), and metabolism in five patients with stable aphasia resulting from ischemic cerebral infarction. Local cerebral metabolic activity was diminished in an area larger than the area of infarction demonstrated by CT. In one patient, FDG PECT revealed a metabolic lesion that probably caused the aphasic syndrome and was not apparent by CT. The data suggest that reliance on CT in delineating the extent of the brain lesion in aphasia or other neuropsychological defects can be misleading; FDG PECT may provide important additional information. Two patients with similar metabolic lesions had very different clinical syndromes, showing that even when currently available methods are combined, major gaps remain in clinicoanatomical correlations in aphasia.

  17. 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.

  18. Helicopter fuselage drag - combined computational fluid dynamics and experimental studies

    NASA Astrophysics Data System (ADS)

    Batrakov, A.; Kusyumov, A.; Mikhailov, S.; Pakhov, V.; Sungatullin, A.; Valeev, M.; Zherekhov, V.; Barakos, G.

    2015-06-01

    In this paper, wind tunnel experiments are combined with Computational Fluid Dynamics (CFD) aiming to analyze the aerodynamics of realistic fuselage configurations. A development model of the ANSAT aircraft and an early model of the AKTAI light helicopter were employed. Both models were tested at the subsonic wind tunnel of KNRTU-KAI for a range of Reynolds numbers and pitch and yaw angles. The force balance measurements were complemented by particle image velocimetry (PIV) investigations for the cases where the experimental force measurements showed substantial unsteadiness. The CFD results were found to be in fair agreement with the test data and revealed some flow separation at the rear of the fuselages. Once confidence on the CFD method was established, further modifications were introduced to the ANSAT-like fuselage model to demonstrate drag reduction via small shape changes.

  19. 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.

  20. 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.

  1. 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

  2. Computational Modeling and Molecular Physiology Experiments Reveal New Insights into Shoot Branching in Pea[C][W

    PubMed Central

    Dun, Elizabeth A.; Hanan, Jim; Beveridge, Christine A.

    2009-01-01

    Bud outgrowth is regulated by the interplay of multiple hormones, including auxin, cytokinin, strigolactones, and an unidentified long-distance feedback signal that moves from shoot to root. The model of bud outgrowth regulation in pea (Pisum sativum) includes these signals and a network of five RAMOSUS (RMS) genes that operate in a shoot-root-shoot loop to regulate the synthesis of, and response to, strigolactones. The number of components in this network renders the integration of new and existing hypotheses both complex and cumbersome. A hypothesis-driven computational model was therefore developed to help understand regulation of shoot branching. The model evolved in parallel with stepwise laboratory research, helping to define and test key hypotheses. The computational model was used to verify new mechanisms involved in the regulation of shoot branching by confirming that the new hypotheses captured all relevant biological data sets. Based on cytokinin and RMS1 expression analyses, this model is extended to include subtle but important differences in the function of RMS3 and RMS4 genes in the shoot and rootstock. Additionally, this research indicates that a branch-derived signal upregulates RMS1 expression independent of the other feedback signal. Furthermore, we propose xylem-sap cytokinin promotes sustained bud outgrowth, rather than acting at the earlier stage of bud release. PMID:19948786

  3. Multidetector Computed Tomography-Based Microstructural Analysis Reveals Reduced Bone Mineral Content and Trabecular Bone Changes in the Lumbar Spine after Transarterial Chemoembolization Therapy for Hepatocellular Carcinoma

    PubMed Central

    Takasu, Miyuki; Yamagami, Takuji; Nakamura, Yuko; Komoto, Daisuke; Kaichi, Yoko; Tani, Chihiro; Date, Shuji; Kiguchi, Masao; Awai, Kazuo

    2014-01-01

    Purpose It is well recognized that therapeutic irradiation can result in bone damage. However, long-term bone toxicity associated with computed tomography (CT) performed during interventional angiography has received little attention. The purpose of this study was to determine the prevalence of osteoporosis and trabecular microstructural changes in patients after transarterial chemoembolization (TACE) for hepatocellular carcinoma therapy using an interventional-CT system. Materials and Methods Spinal microarchitecture was examined by 64-detector CT in 81 patients who underwent TACE, 35 patients with chronic hepatitis, and 79 controls. For each patient, the volumetric CT dose index (CTDIv) during TACE (CTDIv (TACE)), the dose-length product (DLP) during TACE (DLP (TACE)), and CTDIv and DLP of routine dynamic CT scans (CTDIv (CT) and DLP (CT), respectively), were calculated as the sum since 2008. Using a three dimensional (3D) image analysis system, the tissue bone mineral density (tBMD) and trabecular parameters of the 12th thoracic vertebra were calculated. Using tBMD at a reported cutoff value of 68 mg/cm3, the prevalence of osteoporosis was assessed. Results The prevalence of osteoporosis was significantly greater in the TACE vs. the control group (39.6% vs. 18.2% for males, P<0.05 and 60.6% vs. 34.8% for females, P<0.01). Multivariate regression analysis demonstrated that sex, age, and CTDIv (CT) significantly affected the risk of osteoporosis. Of these indices, CTDIv (CT) had the highest area under the curve (AUC) (0.735). Correlation analyses of tBMD with cumulative radiation dose revealed weak correlations between tBMD and CTDIv (CT) (r2 = 0.194, P<0.001). Conclusion The prevalence of osteoporosis was significantly higher in post TACE patients than in control subjects. The cumulative radiation dose related to routine dynamic CT studies was a significant contributor to the prevalence of osteoporosis. PMID:25329933

  4. 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.

  5. 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.

  6. Experimental study of radiometric forces with comparison to computational results

    NASA Astrophysics Data System (ADS)

    Selden, Nathaniel P.

    A study of the radiometric forces on heated plates has been conducted both experimentally and computationally. The experiments were carried out at USC in two vacuum chambers up to a maximum pressure of 6 Pa for various carrier gases. The computations were performed with both the DSMC and ES-BGK methods for a 2-D gas flow over a comparable range of pressures. It is shown that the radiometric devices provide maximum force at a Knudsen number approximating 0.1. Of the various gases tested, helium provides the largest peak force. Qualitatively, the experimental data and computational results are similar. A lack of experimental data on gas-surface accommodation and flow three-dimensionality yields up to a 40% difference in the magnitude of the measured and computed forces, but it is shown that this discrepancy can be used to predict accommodation values. Comparison of four geometric configurations has shown that the effect of the area is significant at pressures up to where the force is maximum. It is also demonstrated that the size of the chamber in which the radiometer resides is of primary importance, where the chamber dimensions are inversely related to the generated force. Finally, simulation of multi-vane configurations have shown that the optimal spacing of vanes can be tailored for specific uses; for maximum force production a tight spacing should be used, while maximum efficiency requires spacing on the order of a vane dimension. While the results so far are encouraging, they are far from complete. Further improvements would include: a new experimental setup to reduce uncertainty with highly accurate temperature control and measurement, an in situ way to prepare the surface as well as measure its cleanliness, and an in depth iterative computational study observing the impact of multiple radiometer vanes at numerous seperations.

  7. 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.

  8. Computer vision as a tool to study plant development.

    PubMed

    Spalding, Edgar P

    2009-01-01

    Morphological phenotypes due to mutations frequently provide key information about the biological function of the affected genes. This has long been true of the plant Arabidopsis thaliana, though phenotypes are known for only a minority of this model organism's approximately 25,000 genes. One common explanation for lack of phenotype in a given mutant is that a genetic redundancy masks the effect of the missing gene. Another possibility is that a phenotype escaped detection or manifests itself only in a certain unexamined condition. Addressing this potentially nettlesome alternative requires the development of more sophisticated tools for studying morphological development. Computer vision is a technical field that holds much promise in this regard. This chapter explains in general terms how computer algorithms can extract quantitative information from images of plant structures undergoing development. Automation is a central feature of a successful computer vision application as it enables more conditions and more dependencies to be characterized. This in turn expands the concept of phenotype into a point set in multidimensional condition space. New ways of measuring and thinking about phenotypes, and therefore the functions of genes, are expected to result from expanding the role of computer vision in plant biology. PMID:19588113

  9. 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.

  10. Computer microworld development adapted to children's conceptions: A case study

    NASA Astrophysics Data System (ADS)

    Couturier, Russell Lawrence

    This research studied changes in ten middle school students' scientific conceptions during interaction with a computer microworld designed adaptively for exploring phases of the moon. Following direct observations of lunar phenomena, five students participated in the development of the computer microworld. The researcher implemented software design requests from the students based on their real world and microworld experience. Five different students used the final revised microworld and provided additional feedback. All sessions were transcribed and analyzed. Evidence from this case study suggests that this constructionist activity was a good catalyst for inducing conceptual change in learners---especially the five who had considerable ownership in the software development. Implications for classroom teaching strategies and suggestions for future research are offered.

  11. 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

  12. 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),…

  13. 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.

  14. 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.

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

    DOE PAGESBeta

    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

  16. 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)

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

    PubMed

    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

  18. 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

  19. Computational analysis of four human adenovirus type 4 genomes reveals molecular evolution through two interspecies recombination events

    PubMed Central

    Dehghan, Shoaleh; Seto, Jason; Liu, Elizabeth B.; Walsh, Michael P.; Dyer, David W.; Chodosh, James; Seto, Donald

    2013-01-01

    Computational analysis of human adenovirus type 4 (HAdV-E4), a pathogen that is the only HAdV member of species E, provides insights into its zoonotic origin and molecular adaptation. Its genome encodes a domain of the major capsid protein, hexon, from HAdV-B16 recombined into the genome chassis of a simian adenovirus. Genomes of two recent field strains provide a clue to its adaptation to the new host: recombination of a NF-I binding site motif, which is required for efficient viral replication, from another HAdV genome. This motif is absent in the chimpanzee adenoviruses and the HAdV-E4 prototype, but is conserved amongst other HAdVs. This is the first report of an interspecies recombination event for HAdVs, and the first documentation of a lateral partial gene transfer from a chimpanzee AdV. The potential for such recombination events are important when considering chimpanzee adenoviruses as candidate gene delivery vectors for human patients. PMID:23763770

  20. A novel periodic boundary condition for computational hemodynamics studies.

    PubMed

    Bahramian, Fereshteh; Mohammadi, Hadi

    2014-07-01

    In computational fluid dynamics models for hemodynamics applications, boundary conditions remain one of the major issues in obtaining accurate fluid flow predictions. For major cardiovascular models, the realistic boundary conditions are not available. In order to address this issue, the whole computational domain needs to be modeled, which is practically impossible. For simulating fully developed turbulent flows using the large eddy simulation and dynamic numerical solution methods, which are very popular in hemodynamics studies, periodic boundary conditions are suitable. This is mainly because the computational domain can be reduced considerably. In this study, a novel periodic boundary condition is proposed, which is based on mass flow condition. The proposed boundary condition is applied on a square duct for the sake of validation. The mass-based condition was shown to obtain the solution in 15% less time. As such, the mass-based condition has two decisive advantages: first, the solution for a given Reynolds number can be obtained in a single simulation because of the direct specification of the mass flow, and second, simulations can be made more quickly. PMID:25015666

  1. 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

  2. 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.

  3. 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

  4. 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

  5. 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.

  6. 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

  7. 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…

  8. 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,…

  9. 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

  10. 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

  11. 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

  12. Ocean predictability studies in a parallel computing environment. Final report

    SciTech Connect

    Leary, R.H.

    1992-11-01

    The goal of the SDSC effort described here is to evaluate the performance potential of the Oberhuber isopycnal (OPYC) ocean global circulation model on the 64-node iPSC/860 parallel computer at SDSC and its near term successor, the Intel Paragon, relative to that of a single vector processor of a CRAY Y-MP and its near term successor, the CRAY C90. This effort is in support of a larger joint project with researchers at Scripps Institution of Oceanography to study the properties of long (10 to 100-year scale), computationally intensive integrations of ocean global circulation models. Generally, performance of the OPYC model on the iPSC/860 has proved quite disappointing, with a simplified version of the entire model running at approximately 1.4 Mflops on a single i860 node in its original form and after extensive optimization, including coding in assembler, at 3.2 Mflops. The author estimates overall performance to be limited to 75 Mflops or less on the 64-node machine, as compared to 180 Mflops for a single CRAY Y-MP processor and 500 Mflops for a single CRAY C90 processor. Similarly, he believes an implementation on an Intel Paragon, even with several hundred nodes, will not be competitive with a single processor C90 implementation. Additionally, the Hamburg Large Scale Geostrophic (LSG) model has been implemented on high-performance workstations and evaluated for its computational potential as an alternative to OPYC for the long term integrations.

  13. Revealing Praxis: A Study of Professional Learning and Development as a Beginning Social Studies Teacher Educator

    ERIC Educational Resources Information Center

    Ritter, Jason K.

    2010-01-01

    This self-study reports on the professional learning and development of a beginning social studies teacher educator via an examination of the evolving relationship between the author's beliefs and practices during his first three years preparing social studies teachers. Throughout this time data were systematically collected in the form of written…

  14. 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.

  15. Dandy-Walker syndrome studied by computed tomography and pneumoencephalography

    SciTech Connect

    Masdeu, J.C.; Dobben, G.D.; Azar-Kia, B.

    1983-04-01

    Based on air studies, some authors have disputed the ability of computed tomography (CT) to diagnose posterior fossa cysts. The authors correlated the pneumoencephalographic, CT, and pathological findings in 4 patients with classic Dandy-Walker syndrome. Three cases had been misdiagnosed as retrocerebellar arachnoid cysts because the fourth ventricle was incorrectly considered normal on brow-up or erect air studies, reflecting the inability of such studies to evaluate an agenetic vermis and deficient posterior medullary velum which are characteristic of Dandy-Walker malformation. Careful correlation with autopsy findings showed that even with complete agenesis of the inferior vermis, if the slit between the cerebellar hemispheres is narrow, the fourth ventricle could be misinterpreted as normal on pneumoencephalography and sagittal CT. Radionuclide studies, a small amount of air, or metrizamide may be needed to determine whether the cyst communicates with the subarachnoid space.

  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 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.

  18. 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.

  19. 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.

  20. Synchrotron radiation computed laminography for polymer composite failure studies.

    PubMed

    Xu, Feng; Helfen, Lukas; Moffat, Andrew J; Johnson, Gregory; Sinclair, Ian; Baumbach, Tilo

    2010-03-01

    Synchrotron radiation computed laminography is applied to the three-dimensional micro-imaging of damage in large polymer composite plates with high spatial resolution. The influence of different experimental conditions is studied with respect to measurement time optimization, dose minimization and reduction of artefacts in the reconstructed images. Failures like delaminations, transverse ply cracks and splits are observed under in situ loads. The propagation of up to 2 mm-long cracks is non-destructively followed in situ and investigated in detail. By phase retrieval using a single detector distance, the failures can be easily visualized in three dimensions. PMID:20157275

  1. Synchrotron radiation computed laminography for polymer composite failure studies

    PubMed Central

    Xu, Feng; Helfen, Lukas; Moffat, Andrew J.; Johnson, Gregory; Sinclair, Ian; Baumbach, Tilo

    2010-01-01

    Synchrotron radiation computed laminography is applied to the three-dimensional micro-imaging of damage in large polymer composite plates with high spatial resolution. The influence of different experimental conditions is studied with respect to measurement time optimization, dose minimization and reduction of artefacts in the reconstructed images. Failures like delaminations, transverse ply cracks and splits are observed under in situ loads. The propagation of up to 2 mm-long cracks is non-destructively followed in situ and investigated in detail. By phase retrieval using a single detector distance, the failures can be easily visualized in three dimensions. PMID:20157275

  2. 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.

  3. Computational Studies of Protein Aggregation: Methods and Applications

    NASA Astrophysics Data System (ADS)

    Morriss-Andrews, Alex; Shea, Joan-Emma

    2015-04-01

    Protein aggregation involves the self-assembly of normally soluble proteins into large supramolecular assemblies. The typical end product of aggregation is the amyloid fibril, an extended structure enriched in β-sheet content. The aggregation process has been linked to a number of diseases, most notably Alzheimer's disease, but fibril formation can also play a functional role in certain organisms. This review focuses on theoretical studies of the process of fibril formation, with an emphasis on the computational models and methods commonly used to tackle this problem.

  4. 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

  5. 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.

  6. Computational Study on Chemical Reaction Mechanisms of Octafluorocarbon Molecules

    NASA Astrophysics Data System (ADS)

    Choi, Heechol; Song, Mi-Young; Yoon, Jung-Sik; Plasma Fundamental Technology Research Team

    2015-09-01

    Saturated or unsaturated octafluorocarbons(OFCs) have been used extensively in dry etching processes due to their relatively low global warming potential and their high CF2 radical levels in commercial plasma treatments. Many experimental and theoretical studies of these species have been performed for useful information about physical and chemical properties of OFCs. However, direct experimental studies of these chemicals are difficult because of their high reactivity in plasma state and high-level theoretical approaches such as G3(MP2) and CCSD(T)/CBS need huge computational cost. Recently, it has been shown that the ωB97X-D/aVTZ method is strongly recommended as the best practical density functional theory(DFT) for rigorous and extensive studies of OFCs because of its high performance and reliability for van der Waals interactions. All the feasible isomerization and dissociation paths of OFCs were investigated at ωB97X-D/aVTZ and rate constants of their chemical reactions were computed by using variational transition-state theory(VTST) for a deep insight into OFCs' reaction mechanisms. Fates and roles of OFCs and their fragments in plasma phases could be clearly explained based on the obtained reaction mechanisms. This work was supported by R&D Program of ``Plasma Convergence & Fundamental Research'' through NFRI of Korea funded by the Government funds.

  7. 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.

  8. Computer Competencies for MLS Graduates: A Study of the UH Graduate School of Library Studies.

    ERIC Educational Resources Information Center

    Davies, Denise M.

    This study is designed to identify the computer competencies that should be required of library/information studies (LIS) graduates of the Graduate School of Library Studies (GSLS) at the University of Hawaii at Manoa. The long term objective of the study is to provide information for the policy and planning of GSLS. The study examines how certain…

  9. 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.

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

    PubMed Central

    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

  11. 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

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

    PubMed

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

    2016-06-01

    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

  13. Computer modelling studies of the bilayer/water interface.

    PubMed

    Pasenkiewicz-Gierula, Marta; Baczynski, Krzysztof; Markiewicz, Michal; Murzyn, Krzysztof

    2016-10-01

    This review summarises high resolution studies on the interface of lamellar lipid bilayers composed of the most typical lipid molecules which constitute the lipid matrix of biomembranes. The presented results were obtained predominantly by computer modelling methods. Whenever possible, the results were compared with experimental results obtained for similar systems. The first and main section of the review is concerned with the bilayer-water interface and is divided into four subsections. The first describes the simplest case, where the interface consists only of lipid head groups and water molecules and focuses on interactions between the lipid heads and water molecules; the second describes the interface containing also mono- and divalent ions and concentrates on lipid-ion interactions; the third describes direct inter-lipid interactions. These three subsections are followed by a discussion on the network of direct and indirect inter-lipid interactions at the bilayer interface. The second section summarises recent computer simulation studies on the interactions of antibacterial membrane active compounds with various models of the bacterial outer membrane. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg. PMID:26825705

  14. 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.

  15. 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

  16. 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…

  17. 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…

  18. Computer Self-Efficacy, Computer Anxiety, and Attitudes toward the Internet: A Study among Undergraduates in Unimas

    ERIC Educational Resources Information Center

    Sam, Hong Kian; Othman, Abang Ekhsan Abang; Nordin, Zaimuarifuddin Shukri

    2005-01-01

    Eighty-one female and sixty-seven male undergraduates at a Malaysian university, from seven faculties and a Center for Language Studies completed a Computer Self-Efficacy Scale, Computer Anxiety Scale, and an Attitudes toward the Internet Scale and give information about their use of the Internet. This survey research investigated undergraduates'…

  19. 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.

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

    PubMed

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

    2015-11-01

    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

  2. Field and computer modeling studies of Appalachian cyclic carbonates

    SciTech Connect

    Read, J.F.

    1988-01-01

    Cyclic carbonates in the Cambrian of the Appalachians have been studied using field data integrated with computer modeling studies. The models incorporate 1 to 3-m.y. and 20,000 to 100,000-year low-amplitude sea level fluctuations, water depth-dependent sedimentation rates, lag time, and subsidence. The 1 to 3-m.y. sea level fluctuations are defined by Fischer plots, which are readily compared to the model output. Cycles decrease in number toward regional highs, because lower subsidence rates only allow 40 to 60% of the Milankovitch sea level fluctuations to affect the highs and highs subside lower than third-order sea levels fall, which truncate 50% of cycles. Furthermore, 2 cycles/100,000 years are deposited on the outer shelf, compared to 1 to 1.4 cycles/100,000 years on inner shelf highs. Consequently, cycles have longer average periods toward the highs.

  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. A computational study of discrete mechanical tissue models.

    PubMed

    Pathmanathan, P; Cooper, J; Fletcher, A; Mirams, G; Murray, P; Osborne, J; Pitt-Francis, J; Walter, A; Chapman, S J

    2009-01-01

    A computational study of discrete 'cell-centre' approaches to modelling the evolution of a collection of cells is undertaken. The study focuses on the mechanical aspects of the tissue, in order to separate the passive mechanical response of the model from active effects such as cell-growth and cell division. Issues which arise when implementing these models are described, and a series of numerical mechanical experiments is performed. It is shown that discrete tissues modelled this way typically exhibit elastic-plastic behaviour under slow compression, and act as a brittle linear elastic solid under slow tension. Both overlapping spheres and Voronoi-tessellation-based models are examined, and the effect of different cell-cell interaction force laws on the bulk mechanical properties of the tissue is determined. This correspondence allows parameters in the cell-based model to be chosen to be compatible with bulk tissue measurements. PMID:19369704

  5. A computer simulation study of compressor tuning phenomena

    NASA Astrophysics Data System (ADS)

    Nieter, J. J.; Singh, R.

    1984-12-01

    Basic thermofluid processes of a positive displacement compressor are strongly dependent upon the acoustic behavior of the manifolds. The tuning process of such a compressor is fairly complex as increases in the mass flow rate may not correspond with higher energy efficiencies. In this paper a computer simulation program is described, which includes the manifold back pressure effect, developed to investigate and explain the tuning phenomena for a single or two-cylinder reciprocating compressor. A symmetric suction manifold system for a two-cylinder refrigeration compressor has been considered as the example case in this tuning study. Results for flow efficiency, energy efficiency, and pressure pulsations at the valve exit are presented in terms of the acoustic natural frequencies of the manifold system. Predicted results compare reasonably well with experimental data. Based on this study, it is possible to choose optimal manifold dimensions which will provide higher efficiencies with lower pressure pulsations.

  6. Computational Study of Savonius Wind Turbines with Stators

    NASA Astrophysics Data System (ADS)

    Alexander, Aaron; Santhanakrishnan, Arvind

    2015-11-01

    The dynamics of a stator assembly that directs incoming wind into an internal cylindrical trapped flow that exits vertically has been previously studied using particle image velocimetry and computational fluid dynamics (CFD). The present study uses the commercial CFD package Star-CCM + (CD-adapco) to investigate how a Savonius rotor is affected by the introduction of cylindrical flow trapped by a stator enclosure. The results are then compared with the flow field around an identical Savonius rotor without a stator assembly. The flow characteristics are investigated at Reynolds numbers on the order of one million to examine local flow effects around the rotor as well as downstream wake vorticity. Additionally, the minimum free stream wind velocity needed for rotor start-up and rotor output power will be compared with and without the use of a stator.

  7. Computational and experimental study of a railplug ignitor

    SciTech Connect

    Ellzey, J.L.; Hall, M.J.; Zhao, X. . Dept. of Mechanical Engineering); Tajima, H. . Dept. of Mechanical Engineering)

    1992-01-01

    The plasma plume generated by a new type of high energy Janitor known as the railplug, is examined. The railplug is a miniaturized railgun that has the potential for improving ignition characteristics of combustible mixtures in engines. The objective of the study is to gain an uderstanding of the characteristics of the plasma created by a transparent railplug, and to validate a multidimensional computer simulation of the plasma and shock fronts. The nature of the plume emitted by the railplug was examined for three levels of electrical energy while firing into air at a pressure of 1 atm. The computer model is to be used to predict trends in railplug performance for various railplug designs, energies, and ambient conditions. The velocity of the plasma movement inside a transparent railplug was measured, as well as the velocity of the plume ejected from the cavity. A shock is produced at the initiation point of the arc and propagates down the cavity, eventually exiting the plug. The velocity of the shock was both measured experimentally and simulated by the model. The computer simulation produces a mushroom-shaped plasma plume at the railplug exit similar to that observed in the shadowgraph photos: The simulation also reproduced the toroidal circulation observed at the plug exit in the shadowgraphs, the radial expansion and the penetration depth of the plume. The trend of linearly increasing plasma kinetic energy with stored electrical energy predicted by the simulation was verified by shadowgraph photos. The agreement between the experiments and the simulations suggests that the multidimensional model holds promise is a predictive design tool.

  8. Computational and experimental study of a railplug ignitor

    SciTech Connect

    Ellzey, J.L.; Hall, M.J.; Zhao, X.; Tajima, H.

    1992-12-31

    The plasma plume generated by a new type of high energy Janitor known as the railplug, is examined. The railplug is a miniaturized railgun that has the potential for improving ignition characteristics of combustible mixtures in engines. The objective of the study is to gain an uderstanding of the characteristics of the plasma created by a transparent railplug, and to validate a multidimensional computer simulation of the plasma and shock fronts. The nature of the plume emitted by the railplug was examined for three levels of electrical energy while firing into air at a pressure of 1 atm. The computer model is to be used to predict trends in railplug performance for various railplug designs, energies, and ambient conditions. The velocity of the plasma movement inside a transparent railplug was measured, as well as the velocity of the plume ejected from the cavity. A shock is produced at the initiation point of the arc and propagates down the cavity, eventually exiting the plug. The velocity of the shock was both measured experimentally and simulated by the model. The computer simulation produces a mushroom-shaped plasma plume at the railplug exit similar to that observed in the shadowgraph photos: The simulation also reproduced the toroidal circulation observed at the plug exit in the shadowgraphs, the radial expansion and the penetration depth of the plume. The trend of linearly increasing plasma kinetic energy with stored electrical energy predicted by the simulation was verified by shadowgraph photos. The agreement between the experiments and the simulations suggests that the multidimensional model holds promise is a predictive design tool.

  9. Computers in the Social Studies Classroom. How to Do It Series, Series 2, No. 14.

    ERIC Educational Resources Information Center

    Diem, Richard A.

    Designed to introduce social studies teachers to computers and to suggest ideas for their potential applications in social studies classrooms, this booklet is arranged in various sections. One section describes the origins of the modern computer, another defines computer terminology, and two sections explain computer hardware and computer…

  10. 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…

  11. 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…

  12. 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…

  13. 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…

  14. Computer Ethics: New Study Area for Engineering Science Students

    ERIC Educational Resources Information Center

    Johnson, Deborah G.

    1978-01-01

    Computer professionals are beginning to look toward codes of ethics and legislation to control the use of software. A project has been established at Rensselaer Polytechnic Institute to develop teaching materials on computer ethics. (BB)

  15. 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.

  16. 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…

  17. 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…

  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. 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.

  20. 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.

  1. Computed microtomography and numerical study of porous rock samples

    NASA Astrophysics Data System (ADS)

    Bielecki, J.; Jarzyna, J.; Bożek, S.; Lekki, J.; Stachura, Z.; Kwiatek, W. M.

    2013-12-01

    Measurement of physical properties of porous geological materials is a crucial issue in oil and gas recovery industry. A conventional experimental way to obtain information on porosity, pore size distribution, specific surface area and permeability are the intrusion porosimetry and permeameter measurement. However, in this approach Washburn's equation is usually used, thus approximation of cylindrical pore shapes is made. However, in recent times the computed microtomography (CMT) technique is more widely used in geoscience (Appoloni et al., 2007). We have already reported preliminary results of investigation of elemental content, microporosity, and specific surface area of porous rocks by means of the CMT technique based on a laboratory source (Bielecki et al., 2012). In this paper, results of complex study of porous rock samples with the use of X-ray CMT (laboratory-source-based facility and synchrotron radiation source) combined with permeability tensor computation by means of the Lattice Boltzmann Method (LBM) are presented. Moreover, the proton induced X-ray emission (PIXE) method was additionally used for elemental content determination of pores-filling substance.

  2. 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

  3. 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.

  4. Photoisomerization among ring-open merocyanines. II. A computational study

    NASA Astrophysics Data System (ADS)

    Walter, Christof; Ruetzel, Stefan; Diekmann, Meike; Nuernberger, Patrick; Brixner, Tobias; Engels, Bernd

    2014-06-01

    The photochemical isomerization of the trans-trans-cis to the trans-trans-trans isomer of the merocyanine form of 6-nitro BIPS, which has been studied with femtosecond transient absorption spectroscopy [S. Ruetzel, M. Diekmann, P. Nuernberger, C. Walter, B. Engels, and T. Brixner, J. Chem. Phys. 140, 224310 (2014)], is investigated using time-dependent density functional theory in conjunction with polarizable continuum models. Benchmark calculations against SCS-ADC(2) evaluate the applicability of the CAM-B3LYP functional. Apart from a relaxed scan in the ground state with additional computation of the corresponding excitation energies, which produces the excited-state surface vertical to the ground-state isomerization coordinate, a relaxed scan in the S1 gives insight into the geometric changes orthogonal to the reaction coordinate and the fluorescence conditions. The shape of the potential energy surface (PES) along the reaction coordinate is found to be highly sensitive to solvation effects, with the method of solvation (linear response vs. state-specific) being critical. The shape of the PES as well as the computed harmonic frequencies in the S1 minima are in line with the experimental results and offer a straightforward interpretation.

  5. Deviated nasal septum hinders intranasal sprays: A computer simulation study

    PubMed Central

    Frank, Dennis O.; Kimbell, Julia S.; Cannon, Daniel; Pawar, Sachin S.; Rhee, John S.

    2013-01-01

    Background This study investigates how deviated nasal septum affects the quantity and distribution of spray particles, and examines the effects of inspiratory airflow and head position on particle transport. Methods Deposition of spray particles was analysed using a three-dimensional computational fluid dynamics model created from a computed tomography scan of a human nose with leftward septal deviation and a right inferior turbinate hypertrophy. Five simulations were conducted using Fluent™ software, with particle sizes ranging from 20-110μm, a spray speed of 3m/s, plume angle of 68°, and with steady state inspiratory airflow either present (15.7L/min) or absent at varying head positions. Results With inspiratory airflow present, posterior deposition on the obstructed side was approximately four times less than the contralateral side, regardless of head position, and was statistically significant (p<0.05). When airflow was absent, predicted deposition beyond the nasal valve on the left and right sides were between 16% and 69% lower and positively influenced by a dependent head position. Conclusions Simulations predicted that septal deviation significantly diminished drug delivery on the obstructed side. Furthermore, increased particle penetration was associated with presence of nasal airflow. Head position is an important factor in particle deposition patterns when inspiratory airflow is absent. PMID:22888490

  6. Accurate Computation of Survival Statistics in Genome-Wide Studies

    PubMed Central

    Vandin, Fabio; Papoutsaki, Alexandra; Raphael, Benjamin J.; Upfal, Eli

    2015-01-01

    A key challenge in genomics is to identify genetic variants that distinguish patients with different survival time following diagnosis or treatment. While the log-rank test is widely used for this purpose, nearly all implementations of the log-rank test rely on an asymptotic approximation that is not appropriate in many genomics applications. This is because: the two populations determined by a genetic variant may have very different sizes; and the evaluation of many possible variants demands highly accurate computation of very small p-values. We demonstrate this problem for cancer genomics data where the standard log-rank test leads to many false positive associations between somatic mutations and survival time. We develop and analyze a novel algorithm, Exact Log-rank Test (ExaLT), that accurately computes the p-value of the log-rank statistic under an exact distribution that is appropriate for any size populations. We demonstrate the advantages of ExaLT on data from published cancer genomics studies, finding significant differences from the reported p-values. We analyze somatic mutations in six cancer types from The Cancer Genome Atlas (TCGA), finding mutations with known association to survival as well as several novel associations. In contrast, standard implementations of the log-rank test report dozens-hundreds of likely false positive associations as more significant than these known associations. PMID:25950620

  7. 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. PMID:26891818

  8. 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

  9. 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.

  10. 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

  11. 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…

  12. Computational design and structure-property relationship studies on heptazines.

    PubMed

    Ghule, Vikas D; Sarangapani, Radhakrishnan; Jadhav, Pandurang M; Pandey, Raj Kishore

    2011-11-01

    This study aimed to design novel nitrogen-rich heptazine derivatives as high energy density materials (HEDM) by exploiting systematic structure-property relationships. Molecular structures with diverse energetic substituents at varying positions in the basic heptazine ring were designed. Density functional techniques were used for prediction of gas phase heat of formation by employing an isodesmic approach, while crystal density was assessed by packing calculations. The results reveal that nitro derivatives of heptazine possess a high heat of formation and further enhancement was achieved by the substitution of nitro heterocycles. The crystal packing density of the designed compounds varied from 1.8 to 2 g cm(-3), and hence, of all the designed molecules, nitro derivatives of heptazine exhibit better energetic performance characteristics in terms of detonation velocity and pressure. The calculated band gap of the designed molecules was analyzed to establish sensitivity correlations, and the results reveal that, in general, amino derivatives possess better insensitivity characteristics. The overall performance of the designed compounds was moderate, and such compounds may find potential applications in gas generators and smoke-free pyrotechnic fuels as they are rich in nitrogen content. PMID:21318236

  13. 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…

  14. 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.

  15. 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

  16. Arsine and its fluoro, chloro derivatives: a computational thermochemical study

    NASA Astrophysics Data System (ADS)

    Bagchi, Sabyasachi; Mondal, Bhaskar; Ghosh, Deepanwita; Das, Abhijit K.

    2010-01-01

    The structures, vibrational frequencies, enthalpies of formation and dissociation energies of arsine, arsenic hydrides and their fluoro, chloro derivatives have been studied using density functional B3LYP/cc-pVDZ, ab-initio MP2/cc-pVDZ and composite CBS-QB3 and CBS-Q methods. Computed standard enthalpies of formation at 298 K by atomisation scheme are compared with reported values. Bond dissociation energies at 0 K are calculated for all possible thermal dissociation of the molecular species in gas phase, from which the energetically most favourable dissociation pathways are predicted. The calculated enthalpies of formation and bond dissociation energies are correlated with the nature of bonding in arsine and its fluoro, chloro derivatives. Energy barriers at 0 K are calculated and transition states are located for the molecular fragment elimination of the thermal dissociation reactions.

  17. 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.

  18. 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

  19. 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

  20. 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

  1. 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

  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 of quantum dot sensitized solar cells

    NASA Astrophysics Data System (ADS)

    Kolesov, Grigory

    This thesis presents a computational study of quantum dot (QD) sensitized solar cells. First part deals with the non-equilibrium many-body theory or non-equilibrium Green's function (NEGF) theory. In this approach I study electron dynamics in the quantum-dot sensitized solar cell subjected to time-dependent fields. NEGF theory, because it does not impose any conditions on a perturbation, is the fundamental one to describe ultrafast processes in small, strongly correlated systems and/or in strong fields. In this research I do not only perform analytical derivation, but also design and implement spectral numerical solution for the resulting complex system of partial integrodifferential equations. This numerical solution yielded an order of magnitude speedup over the methods used previously in the field. The forth chapter of this thesis deals with calculation of optical properties and the ground state configuration of Zn2SnO4 (ZTO). ZTO is used by experimentalists in UW to grow nanorods which are then sensitized by QDs. ZTO is a challenging material for computational analysis because of its inverse spinel structure; thus it has an immense number of configurations matching the X-ray diffraction experiments. I've applied a cluster expansion method and have found the ground state configuration and phase diagram for ZTO. Calculations of optical properties of ground state bulk ZTO were done with a recently developed DFT functional. The optical band gap obtained in these calculations matched the experimental value. The last chapter describes development of the general simulator for interdigitated array electrodes. The application of this simulation together with the experiments may lead to understanding of reaction parameters and mechanisms important for development of electrochemical solar cells.

  4. 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.

  5. 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

  6. 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

  7. Computational and analytical studies of magnetization switching in iron nanopillars

    NASA Astrophysics Data System (ADS)

    Thompson, Sam Hill

    In this dissertation we study the behavior of several computational models of a magnetic nanopillar. We first compare the effect that coarse-graining the computational lattice has on the magnetization switching for three degrees of discretization. Bimodal switching-time distributions are found for all three models, however the underlying mechanism is different for each one. In the lowest-resolution, single-spin model, a bimodal distribution is the result of spin precession which sometimes crosses the threshold defining a switching event early or in the next precession period, depending on thermal fluctuations. For the medium-resolution, stack-of-spins model, the presence of either one or two propagating domain walls during the switching event determines the total switching time, leading to the observed bimodal distribution. The most realistic model, which employs a high-resolution computational lattice, permits multiple switching paths, some of which are characterized by their visitation to a metastable free-energy well and consequently longer lifetimes. It is also notable that the medium-resolution model exhibits reentrant behavior for reversal fields that are applied close to the easy axis. The highest-resolution model is studied in detail, due to its complexity, which precludes a simple description of the mechanism resulting in bimodal switching-time behavior. Phase-space portraits of components of the total energy indicate that the metastable free-energy basin is circumvented for short-lived trials. Sufficient statistics are gathered to allow Markov matrices describing the average behavior of each mode to be investigated. Eigenvectors of these matrices provide estimates of the probability distribution of the largest transient for each mode in the energy space, while the projective dynamics technique identifies the location of the free-energy saddle point. The hypothesis that the visitation of the metastable well underlies the bimodal behavior is further

  8. Mechanistic Studies of Bismuth(V)-Mediated Thioglycoside Activation Reveal Differential Reactivity of Anomers.

    PubMed

    Goswami, Manibarsha; Ashley, Daniel C; Baik, Mu-Hyun; Pohl, Nicola L B

    2016-07-15

    The mechanism of bismuth(V)-mediated thioglycoside activation was examined using reaction kinetics and quantum chemical reaction models. NMR experiments show an unusual nonlinear growth/decay curve for the glycosylation reaction. Further studies suggest an anomeric inversion of the β-glycoside donor to the α-donor during its activation, even in the presence of a neighboring 2-position acetate. Interestingly, in situ anomerization was not observed in the activation of an α-glycoside donor, and this anomer also showed faster reaction times and higher product diastereoselectivites. Density functional theory calculations identify the structure of the promoter triphenyl bismuth ditriflate, [Ph3Bi(OTf)2, 1], in solution and map out the energetics of its interactions with the two thioglycoside anomers. These calculations suggest that 1 must bind the thiopropyl arm to induce triflate loss. The computational analyses also show that, unlike most O-glycosides, the β- and α-donor S-glycosides are similar in energy. One energetically reasonable anomerization pathway of the donors is an SN1-like mechanism promoted by forming a bismuth-sulfonium adduct with the Lewis acidic Bi(V) for the formation of an oxacarbenium intermediate. Finally, the computed energy compensations needed to form these α vs β Bi adducts is a possible explanation for the differential reactivity of these donors. PMID:27295299

  9. 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

  10. 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…

  11. Computational study on the molecular inclusion of andrographolide by cyclodextrin.

    PubMed

    Zhou, Hongwei; Lai, Wai-Ping; Zhang, Zhiqiang; Li, Wai-Kee; Cheung, Hon-Yeung

    2009-03-01

    Due to the poor water solubility of andrographolide (andro), an inclusion technique has been developed to modify its physical and chemical properties so as to improve its bioavailability. In contrast with the immense experimental studies on the inclusion complexes of andro:cyclodextrin, no computational study has so far been carried out on this system. In this work, preliminary docking experiments with AutoDock were performed. Density Functional Theory (DFT) and Austin Model 1 (AM1) calculations upon the docking instances were applied to investigate the two possible modes of molecular inclusions between andro and x-cyclodextrin (xCD, where x is alpha, beta or gamma). Atoms-in-Molecules (AIM) analysis based on the B3LYP/cc-pVDZ wavefunction was applied to verify the existence of the intermolecular hydrogen bonds. It was found that the most stable complex among the six possible inclusion complexes was the one formed between andro and betaCD with andro's decalin ring moiety wrapped by CD at a ratio of 1:1. The hydrogen bonds between andro and CD were responsible for the stability of the inclusion complexes. The calculated data were found to be consistent with the experimental results. Thus, the results of this study can aid new drug design processes. PMID:18841328

  12. 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.

  13. An oculomotor and computational study of a patient with diagonistic dyspraxia.

    PubMed

    Pouget, Pierre; Pradat-Diehl, Pascale; Rivaud-Péchoux, Sophie; Wattiez, Nicolas; Gaymard, Bertrand

    2011-04-01

    Diagonistic dyspraxia (DD) is a behavioural disorder encountered in split-brain subjects in which the left arm acts against the subject's will, deliberately counteracting what the right arm does. We report here an oculomotor and computational study of a patient with a long lasting form of DD. A first series of oculomotor paradigms revealed marked and unprecedented saccade impairments. We used a computational model in order to provide information about the impaired decision-making process: the analysis of saccade latencies revealed that variations of decision times were explained by adjustments of response criterion. This result and paradoxical impairments observed in additional oculomotor paradigms allowed to propose that this adjustment of the criterion level resulted from the co-existence of counteracting oculomotor programs, consistent with the existence of antagonist programs in homotopic cortical areas. In the intact brain, trans-hemispheric inhibition would allow suppression of these counter programs. Depending on the topography of the disconnected areas, various motor and/or behavioural impairments would arise in split-brain subjects. In motor systems, such conflict would result in increased criteria for desired movement execution (oculomotor system) or in simultaneous execution of counteracting movements (skeletal motor system). At higher cognitive levels, it may result in conflict of intentions. PMID:20457451

  14. 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

  15. Revealing the Strong Functional Association of adipor2 and cdh13 with adipoq: A Gene Network Study.

    PubMed

    Bag, Susmita; Anbarasu, Anand

    2015-04-01

    In the present study, we have analyzed functional gene interactions of adiponectin gene (adipoq). The key role of adipoq is in regulating energy homeostasis and it functions as a novel signaling molecule for adipose tissue. Modules of highly inter-connected genes in disease-specific adipoq network are derived by integrating gene function and protein interaction data. Among twenty genes in adipoq web, adipoq is effectively conjoined with two genes: Adiponectin receptor 2 (adipor2) and cadherin 13 (cdh13). The functional analysis is done via ontological briefing and candidate disease identification. We observed that the highly efficient-interlinked genes connected with adipoq are adipor2 and cdh13. Interestingly, the ontological aspect of adipor2 and cdh13 in the adipoq network reveal the fact that adipoq and adipor2 are involved mostly in glucose and lipid metabolic processes. The gene cdh13 indulge in cell adhesion process with adipoq and adipor2. Our computational gene web analysis also predicts potential candidate disease recognition, thus indicating the involvement of adipoq, adipor2, and cdh13 with not only with obesity but also with breast cancer, leukemia, renal cancer, lung cancer, and cervical cancer. The current study provides researchers a comprehensible layout of adipoq network, its functional strategies and candidate disease approach associated with adipoq network. PMID:25388841

  16. A bioinformatic and computational study of myosin phosphatase subunit diversity

    PubMed Central

    Dippold, Rachael P.

    2014-01-01

    Variability in myosin phosphatase (MP) subunits may provide specificity in signaling pathways that regulate muscle tone. We utilized public databases and computational algorithms to investigate the phylogenetic diversity of MP regulatory (PPP1R12A-C) and inhibitory (PPP1R14A-D) subunits. The comparison of exonic coding sequences and expression data confirmed or refuted the existence of isoforms and their tissue-specific expression in different model organisms. The comparison of intronic and exonic sequences identified potential expressional regulatory elements. As examples, smooth muscle MP regulatory subunit (PPP1R12A) is highly conserved through evolution. Its alternative exon E24 is present in fish through mammals with two invariant features: 1) a reading frame shift generating a premature termination codon and 2) a hexanucleotide sequence adjacent to the 3′ splice site hypothesized to be a novel suppressor of exon splicing. A characteristic of the striated muscle MP regulatory subunit (PPP1R12B) locus is numerous and phylogenetically variable transcriptional start sites. In fish this locus only codes for the small (M21) subunit, suggesting the primordial function of this gene. Inhibitory subunits show little intragenic variability; their diversity is thought to have arisen by expansion and tissue-specific expression of different gene family members. We demonstrate differences in the regulatory landscape between smooth muscle enriched (PPP1R14A) and more ubiquitously expressed (PPP1R14B) family members and identify deeply conserved intronic sequence and predicted transcriptional cis-regulatory elements. This bioinformatic and computational study has uncovered a number of attributes of MP subunits that supports selection of ideal model organisms and testing of hypotheses regarding their physiological significance and regulated expression. PMID:24898838

  17. A computational study of circulating large tumor cells traversing microvessels.

    PubMed

    Kojić, Nikola; Milošević, Miljan; Petrović, Dejan; Isailović, Velibor; Sarioglu, A Fatih; Haber, Daniel A; Kojić, Miloš; Toner, Mehmet

    2015-08-01

    Circulating tumor cells (CTCs) are known to be a harbinger of cancer metastasis. The CTCs are known to circulate as individual cells or as a group of interconnected cells called CTC clusters. Since both single CTCs and CTC clusters have been detected in venous blood samples of cancer patients, they needed to traverse at least one capillary bed when crossing from arterial to venous circulation. The diameter of a typical capillary is about 7µm, whereas the size of an individual CTC or CTC clusters can be greater than 20µm and thus size exclusion is believed to be an important factor in the capillary arrest of CTCs - a key early event in metastasis. To examine the biophysical conditions needed for capillary arrest, we have developed a custom-built viscoelastic solid-fluid 3D computational model that enables us to calculate, under physiological conditions, the maximal CTC diameter that will pass through the capillary. We show that large CTCs and CTC clusters can successfully cross capillaries if their stiffness is relatively small. Specifically, under physiological conditions, a 13µm diameter CTC passes through a 7µm capillary only if its stiffness is less than 500Pa and conversely, for a stiffness of 10Pa the maximal passing diameter can be as high as 140µm, such as for a cluster of CTCs. By exploring the parameter space, a relationship between the capillary blood pressure gradient and the CTC mechanical properties (size and stiffness) was determined. The presented computational platform and the resulting pressure-size-stiffness relationship can be employed as a tool to help study the biomechanical conditions needed for capillary arrest of CTCs and CTC clusters, provide predictive capabilities in disease progression based on biophysical CTC parameters, and aid in the rational design of size-based CTC isolation technologies where CTCs can experience large deformations due to high pressure gradients. PMID:26093786

  18. A computational study of circulating large tumor cells traversing microvessels

    PubMed Central

    Kojić, Nikola; Milošević, Miljan; Petrović, Dejan; Isailović, Velibor; Sarioglu, A. Fatih; Haber, Daniel A.; Kojić, Miloš; Toner, Mehmet

    2016-01-01

    Circulating tumor cells (CTCs) are known to be a harbinger of cancer metastasis. The CTCs are known to circulate as individual cells or as a group of interconnected cells called CTC clusters. Since both single CTCs and CTC clusters have been detected in venous blood samples of cancer patients, they needed to traverse at least one capillary bed when crossing from arterial to venous circulation. The diameter of a typical capillary is about 7 μm, whereas the size of an individual CTC or CTC clusters can be greater than 20 μm and thus size exclusion is believed to be an important factor in the capillary arrest of CTCs – a key early event in metastasis. To examine the biophysical conditions needed for capillary arrest, we have developed a custom-built viscoelastic solid–fluid 3D computational model that enables us to calculate, under physiological conditions, the maximal CTC diameter that will pass through the capillary. We show that large CTCs and CTC clusters can successfully cross capillaries if their stiffness is relatively small. Specifically, under physiological conditions, a 13 μm diameter CTC passes through a 7 μm capillary only if its stiffness is less than 500 Pa and conversely, for a stiffness of 10 Pa the maximal passing diameter can be as high as 140 μm, such as for a cluster of CTCs. By exploring the parameter space, a relationship between the capillary blood pressure gradient and the CTC mechanical properties (size and stiffness) was determined. The presented computational platform and the resulting pressure–size–stiffness relationship can be employed as a tool to help study the biomechanical conditions needed for capillary arrest of CTCs and CTC clusters, provide predictive capabilities in disease progression based on biophysical CTC parameters, and aid in the rational design of size-based CTC isolation technologies where CTCs can experience large deformations due to high pressure gradients. PMID:26093786

  19. The bacteriological examination of urine: a computer-aided study

    PubMed Central

    Meers, P. D.

    1974-01-01

    For 6 months details of every patient who had his or her urine sent to a laboratory for bacteriological examination and the result of such examination were entered on a computer-card. A total of 15,606 cards were completed with information in code recording the sex and age of a patient, the origin of the request, the presence or absence in the urine of an excess of protein or cells, the culture result and the name of any significant organism isolated together with its sensitivity to various antimicrobial drugs. This information was interrelated in a computer, and in some cases the resulting numerical details were expressed as rates so as to eliminate the effect of uneven sex and age distribution. In this way the occurrence of urinary tract infection and the type of infecting organism in persons of either sex at various ages was examined according to whether the patient was in hospital or general practice. The sensitivity pattern of each type of significant organism isolated was established according to its source. The association between patients of either sex and various ages who had, or did not have, bacteriologically evident infections and the presence in their urine of an inflammatory exudate was investigated. Finally, the capacity of each type of infecting organism to produce such an exudate was estimated. It was shown that hospital and general practice experience of urinary tract infections differed widely, with regard both to the age and sex distribution of those suffering from it, and to the causative organisms concerned and their sensitivities to antimicrobial drugs. It is suggested that these differences were so great that conclusions drawn from any study of this subject conducted in one of the two areas cannot be applied to the other, and that those derived from a mixture of the two will vary according to the relative sizes of each of the components. PMID:4595089

  20. A computational study of Na behavior on graphene

    NASA Astrophysics Data System (ADS)

    Malyi, Oleksandr I.; Sopiha, Kostiantyn; Kulish, Vadym V.; Tan, Teck L.; Manzhos, Sergei; Persson, Clas

    2015-04-01

    We present the first ab initio and molecular dynamics study of Na adsorption and diffusion on ideal graphene that considers Na-Na interaction and dispersion forces. From density functional theory (DFT) calculations using the generalized gradient approximation (GGA), the binding energy (vs. the vacuum reference state) of -0.75 eV is higher than the cohesive energy of Na metal (Ecomputed migration barriers are significantly lower for the dimer than that for the single atom diffusion. This indicates that Na-Na interaction should be taken into account during the analysis of Na transport on graphene. Finally, we show that the typical defects (vacancy and divacancy) induce significant strengthening of the Nasbnd C interaction. In particular, the largest change to the interaction is computed for vacancy-defected graphene, where the found lowest binding energy (vs. the metal reference state) is about 1.15 eV (1.21 eV for DFT) lower than that for ideal graphene.

  1. 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.

  2. 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.

  3. 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

  4. Field and computer modeling studies of Appalachian cyclic carbonates

    SciTech Connect

    Read, J.F.

    1988-02-01

    Cyclic carbonates in the Cambrian of the Appalachians have been studied using field data integrated with computer modeling studies. The models incorporate 1 to 3-m.y. and 20,000 to 100,000-year low-amplitude sea level fluctuations, water depth-dependent sedimentation rates, lag time, and subsidence. The 1 to 3-m.y. sea level fluctuations are defined by Fischer plots, which are readily compared to the model output. Cycles decrease in number toward regional highs, because (1) lower subsidence rates only allow 40 to 60% of the Milankovitch sea level fluctuations to affect the highs and (2) highs subside lower than third-order sea levels fall, which truncate 50% of cycles. Furthermore, 2 cycles/100,000 years are deposited on the outer shelf, compared to 1 to 1.4 cycles/100,000 years on inner shelf highs. Consequently cycles have longer average periods toward the highs. Furthermore, average thickness shows only a slight decrease landward, even though formation thicknesses may be halved. The field data and modeling constrain amplitudes of 1 to 3-m.y. sea level changes because significant unconformities are absent from the shelf sequence, indicating third-order sea levels fell slower than subsidence rates, thus were considerably less than 50 m.

  5. Flux Solitons Studied for Energy-Conserving Reversible Computing

    NASA Astrophysics Data System (ADS)

    Osborn, Kevin D.; Wustmann, Waltraut

    2015-03-01

    On-chip logic is desired for controlling superconducting qubits. Since qubits are very sensitive to photon field noise, it is desirable to develop an energy-conserving reversible logic, i.e. one which can compute without substantial energy dissipation or applied drive fields. With this goal in mind, simulations on discretized long Josephson junctions (DLJJs) have been performed, where the flux soliton is studied as a potential information carrier. Undriven soliton propagation is studied as a function of discreteness, dissipation, and uncertainty in the junction critical current. The perturbing parameters are low in the simulations such that the solitons fit well to an ideal Sine-Gordon soliton. Surprisingly, using realizable parameters a single flux soliton in a DLJJ is found to travel hundreds of Josephson penetration depths without backscattering in the absence of a driving force. In addition, even with a non-ideal launch, solitons are found to propagate predictably such that they show potential for synchronous routing into reversible logic gates.

  6. 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.

  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. Computed tomography studies of lung ventilation and perfusion.

    PubMed

    Hoffman, Eric A; Chon, Deokiee

    2005-01-01

    With the emergence of multidetector-row computed tomography (CT) it is now possible to image both structure and function via use of a single imaging modality. Breath-hold spiral CT provides detail of the airway and vascular trees along with texture reflective of the state of the lung parenchyma. Use of stable xenon gas wash-in and/or wash-out methods using an axial mode of the CT scanner whereby images are acquired through gating to the respiratory cycle provide detailed images of regional ventilation with isotropic voxel dimensions now on the order of 0.4 mm. Axial scanning during a breath hold and gating to the electrocardiogram during the passage of a sharp bolus injection of iodinated contrast agent provide detailed images of regional pulmonary perfusion. These dynamic CT methods for the study of regional lung function are discussed in the context of other methods that have been used to study heterogeneity of lung function. PMID:16352755

  9. 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

  10. 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…

  11. 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…

  12. 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…

  13. 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…

  14. 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.

  15. 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

  16. 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

  17. A HUPO test sample study reveals common problems in mass spectrometry-based proteomics.

    PubMed

    Bell, Alexander W; Deutsch, Eric W; Au, Catherine E; Kearney, Robert E; Beavis, Ron; Sechi, Salvatore; Nilsson, Tommy; Bergeron, John J M

    2009-06-01

    We performed a test sample study to try to identify errors leading to irreproducibility, including incompleteness of peptide sampling, in liquid chromatography-mass spectrometry-based proteomics. We distributed an equimolar test sample, comprising 20 highly purified recombinant human proteins, to 27 laboratories. Each protein contained one or more unique tryptic peptides of 1,250 Da to test for ion selection and sampling in the mass spectrometer. Of the 27 labs, members of only 7 labs initially reported all 20 proteins correctly, and members of only 1 lab reported all tryptic peptides of 1,250 Da. Centralized analysis of the raw data, however, revealed that all 20 proteins and most of the 1,250 Da peptides had been detected in all 27 labs. Our centralized analysis determined missed identifications (false negatives), environmental contamination, database matching and curation of protein identifications as sources of problems. Improved search engines and databases are needed for mass spectrometry-based proteomics. PMID:19448641

  18. 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. PMID:24942044

  19. 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.

  20. Studying allosteric regulation in metal sensor proteins using computational methods.

    PubMed

    Chakravorty, Dhruva K; Merz, Kenneth M

    2014-01-01

    In this chapter, we describe advances made in understanding the mechanism of allosteric regulation of DNA operator binding in the ArsR/SmtB family of metal-sensing proteins using computational methods. The paradigm, zinc-sensing transcriptional repressor Staphylococcus aureus CzrA represents an excellent model system to understand how metal sensor proteins maintain cellular metal homeostasis. Here, we discuss studies that helped to characterize a metal ion-mediated hydrogen-bonding pathway (HBP) that plays a dominant role in the allosteric mechanism of DNA operator binding in these proteins. The chapter discusses computational methods used to provide a molecular basis for the large conformational motions and allosteric coupling free energy (~6kcal/mol) associated with Zn(II) binding in CzrA. We present an accurate and convenient means by which to include metal ions in the nuclear magnetic resonance (NMR) structure determination process using molecular dynamics (MD) constrained by NMR-derived data. The method provides a realistic and physically viable description of the metal-binding site(s) and has potentially broad applicability in the structure determination of metal ion-bound proteins, protein folding, and metal template protein-design studies. Finally, our simulations provide strong support for a proposed HBP that physically connects the metal-binding residue, His97, to the DNA-binding interface through the αR helix that is present only in the Zn(II)-bound state. We find the interprotomer hydrogen bond interaction to be significantly stronger (~8kcal/mol) at functional allosteric metal-binding sites compared to the apo proteins. This interaction works to overcome the considerable disorder at these hydrogen-bonding sites in apo protein and functions as a "switch" to lock in a weak DNA-binding conformation once metal is bound. This interaction is found to be considerably weaker in nonresponsive metal-binding sites. These findings suggest a conserved functional

  1. 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…

  2. Computational Characterization of Osteoporosis Associated SNPs and Genes Identified by Genome-Wide Association Studies

    PubMed Central

    Wang, Ya; Wu, Guiju; Chen, Jie; Ye, Weiyuan; Yang, Jiancai; Huang, Qingyang

    2016-01-01

    Objectives Genome-wide association studies (GWASs) have revealed many SNPs and genes associated with osteoporosis. However, influence of these SNPs and genes on the predisposition to osteoporosis is not fully understood. We aimed to identify osteoporosis GWASs-associated SNPs potentially influencing the binding affinity of transcription factors and miRNAs, and reveal enrichment signaling pathway and “hub” genes of osteoporosis GWAS-associated genes. Methods We conducted multiple computational analyses to explore function and mechanisms of osteoporosis GWAS-associated SNPs and genes, including SNP conservation analysis and functional annotation (influence of SNPs on transcription factors and miRNA binding), gene ontology analysis, pathway analysis and protein-protein interaction analysis. Results Our results suggested that a number of SNPs potentially influence the binding affinity of transcription factors (NFATC2, MEF2C, SOX9, RUNX2, ESR2, FOXA1 and STAT3) and miRNAs. Osteoporosis GWASs-associated genes showed enrichment of Wnt signaling pathway, basal cell carcinoma and Hedgehog signaling pathway. Highly interconnected “hub” genes revealed by interaction network analysis are RUNX2, SP7, TNFRSF11B, LRP5, DKK1, ESR1 and SOST. Conclusions Our results provided the targets for further experimental assessment and further insight on osteoporosis pathophysiology. PMID:26930606

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

    PubMed

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

    2010-09-01

    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

  4. 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.

  5. Role of Active Site Residues in Promoting Cobalt-Carbon Bond Homolysis in Adenosylcobalamin-Dependent Mutases Revealed Through Experiment and Computation

    PubMed Central

    Román-Meléndez, Gabriel D.; von Glehn, Patrick; Harvey, Jeremy N.; Mulholland, Adrian J.; Marsh, E. Neil G.

    2014-01-01

    Adenosylcobalamin serves as a source of reactive free radicals that are generated by homolytic scission of the coenzyme’s cobalt-carbon bond. AdoCbl-dependent enzymes accelerate AdoCbl homolysis by ~1012-fold, but the mechanism by which this is accomplished remains unclear. We have combined experimental and computational approaches to gain molecular-level insight into this process for glutamate mutase. Two residues, glutamate-330 and lysine-326, form hydrogen bonds with the adenosyl group of the coenzyme. A series of mutations were introduced at these positions that impair the enzyme’s ability to catalyze coenzyme homolysis and tritium exchange with the substrate by 2 – 4 orders of magnitude. These mutations, together with the wild-type enzyme, were also characterized in silico by molecular dynamics simulations of the enzyme:AdoCbl:substrate with AdoCbl modeled in either the associated (Co-C bond formed) or the dissociated (adenosyl radical + CblII) state. The simulations reveal that the number of hydrogen bonds between the adenosyl group and the protein side-chains increases in the homolytically-dissociated state, with respect to the associated state, for both the wild-type and mutant enzymes. The mutations also cause a progressive increase in the mean distance between the 5′-carbon of the adenosyl radical and the abstractable hydrogen of the substrate. Interestingly, the distance between the 5′-carbon and substrate hydrogen, determined computationally, was found to inversely correlate with the logk for tritium exchange (r = 0.93) determined experimentally. Taken together, these results point to a dual role for these residues: they both stabilize the homolytic state through electrostatic interactions between the protein and the dissociated coenzyme, and correctly position the adenosyl radical to facilitate hydrogen abstraction from the substrate. PMID:24341954

  6. Revealing halogen bonding interactions with anomeric systems: an ab initio quantum chemical studies.

    PubMed

    Lo, Rabindranath; Ganguly, Bishwajit

    2015-02-01

    A computational study has been performed using MP2 and CCSD(T) methods on a series of O⋯X (X=Br, Cl and I) halogen bonds to evaluate the strength and characteristic of such highly directional noncovalent interactions. The study has been carried out on a series of dimeric complexes formed between interhalogen compounds (such as BrF, BrCl and BrI) and oxygen containing electron donor molecule. The existence and consequences of the anomeric effect of the electron donor molecule has also been investigated through an exploration of halogen bonding interactions in this halogen bonded complexes. The ab initio quantum chemical calculations have been employed to study both the nature and directionality of the halogen molecules toward the sp(3) oxygen atom in anomeric systems. The presence of anomeric nO→σ*CN interaction involves a dominant role for the availability of the axial and equatorial lone pairs of donor O atom to participate with interhalogen compounds in the halogen-bonded complexes. The energy difference between the axial and equatorial conformers with interhalogen compounds reaches up to 4.60 kJ/mol, which however depends upon the interacting halogen atoms and its attaching atoms. The energy decomposition analysis further suggests that the total halogen bond interaction energies are mainly contributed by the attractive electrostatic and dispersion components. The role of substituents attached with the halogen atoms has also been evaluated in this study. With the increase of halogen atom size and the positive nature of σ-hole, the halogen atom interacted more with the electron donor atom and the electrostatic contribution to the total interaction energy enhances appreciably. Further, noncovalent interaction (NCI) studies have been carried out to locate the noncovalent halogen bonding interactions in real space. PMID:25522359

  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. Helicopter mission optimization study. [portable computer technology for flight optimization

    NASA Technical Reports Server (NTRS)

    Olson, J. R.

    1978-01-01

    The feasibility of using low-cost, portable computer technology to help a helicopter pilot optimize flight parameters to minimize fuel consumption and takeoff and landing noise was demonstrated. Eight separate computer programs were developed for use in the helicopter cockpit using a hand-held computer. The programs provide the helicopter pilot with the ability to calculate power required, minimum fuel consumption for both range and endurance, maximum speed and a minimum noise profile for both takeoff and landing. Each program is defined by a maximum of two magnetic cards. The helicopter pilot is required to key in the proper input parameter such as gross weight, outside air temperature or pressure altitude.

  9. Computational studies on conditions of the emergence of autopoietic protocells.

    PubMed

    Ono, Naoaki

    2005-09-01

    It has been pointed out that the acquisition of self-maintaining protocells was one of the most important evolutionary steps in the earliest stage of life. However, there remains little evidence to show what the components of the protocells were and how they were acquired. A theoretical study to investigate the possible process of the emergence of protocells is therefore required. In this paper, we present a computational model that demonstrates the emergence and evolution of self-maintaining and self-reproducing structures to analyze conditions under which precellular autocatalytic molecules could evolve into self-reproducing protocells. We focused on the supply rates of molecular resources as environmental parameters and explored the pathways of evolution from molecular replication to cellular reproduction under various conditions. The results showed that the spontaneous organization of protocells from a random initial state takes place in a parameter region where the metabolism becomes difficult because of an insufficient supply of resources, but once cell structures are organized, they can survive in a wider range of environments. We investigated the evolution in temporally or spatially changing environments and found that the protocells can take over the precellular metabolic system after the transition. These results suggest a possible scenario for the evolution from precellular to cellular reproduction. PMID:15982803

  10. A computational study of λ-lac mutants

    NASA Astrophysics Data System (ADS)

    Werner, Maria; Aurell, Erik

    2009-12-01

    We present a comprehensive, computational study of the properties of bacteriophage λ mutants designed by Atsumi and Little (2006 Proc. Natl. Acad. Sci. 103 4558-63). These phages underwent a genetic reconstruction where Cro was replaced by a dimeric form of the Lac repressor. To clarify the theoretical characteristics of these mutants, we built a detailed thermodynamic model. The mutants all have a different genetic wiring than the wild-type λ. One group lacks regulation of PRM by the lytic protein. These mutants only exhibit the lysogenic equilibrium, with no transiently active PR. The other group lacks the negative feedback from CI. In this group, we identify a handful of bi-stable mutants, although the majority only exhibit the lysogenic equilibrium. The experimental identification of functional phages differs from our predictions. From a theoretical perspective, there is no reason why only 4 out of 900 mutants should be functional. The differences between theory and experiment can be explained in two ways. Either, the view of the λ phage as a bi-stable system needs to be revised, or the mutants have in fact not undergone a modular replacement, as intended by Atsumi and Little, but constitute instead a wider systemic change.

  11. 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.

  12. Computational study of Met-Car analogue heterofullerenes

    NASA Astrophysics Data System (ADS)

    Domingos, H. S.

    2006-06-01

    Structural, chemical and electronic properties of a number of Met-Car analogue heterofullerenes were investigated using a combination of ab initio and semi-empirical quantum mechanical calculations.Met-Car clusters of known structure and chemistry were studied together with some new hypothetical configurations. In particular, the stability of clusters of the form Y8C12 (Y = Al, S, Si, Ti, As, Bi, Sb, P, N, B, Sn, Sc, Cr, V), XY7C12 (X, Y = B, N, Si) and Y8Z12 (Y, Z = N, B, Si) were investigated based on computed binding energies, Mulliken charges, bond orders and ionization potentials. The results indicate that some novel clusters are due for observation. Clusters of this type are known to form the building blocks of new polymerized solids and may exhibit some novel dielectric, magnetic and superconducting properties. Isomers of D3d symmetry, which are possible global energy minima for Cr, V and Sc carbide clusters, were also identified.

  13. [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. PMID:24467957

  14. Computer-aided target tracking in motion analysis studies

    NASA Astrophysics Data System (ADS)

    Burdick, Dominic C.; Marcuse, M. L.; Mislan, J. D.

    1990-08-01

    Motion analysis studies require the precise tracking of reference objects in sequential scenes. In a typical situation, events of interest are captured at high frame rates using special cameras, and selected objects or targets are tracked on a frame by frame basis to provide necessary data for motion reconstruction. Tracking is usually done using manual methods which are slow and prone to error. A computer based image analysis system has been developed that performs tracking automatically. The objective of this work was to eliminate the bottleneck due to manual methods in high volume tracking applications such as the analysis of crash test films for the automotive industry. The system has proven to be successful in tracking standard fiducial targets and other objects in crash test scenes. Over 95 percent of target positions which could be located using manual methods can be tracked by the system, with a significant improvement in throughput over manual methods. Future work will focus on the tracking of clusters of targets and on tracking deformable objects such as airbags.

  15. 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).

  16. A computational study of radio relics in galaxy cluster mergers

    NASA Astrophysics Data System (ADS)

    Owen, Dane Patrick

    Radio relics are extended regions of synchrotron radio emission that have been found in the outskirts of a few dozen galaxy clusters. Relics are often associated with clusters undergoing merger activity. They are not associated optically with a particular member of the cluster and are thought to arise from relativistic electron populations in the intra-cluster medium. The radio phoenix model, where shockwaves from merger activity re-energize a fossil radio plasma through adiabatic compression of the plasma, is one possible method of relic formation. This thesis uses gravitational N-body + SPH simulations with added synchrotron physics to present the largest computational study of radio relics in the radio phoenix model to date, totaling over 50,000 CPU-hours of computation and 4.7 TB of data. I have created a simulation data set of cluster mergers, with 25 different combinations of cluster mass, impact parameter, kinetic energies, cluster concentrations, and cluster-subcluster mass ratios. Using these simulations, I will discuss how high mass ratio collisions of 7:1 (cluster:subcluster mass) are most effective at reviving emission and creating a relic. I also show how this model predicts that clusters with total masses on the order of 6.25 x 10. 14 solar masses are most efficient at creating relics. By varyingthe magnetic pressure in the simulations, I demonstrate how relic formation is relatively insensitive to a wide range of magnetic field strengths. I also examine the great steepening of the spectral index of relics at even moderate (z ~ 0.4) redshifts predicted by the simulations, with the implications for future low-frequency telescope arrays. Finally, I present specific merger simulations for the clusters Abell 85 and 2443. The relic emission in Abell 85 is shown to be well predicted by the radio phoenix model, while the possible merger of Abell 2443 with its subcluster ZwCl 2224.2+1651 is shown to be unlikely as the cause of the relic in that system.

  17. Visual Stability and the Motion Aftereffect: A Psychophysical Study Revealing Spatial Updating

    PubMed Central

    Biber, Ulrich; Ilg, Uwe J.

    2011-01-01

    Eye movements create an ever-changing image of the world on the retina. In particular, frequent saccades call for a compensatory mechanism to transform the changing visual information into a stable percept. To this end, the brain presumably uses internal copies of motor commands. Electrophysiological recordings of visual neurons in the primate lateral intraparietal cortex, the frontal eye fields, and the superior colliculus suggest that the receptive fields (RFs) of special neurons shift towards their post-saccadic positions before the onset of a saccade. However, the perceptual consequences of these shifts remain controversial. We wanted to test in humans whether a remapping of motion adaptation occurs in visual perception. The motion aftereffect (MAE) occurs after viewing of a moving stimulus as an apparent movement to the opposite direction. We designed a saccade paradigm suitable for revealing pre-saccadic remapping of the MAE. Indeed, a transfer of motion adaptation from pre-saccadic to post-saccadic position could be observed when subjects prepared saccades. In the remapping condition, the strength of the MAE was comparable to the effect measured in a control condition (33±7% vs. 27±4%). Contrary, after a saccade or without saccade planning, the MAE was weak or absent when adaptation and test stimulus were located at different retinal locations, i.e. the effect was clearly retinotopic. Regarding visual cognition, our study reveals for the first time predictive remapping of the MAE but no spatiotopic transfer across saccades. Since the cortical sites involved in motion adaptation in primates are most likely the primary visual cortex and the middle temporal area (MT/V5) corresponding to human MT, our results suggest that pre-saccadic remapping extends to these areas, which have been associated with strict retinotopy and therefore with classical RF organization. The pre-saccadic transfer of visual features demonstrated here may be a crucial determinant for a

  18. 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).

  19. A three-dimensional computer simulation model reveals the mechanisms for self-organization of plant cortical microtubules into oblique arrays.

    PubMed

    Eren, Ezgi Can; Dixit, Ram; Gautam, Natarajan

    2010-08-01

    The noncentrosomal cortical microtubules (CMTs) of plant cells self-organize into a parallel three-dimensional (3D) array that is oriented transverse to the cell elongation axis in wild-type plants and is oblique in some of the mutants that show twisted growth. To study the mechanisms of CMT array organization, we developed a 3D computer simulation model based on experimentally observed properties of CMTs. Our computer model accurately mimics transverse array organization and other fundamental properties of CMTs observed in rapidly elongating wild-type cells as well as the defective CMT phenotypes observed in the Arabidopsis mor1-1 and fra2 mutants. We found that CMT interactions, boundary conditions, and the bundling cutoff angle impact the rate and extent of CMT organization, whereas branch-form CMT nucleation did not significantly impact the rate of CMT organization but was necessary to generate polarity during CMT organization. We also found that the dynamic instability parameters from twisted growth mutants were not sufficient to generate oblique CMT arrays. Instead, we found that parameters regulating branch-form CMT nucleation and boundary conditions at the end walls are important for forming oblique CMT arrays. Together, our computer model provides new mechanistic insights into how plant CMTs self-organize into specific 3D arrangements. PMID:20519434

  20. A Three-Dimensional Computer Simulation Model Reveals the Mechanisms for Self-Organization of Plant Cortical Microtubules into Oblique Arrays

    PubMed Central

    Eren, Ezgi Can; Gautam, Natarajan

    2010-01-01

    The noncentrosomal cortical microtubules (CMTs) of plant cells self-organize into a parallel three-dimensional (3D) array that is oriented transverse to the cell elongation axis in wild-type plants and is oblique in some of the mutants that show twisted growth. To study the mechanisms of CMT array organization, we developed a 3D computer simulation model based on experimentally observed properties of CMTs. Our computer model accurately mimics transverse array organization and other fundamental properties of CMTs observed in rapidly elongating wild-type cells as well as the defective CMT phenotypes observed in the Arabidopsis mor1-1 and fra2 mutants. We found that CMT interactions, boundary conditions, and the bundling cutoff angle impact the rate and extent of CMT organization, whereas branch-form CMT nucleation did not significantly impact the rate of CMT organization but was necessary to generate polarity during CMT organization. We also found that the dynamic instability parameters from twisted growth mutants were not sufficient to generate oblique CMT arrays. Instead, we found that parameters regulating branch-form CMT nucleation and boundary conditions at the end walls are important for forming oblique CMT arrays. Together, our computer model provides new mechanistic insights into how plant CMTs self-organize into specific 3D arrangements. PMID:20519434

  1. 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.

  2. A computational study of the phosphorylation mechanism of the insulin receptor tyrosine kinase.

    PubMed

    Zhou, Baojing; Wong, Chung F

    2009-04-30

    Although various groups have studied the phosphorylation mechanism of the insulin receptor tyrosine kinase (IRK), an unanimous picture has not yet emerged. In this work, we performed a computational study to gain further insights. We first built a structural model of the reactant complex with the guide of several crystal structures and previous computational studies of the cyclic AMP-dependent protein kinase. We then optimized the structure by performing geometry optimization using a quantum mechanical model containing nearly 300 atoms. A reaction path was then traced between the reactant and the product by using a multiple coordinate-driven method. The calculations mapped out a sequence of structural changes depicting the conversion of the reactant to the product. Analysis of the structural changes revealed the formation of a dissociative transition state and the involvement of a proton transfer from the hydroxyl group of the tyrosyl residue of the peptide substrate to a conserved aspartate in the active site of the enzyme. The proton transfer began well before the transition state was reached and finished only shortly before the product was completely formed. In addition, the formation of a hydrogen bonding network among Arg1136, Asp1132, the gamma-phosphate of ATP, and the tyrosine residue of the substrate appeared to hold the latter two in a near-attack position for reaction. The model estimated a reaction barrier of 14 kcal/mol, semiquantitatively in accord with experiment. PMID:19334696

  3. The Effects of Study Tasks in a Computer-Based Chemistry Learning Environment

    NASA Astrophysics Data System (ADS)

    Urhahne, Detlef; Nick, Sabine; Poepping, Anna Christin; Schulz, Sarah Jayne

    2013-12-01

    The present study examines the effects of different study tasks on the acquisition of knowledge about acids and bases in a computer-based learning environment. Three different task formats were selected to create three treatment conditions: learning with gap-fill and matching tasks, learning with multiple-choice tasks, and learning only from text and figures without any additional tasks. Participants were 196 ninth-grade students who learned with a self-developed multimedia program in a pretest-posttest control group design. Research results reveal that gap-fill and matching tasks were most effective in promoting knowledge acquisition, followed by multiple-choice tasks, and no tasks at all. The findings are in line with previous research on this topic. The effects can possibly be explained by the generation-recognition model, which predicts that gap-fill and matching tasks trigger more encompassing learning processes than multiple-choice tasks. It is concluded that instructional designers should incorporate more challenging study tasks for enhancing the effectiveness of computer-based learning environments.

  4. Infrared spectroscopic characterization of carbonated apatite: a combined experimental and computational study.

    PubMed

    Ren, Fuzeng; Ding, Yonghui; Leng, Yang

    2014-02-01

    A combined experimental and computational approach was employed to investigate the feasibility and effectiveness of characterizing carbonated apatite (CAp) by infrared (IR) spectroscopy. First, an experimental comparative study was conducted to identify characteristic IR vibrational bands of carbonate substitution in the apatite lattice. The IR spectra of pure hydroxyapatite (HA), carbonate adsorbed on the HA surface, a physical mixture of HA and sodium carbonate monohydrate, a physical mixture of HA and calcite, synthetic CAps prepared using three methods (precipitation method, hydrothermal route, and solid-gas reaction at high temperature) and biological apatites (human enamel, human cortical bone, and two animal bones) were compared. Then, the IR vibrational bands of carbonate in CAp were calculated with density functional theory. The experimental study identified characteristic IR bands of carbonate that cannot be generated from surface adsorption or physical mixtures and the results show that the bands at ∼880, 1413, and 1450 cm(-1) should not be used as characteristic bands of CAp since they could result from carbonate adsorbed on the apatite crystals surface or present as a separate phase. The combined experimental and computational study reveals that the carbonate v3 bands at ∼1546 and 1465 cm(-1) are, respectively, the IR signature bands for type A CAp and type B CAp. PMID:23533194

  5. Computational study of dislocation based mechanisms in FCC materials

    NASA Astrophysics Data System (ADS)

    Yellakara, Ranga Nikhil

    Understanding the relationships between microstructures and properties of materials is a key to developing new materials with more suitable qualities or employing the appropriate materials in special uses. In the present world of material research, the main focus is on microstructural control to cost-effectively enhance properties and meet performance specifications. This present work is directed towards improving the fundamental understanding of the microscale deformation mechanisms and mechanical behavior of metallic alloys, particularly focusing on face centered cubic (FCC) structured metals through a unique computational methodology called three-dimensional dislocation dynamics (3D-DD). In these simulations, the equations of motion for dislocations are mathematically solved to determine the evolution and interaction of dislocations. Microstructure details and stress-strain curves are a direct observation in the simulation and can be used to validate experimental results. The effect of initial dislocation microstructure on the yield strength has been studied. It has been shown that dislocation density based crystal plasticity formulations only work when dislocation densities/numbers are sufficiently large so that a statistically accurate description of the microstructure can be obtainable. The evolution of the flow stress for grain sizes ranging from 0.5 to 10 mum under uniaxial tension was simulated using an improvised model by integrating dislocation pile-up mechanism at grain boundaries has been performed. This study showed that for a same initial dislocation density, the Hall--Petch relationship holds well at small grain sizes (0.5--2 mum), beyond which the yield strength remains constant as the grain size increases. Various dislocation-particle interaction mechanisms have been introduced and investigations were made on their effect on the uniaxial tensile properties. These studies suggested that increase in particle volume fraction and decrease in particle

  6. The study on computer aided peripheral visual field diagnosis.

    PubMed

    Shuyi, Wang; Xingsan, Qian

    2005-01-01

    Background Despite the widespread adoption of automated perimetry, there is still a role for peripheral perimetry. So far there was no accurate quantitative analysis on the change of visual field, most analysis were qualitative and depend on doctor's experience. Method Computer aided diagnose system was designed to judge the accurate change in visual field. Tabu Seach technology was used to identify visual field from the result of Peripheral perimeter test, and accurate visual filed defect dimension can be concluded by compared with point to point. At the same time liable eye diseases were predicted by computer. Conclusion Computer aided peripheral visual field diagnose system can identify defect in visual field, and provide reliable clinical diagnosis. Key words peripheral visual field, Computer aided diagnose, tabu search. PMID:17282924

  7. 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.

  8. 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.

  9. 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

  10. 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

  11. Computing and information sciences preliminary engineering design study

    SciTech Connect

    Schroeder, J O; Pearson, E W; Thomas, J J; Brothers, J W; Campbell, W K; DeVaney, D M; Jones, D R; Littlefield, R J; Peterson, M J

    1991-04-01

    This document presents the preliminary design concept for the integrated computing and information system to be included in the Environmental and Molecular Sciences Laboratory (EMSL) at the Pacific Northwest Laboratory, Richland, Washington, for the US Department of Energy (DOE). The EMSL is scheduled for completion and occupancy in 1994 or 1995 and will support the DOE environmental mission, in particular hazardous waste remediation. The focus of the report is on the Computing and Information Sciences engineering task of providing a fully integrated state-of-the-art computing environment for simulation, experimentation and analysis in support of molecular research. The EMSL will house two major research organizations, the Molecular Sciences Research Center (MSRC) and part of the Environmental Sciences Research Center (ESRC). Included in the report is a preliminary description of the computing and information system to be included. The proposed system architecture is based on a preliminary understanding of the EMSL users' needs for computational resources. As users understand more about the scientific challenges they face, the definition of the functional requirements will change. At the same time, the engineering team will be gaining experience with new computing technologies. Accordingly, the design architecture must evolve to reflect this new understanding of functional requirements and enabling technologies. 3 figs., 2 tabs.

  12. Blood flow through sutured and coupled microvascular anastomoses: a comparative computational study.

    PubMed

    Wain, Richard A J; Whitty, Justin P M; Dalal, Milind D; Holmes, Michael C; Ahmed, Waqar

    2014-07-01

    This study uses computational fluid dynamics (CFD) to model blood flow through idealised sutured and coupled arterial anastomoses to investigate the affect of each technique on intravascular blood flow. Local flow phenomena are examined in detail to study characteristics that potentially initiate thrombus formation; for example, changes in velocity profile, wall shear stress (WSS), and shear strain rate (SSR). Idealised geometries of sutured and coupled anastomoses were created with dimensions identical to microvascular suture material and a commercially available coupling device using CFD software. Vessels were modelled as non-compliant 1 mm diameter ducts, and blood was simulated as a Newtonian fluid, in keeping with previous studies. All analyses were steady-state and performed on arteries. The sutured simulation revealed a reduced boundary velocity profile; high WSS; and high SSR at the suture sites. The coupled anastomosis simulation showed a small increase in maximum WSS at the anastomotic region compared to a pristine vessel, however, this was less than half that of the sutured model. The coupled vessel displayed an average WSS equivalent to a pristine vessel simulation. Taken together these observations demonstrate a theoretically more thrombogenic profile in a sutured anastomosis when compared to a coupled vessel. Data from simulations on a coupled anastomosis reveal a profile that is nearly equivalent to that of a pristine vessel. Based purely on the combination of less favourable flow properties shown using these idealised arterial models, the sutured method is potentially more thrombogenic than a coupled anastomosis. PMID:24731801

  13. 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

  14. New Insights into Sulfur Metabolism in Yeasts as Revealed by Studies of Yarrowia lipolytica

    PubMed Central

    Hébert, Agnès; Forquin-Gomez, Marie-Pierre; Roux, Aurélie; Aubert, Julie; Junot, Christophe; Heilier, Jean-François; Landaud, Sophie; Bonnarme, Pascal

    2013-01-01

    Yarrowia lipolytica, located at the frontier of hemiascomycetous yeasts and fungi, is an excellent candidate for studies of metabolism evolution. This yeast, widely recognized for its technological applications, in particular produces volatile sulfur compounds (VSCs) that fully contribute to the flavor of smear cheese. We report here a relevant global vision of sulfur metabolism in Y. lipolytica based on a comparison between high- and low-sulfur source supplies (sulfate, methionine, or cystine) by combined approaches (transcriptomics, metabolite profiling, and VSC analysis). The strongest repression of the sulfate assimilation pathway was observed in the case of high methionine supply, together with a large accumulation of sulfur intermediates. A high sulfate supply seems to provoke considerable cellular stress via sulfite production, resulting in a decrease of the availability of the glutathione pathway's sulfur intermediates. The most limited effect was observed for the cystine supply, suggesting that the intracellular cysteine level is more controlled than that of methionine and sulfate. Using a combination of metabolomic profiling and genetic experiments, we revealed taurine and hypotaurine metabolism in yeast for the first time. On the basis of a phylogenetic study, we then demonstrated that this pathway was lost by some of the hemiascomycetous yeasts during evolution. PMID:23220962

  15. 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.

  16. A computational study of an atomizing liquid sheet

    NASA Astrophysics Data System (ADS)

    Deshpande, Suraj S.; Gurjar, Soumil R.; Trujillo, Mario F.

    2015-08-01

    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.

  17. 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

  18. 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

  19. Using 4D Cardiovascular Magnetic Resonance Imaging to Validate Computational Fluid Dynamics: A Case Study.

    PubMed

    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

  20. 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

  1. Sensitivity and uncertainty studies of the CRAC2 computer code.

    PubMed

    Kocher, D C; Ward, R C; Killough, G G; Dunning, D E; Hicks, B B; Hosker, R P; Ku, J Y; Rao, K S

    1987-12-01

    We have studied the sensitivity of health impacts from nuclear reactor accidents, as predicted by the CRAC2 computer code, to the following sources of uncertainty: (1) the model for plume rise, (2) the model for wet deposition, (3) the meteorological bin-sampling procedure for selecting weather sequences with rain, (4) the dose conversion factors for inhalation as affected by uncertainties in the particle size of the carrier aerosol and the clearance rates of radionuclides from the respiratory tract, (5) the weathering half-time for external ground-surface exposure, and (6) the transfer coefficients for terrestrial foodchain pathways. Predicted health impacts usually showed little sensitivity to use of an alternative plume-rise model or a modified rain-bin structure in bin-sampling. Health impacts often were quite sensitive to use of an alternative wet-deposition model in single-trial runs with rain during plume passage, but were less sensitive to the model in bin-sampling runs. Uncertainties in the inhalation dose conversion factors had important effects on early injuries in single-trial runs. Latent cancer fatalities were moderately sensitive to uncertainties in the weathering half-time for ground-surface exposure, but showed little sensitivity to the transfer coefficients for terrestrial foodchain pathways. Sensitivities of CRAC2 predictions to uncertainties in the models and parameters also depended on the magnitude of the source term, and some of the effects on early health effects were comparable to those that were due only to selection of different sets of weather sequences in bin-sampling. PMID:3444936

  2. 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.

  3. Computational study of vortex shedding about slender bodies

    NASA Astrophysics Data System (ADS)

    Murman, Scott Michael

    2000-10-01

    The flow about slender, pointed bodies can be characterized by different states with angle of attack. At moderate-to-high angles of attack (alpha ≈ 40°), a steady, asymmetric vortex pattern develops along the body, leading to a net lateral force. At higher angles of attack (alpha ≈ 60°), the aft-end of the body develops an unsteady von Karman shedding. As the angle of attack approaches 90°, the entire body length exhibits a time-dependent vortex shedding pattern. The current work develops numerical methods capable of simulating both the steady and unsteady vortex shedding about slender bodies at sub-scale (low Mach number, high laminar Reynolds number) test conditions. At these conditions a large database of experimental and numerical results exists for asymmetric vortex shedding. Emphasis is placed upon minimizing the computational cost for simulating three-dimensional, unsteady vortex shedding without sacrificing accuracy. Requirements for the crossflow resolution, time integration, and viscous stress modeling are developed. These methods are utilized to examine the physical mechanisms involved in flows about pointed bodies at angle of attack. The development of an asymmetric vortex pattern via a convective instability mechanism is investigated using tip bumps, surface roughness, and tip curvature. A model for the initiation of an asymmetric flow state from tip perturbations is presented. The development of Von Karman shedding on a semi-infinite pointed body is also studied. Numerical experiments are performed to determine whether the region of unsteady shedding on the aft-end of a body at angle of attack stems from a convective or absolute instability of the flow. The interactions between the regions of steady, asymmetric and unsteady von Karman vortex shedding are examined.

  4. 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.

  5. 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

  6. 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

  7. A resurrection study reveals rapid adaptive evolution within populations of an invasive plant

    PubMed Central

    Sultan, Sonia E; Horgan-Kobelski, Tim; Nichols, Lauren M; Riggs, Charlotte E; Waples, Ryan K

    2013-01-01

    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. PMID:23798976

  8. 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

  9. 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

  10. 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. PMID:22486330

  11. Fault-tolerant building-block computer study

    NASA Technical Reports Server (NTRS)

    Rennels, D. A.

    1978-01-01

    Ultra-reliable core computers are required for improving the reliability of complex military systems. Such computers can provide reliable fault diagnosis, failure circumvention, and, in some cases serve as an automated repairman for their host systems. A small set of building-block circuits which can be implemented as single very large integration devices, and which can be used with off-the-shelf microprocessors and memories to build self checking computer modules (SCCM) is described. Each SCCM is a microcomputer which is capable of detecting its own faults during normal operation and is described to communicate with other identical modules over one or more Mil Standard 1553A buses. Several SCCMs can be connected into a network with backup spares to provide fault-tolerant operation, i.e. automated recovery from faults. Alternative fault-tolerant SCCM configurations are discussed along with the cost and reliability associated with their implementation.

  12. An Imaging and Spectroscopic Study of Four Strong Mg II Absorbers Revealed by GRB 060418

    NASA Astrophysics Data System (ADS)

    Pollack, L. K.; Chen, H.-W.; Prochaska, J. X.; Bloom, J. S.

    2009-08-01

    We present results from an imaging and spectroscopic study of four strong Mg II absorbers of W(2796) gsim 1 Å revealed by the afterglow of GRB 060418 at z GRB = 1.491. These absorbers, at z = 0.603, 0.656, 1.107, and z GRB, exhibit large ion abundances that suggest neutral gas columns characteristic of damped Lyα 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 Δ θ lsim 3farcs5 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 ≈0.1 - 1 L * at impact parameter of ρ lsim 10 h -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 ρ = 2 - 12 h -1 kpc from the afterglow. At the afterglow's position, we derive a 2σ upper limit to the underlying star-formation rate intensity of 0.0074 M sun yr-1 kpc-2. Based in part on observations made with the NASA/ESA Hubble Space Telescope

  13. 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

  14. 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

  15. 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

  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. PMID:25306098

  18. Case Study of a Computer Based Examination System

    ERIC Educational Resources Information Center

    Fluck, Andrew; Pullen, Darren; Harper, Colleen

    2009-01-01

    Electronic supported assessment or e-Assessment is a field of growing importance, but it has yet to make a significant impact in the Australian higher education sector (Byrnes & Ellis, 2006). Current computer based assessment models focus on the assessment of knowledge rather than deeper understandings, using multiple choice type questions, and…

  19. 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…

  20. 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. PMID:26280078

  1. A Computer Simulation for the Study of Waves.

    ERIC Educational Resources Information Center

    Bork, Alfred M.; Robson, John

    A computer program, designed for use in the second quarter of the beginning course for science and engineering majors at the University of California, Irvine, simulates an experimental investigation of a pulse in a rope. A full trial run is given, in which the student's problem is to discover enough about the disturbance of the rope to answer…

  2. 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…

  3. 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

  4. 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…

  5. Developing Computer Model-Based Assessment of Chemical Reasoning: A Feasibility Study

    ERIC Educational Resources Information Center

    Liu, Xiufeng; Waight, Noemi; Gregorius, Roberto; Smith, Erica; Park, Mihwa

    2012-01-01

    This paper reports a feasibility study on developing computer model-based assessments of chemical reasoning at the high school level. Computer models are flash and NetLogo environments to make simultaneously available three domains in chemistry: macroscopic, submicroscopic, and symbolic. Students interact with computer models to answer assessment…

  6. 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…

  7. Use of Computer-Based Case Studies in a Problem-Solving Curriculum.

    ERIC Educational Resources Information Center

    Haworth, Ian S.; And Others

    1997-01-01

    Describes the use of three case studies, on computer, to enhance problem solving and critical thinking among doctoral pharmacy students in a physical chemistry course. Students are expected to use specific computer programs, spreadsheets, electronic mail, molecular graphics, word processing, online literature searching, and other computer-based…

  8. Human-Supplied versus Computer-Supplied Feedback: An Empirical and Pragmatic Study.

    ERIC Educational Resources Information Center

    Croy, Marvin J.; And Others

    1994-01-01

    Reports on a study of 29 students of deductive logic that compared instructor-supplied and computer-supplied diagnostic feedback used with computer-assisted instruction programs. Dependent measures included exam performance, class attendance and responsiveness, and attitudes toward the instructor, computers, other students, and the course.…

  9. 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…

  10. 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,…

  11. 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…

  12. 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

  13. Computational and Observational Studies of Interstellar Thioformaldehyde Masers

    NASA Astrophysics Data System (ADS)

    Simpson, Lisa; Hoffman, I. M.

    2013-06-01

    Interstellar spectroscopy of thioformaldehyde (H2CS) holds considerable promise because of the close relationship between the H2CS molecule and the well-studied formaldehyde (H2CO) molecule. In particular, the well-known J(Ka,Kc) = 1(1,0) to 1(1,1) transition of H2CO at 6 cm (4.8 GHz) has an analogous H2CS transition at 1046 MHz. However, the 1046-MHz line of H2CS has never been detected astronomically. We present here a summary of: (1) a computational investigation of H2CS level populations related to known H2CO 6-cm masers, and (2) an observational campaign of four isotopologues of H2CS. Maser emission from H2CO has been observed at 6 cm for which Boland and de Jong (1981) have developed a pump model. We have extended this model to H2CS and we present preliminary calculations for a 1046-MHz maser. We intend to develop a quantitative tool for interpreting H2CS observations toward Galactic and extragalactic locations of H2CO maser emission by constructing a radiative-transfer maser model for H2CS. Thioformaldehyde has been detected in a few Galactic sources via J>1 transitions. However, interpretation of these results has two outstanding problems: the H2CS/H2CO abundances do not agree with known sulfur-to-oxygen ratios nor do the J>1 populations have the expected Boltzmann relationship to the J=1 states. A detection of the 1046-MHz transition of H2CS with J=1 would alleviate many of the ambiguities in the interpretation of existing observational results. We describe our forthcoming experiment to search in a Galactic star-forming region for thermal and nonthermal emission and absorption from four thioformaldehyde isotopologues: H2(12C)(32S), H2(13C)(32S), H2(12C)(34S), and D2(12C)(32S). Taken together, both parts of this research effort will provide valuable and novel constraints on H2CS and H2CO. New observations of H2CS isotopologues will yield new measurements of deuterium-to-hydrogen and sulfur-to-oxygen ratios in star-forming environments. Also, the application

  14. Functional studies of Drosophila zinc transporters reveal the mechanism for dietary zinc absorption and regulation

    PubMed Central

    2013-01-01

    Background Zinc is key to the function of many proteins, but the process of dietary zinc absorption is not well clarified. Current knowledge about dietary zinc absorption is fragmented, and mostly derives from incomplete mammalian studies. To gain a comprehensive picture of this process, we systematically characterized all zinc transporters (that is, the Zip and ZnT family members) for their possible roles in dietary zinc absorption in a genetically amenable model organism, Drosophila melanogaster. Results A set of plasma membrane-resident zinc transporters was identified to be responsible for absorbing zinc from the lumen into the enterocyte and the subsequent exit of zinc to the circulation. dZip1 and dZip2, two functionally overlapping zinc importers, are responsible for absorbing zinc from the lumen into the enterocyte. Exit of zinc to the circulation is mediated through another two functionally overlapping zinc exporters, dZnT1, and its homolog CG5130 (dZnT77C). Somewhat surprisingly, it appears that the array of intracellular ZnT proteins, including the Golgi-resident dZnT7, is not directly involved in dietary zinc absorption. By modulating zinc status in different parts of the body, we found that regulation of dietary zinc absorption, in contrast to that of iron, is unresponsive to bodily needs or zinc status outside the gut. The zinc transporters that are involved in dietary zinc absorption, including the importers dZip1 and dZip2, and the exporter dZnT1, are respectively regulated at the RNA and protein levels by zinc in the enterocyte. Conclusions Our study using the model organism Drosophila thus starts to reveal a comprehensive sketch of dietary zinc absorption and its regulatory control, a process that is still incompletely understood in mammalian organisms. The knowledge gained will act as a reference for future mammalian studies, and also enable an appreciation of this important process from an evolutionary perspective. PMID:24063361

  15. 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

  16. Experimental evolution and gene knockout studies reveal AcrA-mediated isobutanol tolerance in Ralstonia eutropha.

    PubMed

    Bernardi, Amanda C; Gai, Claudia S; Lu, Jingnan; Sinskey, Anthony J; Brigham, Christopher J

    2016-07-01

    Isobutanol (IBT) has attracted much attention from researchers as a next generation drop-in biofuel. Ralstonia eutropha is a gram-negative bacterium which naturally produces polyhydroxybutyrate (PHB), and has been reported to produce IBT after metabolic engineering. Similar to other microbes, R. eutropha experiences toxicity from branched-chain alcohols and is unable to grow in the presence of IBT concentrations higher than 0.5% (v v(-1)). Such low tolerance greatly limits the ability of R. eutropha to grow and produce IBT. In order to study toxicity to the cells, IBT-tolerant strains were developed by experimental evolution, revealing that two genes, previously described as being related to IBT tolerance in Escherichia coli (acrA and acrA6), also presented mutations in R. eutropha evolved strains. The effect on the physiology of the cells of in-frame deletions of each of these genes was assessed in wild type and engineered IBT-producing strains in an attempt to reproduce a tolerant phenotype. The mutant strains' ability to tolerate, consume, and produce IBT were also analyzed. Although deletions of acrA6 and acrA did not significantly improve R. eutropha growth in the presence of IBT, these deletions improved cell survival in the presence of high concentrations of IBT in the extracellular milieu. Moreover, an in-frame acrA deletion in an engineered IBT-producing R. eutropha enhanced the strain's ability to produce IBT, which could potentially be associated with enhanced survival at high IBT concentrations. PMID:26811221

  17. Field Studies Reveal Strong Postmating Isolation between Ecologically Divergent Butterfly Populations

    PubMed Central

    McBride, Carolyn S.; Singer, Michael C.

    2010-01-01

    Gene flow between populations that are adapting to distinct environments may be restricted if hybrids inherit maladaptive, intermediate phenotypes. This phenomenon, called extrinsic postzygotic isolation (EPI), is thought to play a critical role in the early stages of speciation. However, despite its intuitive appeal, we know surprisingly little about the strength and prevalence of EPI in nature, and even less about the specific phenotypes that tend to cause problems for hybrids. In this study, we searched for EPI among allopatric populations of the butterfly Euphydryas editha that have specialized on alternative host plants. These populations recall a situation thought typical of the very early stages of speciation. They lack consistent host-associated genetic differentiation at random nuclear loci and show no signs of reproductive incompatibility in the laboratory. However, they do differ consistently in diverse host-related traits. For each of these traits, we first asked whether hybrids between populations that use different hosts (different-host hybrids) were intermediate to parental populations and to hybrids between populations that use the same host (same-host hybrids). We then conducted field experiments to estimate the effects of intermediacy on fitness in nature. Our results revealed strong EPI under field conditions. Different-host hybrids exhibited an array of intermediate traits that were significantly maladaptive, including four behaviors. Intermediate foraging height slowed the growth of larvae, while intermediate oviposition preference, oviposition site height, and clutch size severely reduced the growth and survival of the offspring of adult females. We used our empirical data to construct a fitness surface on which different-host hybrids can be seen to fall in an adaptive valley between two peaks occupied by same-host hybrids. These findings demonstrate how ecological selection against hybrids can create a strong barrier to gene flow at the early

  18. 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. PMID:25453169

  19. 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

  20. 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

  1. 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.

  2. Experimental and computational studies of two-dimensional compressible vortex-shock interaction

    NASA Astrophysics Data System (ADS)

    Kao, Chun-Teh

    The problem of two-dimensional compressible vortex-shock interaction is studied both experimentally and numerically. On the experimental side, a strong compressible vortex and a shock wave are produced in the open test section of a shock tube. The shock wave of strength M ≈ 1.2 then collides with the vortex that possesses a density drop at the vortex center exceeding 60% of the free stream value. Shadowgraphs and schlieren pictures of the event are taken in a sequence of experiments with progressive time delays. The pictures show that the shock profile is significantly modified by the interaction, with substantial distortion, disconnection, and a local nonlinear focusing structure. In the computational work, both the Euler equations and the Navier-Stokes equations are solved to simulate the problem. Two flux-splitting techniques are employed: (1) first-order-accurate Modified Steger-Warming method and (2) second-order-accurate variable-extrapolation method satisfying the total-variation-diminishing (TVD) condition. Based on the numerical data, the respective behaviors of the vortex, the shock wave, and the secondary wave generated during the interaction are analyzed. The simulation also reveals that the focal region of the distorted shock structure is bounded by a Mach stem and two slipstreams, in which local intensified pressure, density, and temperature peaks occur. It is found that the local intensification of fluid properties and the secondary wave possess essentially nonlinear characteristics at their early stages. The computational results agree well, qualitatively, with the experimental observations.

  3. 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

  4. 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

  5. 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

  6. Theoretical and computational studies in protein folding, design, and function

    NASA Astrophysics Data System (ADS)

    Morrissey, Michael Patrick

    2000-10-01

    In this work, simplified statistical models are used to understand an array of processes related to protein folding and design. In Part I, lattice models are utilized to test several theories about the statistical properties of protein-like systems. In Part II, sequence analysis and all-atom simulations are used to advance a novel theory for the behavior of a particular protein. Part I is divided into five chapters. In Chapter 2, a method of sequence design for model proteins, based on statistical mechanical first-principles, is developed. The cumulant design method uses a mean-field approximation to expand the free energy of a sequence in temperature. The method successfully designs sequences which fold to a target lattice structure at a specific temperature, a feat which was not possible using previous design methods. The next three chapters are computational studies of the double mutant cycle, which has been used experimentally to predict intra-protein interactions. Complete structure prediction is demonstrated for a model system using exhaustive, and also sub-exhaustive, double mutants. Nonadditivity of enthalpy, rather than of free energy, is proposed and demonstrated to be a superior marker for inter-residue contact. Next, a new double mutant protocol, called exchange mutation, is introduced. Although simple statistical arguments predict exchange mutation to be a more accurate contact predictor than standard mutant cycles, this hypothesis was not upheld in lattice simulations. Reasons for this inconsistency will be discussed. Finally, a multi-chain folding algorithm is introduced. Known as LINKS, this algorithm was developed to test a method of structure prediction which utilizes chain-break mutants. While structure prediction was not successful, LINKS should nevertheless be a useful tool for the study of protein-protein and protein-ligand interactions. The last chapter of Part I utilizes the lattice to explore the differences between standard folding, from

  7. 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.

  8. Computational study of sodium magnesium hydride for hydrogen storage applications

    NASA Astrophysics Data System (ADS)

    Soto Valle, Fernando Antonio

    Hydrogen offers considerable potential benefits as an energy carrier. However, safe and convenient storage of hydrogen is one of the biggest challenges to be resolved in the near future. Sodium magnesium hydride (NaMgH 3) has attracted attention as a hydrogen storage material due to its light weight and high volumetric hydrogen density of 88 kg/m3. Despite the advantages, hydrogen release in this material occurs at approximately 670 K, which is well above the operable range for on-board hydrogen storage applications. In this regard, hydrogen release may be facilitated by substitution doping of transition-metals. This dissertation describes first-principles computational methods that enable an examination of the hydrogen storage properties of NaMgH3. The novel contribution of this dissertation includes a combination of crystal, supercell, and surface slab calculations that provides new and relevant insights about the thermodynamic and kinetic properties of NaMgH3. First-principles calculations on the pristine crystal structure provide a starting reference point for the study of this material as a hydrogen storage material. To the best of our knowledge, it is reported for the first time that a 25% mol doping concentration of Ti, V, Cu, and Zn dopants reduce the reaction enthalpy of hydrogen release for NaMgH3. The largest decrease in the DeltaH(298 K) value corresponds to the Zn-doped model (67.97 kJ/(mol H2)). Based on cohesive energy calculations, it is reported that at the 6.25% mol doping concentration, Ti and Zn dopants are the only transition metals that destabilize the NaMgH3 hydride. In terms of hydrogen removal energy, it is quantified that the energy cost to remove a single H from the Ti-doped supercell model is 0.76 eV, which is lower with respect to the pristine model and other prototypical hydrogen storage materials. From the calculation of electronic properties such as density of states, electron density difference, and charge population analysis

  9. 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.

  10. 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

  11. 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.

  12. Study of the tevatron nonlinear acceptance by computer simulation

    SciTech Connect

    Willeke, F.

    1983-11-01

    In this report, the results of computer calculations of nonlinear acceptance reduction caused by nonlinear fields in the TEVATRON are presented. A set of test particles has been traced during many revolutions in the accelerator in order to determine the maximum stable amplitude in the presence of nonlinear fields. Sources of nonlinear fields are designed imperfections of dipole and quadrupole magnets, fluctuations due to manufacturing tolerances, and sextupole fields needed to compensate for chromaticity.

  13. 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).

  14. Computational genomic analysis of PARK7 interactome reveals high BBS1 gene expression as a prognostic factor favoring survival in malignant pleural mesothelioma.

    PubMed

    Vavougios, Georgios D; Solenov, Evgeniy I; Hatzoglou, Chrissi; Baturina, Galina S; Katkova, Liubov E; Molyvdas, Paschalis Adam; Gourgoulianis, Konstantinos I; Zarogiannis, Sotirios G

    2015-10-01

    The aim of our study was to assess the differential gene expression of Parkinson protein 7 (PARK7) interactome in malignant pleural mesothelioma (MPM) using data mining techniques to identify novel candidate genes that may play a role in the pathogenicity of MPM. We constructed the PARK7 interactome using the ConsensusPathDB database. We then interrogated the Oncomine Cancer Microarray database using the Gordon Mesothelioma Study, for differential gene expression of the PARK7 interactome. In ConsensusPathDB, 38 protein interactors of PARK7 were identified. In the Gordon Mesothelioma Study, 34 of them were assessed out of which SUMO1, UBC3, KIAA0101, HDAC2, DAXX, RBBP4, BBS1, NONO, RBBP7, HTRA2, and STUB1 were significantly overexpressed whereas TRAF6 and MTA2 were significantly underexpressed in MPM patients (network 2). Furthermore, Kaplan-Meier analysis revealed that MPM patients with high BBS1 expression had a median overall survival of 16.5 vs. 8.7 mo of those that had low expression. For validation purposes, we performed a meta-analysis in Oncomine database in five sarcoma datasets. Eight network 2 genes (KIAA0101, HDAC2, SUMO1, RBBP4, NONO, RBBP7, HTRA2, and MTA2) were significantly differentially expressed in an array of 18 different sarcoma types. Finally, Gene Ontology annotation enrichment analysis revealed significant roles of the PARK7 interactome in NuRD, CHD, and SWI/SNF protein complexes. In conclusion, we identified 13 novel genes differentially expressed in MPM, never reported before. Among them, BBS1 emerged as a novel predictor of overall survival in MPM. Finally, we identified that PARK7 interactome is involved in novel pathways pertinent in MPM disease. PMID:26254420

  15. 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

  16. 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.

  17. Computer-assisted surgery patterns of ligamentous deformity of the knee: a clinical and cadaveric study.

    PubMed

    Schwarzkopf, Ran; Hadley, Scott; Abbasi, Mohammed; Meere, Patrick A

    2013-08-01

    Knee malalignment during total knee arthroplasty (TKA) is commonly classified as either varus or valgus on the basis of a standing anteroposterior radiograph. Computer-assisted surgery (CAS) navigation TKA provides precise dynamic evaluation of knee alignment throughout the full range of motion (FROM). The goal of this study was to classify patterns of CAS-generated knee deformity curves that match specific soft tissue contracture combinations. This can then be applied as an algorithm for soft tissue balancing on the basis of the preoperative knee deformity curve. Computer navigation-generated graphs from 65 consecutive TKA procedures performed by a single surgeon were analyzed. A stress-strain curve of the coronal alignment of the knee was recorded throughout FROM before bony resection. All graphs were classified into groups according to their pattern. Cadaveric knee models were then used to test the correlation between isolated and combined ligamentous contractures and identified CAS deformity curves. An analysis of the intraoperative knee alignment graphs revealed four distinct patterns of coronal deformity on the basis of intraoperative data: 13% diagonal, 18.5% C-shaped, 43.5% comma shaped, and 25% S-shaped. Each represents the change in varus and valgus alignment during FROM. All patterns were reproduced with cadaveric knees by recreating specific contracture constellations. A tight posterior capsule gave an S-shaped curve, a tight lateral collateral ligament gave a C-shaped curve, tight medial collateral ligament gave a diagonal curve, and a tight posterior lateral corner gave a comma-shaped curve. Release of the specific contractures resulted in correction of all patterns of deformity as measured by CAS. We propose a new classification system for coronal plane knee deformity throughout FROM. This system intends to match individual and combined soft tissue pathological contractures to specific stress-strain curves obtained through routine knee CAS

  18. 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.

  19. 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…

  20. 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…

  1. 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…

  2. 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

  3. CFD spinoff - Computational electromagnetics for radar cross section (RCS) studies

    NASA Technical Reports Server (NTRS)

    Shankar, Vijaya; Mohammadian, Alireza H.; Hall, William F.; Erickson, Roy

    1990-01-01

    A finite-volume discretization procedure derived from proven CFD methods is used to solve the conservation form of the time-domain Maxwell's equations, in order to compute EM scattering from layered objects. This time-domain approach handles both single-frequency/continuous wave and broadband-frequency/pulse incident excitation. Arbitrarily shaped objects are modeled by means of a body-fitted coordinate transformation; complex internal/external structures with many material layers are treated through the implementation of a multizone framework capable of handling any type of zonal boundary condition. Results are presented for various two- and three-dimensional problems.

  4. 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.

  5. Periodic local-MP2 computational study of crystalline neon.

    PubMed

    Halo, Migen; Casassa, Silvia; Maschio, Lorenzo; Pisani, Cesare

    2009-01-21

    Face-centered-cubic crystalline Neon is taken as a test system to explore the influence of computational parameters on the quality of the MP2 solution provided by the Cryscor program using a local-correlation approach. The effect of the various approximations adopted is analyzed: basis set limitations, finite size of excitation domains, truncation of the tails of the local functions, approximate evaluation of two-electron integrals, estimate (by extrapolation) of long-range contributions are shown to play roles of different importance. The Ne2 dimer is used as an auxiliary test case in order to allow comparison with recent and accurate literature data. PMID:19283277

  6. 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.

  7. Retrospective Study on Mathematical Modeling Based on Computer Graphic Processing

    NASA Astrophysics Data System (ADS)

    Zhang, Kai Li

    Graphics & image making is an important field in computer application, in which visualization software has been widely used with the characteristics of convenience and quick. However, it was thought by modeling designers that the software had been limited in it's function and flexibility because mathematics modeling platform was not built. A non-visualization graphics software appearing at this moment enabled the graphics & image design has a very good mathematics modeling platform. In the paper, a polished pyramid is established by multivariate spline function algorithm, and validate the non-visualization software is good in mathematical modeling.

  8. Predictive Factors for Anastomotic Leakage After Colorectal Surgery: Study Protocol for a Prospective Observational Study (REVEAL Study)

    PubMed Central

    Bosmans, Joanna WAM; Kartal, Serdar; Lubbers, Tim; Sosef, Meindert; Slooter, Gerrit D; Stoot, Jan H; van Schooten, Frederik-Jan; Bouvy, Nicole D; Derikx, Joep PM

    2016-01-01

    Background Anastomotic leakage (AL) remains the most important complication following colorectal surgery, and is associated with high morbidity and mortality rates. Previous research has focused on identifying risk factors and potential biomarkers for AL, but the sensitivity of these tests remains poor. Objective This prospective multicenter observational study aims at combining multiple parameters to establish a diagnostic algorithm for colorectal AL. Methods This study aims to include 588 patients undergoing surgery for colorectal carcinoma. Patients will be eligible for inclusion when surgery includes the construction of a colorectal anastomosis. Patient characteristics will be collected upon consented inclusion, and buccal swabs, breath, stool, and blood samples will be obtained prior to surgery. These samples will allow for the collection of information regarding patients’ inflammatory status, genetic predisposition, and intestinal microbiota. Additionally, breath and blood samples will be taken postoperatively and patients will be strictly observed during their in-hospital stay, and the period shortly thereafter. Results This study has been open for inclusion since August 2015. Conclusions An estimated 8-10% of patients will develop AL following surgery, and they will be compared to non-leakage patients. The objectives of this study are twofold. The primary aim is to establish and validate a diagnostic algorithm for the pre-operative prediction of the risk of AL development using a combination of inflammatory, immune-related, and genetic parameters. Previously established risk factors and novel parameters will be incorporated into this algorithm, which will aid in the recognition of patients who are at risk for AL. Based on these results, recommendations can be made regarding the construction of an anastomosis or deviating stoma, and possible preventive strategies. Furthermore, we aim to develop a new algorithm for the post-operative diagnosis of AL at an

  9. Analysis of Nidogen-1/Laminin γ1 Interaction by Cross-Linking, Mass Spectrometry, and Computational Modeling Reveals Multiple Binding Modes

    PubMed Central

    Lössl, Philip; Kölbel, Knut; Tänzler, Dirk; Nannemann, David; Ihling, Christian H.; Keller, Manuel V.; Schneider, Marian; Zaucke, Frank; Meiler, Jens; Sinz, Andrea

    2014-01-01

    We describe the detailed structural investigation of nidogen-1/laminin γ1 complexes using full-length nidogen-1 and a number of laminin γ1 variants. The interactions of nidogen-1 with laminin variants γ1 LEb2–4, γ1 LEb2–4 N836D, γ1 short arm, and γ1 short arm N836D were investigated by applying a combination of (photo-)chemical cross-linking, high-resolution mass spectrometry, and computational modeling. In addition, surface plasmon resonance and ELISA studies were used to determine kinetic constants of the nidogen-1/laminin γ1 interaction. Two complementary cross-linking strategies were pursued to analyze solution structures of laminin γ1 variants and nidogen-1. The majority of distance information was obtained with the homobifunctional amine-reactive cross-linker bis(sulfosuccinimidyl)glutarate. In a second approach, UV-induced cross-linking was performed after incorporation of the diazirine-containing unnatural amino acids photo-leucine and photo-methionine into laminin γ1 LEb2–4, laminin γ1 short arm, and nidogen-1. Our results indicate that Asn-836 within laminin γ1 LEb3 domain is not essential for complex formation. Cross-links between laminin γ1 short arm and nidogen-1 were found in all protein regions, evidencing several additional contact regions apart from the known interaction site. Computational modeling based on the cross-linking constraints indicates the existence of a conformational ensemble of both the individual proteins and the nidogen-1/laminin γ1 complex. This finding implies different modes of interaction resulting in several distinct protein-protein interfaces. PMID:25387007

  10. 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

  11. 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.

  12. 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

  13. A computational study of systemic hydration in vocal fold collision.

    PubMed

    Bhattacharya, Pinaki; Siegmund, Thomas

    2014-01-01

    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-fidelity numerical computations are described, taking into account fully 3D 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 airflow 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 tend to increase the state of hydration of the VF tissue, whereas VF collision works to reduce hydration. PMID:23531170

  14. 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

  15. 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.

  16. How Do Multiple-Star Systems Form? VLA Study Reveals "Smoking Gun"

    NASA Astrophysics Data System (ADS)

    2006-12-01

    system, all the antennas could provide data for us. In addition, we improved the level of detail by using the Pie Town, NM, antenna of the Very Long Baseline Array, as part of an expanded system," Lim said. The implementation and improvement of the 43 GHz receiving system was a collaborative program among the German Max Planck Institute, the Mexican National Autonomous University, and the U.S. National Radio Astronomy Observatory. Two popular theoretical models for the formation of multiple-star systems are, first, that the two protostars and their surrounding dusty disks fragment from a larger parent disk, and, second, that the protostars form independently and then one captures the other into a mutual orbit. "Our new study shows that the disks of the two main protostars are aligned with each other, and also are aligned with the larger, surrounding disk. In addition, their orbital motion resembles the rotation of the larger disk. This is a 'smoking gun' supporting the fragmentation model," Lim said. However, the new study also revealed a third young star with a dust disk. "The disk of this one is misaligned with those of the other two, so it may be the result of either fragmentation or capture," Takakuwa said. The misalignment of the third disk could have come through gravitational interactions with the other two, larger, protostars, the scientists said. They plan further observations to try to resolve the question. "We have a very firm indication that two of these protostars and their dust disks formed from the same, larger disk-like cloud, then broke out from it in a fragmentation process. That strongly supports one theoretical model for how multiple-star systems are formed. The misalignment of the third protostar and its disk leaves open the possibility that it could have formed elsewhere and been captured, and we'll continue to work on reconstructing the history of this fascinating system," Lim summarized. The National Radio Astronomy Observatory is a facility of

  17. Different precursor populations revealed by microscopic studies of bulk damage in KDP and DKDP crystals

    SciTech Connect

    DeMange, P; Negres, R A; Radousky, H B; Demos, S G

    2005-10-31

    We present experimental results aiming to reveal the relationship between damage initiating defect populations in KDP and DKDP crystals under irradiation at different wavelengths. Our results indicate that there is more than one type of defects leading to damage initiation, each defect acting as damage initiators over a different wavelength range. Results showing disparities in the morphology of damage sites from exposure at different wavelengths provides additional evidence for the presence of multiple types of defects responsible for damage initiation.

  18. 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

  19. 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

  20. 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