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Sample records for computational studies reveal

  1. Attitude towards computer-based learning: determinants as revealed by a controlled interventional study.

    PubMed

    Hahne, Amina Katharina; Benndorf, Ralf; Frey, Peter; Herzig, Stefan

    2005-09-01

    Curriculum-wide implementation of computer-based learning (CBL) in undergraduate medical education remains elusive. Unlike many pilot tests of singular learning programmes, dropout rates are high and acceptance seems low in the long run. We studied the effect of a new CBL programme, suitable for curriculum-wide implementation, on Year 3 medical students' attitudes towards CBL. Students from 2 universities participating in a mandatory pharmacology course were given access to a CBL programme covering cardiovascular drug therapy in a controlled randomised study (n = 167). Learner properties and attitude towards CBL were measured using psychometric scales, and knowledge by multiple-choice questions (pre- and post-test). Attitude towards CBL worsened in the CBL group (n = 70). Individual learners' properties did not explain this effect. The perceived programme quality was rated only 'average', which may contribute to the lower post-test values of attitude towards CBL. Learning outcomes were similar between the control group (n = 97) and students using CBL (n = 44). Learning efforts were shifted from self-study towards CBL. The initial enthusiasm of students was not maintained when using a programme designed to complement or even replace traditional teaching. Curriculum-wide implementation of CBL might be hampered by the discouragement of users.

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

    PubMed

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

    2016-01-15

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

  3. Novel Polyurethane Matrix Systems Reveal a Particular Sustained Release Behavior Studied by Imaging and Computational Modeling.

    PubMed

    Campiñez, María Dolores; Caraballo, Isidoro; Puchkov, Maxim; Kuentz, Martin

    2017-07-01

    The aim of the present work was to better understand the drug-release mechanism from sustained release matrices prepared with two new polyurethanes, using a novel in silico formulation tool based on 3-dimensional cellular automata. For this purpose, two polymers and theophylline as model drug were used to prepare binary matrix tablets. Each formulation was simulated in silico, and its release behavior was compared to the experimental drug release profiles. Furthermore, the polymer distributions in the tablets were imaged by scanning electron microscopy (SEM) and the changes produced by the tortuosity were quantified and verified using experimental data. The obtained results showed that the polymers exhibited a surprisingly high ability for controlling drug release at low excipient concentrations (only 10% w/w of excipient controlled the release of drug during almost 8 h). The mesoscopic in silico model helped to reveal how the novel biopolymers were controlling drug release. The mechanism was found to be a special geometrical arrangement of the excipient particles, creating an almost continuous barrier surrounding the drug in a very effective way, comparable to lipid or waxy excipients but with the advantages of a much higher compactability, stability, and absence of excipient polymorphism.

  4. 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

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

    PubMed

    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

    2015-06-01

    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 [(14)C]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 [(14)C]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. © FASEB.

  6. 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

  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.

  8. Sawfishes stealth revealed using computational fluid dynamics.

    PubMed

    Bradney, D R; Davidson, A; Evans, S P; Wueringer, B E; Morgan, D L; Clausen, P D

    2017-02-27

    Detailed computational fluid dynamics simulations for the rostrum of three species of sawfish (Pristidae) revealed that negligible turbulent flow is generated from all rostra during lateral swipe prey manipulation and swimming. These results suggest that sawfishes are effective stealth hunters that may not be detected by their teleost prey's lateral line sensory system during pursuits. Moreover, during lateral swipes, the rostra were found to induce little velocity into the surrounding fluid. Consistent with previous data of sawfish feeding behaviour, these data indicate that the rostrum is therefore unlikely to be used to stir up the bottom to uncover benthic prey. Whilst swimming with the rostrum inclined at a small angle to the horizontal, the coefficient of drag of the rostrum is relatively low and the coefficient of lift is zero.

  9. Studies to reveal the nature of interactions between catalase and curcumin using computational methods and optical techniques.

    PubMed

    Mofidi Najjar, Fayezeh; Ghadari, Rahim; Yousefi, Reza; Safari, Naser; Sheikhhasani, Vahid; Sheibani, Nader; Moosavi-Movahedi, Ali Akbar

    2017-02-01

    Curcumin is an important antioxidant compound, and is widely reported as an effective component for reducing complications of many diseases. However, the detailed mechanisms of its activity remain poorly understood. We found that curcumin can significantly increase catalase activity of BLC (bovine liver catalase). The mechanism of curcumin action was investigated using a computational method. We suggested that curcumin may activate BLC by modifying the bottleneck of its narrow channel. The molecular dynamic simulation data showed that placing curcumin on the structure of enzyme can increase the size of the bottleneck in the narrow channel of BLC, and readily allow the access of substrate to the active site. Because of the increase of the distance between amino acids of the bottleneck in the presence of curcumin, the entrance space of substrate increased from 250Å(3) to 440Å(3). In addition, the increase in emission of intrinsic fluorescence of BLC in presence of curcumin demonstrated changes in tertiary structure of catalase, and possibility of less quenching. We also used circular dichroism (CD) spectropolarimetry to determine how curcumin may alter the enzyme secondary structure. Catalase spectra in the presence of various concentrations of curcumin showed an increase in the amount of α-helix content.

  10. Computational study of the fibril organization of polyglutamine repeats reveals a common motif identified in beta-helices.

    PubMed

    Zanuy, David; Gunasekaran, Kannan; Lesk, Arthur M; Nussinov, Ruth

    2006-04-21

    The formation of fibril aggregates by long polyglutamine sequences is assumed to play a major role in neurodegenerative diseases such as Huntington. Here, we model peptides rich in glutamine, through a series of molecular dynamics simulations. Starting from a rigid nanotube-like conformation, we have obtained a new conformational template that shares structural features of a tubular helix and of a beta-helix conformational organization. Our new model can be described as a super-helical arrangement of flat beta-sheet segments linked by planar turns or bends. Interestingly, our comprehensive analysis of the Protein Data Bank reveals that this is a common motif in beta-helices (termed beta-bend), although it has not been identified so far. The motif is based on the alternation of beta-sheet and helical conformation as the protein sequence is followed from the N to the C termini (beta-alpha(R)-beta-polyPro-beta). We further identify this motif in the ssNMR structure of the protofibril of the amyloidogenic peptide Abeta(1-40). The recurrence of the beta-bend suggests a general mode of connecting long parallel beta-sheet segments that would allow the growth of partially ordered fibril structures. The design allows the peptide backbone to change direction with a minimal loss of main chain hydrogen bonds. The identification of a coherent organization beyond that of the beta-sheet segments in different folds rich in parallel beta-sheets suggests a higher degree of ordered structure in protein fibrils, in agreement with their low solubility and dense molecular packing.

  11. Revealing the potency of Annona muricata leaves extract as FOXO1 inhibitor for diabetes mellitus treatment through computational study.

    PubMed

    Damayanti, Dini Sri; Utomo, Didik Huswo; Kusuma, Chandra

    2016-12-01

    FOXO1 protein inactivation in the nucleus is one of targets for the treatment of diabetes mellitus. Annona muricata leaves contain flavonoid and phenolic compound alkaloids that were known to be able to increase pancreatic β cell proliferation in animal experiment. This research aimed to predict the active compound ability of the Annona muricata leaves to bind and inhibit FOXO1 protein through in silico study. Analysis of molecular docking was performed by using Autodock Vina PyRx. this research proved that anonaine, rutin, muricatocin a, isolaureline, xylopine, and kaempferol 3-O-rutinoside had an equal or smaller free binding energy compared to the control compound. Rutin and Muricatocin A had the same binding ability toward 66% amino acid residues, compared to control compound with hydrogen bond type, while xylopine, anonaine, isolaureline, kaempferol 3-O-rutinoside had a similar binding ability towards 33% amino acid residues compared to control compound with hydrogen bond type.

  12. Structural, Biochemical, and Computational Studies Reveal the Mechanism of Selective Aldehyde Dehydrogenase 1A1 Inhibition by Cytotoxic Duocarmycin Analogues.

    PubMed

    Koch, Maximilian F; Harteis, Sabrina; Blank, Iris D; Pestel, Galina; Tietze, Lutz F; Ochsenfeld, Christian; Schneider, Sabine; Sieber, Stephan A

    2015-11-09

    Analogues of the natural product duocarmycin bearing an indole moiety were shown to bind aldehyde dehydrogenase 1A1 (ALDH1A1) in addition to DNA, while derivatives without the indole solely addressed the ALDH1A1 protein. The molecular mechanism of selective ALDH1A1 inhibition by duocarmycin analogues was unraveled through cocrystallization, mutational studies, and molecular dynamics simulations. The structure of the complex shows the compound embedded in a hydrophobic pocket, where it is stabilized by several crucial π-stacking and van der Waals interactions. This binding mode positions the cyclopropyl electrophile for nucleophilic attack by the noncatalytic residue Cys302, thereby resulting in covalent attachment, steric occlusion of the active site, and inhibition of catalysis. The selectivity of duocarmycin analogues for ALDH1A1 is unique, since only minor alterations in the sequence of closely related protein isoforms restrict compound accessibility. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Carbohydrate-protein interactions that drive processive polysaccharide translocation in enzymes revealed from a computational study of cellobiohydrolase processivity.

    PubMed

    Knott, Brandon C; Crowley, Michael F; Himmel, Michael E; Ståhlberg, Jerry; Beckham, Gregg T

    2014-06-18

    Translocation of carbohydrate polymers through protein tunnels and clefts is a ubiquitous biochemical phenomenon in proteins such as polysaccharide synthases, glycoside hydrolases, and carbohydrate-binding modules. Although static snapshots of carbohydrate polymer binding in proteins have long been studied via crystallography and spectroscopy, the molecular details of polysaccharide chain processivity have not been elucidated. Here, we employ simulation to examine how a cellulose chain translocates by a disaccharide unit during the processive cycle of a glycoside hydrolase family 7 cellobiohydrolase. Our results demonstrate that these biologically and industrially important enzymes employ a two-step mechanism for chain threading to form a Michaelis complex and that the free energy barrier to chain threading is significantly lower than the hydrolysis barrier. Taken with previous studies, our findings suggest that the rate-limiting step in enzymatic cellulose degradation is the glycosylation reaction, not chain processivity. Based on the simulations, we find that strong electrostatic interactions with polar residues that are conserved in GH7 cellobiohydrolases, but not in GH7 endoglucanases, at the leading glucosyl ring provide the thermodynamic driving force for polysaccharide chain translocation. Also, we consider the role of aromatic-carbohydrate interactions, which are widespread in carbohydrate-active enzymes and have long been associated with processivity. Our analysis suggests that the primary role for these aromatic residues is to provide tunnel shape and guide the carbohydrate chain to the active site. More broadly, this work elucidates the role of common protein motifs found in carbohydrate-active enzymes that synthesize or depolymerize polysaccharides by chain translocation mechanisms coupled to catalysis.

  14. 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

    2014-08-07

    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.

  15. Computational modeling reveals molecular details of epidermal growth factor binding

    PubMed Central

    Mayawala, Kapil; Vlachos, Dionisios G; Edwards, Jeremy S

    2005-01-01

    Background The ErbB family of receptors are dysregulated in a number of cancers, and the signaling pathway of this receptor family is a critical target for several anti-cancer drugs. Therefore a detailed understanding of the mechanisms of receptor activation is critical. However, despite a plethora of biochemical studies and recent single particle tracking experiments, the early molecular mechanisms involving epidermal growth factor (EGF) binding and EGF receptor (EGFR) dimerization are not as well understood. Herein, we describe a spatially distributed Monte Carlo based simulation framework to enable the simulation of in vivo receptor diffusion and dimerization. Results Our simulation results are in agreement with the data from single particle tracking and biochemical experiments on EGFR. Furthermore, the simulations reveal that the sequence of receptor-receptor and ligand-receptor reaction events depends on the ligand concentration, receptor density and receptor mobility. Conclusion Our computer simulations reveal the mechanism of EGF binding on EGFR. Overall, we show that spatial simulation of receptor dynamics can be used to gain a mechanistic understanding of receptor activation which may in turn enable improved cancer treatments in the future. PMID:16318625

  16. 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…

  17. A Curtin-Hammett mechanism for the copolymerization of ethylene and methyl acrylate monomer using a PymNox nickel catalyst as revealed by DFT computational studies.

    PubMed

    Ramos, Javier; Martínez, Sonia; Cruz, Víctor L; Martínez-Salazar, Javier

    2012-02-01

    In this work, the copolymerization of ethylene and methyl acrylate (MA) as catalyzed by a new Ni-based PymNox organometallic compound was studied computationally. We recently tested the behavior of this type of catalyst in ethylene homopolymerization. Experimental results show that the unsubstituted catalyst Ni2 (aldimino PymNox catalyst) is unable to incorporate the MA monomer, whereas methyl-substituted Ni1 (acetaldimino PymNox catalyst) is able to achieve copolymerization. The reactivities of both catalysts were examined using density functional theory (DFT) models. Based on energy profiles calculated at the BP86 level, a Curtin-Hammett mechanism was proposed to explain the different reactivities of the catalysts in ethylene/MA copolymerization. Our results indicate that the methyl substituent Ni1 introduces additional steric hindrance that results in a catalyst conformation that is better suited to polar monomer incorporation. This model provides insights into the design of new catalysts to produce polar functionalized copolymers based on ethylene.

  18. Revealing the mechanisms underlying embolic stroke using computational modelling.

    PubMed

    Chung, Emma M L; Hague, James P; Evans, David H

    2007-12-07

    Computational forecasting of arterial blockages in a virtual patient has the potential to provide the next generation of advanced clinical monitoring aids for stroke prevention. As a first step towards a physiologically realistic virtual patient, we have created a computer model investigating the effects of emboli (particles or gas bubbles) as they become lodged in the brain. Our model provides a framework for predicting the severity of microvascular obstruction by simulating fundamental interactions between emboli and the fractal geometry of the arterial tree through which they travel. The model vasculature consisted of a bifurcating fractal tree comprising over a million branches ranging between 1 mm and 12 microm in diameter. Motion of emboli through the tree was investigated using a Monte Carlo simulation to evaluate the effects of the embolus size, clearance time and embolization rate on the number and persistence of blocked arterioles. Our simulations reveal with striking clarity that the relationship between embolus properties and vascular obstruction is nonlinear. We observe a rapid change between free-flowing and severely blocked arteries at specific combinations of the embolus size and embolization rate. The model predicts distinct patterns of cerebral injury for solid and gaseous emboli which are consistent with clinical observations. Solid emboli are predicted to be responsible for focal persistent injuries, while fast-clearing gas emboli produce diffuse transient blockages similar to global hypoperfusion. The impact of solid emboli was found to be dramatically reduced by embolus fragmentation. Computer simulations of embolization provide a novel means of investigating the role of emboli in producing neurological injury and assessing effective strategies for stroke prevention.

  19. 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

  20. Case Studies Reveal Camper Growth.

    ERIC Educational Resources Information Center

    Brannan, Steve; Fullerton, Ann

    1999-01-01

    Case studies in the National Camp Evaluation Project and National Inclusive Camp Practices project used interviews with counselors and parents about camper's growth to yield qualitative data for camp program evaluation. The importance, methods, and benefits of case studies are described. Sidebars give examples of comments on perceived camper…

  1. 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.

  2. Computational studies of consciousness.

    PubMed

    Aleksander, Igor; Morton, Helen

    2008-01-01

    In this chapter we present a computational architecture intended to add clarity to the concept of consciousness. We briefly review some of the motivations of work done in this area in various institutes around the world and looks closely at our own work which specifically includes phenomenology, the sense of a self in a perceptual world. This breaks consciousness into five axioms: presence, imagination, attention, volition and emotions. It develops plausible mechanisms of each and how they interact to give a single sensation. An abstract architecture, the kernel architecture, is introduced as a starting point for building computational models. It is shown that through this architecture it is possible to discuss puzzling aspects of consciousness, for example are animals conscious? What happens when we dream? What goes on when we experience an illusion? This paper is intended to elucidate and update some concepts introduced in Aleksander (2005).

  3. Computed tomography: Will the slices reveal the truth

    PubMed Central

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

    2016-01-01

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

  4. 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…

  5. 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

  6. Computer simulations reveal motor properties generating stable antiparallel microtubule interactions.

    PubMed

    Nédélec, François

    2002-09-16

    An aster of microtubules is a set of flexible polar filaments with dynamic plus ends that irradiate from a common location at which the minus ends of the filaments are found. Processive soluble oligomeric motor complexes can bind simultaneously to two microtubules, and thus exert forces between two asters. Using computer simulations, I have explored systematically the possible steady-state regimes reached by two asters under the action of various kinds of oligomeric motors. As expected, motor complexes can induce the asters to fuse, for example when the complexes consist only of minus end-directed motors, or to fully separate, when the motors are plus end directed. More surprisingly, complexes made of two motors of opposite directionalities can also lead to antiparallel interactions between overlapping microtubules that are stable and sustained, like those seen in mitotic spindle structures. This suggests that such heterocomplexes could have a significant biological role, if they exist in the cell.

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

    NASA Astrophysics Data System (ADS)

    Hong, Liang; Smith, Jeremy; CenterMolecular Biophysics Team

    2014-03-01

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

  8. 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.

  9. 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

  10. Spontaneous Movements of a Computer Mouse Reveal Egoism and In-group Favoritism.

    PubMed

    Maliszewski, Norbert; Wojciechowski, Łukasz; Suszek, Hubert

    2017-01-01

    The purpose of the project was to assess whether the first spontaneous movements of a computer mouse, when making an assessment on a scale presented on the screen, may express a respondent's implicit attitudes. In Study 1, the altruistic behaviors of 66 students were assessed. The students were led to believe that the task they were performing was also being performed by another person and they were asked to distribute earnings between themselves and the partner. The participants performed the tasks under conditions with and without distractors. With the distractors, in the first few seconds spontaneous mouse movements on the scale expressed a selfish distribution of money, while later the movements gravitated toward more altruism. In Study 2, 77 Polish students evaluated a painting by a Polish/Jewish painter on a scale. They evaluated it under conditions of full or distracted cognitive abilities. Spontaneous movements of the mouse on the scale were analyzed. In addition, implicit attitudes toward both Poles and Jews were measured with the Implicit Association Test (IAT). A significant association between implicit attitudes (IAT) and spontaneous evaluation of images using a computer mouse was observed in the group with the distractor. The participants with strong implicit in-group favoritism of Poles revealed stronger preference for the Polish painter's work in the first few seconds of mouse movement. Taken together, these results suggest that spontaneous mouse movements may reveal egoism (in-group favoritism), i.e., processes that were not observed in the participants' final decisions (clicking on the scale).

  11. Combined computational and biochemical study reveals the importance of electrostatic interactions between the "pH sensor" and the cation binding site of the sodium/proton antiporter NhaA of Escherichia coli.

    PubMed

    Olkhova, Elena; Kozachkov, Lena; Padan, Etana; Michel, Hartmut

    2009-08-15

    Sodium proton antiporters are essential enzymes that catalyze the exchange of sodium ions for protons across biological membranes. The crystal structure of NhaA has provided a basis to explore the mechanism of ion exchange and its unique regulation by pH. Here, the mechanism of the pH activation of the antiporter is investigated through functional and computational studies of several variants with mutations in the ion-binding site (D163, D164). The most significant difference found computationally between the wild type antiporter and the active site variants, D163E and D164N, are low pK(a) values of Glu78 making them insensitive to pH. Although in the variant D163N the pK(a) of Glu78 is comparable to the physiological one, this variant cannot demonstrate the long-range electrostatic effect of Glu78 on the pH-dependent structural reorganization of trans-membrane helix X and, hence, is proposed to be inactive. In marked contrast, variant D164E remains sensitive to pH and can be activated by alkaline pH shift. Remarkably, as expected computationally and discovered here biochemically, D164E is viable and active in Na(+)/H(+) exchange albeit with increased apparent K(M). Our results unravel the unique electrostatic network of NhaA that connect the coupled clusters of the "pH sensor" with the binding site, which is crucial for pH activation of NhaA.

  12. Spontaneous Movements of a Computer Mouse Reveal Egoism and In-group Favoritism

    PubMed Central

    Maliszewski, Norbert; Wojciechowski, Łukasz; Suszek, Hubert

    2017-01-01

    The purpose of the project was to assess whether the first spontaneous movements of a computer mouse, when making an assessment on a scale presented on the screen, may express a respondent’s implicit attitudes. In Study 1, the altruistic behaviors of 66 students were assessed. The students were led to believe that the task they were performing was also being performed by another person and they were asked to distribute earnings between themselves and the partner. The participants performed the tasks under conditions with and without distractors. With the distractors, in the first few seconds spontaneous mouse movements on the scale expressed a selfish distribution of money, while later the movements gravitated toward more altruism. In Study 2, 77 Polish students evaluated a painting by a Polish/Jewish painter on a scale. They evaluated it under conditions of full or distracted cognitive abilities. Spontaneous movements of the mouse on the scale were analyzed. In addition, implicit attitudes toward both Poles and Jews were measured with the Implicit Association Test (IAT). A significant association between implicit attitudes (IAT) and spontaneous evaluation of images using a computer mouse was observed in the group with the distractor. The participants with strong implicit in-group favoritism of Poles revealed stronger preference for the Polish painter’s work in the first few seconds of mouse movement. Taken together, these results suggest that spontaneous mouse movements may reveal egoism (in-group favoritism), i.e., processes that were not observed in the participants’ final decisions (clicking on the scale). PMID:28163689

  13. In vitro protease cleavage and computer simulations reveal the HIV-1 capsid maturation pathway

    PubMed Central

    Ning, Jiying; Erdemci-Tandogan, Gonca; Yufenyuy, Ernest L.; Wagner, Jef; Himes, Benjamin A.; Zhao, Gongpu; Aiken, Christopher; Zandi, Roya; Zhang, Peijun

    2016-01-01

    HIV-1 virions assemble as immature particles containing Gag polyproteins that are processed by the viral protease into individual components, resulting in the formation of mature infectious particles. There are two competing models for the process of forming the mature HIV-1 core: the disassembly and de novo reassembly model and the non-diffusional displacive model. To study the maturation pathway, we simulate HIV-1 maturation in vitro by digesting immature particles and assembled virus-like particles with recombinant HIV-1 protease and monitor the process with biochemical assays and cryoEM structural analysis in parallel. Processing of Gag in vitro is accurate and efficient and results in both soluble capsid protein and conical or tubular capsid assemblies, seemingly converted from immature Gag particles. Computer simulations further reveal probable assembly pathways of HIV-1 capsid formation. Combining the experimental data and computer simulations, our results suggest a sequential combination of both displacive and disassembly/reassembly processes for HIV-1 maturation. PMID:27958264

  14. In vitro protease cleavage and computer simulations reveal the HIV-1 capsid maturation pathway.

    PubMed

    Ning, Jiying; Erdemci-Tandogan, Gonca; Yufenyuy, Ernest L; Wagner, Jef; Himes, Benjamin A; Zhao, Gongpu; Aiken, Christopher; Zandi, Roya; Zhang, Peijun

    2016-12-13

    HIV-1 virions assemble as immature particles containing Gag polyproteins that are processed by the viral protease into individual components, resulting in the formation of mature infectious particles. There are two competing models for the process of forming the mature HIV-1 core: the disassembly and de novo reassembly model and the non-diffusional displacive model. To study the maturation pathway, we simulate HIV-1 maturation in vitro by digesting immature particles and assembled virus-like particles with recombinant HIV-1 protease and monitor the process with biochemical assays and cryoEM structural analysis in parallel. Processing of Gag in vitro is accurate and efficient and results in both soluble capsid protein and conical or tubular capsid assemblies, seemingly converted from immature Gag particles. Computer simulations further reveal probable assembly pathways of HIV-1 capsid formation. Combining the experimental data and computer simulations, our results suggest a sequential combination of both displacive and disassembly/reassembly processes for HIV-1 maturation.

  15. In vitro protease cleavage and computer simulations reveal the HIV-1 capsid maturation pathway

    NASA Astrophysics Data System (ADS)

    Ning, Jiying; Erdemci-Tandogan, Gonca; Yufenyuy, Ernest L.; Wagner, Jef; Himes, Benjamin A.; Zhao, Gongpu; Aiken, Christopher; Zandi, Roya; Zhang, Peijun

    2016-12-01

    HIV-1 virions assemble as immature particles containing Gag polyproteins that are processed by the viral protease into individual components, resulting in the formation of mature infectious particles. There are two competing models for the process of forming the mature HIV-1 core: the disassembly and de novo reassembly model and the non-diffusional displacive model. To study the maturation pathway, we simulate HIV-1 maturation in vitro by digesting immature particles and assembled virus-like particles with recombinant HIV-1 protease and monitor the process with biochemical assays and cryoEM structural analysis in parallel. Processing of Gag in vitro is accurate and efficient and results in both soluble capsid protein and conical or tubular capsid assemblies, seemingly converted from immature Gag particles. Computer simulations further reveal probable assembly pathways of HIV-1 capsid formation. Combining the experimental data and computer simulations, our results suggest a sequential combination of both displacive and disassembly/reassembly processes for HIV-1 maturation.

  16. What computational chemistry and magnetic resonance reveal concerning the oxygen evolving centre in Photosystem II.

    PubMed

    Terrett, Richard; Petrie, Simon; Stranger, Rob; Pace, Ron J

    2016-09-01

    Density Functional Theory (DFT) computational studies of the Mn4/Ca Oxygen Evolving Complex (OEC) region of Photosystem II in the paramagnetic S2 and S3 states of the water oxdizing catalytic cycle are described. These build upon recent advances in computationally understanding the detailed S1 state OEC geometries, revealed by the recent high resolution Photosystem II crystal structures of Shen et al., at 1.90Å and 1.95Å (Petrie et al., 2015, Angew. Chem. Int. Ed., 54, 7120). The models feature a 'Low Oxidation Paradigm' assumption for the mean Mn oxidation states in the functional enzyme, with the mean oxidation levels being 3.0, 3.25 and 3.5 in S1, S2 and S3, respectively. These calculations are used to infer magnetic exchange interactions within the coupled OEC cluster, particularly in the Electron Paramagnetic Resonance (EPR)-visible S2 and S3 states. Detailed computational estimates of the intrinsic magnitudes and molecular orientations of the (55)Mn hyperfine tensors in the S2 state are presented. These parameters, together with the resultant spin projected hyperfine values are compared with recent appropriate experimental EPR data (Continuous Wave (CW), Electron-Nuclear Double Resonance (ENDOR) and ELDOR (Electron-Electron Double Resonance)-Detected Nuclear Magnetic Resonance (EDNMR)) from the OEC. It is found that an effective Coupled Dimer magnetic organization of the four Mn in the OEC cluster in the S2 and S3 states is able to quantitatively rationalize the observed (55)Mn hyperfine data. This is consistent with structures we propose to represent the likely state of the OEC in the catalytically active form of the enzyme. Copyright © 2016 Elsevier Inc. All rights reserved.

  17. 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…

  18. Computers in Public Education Study.

    ERIC Educational Resources Information Center

    HBJ Enterprises, Highland Park, NJ.

    This survey conducted for the National Institute of Education reports the use of computers in U.S. public schools in the areas of instructional computing, student accounting, management of educational resources, research, guidance, testing, and library applications. From a stratified random sample of 1800 schools in varying geographic areas and…

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

    PubMed

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

    2015-09-01

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

  20. 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

  1. Computer Use in Elementary Social Studies.

    ERIC Educational Resources Information Center

    Freiwald, Wendy D.

    This paper presents a review of the literature regarding use of computers in elementary social studies and a rationale of how computer usage aligns with the constructivist approach to education. Computer use in elementary social studies can be divided into three broad categories: (1) instructional software; (2) productive software; and (3)…

  2. Computer simulation studies of minerals

    NASA Astrophysics Data System (ADS)

    Oganov, Artem Romaevich

    Applications of state-of-the-art computer simulations to important Earth- and rock-forming minerals (Al2SiO5 polymorphs, albite (NaAlSi3O8), and MgSiO3 perovskite) are described. Detailed introductions to equations of state and elasticity, phase transitions, computer simulations, and geophysical background are given. A new general classification of phase transitions is proposed, providing a natural framework for discussion of structural, thermodynamic, and kinetic aspects of phase transitions. The concept of critical bond distances is introduced. For Si-O bonds this critical distance is 2.25 A. Using atomistic simulations, anomalous Al-Si antiordering in albite is explained. A first-order isosymmetric transition associated with a change in the ordering scheme is predicted at high pressures. A quantum-mechanical study is presented for the Al2SiO5 polymorphs: kyanite, andalusite, sillimanite, and hypothetical pseudobrookite-like and V3O5-like phases (the latter phase was believed to be the main Al mineral of the lower mantle). It is shown that above 11 GPa all the Al2SiO5 phases break down into the mixture of oxides: corundum (Al2O3) and stishovite (SiO2). Atomisation energies, crystal structures and equations of state of all the Al2SiO5 polymorphs, corundum, stishovite, quartz (SiO2) have been determined. Metastable pressure-induced transitions in sillimanite and andalusite are predicted at ~30-50 GPa and analysed in terms of structural changes and lattice dynamics. Sillimanite (Pbnm) transforms into incommensurate and isosymmetric (Pbnm) phases; andalusite undergoes pressure-induced amorphisation. Accurate quantum-mechanical thermal equation of state is obtained for MgSiO3 perovskite, the main Earth-forming mineral. Results imply that a pure-perovskite mantle is unlikely. I show that MgSiO3 perovskite is not a Debye-like solid, contrary to a common assumption. First ever ab initio molecular dynamics calculations of elastic constants at finite temperatures are

  3. 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,…

  4. 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…

  5. 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.

  6. Computational and synthetic studies with tetravinylethylenes.

    PubMed

    Lindeboom, Erik J; Willis, Anthony C; Paddon-Row, Michael N; Sherburn, Michael S

    2014-12-05

    Computational and experimental studies offer fresh insights into the neglected tetravinylethylene class of compounds. Both the structures and the outcomes of exploratory reactions of the parent hydrocarbon are predicted and explained in detail through high-level composite ab initio MO G4(MP2) computational studies.

  7. 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…

  8. Education Students' Perceptions of Computers: A Cross-Cultural Study

    ERIC Educational Resources Information Center

    Huang, Shwu-Yong L.

    2003-01-01

    This study investigates education students' perceptions of computers and the factors affecting their perceptions among education students in the United States and Taiwan. Sample subjects were 360 students from six colleges of education in the two places. The results reveal that there were significant differences. Education students in the United…

  9. Interdisciplinary Study with Computer-Based Multimedia.

    ERIC Educational Resources Information Center

    Couch, John D.; And Others

    Interdisciplinary study with computer-based multimedia in the classroom is reviewed. The multimedia revolution involves multiple technologies and multiple modes of sensation, but the computer is at the heart of this revolution. Despite the many challenges, interest is strong for multimedia courseware. The predicted market is enormous, and nowhere…

  10. Report of Computer Selection Study Committee.

    ERIC Educational Resources Information Center

    Botten, LeRoy H.

    A computer selection committee was charged with studying the computer needs of Andrews University in Berrien Springs, Michigan. Major results of the investigation included the findings that campus academic and administrative needs would best be served by one onsite system which could support versatile and concurrent time-sharing, batch processing,…

  11. Interdisciplinary Study with Computer-Based Multimedia.

    ERIC Educational Resources Information Center

    Couch, John D.; And Others

    Interdisciplinary study with computer-based multimedia in the classroom is reviewed. The multimedia revolution involves multiple technologies and multiple modes of sensation, but the computer is at the heart of this revolution. Despite the many challenges, interest is strong for multimedia courseware. The predicted market is enormous, and nowhere…

  12. Beginning a Study Investigating Computer Programming.

    ERIC Educational Resources Information Center

    Stocker, Charlene

    Intended for children from kindergarten through the sixth grade, this booklet teaches about the computer and provides instruction in computer programming in the BASIC language. Thirteen sequential lessons are provided to encourage independent study. Each lesson consists of a set of four pages and explains a BASIC command or statement, presents…

  13. Computer Based Social Studies Instruction: A Qualitative Case Study

    ERIC Educational Resources Information Center

    Ulusoy, Mustafa

    2005-01-01

    In this study, the quality of the computer and Internet based social studies course was investigated. A case study design was chosen to understand, a) how computers are used in the eighth grade classroom, b) what the students' and teachers' perceptions are about the advantages and problems of using computers. Qualitative data sources showed that…

  14. Computer-Assisted Study Skills Improvement Program.

    ERIC Educational Resources Information Center

    Brown, William F.; Forristall, Dorothy Z.

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

  15. 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.

  16. 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.

  17. A computational study of wingtip vortex flowfield

    NASA Technical Reports Server (NTRS)

    Dacles-Mariani, Jennifer; Rogers, Stuart; Kwak, Dochan; Zilliac, Greg; Chow, Jim

    1993-01-01

    The near-field behavior of a wingtip vortex flow is studied computationally using an incompressible flow solver for the Navier-Stokes equations based on the artificial compressibility method. Inaccuracies in current computational studies are addressed, especially, the role of numerical errors and transition/turbulence modeling. A subset problem is devised in order to make the study of vortex preservation more tractable. As part of the numerical checks, the flow is first run laminar while performing a systematic grid refinement study for the subset problem. Further studies on the numerical errors are conducted with the measured Reynolds stresses introduced into the momentum equations as source terms. As a preliminary study of turbulent flows, the one-equation Baldwin-Barth turbulence model is implemented as well as the approximation of the production term. The full-geometry case is computed using 1.1 million grid points. The results are compared with experiment.

  18. 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.

  19. US QCD computational performance studies with PERI

    NASA Astrophysics Data System (ADS)

    Zhang, Y.; Fowler, R.; Huck, K.; Malony, A.; Porterfield, A.; Reed, D.; Shende, S.; Taylor, V.; Wu, X.

    2007-07-01

    We report on some of the interactions between two SciDAC projects: The National Computational Infrastructure for Lattice Gauge Theory (USQCD), and the Performance Engineering Research Institute (PERI). Many modern scientific programs consistently report the need for faster computational resources to maintain global competitiveness. However, as the size and complexity of emerging high end computing (HEC) systems continue to rise, achieving good performance on such systems is becoming ever more challenging. In order to take full advantage of the resources, it is crucial to understand the characteristics of relevant scientific applications and the systems these applications are running on. Using tools developed under PERI and by other performance measurement researchers, we studied the performance of two applications, MILC and Chroma, on several high performance computing systems at DOE laboratories. In the case of Chroma, we discuss how the use of C++ and modern software engineering and programming methods are driving the evolution of performance tools.

  20. 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

  1. Computer simulations reveal mechanisms that organize nuclear dynein forces to separate centrosomes.

    PubMed

    De Simone, Alessandro; Gönczy, Pierre

    2017-07-12

    Centrosome separation along the surface of the nucleus at the onset of mitosis is critical for bipolar spindle assembly. Dynein anchored on the nuclear envelope is known to be important for centrosome separation, but it is unclear how nuclear dynein forces are organized in an anisotropic manner to promote the movement of centrosomes away from each other. Here, we use computational simulations of C. elegans embryos to address this fundamental question, testing three potential mechanisms by which nuclear dynein may act. First, our analysis shows that expansion of the nuclear volume per se does not generate forces driving centrosome separation. Second, we uncover that steric interactions between microtubules and centrosomes contribute to robust onset of nuclear dynein-mediated centrosome separation. Third, we find that the initial position of centrosomes, between nucleus and cell cortex at the embryo posterior, is a key determinant in organizing microtubule aster asymmetry to power nuclear dynein-dependent separation. Overall, our work reveals that accurate initial centrosome position, together with steric interactions, ensure proper anisotropic organization of nuclear dynein forces to separate centrosomes, thus ensuring robust bipolar spindle assembly. © 2017 by The American Society for Cell Biology.

  2. 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…

  3. 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.

  4. 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

  5. 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)

  6. 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

  7. A systematic computational study on flavonoids.

    PubMed

    Aparicio, Santiago

    2010-05-03

    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.

  8. Canine tarsal architecture as revealed by high-resolution computed tomography.

    PubMed

    Galateanu, G; Apelt, D; Aizenberg, I; Saragusty, J; Hildebrandt, T B

    2013-06-01

    Central tarsal bone (CTB) fractures are well documented and are a subject of increasing importance in human, equine and canine athletes although the mechanism of these fractures in dogs is not fully understood and an extrapolation from human medicine may not be accurate. This study reports the use of high-resolution computed tomography (CT) of 91 tarsal joints from 47 dogs to generate a more detailed in situ anatomical description of the CTB architecture in order to obtain a better understanding of the pathogenesis of CTB fractures in this species. The dogs studied represented a wide range of ages, breeds and levels of habitual physical activity and the angles of the tarsal joints studied ranged between maximal flexion (16.4°) and maximal extension (159.1°). Regardless of tarsal angle, the CTB articulated with the calcaneus exclusively at the level of its plantar process (PPCTB) in all dogs. The PPCTB presented two distinct parts in all dogs, a head and a neck. The calcaneus tended to rely on the PPCTB neck during flexion and on the PPCTB head during extension. This study describes new tarsal elements for the first time, including the calcaneal articular process, the fourth tarsal bone plantar articular process and the talar plantar prominence of the CTB. Based on calcaneo-PPCTB architecture, it is postulated that the PPCTB is a keystone structure and that at least some of CTB fractures in dogs could either commence at or are induced at this level due to the impingement forces exercised by the calcaneus.

  9. Cyanobacterial biofuels: new insights and strain design strategies revealed by computational modeling.

    PubMed

    Erdrich, Philipp; Knoop, Henning; Steuer, Ralf; Klamt, Steffen

    2014-09-19

    Cyanobacteria are increasingly recognized as promising cell factories for the production of renewable biofuels and chemical feedstocks from sunlight, CO2, and water. However, most biotechnological applications of these organisms are still characterized by low yields. Increasing the production performance of cyanobacteria remains therefore a crucial step. In this work we use a stoichiometric network model of Synechocystis sp. PCC 6803 in combination with CASOP and minimal cut set analysis to systematically identify and characterize suitable strain design strategies for biofuel synthesis, specifically for ethanol and isobutanol. As a key result, improving upon other works, we demonstrate that higher-order knockout strategies exist in the model that lead to coupling of growth with high-yield biofuel synthesis under phototrophic conditions. Enumerating all potential knockout strategies (cut sets) reveals a unifying principle behind the identified strain designs, namely to reduce the ratio of ATP to NADPH produced by the photosynthetic electron transport chain. Accordingly, suitable knockout strategies seek to block cyclic and other alternate electron flows, such that ATP and NADPH are exclusively synthesized via the linear electron flow whose ATP/NADPH ratio is below that required for biomass synthesis. The products of interest are then utilized by the cell as sinks for reduction equivalents in excess. Importantly, the calculated intervention strategies do not rely on the assumption of optimal growth and they ensure that maintenance metabolism in the absence of light remains feasible. Our analyses furthermore suggest that a moderately increased ATP turnover, realized, for example, by ATP futile cycles or other ATP wasting mechanisms, represents a promising target to achieve increased biofuel yields. Our study reveals key principles of rational metabolic engineering strategies in cyanobacteria towards biofuel production. The results clearly show that achieving

  10. 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

  11. A computational study of tip desensitization in axial flow turbines

    NASA Astrophysics Data System (ADS)

    Tallman, James A.

    This study investigates the use of modified blade tip geometries as a means of reducing the leakage flow and vortex in axial flow turbine rotors. Computational Fluid Dynamics (CFD) was used as a tool to compute the flowfield of a low-speed, single stage, experimental turbine. The results from three separate baseline turbine rotor computations all showed good agreement with experimental measurements, validating the numerical procedure's ability to predict complex turbine rotor flowfields. This agreement was, in part, due to an advanced, multi-block method of discretizing the turbine rotor into a computational mesh, which was developed as part of the study. After validating the numerical procedure, three different classifications of tip geometry modification were investigated through CFD simulation: chamfering of the suction side of the blade tip, rounding of the blade tip edge, and squealer-type cavities. Chamfering of the blade tip was shown to cause the leakage flow inside the gap to turn toward the camber direction of the blade. This turning led to reduced mass flow through the gap and a smaller leakage vortex. Rounding of the suction side edge of the blade tip resulted in a considerable reduction in the size and strength of the leakage vortex, while rounding of the pressure side edge of the blade tip greatly increased the mass flow rate through the gap. Rounded squealer cavities acted to reduce the mass flow through the gap and proved advantageous over traditional, square squealer cavities. Final, detailed computations using a very refined mesh reconfirmed the findings of more rapid, preliminary computations. Detailed, three-dimensional analysis of the computed flowfields revealed the physics behind the modified tip geometries' reduction of the leakage flow and vortex.

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

    PubMed

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

    2015-10-13

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

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

    PubMed Central

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

    2015-01-01

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

  14. Computer simulations of cellular group selection reveal mechanism for sustaining cooperation.

    PubMed

    Markvoort, Albert J; Sinai, Sam; Nowak, Martin A

    2014-09-21

    We present a computer simulation of group selection that is inspired by proto-cell division. Two types of replicating molecules, cooperators and defectors, reside inside membrane bound compartments. Cooperators pay a cost for other replicators in the cell to receive a benefit. Defectors pay no cost and distribute no benefits. The total population size fluctuates as a consequence of births and deaths of individual replicators. Replication requires activated substrates that are generated at a constant rate. Our model includes mutation between cooperators and defectors and selection on two levels: within proto-cells and between proto-cells. We find surprising similarities and differences between models with and without cell death. In both cases, a necessary requirement for group selection to favor some level of cooperation is the continuous formation of a minimum fraction of pure cooperator groups. Subsequently these groups become undermined by defectors, because of mutation and selection within cells. Cell division mechanisms which generate pure cooperator groups more efficiently are stronger promoters of cooperation. For example, division of a proto-cell into many daughter cells is more powerful in enhancing cooperation than division into two daughter cells. Our model differs from previous studies of group selection in that we explore a variety of different features and relax several restrictive assumptions that would be needed for analytic calculations.

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

    PubMed

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

    2007-10-09

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

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

    PubMed Central

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

    2007-01-01

    The American sabercat Smilodon fatalis is among the most charismatic of fossil carnivores. Despite broad agreement that its extraordinary anatomy reflects unique hunting techniques, after >150 years of study, many questions remain concerning its predatory behavior. Were the “sabers” used to take down large prey? Were prey killed with an eviscerating bite to the abdomen? Was its bite powerful or weak compared with that of modern big cats? Here we quantitatively assess the sabercat's biomechanical performance using the most detailed computer reconstructions yet developed for the vertebrate skull. Our results demonstrate that bite force driven by jaw muscles was relatively weak in S. fatalis, one-third that of a lion (Panthera leo) of comparable size, and its skull was poorly optimized to resist the extrinsic loadings generated by struggling prey. Its skull is better optimized for bites on restrained prey where the bite is augmented by force from the cervical musculature. We conclude that prey were brought to ground and restrained before a killing bite, driven in large part by powerful cervical musculature. Because large prey is easier to restrain if its head is secured, the killing bite was most likely directed to the neck. We suggest that the more powerful jaw muscles of P. leo may be required for extended, asphyxiating bites and that the relatively low bite forces in S. fatalis might reflect its ability to kill large prey more quickly, avoiding the need for prolonged bites. PMID:17911253

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2013-07-07

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

  19. 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,…

  20. 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,…

  1. Experimental and computational studies of dynamic stall

    NASA Technical Reports Server (NTRS)

    Carr, L. W.; Platzer, M. F.; Chandrasekhara, M. S.; Ekaterinaris, J.

    1989-01-01

    A review of dynamic stall research in progress under the Navy-NASA Joint Institute of Aeronautics is presented. This effort, which includes both experimental and computational studies of the dynamic stall process, is directed toward better understanding and modeling of the fluid flow that occurs on helicopters and aircraft flying in conditions that induce dynamic stall. The results of research now in progress are presented, with discussion of the experimental program on compressibility effects on dynamic stall, related CFD studies of the stall process based on Navier-Stokes modeling, and viscous-inviscid flow modeling of the incipient stall process.

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

    SciTech Connect

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

    2014-01-10

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

  3. 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.

  4. 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.

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

    NASA Astrophysics Data System (ADS)

    Derickson, Russell G.; Pielke, Roger A.

    2000-07-01

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

  6. A Computer-Supported Method to Reveal and Assess Personal Professional Theories in Vocational Education

    ERIC Educational Resources Information Center

    van den Bogaart, Antoine C. M.; Bilderbeek, Richel J. C.; Schaap, Harmen; Hummel, Hans G. K.; Kirschner, Paul A.

    2016-01-01

    This article introduces a dedicated, computer-supported method to construct and formatively assess open, annotated concept maps of Personal Professional Theories (PPTs). These theories are internalised, personal bodies of formal and practical knowledge, values, norms and convictions that professionals use as a reference to interpret and acquire…

  7. A Computer-Supported Method to Reveal and Assess Personal Professional Theories in Vocational Education

    ERIC Educational Resources Information Center

    van den Bogaart, Antoine C. M.; Bilderbeek, Richel J. C.; Schaap, Harmen; Hummel, Hans G. K.; Kirschner, Paul A.

    2016-01-01

    This article introduces a dedicated, computer-supported method to construct and formatively assess open, annotated concept maps of Personal Professional Theories (PPTs). These theories are internalised, personal bodies of formal and practical knowledge, values, norms and convictions that professionals use as a reference to interpret and acquire…

  8. 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

  9. Computational Study of a Primitive Life Model

    NASA Astrophysics Data System (ADS)

    Andrecut, Mircea

    We present a computational study of a primitive life model. The calculation involves a discrete treatment of a partial differential equation and some details of that problems are explained. We show that the investigated model is equivalent to a diffusively coupled logistic lattice. The bifurcation diagrams were calculated for different values of the control parameters. The obtained diagrams have shown that the time dependence of the population of the investigated model exhibits transitions between ordered and chaotic behavior. We have investigated also the patterns formation in this system.

  10. Computational vibrational study on coordinated nicotinamide

    NASA Astrophysics Data System (ADS)

    Bolukbasi, Olcay; Akyuz, Sevim

    2005-06-01

    The molecular structure and vibrational spectra of zinc (II) halide complexes of nicotinamide (ZnX 2(NIA) 2; X=Cl or Br; NIA=Nicotinamide) were investigated by computational vibrational study and scaled quantum mechanical (SQM) analysis. The geometry optimisation and vibrational wavenumber calculations of zinc halide complexes of nicotinamide were carried out by using the DFT/RB3LYP level of theory with 6-31G(d,p) basis set. The calculated wavenumbers were scaled by using scaled quantum mechanical (SQM) force field method. The fundamental vibrational modes were characterised by their total energy distribution. The coordination effects on nicotinamide through the ring nitrogen were discussed.

  11. Computational analysis reveals abundance of potential glycoproteins in Archaea, Bacteria and Eukarya.

    PubMed

    Zafar, Sadia; Nasir, Arshan; Bokhari, Habib

    2011-01-01

    Glycosylation is the most common type of post-translational modification (PTM) and is known to affect protein stability, folding and activity. Inactivity of enzymes mediating glycosylation can result in serious disorders including colon cancer and brain disorders. Out of five main types of glycosylation, N-linked glycosylation is most abundant and characterized by the addition of a sugar group to an Asparagine residue at the N-X-S/T motif. Enzyme mediating such transfer is known as oligosaccharyl transferase (OST). It has been hypothesized before that a significant number of proteins serve as glycoproteins. In this study, we used programming implementations of Python to statistically quantify the representation of glycoproteins by scanning all the available proteome sequence data at ExPASy server for the presence of glycoproteins and also the enzyme which plays critical role in glycosylation i.e. OST. Our results suggest that more than 50% of the proteins carry N-X-S/T motif i.e. they could be potential glycoproteins. Furthermore, approximately 28-36% (1/3) of proteins possesses signature motifs which are characteristic features of enzyme OST. Quantifying this bias individually reveals that both the number of proteins tagged with N-X-S/T motif and the average number of motifs per protein is significantly higher in case of eukaryotes when compared to prokaryotes. In the light of these results we conclude that there is a significant bias in the representation of glycoproteins in the proteomes of all species and is manifested substantially in eukaryotes and claim for glycosylation to be the most common and ubiquitous PTM in cells, especially in eukaryotes.

  12. 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.

  13. 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.

  14. Computational Prediction of CRISPR/Cas9 Target Sites Reveals Potential Off-Target Risks in Human and Mouse.

    PubMed

    Wang, Qingbo; Ui-Tei, Kumiko

    2017-01-01

    The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) system is a prominent genome engineering technology. In the CRISPR/Cas system, the RNA-guided endonuclease Cas protein introduces a DNA double-stranded break at the genome position recognized by a guide RNA (gRNA) based on complementary base-pairing of about 20-nucleotides in length. The 8- or 12-mer gRNA sequence in the proximal region is especially important for target recognition, and the genes with sequence complementarity to such regions are often disrupted. To carry out target site-specific genome editing, we released the CRISPRdirect ( http://crispr.dbcls.jp /) website. This website allows us to select target site-specific gRNA sequences by performing exhaustive searches against entire genomic sequences. In this study, target site-specific gRNA sequences were designed for human, mouse, Drosophila melanogaster, and Caenorhabditis elegans. The calculation results revealed that at least five gRNA sequences, each of them having only one perfectly complementary site in the whole genome, could be designed for more than 95% of genes, regardless of the organism. Next, among those gRNAs, we selected gRNAs that did not have any other complementary site to the unique 12-mer proximal sequences to avoid possible off-target effects. This computational prediction revealed that target site-specific gRNAs are selectable for the majority of genes in D. melanogaster and C. elegans. However, for >50% of genes in humans and mice, there are no target sites without possible off-target effects.

  15. Computational Prediction of Intronic microRNA Targets using Host Gene Expression Reveals Novel Regulatory Mechanisms

    PubMed Central

    Radfar, M. Hossein; Wong, Willy; Morris, Quaid

    2011-01-01

    Approximately half of known human miRNAs are located in the introns of protein coding genes. Some of these intronic miRNAs are only expressed when their host gene is and, as such, their steady state expression levels are highly correlated with those of the host gene's mRNA. Recently host gene expression levels have been used to predict the targets of intronic miRNAs by identifying other mRNAs that they have consistent negative correlation with. This is a potentially powerful approach because it allows a large number of expression profiling studies to be used but needs refinement because mRNAs can be targeted by multiple miRNAs and not all intronic miRNAs are co-expressed with their host genes. Here we introduce InMiR, a new computational method that uses a linear-Gaussian model to predict the targets of intronic miRNAs based on the expression profiles of their host genes across a large number of datasets. Our method recovers nearly twice as many true positives at the same fixed false positive rate as a comparable method that only considers correlations. Through an analysis of 140 Affymetrix datasets from Gene Expression Omnibus, we build a network of 19,926 interactions among 57 intronic miRNAs and 3,864 targets. InMiR can also predict which host genes have expression profiles that are good surrogates for those of their intronic miRNAs. Host genes that InMiR predicts are bad surrogates contain significantly more miRNA target sites in their 3′ UTRs and are significantly more likely to have predicted Pol II and Pol III promoters in their introns. We provide a dataset of 1,935 predicted mRNA targets for 22 intronic miRNAs. These prediction are supported both by sequence features and expression. By combining our results with previous reports, we distinguish three classes of intronic miRNAs: Those that are tightly regulated with their host gene; those that are likely to be expressed from the same promoter but whose host gene is highly regulated by miRNAs; and those

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-10-19

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

  19. 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.

  20. Effects of age-associated regional changes in aortic stiffness on human hemodynamics revealed by computational modeling

    PubMed Central

    Cuomo, Federica; Roccabianca, Sara; Dillon-Murphy, Desmond; Xiao, Nan; Humphrey, Jay D.

    2017-01-01

    Although considered by many as the gold standard clinical measure of arterial stiffness, carotid-to-femoral pulse wave velocity (cf-PWV) averages material and geometric properties over a large portion of the central arterial tree. Given that such properties may evolve differentially as a function of region in cases of hypertension and aging, among other conditions, there is a need to evaluate the potential utility of cf-PWV as an early diagnostic of progressive vascular stiffening. In this paper, we introduce a data-driven fluid-solid-interaction computational model of the human aorta to simulate effects of aging-related changes in regional wall properties (e.g., biaxial material stiffness and wall thickness) and conduit geometry (e.g., vessel caliber, length, and tortuosity) on several metrics of arterial stiffness, including distensibility, augmented pulse pressure, and cyclic changes in stored elastic energy. Using the best available biomechanical data, our results for PWV compare well to findings reported for large population studies while rendering a higher resolution description of evolving local and global metrics of aortic stiffening. Our results reveal similar spatio-temporal trends between stiffness and its surrogate metrics, except PWV, thus indicating a complex dependency of the latter on geometry. Lastly, our analysis highlights the importance of the tethering exerted by external tissues, which was iteratively estimated until hemodynamic simulations recovered typical values of tissue properties, pulse pressure, and PWV for each age group. PMID:28253335

  1. Bioreactor studies and computational fluid dynamics.

    PubMed

    Singh, H; Hutmacher, D W

    2009-01-01

    The hydrodynamic environment "created" by bioreactors for the culture of a tissue engineered construct (TEC) is known to influence cell migration, proliferation and extra cellular matrix production. However, tissue engineers have looked at bioreactors as black boxes within which TECs are cultured mainly by trial and error, as the complex relationship between the hydrodynamic environment and tissue properties remains elusive, yet is critical to the production of clinically useful tissues. It is well known in the chemical and biotechnology field that a more detailed description of fluid mechanics and nutrient transport within process equipment can be achieved via the use of computational fluid dynamics (CFD) technology. Hence, the coupling of experimental methods and computational simulations forms a synergistic relationship that can potentially yield greater and yet, more cohesive data sets for bioreactor studies. This review aims at discussing the rationale of using CFD in bioreactor studies related to tissue engineering, as fluid flow processes and phenomena have direct implications on cellular response such as migration and/or proliferation. We conclude that CFD should be seen by tissue engineers as an invaluable tool allowing us to analyze and visualize the impact of fluidic forces and stresses on cells and TECs.

  2. Bioreactor Studies and Computational Fluid Dynamics

    NASA Astrophysics Data System (ADS)

    Singh, H.; Hutmacher, D. W.

    The hydrodynamic environment “created” by bioreactors for the culture of a tissue engineered construct (TEC) is known to influence cell migration, proliferation and extra cellular matrix production. However, tissue engineers have looked at bioreactors as black boxes within which TECs are cultured mainly by trial and error, as the complex relationship between the hydrodynamic environment and tissue properties remains elusive, yet is critical to the production of clinically useful tissues. It is well known in the chemical and biotechnology field that a more detailed description of fluid mechanics and nutrient transport within process equipment can be achieved via the use of computational fluid dynamics (CFD) technology. Hence, the coupling of experimental methods and computational simulations forms a synergistic relationship that can potentially yield greater and yet, more cohesive data sets for bioreactor studies. This review aims at discussing the rationale of using CFD in bioreactor studies related to tissue engineering, as fluid flow processes and phenomena have direct implications on cellular response such as migration and/or proliferation. We conclude that CFD should be seen by tissue engineers as an invaluable tool allowing us to analyze and visualize the impact of fluidic forces and stresses on cells and TECs.

  3. Computational Phenotyping of Two-Person Interactions Reveals Differential Neural Response to Depth-of-Thought

    PubMed Central

    Xiang, Ting; Ray, Debajyoti; Lohrenz, Terry; Dayan, Peter; Montague, P. Read

    2012-01-01

    Reciprocating exchange with other humans requires individuals to infer the intentions of their partners. Despite the importance of this ability in healthy cognition and its impact in disease, the dimensions employed and computations involved in such inferences are not clear. We used a computational theory-of-mind model to classify styles of interaction in 195 pairs of subjects playing a multi-round economic exchange game. This classification produces an estimate of a subject's depth-of-thought in the game (low, medium, high), a parameter that governs the richness of the models they build of their partner. Subjects in each category showed distinct neural correlates of learning signals associated with different depths-of-thought. The model also detected differences in depth-of-thought between two groups of healthy subjects: one playing patients with psychiatric disease and the other playing healthy controls. The neural response categories identified by this computational characterization of theory-of-mind may yield objective biomarkers useful in the identification and characterization of pathologies that perturb the capacity to model and interact with other humans. PMID:23300423

  4. Comparative study on computed tomography algorithms

    NASA Astrophysics Data System (ADS)

    Zayed, Nasser; Lawton, Bryan

    1994-09-01

    This study uses Computed Tomography (CT) for reconstructing images of solid propellant rocket motors during static firing tests. Implementation, verification and comparison of four CT algorithms are presented. These four algorithms are: Algebraic Reconstruction Technique, Linear Superposition with Compensation, and Fourier Convolution technique with parallel beams and fan-beam. The phantom used in the comparison between algorithms is similar in cross-section to a solid propellant rocket motor. Comparison between algorithms on the ability to detect artifacts is made. Also, a comparison is made using data obtained by optical tomography of the absorption coefficient inside a 20 mm gas gun barrel. Finally, a comparison of the running time versus number of projections, number of ray sums, and resolution is studied.

  5. Computer analysis of radionuclide esophageal transit studies

    SciTech Connect

    Klein, H.A.; Wald, A.

    1984-09-01

    For detailed examination of the esophageal transit of a swallowed radioactive liquid bolus, three computer-based techniques have been developed: analysis of time-activity curves with decomposition into rapid and residual components, yielding the mean transit time for the former and the residual fraction for the latter; reduction of dynamic image sequences to single condensed images, facilitating subjective assessment; and tracking of the centroid of radioactivity, permitting quantification of retrograde motion. Studies were performed on 12 normal subjects and on six patients with motility disorders. Elevated residual fractions were observed in all the patients, and an abnormal degree of retrograde motion in two. Two normal and two abnormal studies exemplify the variety of patterns observed in condensed images.

  6. Femoral nerve dysfunction after retroperitoneal hemorrhage: pathophysiology revealed by computed tomography.

    PubMed

    Reinstein, L; Alevizatos, A C; Twardzik, F G; DeMarco, S J

    1984-01-01

    In three patients receiving anticoagulation therapy who developed retroperitoneal hemorrhage computed tomography (CT) clearly localized the resulting hematoma in each case. Three distinct syndromes are described. A hemorrhage within the iliacus muscle resulted in femoral nerve dysfunction. A large hemorrhage within the iliacus muscle which extended into the psoas muscle produced both femoral and obturator nerve dysfunction. A retroperitoneal hemorrhage extrinsic to both the iliacus and psoas muscles did not produce peripheral nerve dysfunction. The pathophysiology of peripheral nerve dysfunction in retroperitoneal hemorrhage is reviewed in detail.

  7. 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

  8. 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

  9. Replication Study: Melanoma genome sequencing reveals frequent PREX2 mutations

    PubMed Central

    Horrigan, Stephen K; Courville, Pascal; Sampey, Darryl; Zhou, Faren; Cai, Steve

    2017-01-01

    In 2015, as part of the Reproducibility Project: Cancer Biology, we published a Registered Report (Chroscinski et al., 2014) that described how we intended to replicate selected experiments from the paper "Melanoma genome sequencing reveals frequent PREX2 mutations" (Berger et al., 2012). Here we report the results of those experiments. We regenerated cells stably expressing ectopic wild-type and mutant phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2 (PREX2) using the same immortalized human NRASG12D melanocytes as the original study. Evaluation of PREX2 expression in these newly generated stable cells revealed varying levels of expression among the PREX2 isoforms, which was also observed in the stable cells made in the original study (Figure S6A; Berger et al., 2012). Additionally, ectopically expressed PREX2 was found to be at least 5 times above endogenous PREX2 expression. The monitoring of tumor formation of these stable cells in vivo resulted in no statistically significant difference in tumor-free survival driven by PREX2 variants, whereas the original study reported that these PREX2 mutations increased the rate of tumor incidence compared to controls (Figure 3B and S6B; Berger et al., 2012). Surprisingly, the median tumor-free survival was 1 week in this replication attempt, while 70% of the control mice were reported to be tumor-free after 9 weeks in the original study. The rapid tumor onset observed in this replication attempt, compared to the original study, makes the detection of accelerated tumor growth in PREX2 expressing NRASG12D melanocytes extremely difficult. Finally, we report meta-analyses for each result. DOI: http://dx.doi.org/10.7554/eLife.21634.001 PMID:28100394

  10. The centre of mass of a ‘flying’ body revealed by a computational model

    NASA Astrophysics Data System (ADS)

    Simeão Carvalho, Paulo; José Rodrigues, Marcelo

    2017-01-01

    The interpretation of complex trajectories of rigid bodies by the identification of their centre of mass (CM), has a large potential for improving the understanding of the concept of CM at college and university level. Therefore, it is not surprising that there are several techniques described in the literature concerning how to identify the CM of rigid bodies. However, these techniques fail when the CM’s position in the body’s frame of reference changes when the body is at motion. In this work we present a computational model that allows the identification of the CM with very good accuracy, either when the CM’s position changes or is fixed in the body’s frame of reference. This model can be used for a system of bodies moving in a plane, for which the CM of each body coincides with its geometric centre. The effectiveness of this model is tested with experiments using video acquisition and numerical analysis, and can be done in experimental classes under controlled conditions. Students are then able to compare the computed CM with the experimental CM, and investigate why the bodies sometimes present weird trajectories. This property applies in particular to sports, so the model can be also very useful as an educational resource for the explanation of the motion of athletes, namely as a tool for optimizing their performance.

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

    NASA Astrophysics Data System (ADS)

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

    2005-06-01

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

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

    PubMed

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

    2005-06-08

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

  13. 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

  14. Computational modeling and molecular physiology experiments reveal new insights into shoot branching in pea.

    PubMed

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

    2009-11-01

    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.

  15. Computational study on the vinyl azide decomposition.

    PubMed

    Duarte, Darío J R; Miranda, Margarida S; Esteves da Silva, Joaquim C G

    2014-07-10

    The decomposition mechanism of vinyl azide (CH2CHN3) has been studied by calculations of the electronic structure. In addition, a study based on the topology of the electron charge density distribution and its Laplacian function, within the Quantum Theory of Atoms in Molecules (QTAIM), has been carried out with the aim of comprehending the electron redistribution mechanisms that take place in the formation of vinyl nitrenes. The electronic structure calculations reveal that the decomposition of the s-cis conformer of vinyl azide leads to the formation of ketenimine through a single-step conversion, s-cis-CH2CHN3 → CH2CNH + N2, while the conversion of the s-trans conformer to acetonitrile occurs in two steps, s-trans-CH2CHN3 → cyc-CH2NCH + N2 → CH3CN + N2. The topological analysis of the L(r) function reveals that triplet vinyl nitrene has one lone pair on the valence shell charge concentration (VSCC) of nitrogen and thus could act as a monodentate Lewis base, while singlet vinyl nitrene has two lone pairs on the VSCC of nitrogen and thus could act as a bidentate Lewis base.

  16. 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,…

  17. 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,…

  18. The Computational Studies of Plasmon Interaction

    NASA Astrophysics Data System (ADS)

    Demchuk, Antonina; Bolesta, Ivan; Kushnir, Oleksii; Kolych, Ihor

    2017-04-01

    In this paper, an interaction of metal nanoparticles that appears in the extinction spectra was investigated. The mutual coupling between the nanoparticles, the effect of size difference, and the interparticle separation in silver nanoparticle dimers are studied by computer discrete dipole approximation methods. The obtained results show that nanoparticle interaction results in the distinct collective modes, known as the low-energy bonding modes and the higher-energy antibounding modes. The spectral position of the modes is analyzed as a function of the ratio of interparticle distance to particle size that reduces the dependency on the particle size itself. The optical spectra of nanoparticles that form the fractal cluster were investigated. It was found that the number of spectral bands increase with the growth of the number of nanoparticles in the fractal cluster, which are described within the plasmon hybridization model.

  19. The Computational Studies of Plasmon Interaction.

    PubMed

    Demchuk, Antonina; Bolesta, Ivan; Kushnir, Oleksii; Kolych, Ihor

    2017-12-01

    In this paper, an interaction of metal nanoparticles that appears in the extinction spectra was investigated. The mutual coupling between the nanoparticles, the effect of size difference, and the interparticle separation in silver nanoparticle dimers are studied by computer discrete dipole approximation methods. The obtained results show that nanoparticle interaction results in the distinct collective modes, known as the low-energy bonding modes and the higher-energy antibounding modes. The spectral position of the modes is analyzed as a function of the ratio of interparticle distance to particle size that reduces the dependency on the particle size itself. The optical spectra of nanoparticles that form the fractal cluster were investigated. It was found that the number of spectral bands increase with the growth of the number of nanoparticles in the fractal cluster, which are described within the plasmon hybridization model.

  20. Ethiopian Population Dermatoglyphic Study Reveals Linguistic Stratification of Diversity

    PubMed Central

    2015-01-01

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

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

    PubMed

    Yohannes, Seile; Bekele, Endashaw

    2015-01-01

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

  2. Computational EEG modelling of decision making under ambiguity reveals spatio-temporal dynamics of outcome evaluation.

    PubMed

    Jollans, Lee; Whelan, Robert; Venables, Louise; Turnbull, Oliver H; Cella, Matteo; Dymond, Simon

    2017-03-15

    Complex human cognition, such as decision-making under ambiguity, is reflected in dynamic spatio-temporal activity in the brain. Here, we combined event-related potentials with computational modelling of the time course of decision-making and outcome evaluation during the Iowa Gambling Task. Measures of choice probability generated using the Prospect Valence Learning Delta (PVL-Delta) model, in addition to objective trial outcomes (outcome magnitude and valence), were applied as regressors in a general linear model of the EEG signal. The resulting three-dimensional spatio-temporal characterization of task-related neural dynamics demonstrated that outcome valence, outcome magnitude, and PVL-Delta choice probability were expressed in distinctly separate event related potentials. Our findings showed that the P3 component was associated with an experience-based measure of outcome expectancy. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Thermodynamics of the Purine Nucleoside Phosphorylase Reaction Revealed by Computer Simulations.

    PubMed

    Isaksen, Geir Villy; Åqvist, Johan; Brandsdal, Bjørn Olav

    2017-01-10

    Enzymes are able to catalyze chemical reactions by reducing the activation free energy, yielding significant increases in the reaction rates. This can thermodynamically be accomplished by either reducing the activation enthalpy or increasing the activation entropy. The effect of remote mutations on the thermodynamic activation parameters of human purine nucleoside phosphorylase is examined using extensive molecular dynamics and free energy simulations. More than 2700 independent reaction free energy profiles for six different temperatures have been calculated to obtain high-precision computational Arrhenius plots. On the basis of these, the activation enthalpies and entropies were computed from linear regression of the plots with ΔG(⧧) as a function of 1/T, and the obtained thermodynamic activation parameters are in very good agreement with those from experiments. The Arrhenius plots immediately show that the 6-oxopurines (INO and GUO) have identical slopes, whereas the 6-aminopurine (ADO) has a significantly different slope, indicating that the substrate specificity is related to the difference in thermodynamic activation parameters. Furthermore, the calculations show that the human PNP specificity for 6-oxopurines over 6-aminopurines originates from significant differences in electrostatic preorganization. The effect of the remote double mutation, K22E and H104R (E:R), has also been examined, as it alters human PNP toward the bovine PNP. These residues are situated on the protein surface, 28-35 Å from the active site, and the mutation alters the enthalpy-entropy balance with little effect on the catalytic rates. It is thus quite remarkable that the empirical valence bond method can reproduce the enthalpies and entropies induced by these long-range mutations.

  4. 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

  5. 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…

  6. 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…

  7. 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

  8. 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

  9. Using the Computer in Evolution Studies

    ERIC Educational Resources Information Center

    Mariner, James L.

    1973-01-01

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

  10. Computational mapping reveals dramatic effect of Hoogsteen breathing on duplex DNA reactivity with formaldehyde

    PubMed Central

    Bohnuud, Tanggis; Beglov, Dmitri; Ngan, Chi Ho; Zerbe, Brandon; Hall, David R.; Brenke, Ryan; Vajda, Sandor; Frank-Kamenetskii, Maxim D.; Kozakov, Dima

    2012-01-01

    Formaldehyde has long been recognized as a hazardous environmental agent highly reactive with DNA. Recently, it has been realized that due to the activity of histone demethylation enzymes within the cell nucleus, formaldehyde is produced endogenously, in direct vicinity of genomic DNA. Should it lead to extensive DNA damage? We address this question with the aid of a computational mapping method, analogous to X-ray and nuclear magnetic resonance techniques for observing weakly specific interactions of small organic compounds with a macromolecule in order to establish important functional sites. We concentrate on the leading reaction of formaldehyde with free bases: hydroxymethylation of cytosine amino groups. Our results show that in B-DNA, cytosine amino groups are totally inaccessible for the formaldehyde attack. Then, we explore the effect of recently discovered transient flipping of Watson–Crick (WC) pairs into Hoogsteen (HG) pairs (HG breathing). Our results show that the HG base pair formation dramatically affects the accessibility for formaldehyde of cytosine amino nitrogens within WC base pairs adjacent to HG base pairs. The extensive literature on DNA interaction with formaldehyde is analyzed in light of the new findings. The obtained data emphasize the significance of DNA HG breathing. PMID:22705795

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

    PubMed

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

    2015-07-01

    The perceived low levels of genetic diversity, poor interspecific competitive and defensive ability, and loss of dispersal capacities of insular lineages have driven the view that oceanic islands are evolutionary dead ends. Focusing on the Atlantic bryophyte flora distributed across the archipelagos of the Azores, Madeira, the Canary Islands, Western Europe, and northwestern Africa, we used an integrative approach with species distribution modeling and population genetic analyses based on approximate Bayesian computation to determine whether this view applies to organisms with inherent high dispersal capacities. Genetic diversity was found to be higher in island than in continental populations, contributing to mounting evidence that, contrary to theoretical expectations, island populations are not necessarily genetically depauperate. Patterns of genetic variation among island and continental populations consistently fitted those simulated under a scenario of de novo foundation of continental populations from insular ancestors better than those expected if islands would represent a sink or a refugium of continental biodiversity. We, suggest that the northeastern Atlantic archipelagos have played a key role as a stepping stone for transoceanic migrants. Our results challenge the traditional notion that oceanic islands are the end of the colonization road and illustrate the significant role of oceanic islands as reservoirs of novel biodiversity for the assembly of continental floras. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  12. 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

  13. Heterogeneous vesiculation of 2011 El Hierro xeno-pumice revealed by X-ray computed microtomography

    NASA Astrophysics Data System (ADS)

    Berg, S. E.; Troll, V. R.; Deegan, F. M.; Burchardt, S.; Krumbholz, M.; Mancini, L.; Polacci, M.; Carracedo, J. C.; Soler, V.; Arzilli, F.; Brun, F.

    2016-12-01

    During the first week of the 2011 El Hierro submarine eruption, abundant light-coloured pumiceous, high-silica volcanic bombs coated in dark basanite were found floating on the sea. The composition of the light-coloured frothy material (`xeno-pumice') is akin to that of sedimentary rocks from the region, but the textures resemble felsic magmatic pumice, leaving their exact mode of formation unclear. To help decipher their origin, we investigated representative El Hierro xeno-pumice samples using X-ray computed microtomography for their internal vesicle shapes, volumes, and bulk porosity, as well as for the spatial arrangement and size distributions of vesicles in three dimensions (3D). We find a wide range of vesicle morphologies, which are especially variable around small fragments of rock contained in the xeno-pumice samples. Notably, these rock fragments are almost exclusively of sedimentary origin, and we therefore interpret them as relicts an the original sedimentary ocean crust protolith(s). The irregular vesiculation textures observed probably resulted from pulsatory release of volatiles from multiple sources during xeno-pumice formation, most likely by successive release of pore water and mineral water during incremental heating and decompression of the sedimentary protoliths.

  14. 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

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

    PubMed

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

    2014-12-01

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

  16. Multiple-stage ambiguity in motion perception reveals global computation of local motion directions.

    PubMed

    Rider, Andrew T; Nishida, Shin'ya; Johnston, Alan

    2016-12-01

    The motion of a 1D image feature, such as a line, seen through a small aperture, or the small receptive field of a neural motion sensor, is underconstrained, and it is not possible to derive the true motion direction from a single local measurement. This is referred to as the aperture problem. How the visual system solves the aperture problem is a fundamental question in visual motion research. In the estimation of motion vectors through integration of ambiguous local motion measurements at different positions, conventional theories assume that the object motion is a rigid translation, with motion signals sharing a common motion vector within the spatial region over which the aperture problem is solved. However, this strategy fails for global rotation. Here we show that the human visual system can estimate global rotation directly through spatial pooling of locally ambiguous measurements, without an intervening step that computes local motion vectors. We designed a novel ambiguous global flow stimulus, which is globally as well as locally ambiguous. The global ambiguity implies that the stimulus is simultaneously consistent with both a global rigid translation and an infinite number of global rigid rotations. By the standard view, the motion should always be seen as a global translation, but it appears to shift from translation to rotation as observers shift fixation. This finding indicates that the visual system can estimate local vectors using a global rotation constraint, and suggests that local motion ambiguity may not be resolved until consistencies with multiple global motion patterns are assessed.

  17. 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.

  18. Computational imaging reveals shape differences between normal and malignant prostates on MRI

    PubMed Central

    Rusu, Mirabela; Purysko, Andrei S.; Verma, Sadhna; Kiechle, Jonathan; Gollamudi, Jay; Ghose, Soumya; Herrmann, Karin; Gulani, Vikas; Paspulati, Raj; Ponsky, Lee; Böhm, Maret; Haynes, Anne-Maree; Moses, Daniel; Shnier, Ron; Delprado, Warick; Thompson, James; Stricker, Phillip; Madabhushi, Anant

    2017-01-01

    We seek to characterize differences in the shape of the prostate and the central gland (combined central and transitional zones) between men with biopsy confirmed prostate cancer and men who were identified as not having prostate cancer either on account of a negative biopsy or had pelvic imaging done for a non-prostate malignancy. T2w MRI from 70 men were acquired at three institutions. The cancer positive group (PCa+) comprised 35 biopsy positive (Bx+) subjects from three institutions (Gleason scores: 6–9, Stage: T1–T3). The negative group (PCa−) combined 24 biopsy negative (Bx−) from two institutions and 11 subjects diagnosed with rectal cancer but with no clinical or MRI indications of prostate cancer (Cl−). The boundaries of the prostate and central gland were delineated on T2w MRI by two expert raters and were used to construct statistical shape atlases for the PCa+, Bx− and Cl− prostates. An atlas comparison was performed via per-voxel statistical tests to localize shape differences (significance assessed at p < 0.05). The atlas comparison revealed central gland hypertrophy in the Bx− subpopulation, resulting in significant volume and posterior side shape differences relative to PCa+ group. Significant differences in the corresponding prostate shapes were noted at the apex when comparing the Cl− and PCa+ prostates. PMID:28145532

  19. [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.

  20. 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.

  1. 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.

  2. Computational Study of Multiple Hydrokinetic Turbine Performance

    NASA Astrophysics Data System (ADS)

    Jonas, Joseph David

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

  3. 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.

  4. Computational Studies of Protein Hydration Methods

    NASA Astrophysics Data System (ADS)

    Morozenko, Aleksandr

    It is widely appreciated that water plays a vital role in proteins' functions. The long-range proton transfer inside proteins is usually carried out by the Grotthuss mechanism and requires a chain of hydrogen bonds that is composed of internal water molecules and amino acid residues of the protein. In other cases, water molecules can facilitate the enzymes catalytic reactions by becoming a temporary proton donor/acceptor. Yet a reliable way of predicting water protein interior is still not available to the biophysics community. This thesis presents computational studies that have been performed to gain insights into the problems of fast and accurate prediction of potential water sites inside internal cavities of protein. Specifically, we focus on the task of attainment of correspondence between results obtained from computational experiments and experimental data available from X-ray structures. An overview of existing methods of predicting water molecules in the interior of a protein along with a discussion of the trustworthiness of these predictions is a second major subject of this thesis. A description of differences of water molecules in various media, particularly, gas, liquid and protein interior, and theoretical aspects of designing an adequate model of water for the protein environment are widely discussed in chapters 3 and 4. In chapter 5, we discuss recently developed methods of placement of water molecules into internal cavities of a protein. We propose a new methodology based on the principle of docking water molecules to a protein body which allows to achieve a higher degree of matching experimental data reported in protein crystal structures than other techniques available in the world of biophysical software. The new methodology is tested on a set of high-resolution crystal structures of oligopeptide-binding protein (OppA) containing a large number of resolved internal water molecules and applied to bovine heart cytochrome c oxidase in the fully

  5. 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.

  6. Computational Studies of Strongly Correlated Quantum Matter

    NASA Astrophysics Data System (ADS)

    Shi, Hao

    The study of strongly correlated quantum many-body systems is an outstanding challenge. Highly accurate results are needed for the understanding of practical and fundamental problems in condensed-matter physics, high energy physics, material science, quantum chemistry and so on. Our familiar mean-field or perturbative methods tend to be ineffective. Numerical simulations provide a promising approach for studying such systems. The fundamental difficulty of numerical simulation is that the dimension of the Hilbert space needed to describe interacting systems increases exponentially with the system size. Quantum Monte Carlo (QMC) methods are one of the best approaches to tackle the problem of enormous Hilbert space. They have been highly successful for boson systems and unfrustrated spin models. For systems with fermions, the exchange symmetry in general causes the infamous sign problem, making the statistical noise in the computed results grow exponentially with the system size. This hinders our understanding of interesting physics such as high-temperature superconductivity, metal-insulator phase transition. In this thesis, we present a variety of new developments in the auxiliary-field quantum Monte Carlo (AFQMC) methods, including the incorporation of symmetry in both the trial wave function and the projector, developing the constraint release method, using the force-bias to drastically improve the efficiency in Metropolis framework, identifying and solving the infinite variance problem, and sampling Hartree-Fock-Bogoliubov wave function. With these developments, some of the most challenging many-electron problems are now under control. We obtain an exact numerical solution of two-dimensional strongly interacting Fermi atomic gas, determine the ground state properties of the 2D Fermi gas with Rashba spin-orbit coupling, provide benchmark results for the ground state of the two-dimensional Hubbard model, and establish that the Hubbard model has a stripe order in the

  7. 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.

  8. 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

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

    PubMed

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

    2015-08-07

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

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

    PubMed Central

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

    2015-01-01

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

  11. Computational Tools for Genomic Studies in Plants.

    PubMed

    Martinez, Manuel

    2016-12-01

    In recent years, the genomic sequence of numerous plant species including the main crop species has been determined. Computational tools have been developed to deal with the issue of which plant has been sequenced and where is the sequence hosted. In this mini-review, the databases for genome projects, the databases created to host species/clade projects and the databases developed to perform plant comparative genomics are revised. Because of their importance in modern research, an in-depth analysis of the plant comparative genomics databases has been performed. This comparative analysis is focused in the common and specific computational tools developed to achieve the particular objectives of each database. Besides, emerging high-performance bioinformatics tools specific for plant research are commented. What kind of computational approaches should be implemented in next years to efficiently analyze plant genomes is discussed.

  12. Biological Agent Neutralization/Computational Modeling Studies

    DTIC Science & Technology

    2010-09-01

    Computational Results • Solution of the Navier - Stokes equations for the flow inside the device has been obtained by the GASP solver. • 3rd order of...flkv:.lD ENTERPRISE I OFFICE I PHONE: Ali) -Eugene Stokes / 767-2826 / flL DATE: tt4 PUBLIC AFFAIRS: KJtJJ/,1.1/~A. !ffi / ~ ~ ~uwc:- DATE:’ ti{fr._(-u...to temperatures from 165C to 275C for times between 25ms and 100ms. The data was used to anchor computational fluid dynamics (CFD) flow modeling of

  13. 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…

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

    ERIC Educational Resources Information Center

    Brereton, P.

    2011-01-01

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

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

    ERIC Educational Resources Information Center

    Brereton, P.

    2011-01-01

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

  16. Computer Science and Engineering Students Addressing Critical Issues Regarding Gender Differences in Computing: A Case Study

    ERIC Educational Resources Information Center

    Tsagala, Evrikleia; Kordaki, Maria

    2008-01-01

    This study focuses on how Computer Science and Engineering Students (CSESs) of both genders address certain critical issues for gender differences in the field of Computer Science and Engineering (CSE). This case study is based on research conducted on a sample of 99 Greek CSESs, 43 of which were women. More specifically, these students were asked…

  17. Computer formulations of aircraft models for simulation studies

    NASA Technical Reports Server (NTRS)

    Howard, J. C.

    1979-01-01

    Recent developments in formula manipulation compilers and the design of several symbol manipulation languages, enable computers to be used for symbolic mathematical computation. A computer system and language that can be used to perform symbolic manipulations in an interactive mode are used to formulate a mathematical model of an aeronautical system. The example demonstrates that once the procedure is established, the formulation and modification of models for simulation studies can be reduced to a series of routine computer operations.

  18. 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

  19. 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…

  20. Assessing Moderator Variables: Two Computer Simulation Studies.

    ERIC Educational Resources Information Center

    Mason, Craig A.; And Others

    1996-01-01

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

  1. Literary Studies: A Computer Assisted Teaching Methodology.

    ERIC Educational Resources Information Center

    Mills, Jon; Chandramohan, Balasubramanyam

    1996-01-01

    Describes the use of TACT computer software to teach Joseph Conrad's "Heart of Darkness." Employs TACT to reinforce understanding of the text achieved through a combination of analytic approaches to literary texts with linguistic methods. Argues that exposure to the software made students' interaction with the text more complex and…

  2. Where Computer Science and Cultural Studies Collide

    ERIC Educational Resources Information Center

    Kirschenbaum, Matthew

    2009-01-01

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

  3. 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…

  4. 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…

  5. Computer-Mediated Communication: An Experimental Study.

    ERIC Educational Resources Information Center

    Smith, William E.

    1994-01-01

    Investigates the effectiveness of a computer-mediated communication system in supplementing traditional instruction in a media law course. Finds mixed results on measures of satisfaction and no significant improvement on exam scores. Notes that the system required more time from the instructor and students. (SR)

  6. A computational study of alternate SELEX.

    PubMed

    Seo, Yeon-Jung; Nilsen-Hamilton, Marit; Levine, Howard A

    2014-07-01

    Systematic evolution of ligands by exponential enrichment (SELEX) is a procedure for identifying nucleic acid (NA) molecules with affinities for specific target species, such as proteins, peptides, or small organic molecules. Here, we extend the work in Seo et al. (Bull Math Biol 72:1623-1665, 2010) (multiple-target SELEX or positive SELEX) and examine an alternate SELEX process with multiple targets by incorporating negative selection into a positive SELEX protocol. The alternate SELEX process is done iteratively by alternating several positive selection rounds with several negative selection rounds. At the end of each positive selection round, NAs are eluted from the bound product and amplified by polymerase chain reaction (PCR) to increase the size of the pool of NA species that bind preferentially to the given positive target vector. The enriched population of NAs is then exposed to the negative targets (undesired targets). The free NA species (instead of the bound NA species being eluted) are retained and amplified by PCR (negative selection). The goal is to minimize an enrichment of nonspecifically binding NAs against multiple targets. While positive selection alone results in a pool of NAs that bind tightly to a given target vector, negative selection results in the subset of the NAs that bind best to the nontarget vectors that are also present. By alternating the two processes, we eventually obtain a refined population of nucleic acids that bind to the desired target(s) with high "selectivity" and "specificity." In the present paper, we give formulations of the negative and alternate selection processes and define their efficiencies in a meaningful way. We study the asymptotic behavior of alternate SELEX system as a discrete-time dynamical system. To do this, we use the chemical potential to examine how alternate SELEX leads to the selection of NAs with more specific interactions when the ratio of the number of positive selection rounds to the number of

  7. The quinones of benzocyclobutadiene: a computational study.

    PubMed

    Golas, Ewa; Lewars, Errol; Liebman, Joel F

    2009-08-27

    The conventional (excluding non-Kekulé, singlet diradical structures) quinones of benzocyclobutadiene were studied computationally. Eight structures were examined, namely (based on the CA names for benzocyclobutenedione), benzocyclobutenedione or bicyclo[4.2.0]octa-1,3,5-triene-7,8-dione, bicyclo[4.2.0]octa-3,5,8-triene-2,7-dione, bicyclo[4.2.0]octa-1,4,6-triene-3,8-dione, bicyclo[4.2.0]octa-1(6),4,7-triene-2,3-dione, bicyclo[4.2.0]octa-1(8), 4,6-triene-2,3-dione, bicyclo[4.2.0]octa-1(6),3,7-triene-2,5-dione, bicyclo[4.2.0]octa-1(8),3,6-triene-2,5-dione, and bicyclo[4.2.0]octa-1,5,7-triene-3,4-dione (the question of resonance or tautomerism for the 2,3-dione pair and the 2,5-dione pair is considered). Using DFT (B3LYP/6-31G*) and ab initio (MP2/6-31G*) methods the geometries of the eight species were optimized, giving similar results for the two methods. The heats of formation of the quinones were calculated, placing them in low-energy (-17 kJ mol(-1), 7,8-dione), medium-energy (79-137 kJ mol(-1), 2,7-, 3,8-, and 3,4-diones), and high-energy (260-275 kJ mol(-1), 2,3- and 2,5-diones) groups. Diels-Alder reactivity as dienophiles with butadiene indicated the 2,7-, 3,8-, and particularly the 3,4-quinone may be relatively unreactive toward dimerization or polymerization and are attractive synthesis goals. Isodesmic ring-opening reactions and NICS calculations showed aromatic/nonaromatic properties to be essentially as expected from the presence of a benzene or cyclobutadiene ring. UV spectra, ionization energy electron affinity, and HOMO/LUMO energies were also calculated.

  8. A computational study of diiodomethane photoisomerization

    NASA Astrophysics Data System (ADS)

    Borin, Veniamin A.

    This work gives the detailed description of the dynamics and mechanism of the previously unsuspected photochemical reaction path of diiodomethane (CH2I2), a paradigmatic haloalkane, which is direct intramolecular isomerization upon the excitation of this molecule to the lowest singlet S1 state. The previous liquid-phase ultrafast spectroscopy experiments on the UV photochemistry of di- and polyhalomethanes suggest that following excitation of these molecules, the carbon-halogen bond breaks, leading to formation of the initial radical pair. The radical pair, trapped by a solvent cage collapses into an isomer product species with halogen-halogen bond on a picoseconds timescale (1 ps = 10-12 s). Yet, the results recently obtained in our research group, clearly suggest that in addition to this conventional, in-cage isomerization process, there is another, unconventional isomerization mechanism, which occurs on a sub-100 fs timescale (1 fs = 10 -15 s) and does not require the solvent environment around the excited CH2I2 solute. Indeed, the ultrafast sub-100 fs timescale observed suggests two main considerations: The sub-100 fs photoisomerization in polyhalomethanes is direct, i.e. proceeds via the intramolecular reaction mechanism proceeding without any intermediates (such as a radical pair) and, likely, is mediated by a crossing of excited and ground electronic states. The solvent cage may not be needed, because the timescale of the aforementioned isomerization process is shorter than the 100-200 fs timescale for a single collisional encounter between solvent and solute molecules. Femtosecond transient absorption spectroscopy is a very valuable tool in studying the photochemical reactivity on short timescales. The measured ultrafast time-resolved spectra are complicated by relaxation processes in far from equilibrium solutes, such as intramolecular energy redistribution and flow, and can be understood in detail with the help from state-of-the-art quantum

  9. Computational studies of origins of life scenarios

    NASA Astrophysics Data System (ADS)

    Mathew, Damien Cherian

    Understanding the origins of life on Earth is one of the most intriguing problems facing science today. In the research presented here, we apply computational methods to explore origins of life scenarios. In particular, we focus on the origins of the genetic code and the intersection between geochemistry and a primordial "biochemistry" in which mononucleotides could form short oligoucleotide chains. We also apply quantum chemical methods to a modern biochemical reaction, the charging of tRNA by an aminoacyl-tRNA synthetase, in order to shed light on the possible chemistry one may want to consider in problems relating to the origins of life. The question of how codons came to be associated with specific amino acids in the present form of the genetic code is one fundamental part of gaining insight into the origins of life. Carl Woese and coworkers designed a series of experiments to test associations between amino acids and nucleobases that may have played a role in establishing the genetic code. Through these experiments it was found that a property of amino acids called the polar requirement (PR) is correlated to the organization of the codon table. No other property of amino acids has been found that correlates with the codon table as well as PR, indicating that PR is uniquely related to the modern genetic code. Using molecular dynamics simulations of amino acids in solutions of water and dimethylpyridine used to experimentally measure PR, we show that variations in the partitioning between the two phases as described by radial distribution functions correlate well with the measured PRs. Partition coefficients based on probability densities of the amino acids in each phase have the linear behavior with base concentration as suggested by the PR experiments. We also investigate the possible roles of inorganic mineral surfaces in catalysis and stabilization of reactions essential for early forms of replicating systems that could have evolved into biochemical

  10. Secure Cloud Computing Implementation Study For Singapore Military Operations

    DTIC Science & Technology

    2016-09-01

    COMPUTING IMPLEMENTATION STUDY FOR SINGAPORE MILITARY OPERATIONS by Lai Guoquan September 2016 Thesis Advisor: John D. Fulp Co-Advisor...DATES COVERED Master’s thesis 4. TITLE AND SUBTITLE SECURE CLOUD COMPUTING IMPLEMENTATION STUDY FOR SINGAPORE MILITARY OPERATIONS 5. FUNDING NUMBERS...addition, from the military perspective, the benefits of cloud computing were analyzed from a study of the U.S. Department of Defense. Then, using

  11. 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.

  12. Structural isomerization of the gas-phase 2-norbornyl cation revealed with infrared spectroscopy and computational chemistry.

    PubMed

    Mosley, Jonathan D; Young, Justin W; Agarwal, Jay; Schaefer, Henry F; Schleyer, Paul v R; Duncan, Michael A

    2014-06-02

    In an attempt to produce the 2-norbornyl cation (2NB(+)) in the gas phase, protonation of norbornene was accomplished in a pulsed discharge ion source coupled with a supersonic molecular beam. The C7H11(+) cation was size-selected in a time-of-flight mass spectrometer and investigated with infrared laser photodissociation spectroscopy using the method of "tagging" with argon. The resulting vibrational spectrum, containing sharp bands in the C-H stretching and fingerprint regions, was compared to that predicted by computational chemistry. However, the measured spectrum did not match that of 2NB(+), prompting a detailed computational study of other possible isomers of C7H11(+). This study finds five isomers more stable than 2NB(+). The spectrum obtained corresponds to the 1,3-dimethylcyclopentenyl cation, the global minimum-energy structure for C7H11(+), which is produced through an unanticipated ring-opening rearrangement path.

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

    PubMed

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

    2016-05-01

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

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. 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…

  19. 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…

  20. Computational and experimental study of laminar flames

    SciTech Connect

    Smooke, Mitchell

    2015-05-29

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

  1. Interactive computer program for optimal designs of longitudinal cohort studies.

    PubMed

    Tekle, Fetene B; Tan, Frans E S; Berger, Martijn P F

    2009-05-01

    Many large scale longitudinal cohort studies have been carried out or are ongoing in different fields of science. Such studies need a careful planning to obtain the desired quality of results with the available resources. In the past, a number of researches have been performed on optimal designs for longitudinal studies. However, there was no computer program yet available to help researchers to plan their longitudinal cohort design in an optimal way. A new interactive computer program for the optimization of designs of longitudinal cohort studies is therefore presented. The computer program helps users to identify the optimal cohort design with an optimal number of repeated measurements per subject and an optimal allocations of time points within a given study period. Further, users can compute the loss in relative efficiencies of any other alternative design compared to the optimal one. The computer program is described and illustrated using a practical example.

  2. 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. Copyright 2015, SLACK Incorporated.

  3. Computational imaging analysis of fibrin matrices with the inclusion of erythrocytes from homozygous SS blood reveals agglomerated and amorphous structures.

    PubMed

    Averett, Rodney D; Norton, David G; Fan, Natalie K; Platt, Manu O

    2017-01-01

    Sickle cell disease is a single point mutation disease that is known to alter the coagulation system, leading to hypercoagulable plasma conditions. These hypercoagulable conditions can lead to complications in the vasculature, caused by fibrin clots that form undesirably. There is a need to understand the morphology and structure of fibrin clots from patients with sickle cell disease, as this could lead to further discovery of treatments and life-saving therapies. In this work, a computational imaging analysis method is presented to evaluate fibrin agglomeration in the presence of erythrocytes (RBCs) homozygous for the sickle cell mutation (SS). Numerical algorithms were used to determine agglomeration of fibrin fibers within a matrix with SS RBCs to test the hypothesis that fibrin matrices with the inclusion of SS RBCs possess a more agglomerated structure than native fibrin matrices with AA RBCs. The numerical results showed that fibrin structures with SS RBCs displayed an overall higher degree of agglomeration as compared to native fibrin structures. The computational algorithm was also used to evaluate fibrin fiber overlap (aggregation) and anisotropy (orientation) in normal fibrin matrices compared to fibrin matrices polymerized around SS RBCs; however, there was no statistical difference. Ultrasound measurements of stiffness revealed rigid RBCs in the case of samples derived from homozygous SS blood, and densely evolving matrices, when compared to normal fibrin with the inclusion of AA RBCs. An agglomeration model is suggested to quantify the fibrin aggregation/clustering near RBCs for both normal fibrin matrices and for the altered structures. The results of this work are important in the sense that the understanding of aggregation and morphology in fibrin clots with incorporation of RBCs from persons living with sickle cell anemia may elucidate the complexities of comorbidities and other disease complications.

  4. 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.

  5. A Computational Framework for Evaluating the Efficiency of Arabidopsis Accessions in Response to Nitrogen Stress Reveals Important Metabolic Mechanisms

    PubMed Central

    Kleessen, Sabrina; Fernie, Alisdair R.; Nikoloski, Zoran

    2012-01-01

    High-throughput phenotyping technologies in combination with genetic variability for the plant model species Arabidopsis thaliana (Arabidopsis) offer an excellent experimental platform to reveal the effects of different gene combinations on phenotypes. These developments have been coupled with computational approaches to extract information not only from the multidimensional data, capturing various levels of biochemical organization, but also from various morphological and growth-related traits. Nevertheless, the existing methods usually focus on data aggregation which may neglect accession-specific effects. Here we argue that revealing the molecular mechanisms governing a desired set of output traits can be performed by ranking of accessions based on their efficiencies relative to all other analyzed accessions. To this end, we propose a framework for evaluating accessions via their relative efficiencies which establish a relationship between multidimensional system’s inputs and outputs from different environmental conditions. The framework combines data envelopment analysis (DEA) with a novel valency index characterizing the difference in congruence between the efficiency rankings of accessions under various conditions. We illustrate the advantages of the proposed approach for analyzing genetic variability on a publicly available data set comprising quantitative data on metabolic and morphological traits for 23 Arabidopsis accessions under three conditions of nitrogen availability. In addition, we extend the proposed framework to identify the set of traits displaying the highest influence on ranking based on the relative efficiencies of the considered accessions. As an outlook, we discuss how the proposed framework can be combined with well-established statistical techniques to further dissect the relationship between natural variability and metabolism. PMID:23056002

  6. Role of chronic toxicology studies in revealing new toxicities.

    PubMed

    Galijatovic-Idrizbegovic, Alema; Miller, Judith E; Cornell, Wendy D; Butler, James A; Wollenberg, Gordon K; Sistare, Frank D; DeGeorge, Joseph J

    2016-12-01

    Chronic (>3 months) preclinical toxicology studies are conducted to support the safe conduct of clinical trials exceeding 3 months in duration. We have conducted a review of 32 chronic toxicology studies in non-rodents (22 studies in dogs and 10 in non-human primates) and 27 chronic toxicology studies in rats dosed with Merck compounds to determine the frequency at which additional target organ toxicities are observed in chronic toxicology studies as compared to subchronic studies of 3 months in duration. Our review shows that majority of the findings are observed in the subchronic studies since additional target organs were not observed in 24 chronic non rodent studies and in 21 chronic rodent studies. However, 6 studies in non rodents and 6 studies in rodents yielded new findings that were not seen in studies of 3-month or shorter duration. For 3 compounds the new safety findings did contribute to termination of clinical development plans. Although the incidence of compound termination associated with chronic toxicology study observations is low (∼10%), the observations made in these studies can be important for evaluating human safety risk.

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

    NASA Astrophysics Data System (ADS)

    Cantwell Wilson, Brenda

    2002-03-01

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

  8. 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…

  9. 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

  10. 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.

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

    NASA Astrophysics Data System (ADS)

    Georgiev, K.; Zlatev, Z.

    2010-11-01

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

  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. Dynamic oscillations predicted by computer studies

    SciTech Connect

    Butts, M.M.; Smith, H.S. )

    1991-01-01

    During the latter part of 1988, a study was begun to review the dynamic stability performance of a power company's plant. The scope of the study was to identify any operating conditions that might contribute to system oscillations and to examine alternative solutions that would control these oscillations. The study was performed in several phases. This paper discusses the study process, utilizing two different software packages for the analysis: Dynamic stability studies using time-domain software and Eigenvalue analysis using frequency-domain software.

  14. Verification, validation and sensitivity studies in computational biomechanics.

    PubMed

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

    2007-06-01

    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 (V&V). 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 V&V principles in the field of computational biomechanics, thereby improving the peer acceptance of studies that use computational modeling techniques.

  15. 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

  16. A study of the effectiveness of an interactive computer classroom.

    PubMed

    Ayoub, J L; Vanderboom, C; Knight, M; Walsh, K; Briggs, R; Grekin, K

    1998-01-01

    This study examined the use of an interactive computer classroom (ICC) compared with a traditional lecture/discussion format (LD) for a nursing management course taught from fall semester 1994 through fall semester 1996. The ICC was structured around a group systems support software, a tool previously used in business settings for group decision-making activities. Structured learning activities allowed all students to participate simultaneously and anonymously. Data were collected during the second and final semesters of the study. The outcomes included academic performance, measured by course exams; class participation, measured by direct observation; and attendance records. The control group was a concurrent management course taught with the same objectives and evaluated by identical examinations. The examination scores and the frequency of class participation of the ICC group were significantly higher than those measures of the LD group. There was no significant difference in class attendance. Evaluation forms with open-ended questions were completed by the ICC students and revealed that the students believed that the process enhanced application and understanding. The negative aspects of the ICC experience were the need for increased preparation time for faculty and the students' lack of tolerance when technical difficulties caused delays.

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

    ERIC Educational Resources Information Center

    Strickland, James

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

  18. Academic Computing at Jackson State University. A Case Study.

    ERIC Educational Resources Information Center

    Hunter, Beverly

    Prepared by the Human Resources Research Organization to assist administrators, faculty, staff, and students at other minority institutions, to plan, extend, or improve uses of computers, this case study is one of a series on educational applications of computers. A profile of Jackson State University identifies the location, programs, mission,…

  19. 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…

  20. 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.

  1. 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.…

  2. A Study of Computer Techniques for Music Research. Final Report.

    ERIC Educational Resources Information Center

    Lincoln, Harry B.

    Work in three areas comprised this study of computer use in thematic indexing for music research: (1) acquisition, encoding, and keypunching of data--themes of which now number about 50,000 (primarily 16th Century Italian vocal music) and serve as a test base for program development; (2) development of computer programs to process this data; and…

  3. 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

  4. Multitargeting by curcumin as revealed by molecular interaction studies.

    PubMed

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

    2011-11-01

    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 Ca(2+) 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

  5. 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 some…

  6. 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…

  7. 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…

  8. Computational study of the mechanism of Bcl-2 apoptotic switch

    NASA Astrophysics Data System (ADS)

    Tokár, Tomáš; Uličný, Jozef

    2012-12-01

    In spite of attention devoted to molecular mechanisms of apoptosis, the details of functioning of one crucial component-the Bcl-2 apoptotic switch-are not completely understood. There are two competing mechanisms of its internal working-the indirect activation and the direct activation. In the absence of conclusive experimental data, we have used computational modeling to assess the properties of both mechanisms and their suitability to act as a biological switch. Since the two mechanisms form opposite poles of continuum of Bcl-2 molecular interaction models, we have constructed more general models including these two models as extreme cases. By studying the relationship between model parameters and the steady-state response we have found optimal interaction patterns which reproduce the behavior of the Bcl-2 apoptotic switch. Our results show, that stimulus-response ultrasensitivity is negatively affected by spontaneous activation of Bcl-2 effectors. We found that ultrasensitivity requires effectors activation, mediated by another subgroup of Bcl-2 proteins-activators. We have shown that the auto-activation of monomeric effector forms provides an ultrasensitivity enhancing feedback loop. Thorough robustness analysis revealed that the interaction pattern postulated in the direct activation hypothesis is able to conserve stimulus-response switching characteristics for wide range changes of its internal parameters. The robustness of the switch against the variation of the reaction parameter is strongly reduced for the intermediate hybrid model and even more for the indirect part of the models. Computer simulations of the more general model presented here suggest, that stimulus-response ultrasensitivity is an emergent property of the direct activation model that is unlikely to occur in the model of indirect activation. Introduction of indirect-model-specific interactions does not provide a better explanation of the Bcl-2 switch functionality compared to the direct

  9. Trial-by-Trial Modulation of Associative Memory Formation by Reward Prediction Error and Reward Anticipation as Revealed by a Biologically Plausible Computational Model.

    PubMed

    Aberg, Kristoffer C; Müller, Julia; Schwartz, Sophie

    2017-01-01

    Anticipation and delivery of rewards improves memory formation, but little effort has been made to disentangle their respective contributions to memory enhancement. Moreover, it has been suggested that the effects of reward on memory are mediated by dopaminergic influences on hippocampal plasticity. Yet, evidence linking memory improvements to actual reward computations reflected in the activity of the dopaminergic system, i.e., prediction errors and expected values, is scarce and inconclusive. For example, different previous studies reported that the magnitude of prediction errors during a reinforcement learning task was a positive, negative, or non-significant predictor of successfully encoding simultaneously presented images. Individual sensitivities to reward and punishment have been found to influence the activation of the dopaminergic reward system and could therefore help explain these seemingly discrepant results. Here, we used a novel associative memory task combined with computational modeling and showed independent effects of reward-delivery and reward-anticipation on memory. Strikingly, the computational approach revealed positive influences from both reward delivery, as mediated by prediction error magnitude, and reward anticipation, as mediated by magnitude of expected value, even in the absence of behavioral effects when analyzed using standard methods, i.e., by collapsing memory performance across trials within conditions. We additionally measured trait estimates of reward and punishment sensitivity and found that individuals with increased reward (vs. punishment) sensitivity had better memory for associations encoded during positive (vs. negative) prediction errors when tested after 20 min, but a negative trend when tested after 24 h. In conclusion, modeling trial-by-trial fluctuations in the magnitude of reward, as we did here for prediction errors and expected value computations, provides a comprehensive and biologically plausible description of

  10. Trial-by-Trial Modulation of Associative Memory Formation by Reward Prediction Error and Reward Anticipation as Revealed by a Biologically Plausible Computational Model

    PubMed Central

    Aberg, Kristoffer C.; Müller, Julia; Schwartz, Sophie

    2017-01-01

    Anticipation and delivery of rewards improves memory formation, but little effort has been made to disentangle their respective contributions to memory enhancement. Moreover, it has been suggested that the effects of reward on memory are mediated by dopaminergic influences on hippocampal plasticity. Yet, evidence linking memory improvements to actual reward computations reflected in the activity of the dopaminergic system, i.e., prediction errors and expected values, is scarce and inconclusive. For example, different previous studies reported that the magnitude of prediction errors during a reinforcement learning task was a positive, negative, or non-significant predictor of successfully encoding simultaneously presented images. Individual sensitivities to reward and punishment have been found to influence the activation of the dopaminergic reward system and could therefore help explain these seemingly discrepant results. Here, we used a novel associative memory task combined with computational modeling and showed independent effects of reward-delivery and reward-anticipation on memory. Strikingly, the computational approach revealed positive influences from both reward delivery, as mediated by prediction error magnitude, and reward anticipation, as mediated by magnitude of expected value, even in the absence of behavioral effects when analyzed using standard methods, i.e., by collapsing memory performance across trials within conditions. We additionally measured trait estimates of reward and punishment sensitivity and found that individuals with increased reward (vs. punishment) sensitivity had better memory for associations encoded during positive (vs. negative) prediction errors when tested after 20 min, but a negative trend when tested after 24 h. In conclusion, modeling trial-by-trial fluctuations in the magnitude of reward, as we did here for prediction errors and expected value computations, provides a comprehensive and biologically plausible description of

  11. 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…

  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.

  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 PAGES

    Syamlal, Madhava; O'Brien, Thomas J.; Benyahia, Sofiane; ...

    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. Open -source software in computational research: A case study

    SciTech Connect

    Syamlal, M.; O'Brien, T.; Benyahia, S.; Gel, A.; Pannala, S.

    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.

  17. Trijunctions in crystalline materials: A computer simulation study

    NASA Astrophysics Data System (ADS)

    Srivilliputhur, Srinivasan Gopalan

    The molecular dynamics (MD) method has been extensively used to gain atomistic insight into material properties. Massively parallel computers offer a cost-effective way to dramatically increase the scope and accuracy of MD. Keeping this emerging scenario in mind, we set and realized a two fold goal, (i) to develop an efficient large-scale parallel MD code for atoms interacting via short-range forces, and (ii) to apply our MD method to study the structure and energetics of trijunctions (TJ) in a FCC polycrystal. Using our parallel MD code, we performed atomistic simulations of a three dimensional, periodic Lennard-Jones polycrystalline system and found that the TJ line energies can have a negative value, in agreement with the suggestion of J. W. Gibbs. Our system consisted of three FCC grains rotated 30 degrees about a common <001> axis. This configuration yields six TJ's also along <001>, with symmetries m, 3 and 3m in the color group terminology of Cahn and Kalonji. Associated with these TJ's are three 30sp° and six 60sp° symmetric tilt grain boundaries (STGB). An aluminum specimen with such grains, and highly symmetric TJ's was epitaxially grown on a silicon (111) surface and studied using high-resolution electron-microscopy by Dahmen et al. For the first time it has been possible to simultaneously and unambiguously separate the TJ and STGB contribution to the system's excess energy, in addition to gaining insight into its atomic structure. Interfaces in our energy minimized polycrystal systems were compared with similar STGB's in pure bi-crystals. The polycrystal STGB width was found to be practically the same in all the system sizes investigated. As indicated by the systematic common-neighbor local structure analysis, and the radial and energy distribution functions, there exists a high level of interfacial order and slightly lower overall densities in the TJ systems (compared to a FCC crystal). Further, as indicated by these and the atom centered hydrostatic

  18. Stapled peptides in the p53 pathway: computer simulations reveal novel interactions of the staples with the target protein.

    PubMed

    Joseph, Thomas Leonard; Lane, David; Verma, Chandra S

    2010-11-15

    Atomistic simulations of a set of stapled peptides derived from the transactivation domain of p53 (designed by Verdine & colleagues, JACS 2007 129:2456) and complexed to MDM2 reveal that the good binders are uniquely characterized by higher helicity and by extensive interactions between the hydrocarbon staples and the MDM2 surface; in contrast the poor binders have reduced helicity and their staples are mostly solvent exposed. Our studies also find that the best binders can also potentially inhibit MDMX with similar affinities, suggesting that such stapled peptides can be evolved for dual inhibition with therapeutic potential.

  19. A COMPUTED TOMOGRAPHIC STUDY OF SCHIZOPHRENIA

    PubMed Central

    Siddharatha; Lal, Narottam; Tewari, S.C.; Dalal, P.K.; Kohli, Neera; Srivastava, Shrikant

    1997-01-01

    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

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

    PubMed

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

    2010-06-01

    Among the fossilized ontogenetic series known for tetrapods, only more basal groups like temnospondyl amphibians have been used extensively in developmental studies, whereas reptilian and synapsid data have been largely neglected so far. However, before such ontogenetic series can be subject to study, the relative age and affiliation of putative specimens within a series has to be verified. Bone histology has a long-standing tradition as being a source of palaeobiological and growth history data in fossil amniotes and indeed, the analysis of bone microstructures still remains the most important and most reliable tool for determining the absolute ontogenetic age of fossil vertebrates. It is also the only direct way to reconstruct life histories and growth strategies for extinct animals. Herein the record of bone histology among Reptilia and its application to elucidate and expand fossilized ontogenies as a source of developmental data are reviewed. (c) 2009 Elsevier Ltd. All rights reserved.

  1. 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.

  2. 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

  3. Computer assisted analysis of MR-mammography reveals association between contrast enhancement and occurrence of distant metastasis.

    PubMed

    Baltzer, Pascal A T; Zoubi, Ramy; Burmeister, Hartmut P; Gajda, Mieczyslaw; Camara, Oumar; Kaiser, Werner A; Dietzel, Matthias

    2012-12-01

    Dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) is able to detect breast cancer with high sensitivity. Furthermore, this method provides functional information on tissue composition and vascularization. This study aims to identify the potential of DCE-MRI to predict distant metastasis in breast cancer patients using computer assisted interpretation of dynamic enhancement data. For this purpose, 59 consecutive patients with newly diagnosed invasive breast cancer received pretherapeutic DCE-MRI at 1.5 Tesla according to international recommendations. In all patients, follow up interval and occurrence of distant metastasis was documented. For DCE-MRI analysis dedicated software was used (Brevis, Siemens Healthcare, Erlangen, Germany). It allows semiautomatic identification of the most suspect curve in a lesion analyzed. Enhancement parameters assessed were "Initial Enhancement", "Washout", "Peak-Enhancement", and "Time to Peak Enhancement". Cox proportional hazards regression (CPHR) was used to analyze the effect of these parameters on the probability of metachronous distant metastasis. Median follow up period was 52.0 months. 6 patients developed distant metastases between 11 and 35 months after breast cancer diagnosis. In CPHR, Washout could be identified as significant and independent predictor for occurrence of distant metastasis (P = 0.0134). Our initial data demonstrate an association between computer measured enhancement parameters in DCE-MRI and occurrence of distant metastasis by quantification of Washout.

  4. Computational study of the heterodimerization between μ and δ receptors

    NASA Astrophysics Data System (ADS)

    Liu, Xin; Kai, Ming; Jin, Lian; Wang, Rui

    2009-06-01

    A growing body of evidence indicated that the G protein coupled receptors exist as homo- or hetero-dimers in the living cell. The heterodimerization between μ and δ opioid receptors has attracted researchers' particular interests, it is reported to display novel pharmacological and signalling regulation properties. In this study, we construct the full-length 3D-model of μ and δ opioid receptors using the homology modelling method. Threading program was used to predict the possible templates for the N- and C-terminus domains. Then, a 30 ns molecular dynamics simulations was performed with each receptor embedded in an explicit membrane-water environment to refine and explore the conformational space. Based on the structures extracted from the molecular dynamics, the likely interface of μ-δ heterodimer was investigated through the analysis of protein-protein docking, cluster, shape complementary and interaction energy. The computational modelling works revealed that the most likely interface of heterodimer was formed between the transmembrane1,7 (TM1,7) domains of μ receptor and the TM(4,5) domains of δ receptor, with emphasis on μ-TM1 and δ-TM4, the next likely interface was μ(TM6,7)-δ(TM4,5), with emphasis on μ-TM6 and δ-TM4. Our results were consistent with previous reports.

  5. 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…

  6. Computational Study of Inlet Active Flow Control

    DTIC Science & Technology

    2007-05-01

    respectively. 3 Figure 2: Howard University Baseline Grid File created from Gridgen mesh Howard University also created a refined grid with... Gridgen mesh 4 Simulation Details and Results In total, three solutions were obtained from the study, one using the Howard University Baseline

  7. 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.

  8. A computer controlled pulsatile pump: preliminary study.

    PubMed

    Zwarts, M S; Topaz, S R; Jones, D N; Kolff, W J

    1996-12-01

    A Stepper Motor Driven Reciprocating Pump (SDRP) can replace roller pumps and rotary pumps for cardio pulmonary bypass, hemodialysis and regional perfusion. The blood pumping ventricles are basically the same as ventricles used for air driven artificial hearts and ventricular assist devices. The electric stepper motor uses a flexible linkage belt to produce a reciprocating movement, which pushes a hard sphere into the diaphragm of the blood ventricles. The SDRP generates pulsatile flow and has a small priming volume. The preset power level of the motor driver limits the maximum potential outflow pressure, so the driver acts as a safety device. A double pump can be made by connecting two fluid pumping chambers to opposing sides of the motor base. Each pump generates pulsatile flow. Pressure and flow studies with water were undertaken. Preliminary blood studies showed low hemolysis, even when circulating a small amount of blood up to 16 hours.

  9. Computational Studies of Laminar to Turbulence Transition

    DTIC Science & Technology

    1994-07-14

    model flows. One such flow is the swept Hiemenz flow in which the interaction of stationary and traveling crossflow disturbances can be studied. In...secondary instability of the three-dimensional mean flow modulated by the stationary vortices. Section 2 describes the basic flow for the swept Hiemenz ...Section 5 describes the results from secondary instability analysis and the conclusions are given in § 6. 50 2. The Swept Hiemenz Problem The flow past

  10. Advanced Computational Techniques in Regional Wave Studies

    DTIC Science & Technology

    1990-01-03

    earthquakes on the Cascadia Subduction zone , Pacific Northwest, Pure Appl. Geoph. 129, (in press). Heinrich, R. R. (1941). A contribution to the seismic...and the strength of preexisting zones of weakness (Talwani, 1989). Since the historical record is significantly smaller than one complete recurrence...deter- mined from aftershock studies. Darragh and Bolt (1987) pointed out that there can be a discrepancy between the extent of the aftershock zone

  11. Computational Studies of Magnetically Doped Semiconductor Nanoclusters

    NASA Astrophysics Data System (ADS)

    Gutsev, Lavrenty Gennady

    Spin-polarized unrestricted density functional theory is used to calculate the molecular properties of magnetic semiconductor quantum dots doped with 3d-metal atoms. We calculate total energies of the low spin antiferromagnetically coupled states using a spin-flipping algorithm leading to the broken-symmetry states. Given the novel nature of the materials studied, we simulate experimental observables such as hyperfine couplings, ionization/ energies, electron affinities, first and second order polarizabilities, band gaps and exchange coupling constants. Specifically, we begin our investigation with pure clusters of (CdSe )16 and demonstrate the dependence of molecular observables on geometrical structures. We also show that the many isomers of this cluster are energetically quite closely spaced, and thus it would be necessary to employ a battery of tests to experimentally distinguish them. Next, we discuss Mn-doping into the cage (CdSe)9 cluster as well as the zinc-blende stacking type cluster (CdSe)36. We show that the local exchange coupling mechanism is ligand-mediated superexchange and simulate the isotropic hyperfine constants. Finally, we discuss a novel study where (CdSe)9 is doped with Mn or Fe up to a full replacement of all the Cd's and discuss the transition points for the magnetic behavior and specifically the greatly differing band-gap shifts. We also outline an unexpected pattern in the polarizability of the material as metals are added and compare our results with the results from theoretical studies of the bulk material.

  12. Computational Studies of Venom Peptides Targeting Potassium Channels

    PubMed Central

    Chen, Rong; Chung, Shin-Ho

    2015-01-01

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

  13. Integrating user studies into computer graphics-related courses.

    PubMed

    Santos, B S; Dias, P; Silva, S; Ferreira, C; Madeira, J

    2011-01-01

    This paper presents computer graphics. Computer graphics and visualization are essentially about producing images for a target audience, be it the millions watching a new CG-animated movie or the small group of researchers trying to gain insight into the large amount of numerical data resulting from a scientific experiment. To ascertain the final images' effectiveness for their intended audience or the designed visualizations' accuracy and expressiveness, formal user studies are often essential. In human-computer interaction (HCI), such user studies play a similar fundamental role in evaluating the usability and applicability of interaction methods and metaphors for the various devices and software systems we use.

  14. 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.

  15. 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

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

    PubMed Central

    2013-01-01

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

  17. Faecal microbiota study reveals specific dysbiosis in spondyloarthritis.

    PubMed

    Breban, Maxime; Tap, Julien; Leboime, Ariane; Said-Nahal, Roula; Langella, Philippe; Chiocchia, Gilles; Furet, Jean-Pierre; Sokol, Harry

    2017-09-01

    Altered microbiota composition or dysbiosis is suspected to be implicated in the pathogenesis of chronic inflammatory diseases, such as spondyloarthritis (SpA) and rheumatoid arthritis (RA). 16S ribosomal RNA gene sequencing was performed on faecal DNA isolated from stool samples in two consecutive cross-sectional cohorts, each comprising three groups of adult volunteers: SpA, RA and healthy controls (HCs). In the second study, HCs comprised a majority of aged-matched siblings of patients with known HLA-B27 status. Alpha and beta diversities were assessed using QIIME, and comparisons were performed using linear discriminant analysis effect size to examine differences between groups. In both cohorts, dysbiosis was evidenced in SpA and RA, as compared with HCs, and was disease specific. A restriction of microbiota biodiversity was detected in both disease groups. The most striking change was a twofold to threefold increased abundance of Ruminococcus gnavus in SpA, as compared with both RA and HCs that was significant in both studies and positively correlated with disease activity in patients having a history of inflammatory bowel disease (IBD). Among HCs, significant difference in microbiota composition were also detected between HLA-B27+ and HLA-B27 negative siblings, suggesting that genetic background may influence gut microbiota composition. Our results suggest that distinctive dysbiosis characterise both SpA and RA and evidence a reproducible increase in R. gnavus that appears specific for SpA and a marker of disease activity. This observation is consistent with the known proinflammatory role of this bacteria and its association with IBD. It may provide an explanation for the link that exists between SpA and IBD. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  18. 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..

  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. Computational Studies of Nanostructures of Boron

    NASA Astrophysics Data System (ADS)

    Tandy, P.; Yu, M.; Leahy, C.; Tian, W. Q.; Wu, S. Y.; Jayanthi, C. S.

    2009-03-01

    The goal of this work is to develop a reliable semi-empirical Hamiltonian for boron that may be used to predict nanostructures of boron. It is well known that bonding in boron is complicated as it may form three-center, two-electron bonds. The semi-empirical Hamiltonian used here was recently developed by Leahy et al. in the framework of linear combination of atomic orbitals[1]. The salient feature of this Hamiltonian is that it treats environment dependency and charge redistributions on equal footing. It will be shown that such a parameterized Hamiltonian can predict the B80 cage structure with C1 symmetry as found in a recent first-principles study [2]. Having validated our semi-empirical Hamiltonian for boron with small boron clusters and the B80 cage, we have performed a systematic study of other boron nanostructures: (i) larger cage structures (e.g., B215), (ii) boron clusters cut from the bulk alpha boron, and (iii) boron sheets (triangular sheets with and without holes). We will discuss the ground state structures of these boron nanostructures as well as the energetics and HOMO-LUMO gaps of different families of boron clusters as a function their diameters. 1. C. Leahy et al. Phys. Rev. B74, 155408 (2006). 2. N. G. Szwacki et al. PRL 100, 159901 (2008).

  1. Computational study of materials under pressure

    NASA Astrophysics Data System (ADS)

    Kasinathan, Deepa

    2006-07-01

    Pressure possesses perhaps the greatest of all the physical variables. First principles electronic structure calculations have contributed significantly to high perssure studies, especially of solids. In this work, the results of the first principles analysis of CoN, MnO and Li under pressure are presented. From total energy calculations, we can establish that CoN takes a paramagnetic zincblende structure at ambient pressure, rather than rocksalt as sometimes suggested. We also predict a first order phase transition to a ferromagnetic state at 43 GPa, a weak ferromagnet not far from a ferromagnetic quantum critical point. MnO, a classic prototype for a Mott insulator exibits rich physics as a function of pressure, including structural phase transition, volume collapse, insulator - metal transition, etc. This system has been a long standing challenge to methods based on density functional theory. Our study provides some of the first detailed information on how magnetic moments in a real material may begin to disintegrate without vanishing identically, at or near a Mott transition, when correlation is taken into account. Li, the simplest metal becomes a superconductor under pressure, with the highest Tc observed in any elemental metal. Using both total energy and linear response calculations we observe increasingly strong electron-phonon coupling concentrated along intersections of Kohn anomaly surfaces with the evolving Fermi surface, that drives this simple metal to become a superconductor under pressure.

  2. 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

  3. 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

  4. 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

  5. Studies of recombinant TWA1 reveal constitutive dimerization

    PubMed Central

    Francis, Ore; Baker, Genevieve E.; Race, Paul R.

    2016-01-01

    The mammalian muskelin/RanBP9/C-terminal to LisH (CTLH) complex and the Saccharomyces cerevisiae glucose-induced degradation (GID) complex are large, multi-protein complexes that each contain a RING E3 ubiquitin ligase. The yeast GID complex acts to degrade a key enzyme of gluconeogenesis, fructose 1,6-bisphosphatase, under conditions of abundant fermentable carbon sources. However, the assembly and functions of the mammalian complex remain poorly understood. A striking feature of these complexes is the presence of multiple proteins that contain contiguous lissencephaly-1 homology (LisH), CTLH and C-terminal CT11-RanBP9 (CRA) domains. TWA1/Gid8, the smallest constituent protein of these complexes, consists only of LisH, CTLH and CRA domains and is highly conserved in eukaryotes. Towards better knowledge of the role of TWA1 in these multi-protein complexes, we established a method for bacterial expression and purification of mouse TWA1 that yields tag-free, recombinant TWA1 in quantities suitable for biophysical and biochemical studies. CD spectroscopy of recombinant TWA1 indicated a predominantly α-helical protein. Gel filtration chromatography, size-exclusion chromatography (SEC) with multi-angle light scattering (SEC-MALS) and native PAGE demonstrated a propensity of untagged TWA1 to form stable dimers and, to a lesser extent, higher order oligomers. TWA1 has a single cysteine residue, Cys139, yet the dimeric form was preserved when TWA1 was purified in the presence of the reducing agent tris(2-carboxyethyl)phosphine (TCEP). These findings have implications for understanding the molecular role of TWA1 in the yeast GID complex and related multi-protein E3 ubiquitin ligases identified in other eukaryotes. PMID:27920276

  6. 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

  7. 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.

  8. Computational Study of Combustor-Turbine Interactions

    NASA Technical Reports Server (NTRS)

    Miki, Kenji; Liou, Meng-Sing

    2017-01-01

    The Open National Combustion Code (OpenNCC) is applied to the simulation of a realisticcombustor configuration [Energy Efficient Engine (E(exp. 3))] in order to investigate the unsteady flow fields inside the combustor and around the first stage stator of a high pressure turbine (HPT). We consider one-twelfth (24 degrees) of the full annular E(exp. 3) combustor with three different geometries of the combustor exit: one without the vane, and two others with the vane set at different relative positions in relation to the fuel nozzle (clocking). Although it is common to take the exit flow profiles obtained by separately simulating the combustor and then feed it as the inflow profile when modeling the HPT, our studies show that the unsteady flow fields are influenced by the presence of the vane as well as clocking. More importantly, the characteristics (e.g., distribution and strength) of the high temperature spots (i.e., hot-streaks) appearing on the vane significantly alters. This indicates the importance of simultaneously modeling both the combustor and the HPT to understand the mechanics of the unsteady formulation of hot-streaks.

  9. Computational Studies and Designs for Fast Ignition

    NASA Astrophysics Data System (ADS)

    Nagatomo, H.; Johzaki, T.; Nakamura, T.; Sakagami, H.; Mima, K.

    2006-12-01

    The fast ignition scheme is one of the most fascinating and feasible ignition schemes for the inertial fusion energy. At ILE Osaka University, FIREX (Fast Ignition Realization Experiment) project is in progress. Implosion experiments of the cryogenic target are scheduled in near future. There are two key issues for the fast ignition. One is controlling the implosion dynamics to form high density core plasma in non-spherical implosion, and the other is heating the core plasma efficiently by the short pulse high intense laser. The time and space scale in the fast ignition scheme vary widely from initial laser irradiation to solid target, to relativistic laser plasma interaction and final fusion burning. The numerical simulation plays an important role in demonstrating the performance of the fast ignition, designing the targets, and optimizing laser pulse shapes for the scheme. These all the physics are desired to be self-consistently described. In order to study these physics of FI, we have developed "Fast Ignition Integrated Interconnecting code" (FI3), which consists of collective Particle-in-Cell (PIC) code (FISCOF1D/2D), Relativistic Fokker-Planck with hydro code (FIBMET), and 2-dimensional Arbitrary-Lagrangian-Eulerian (ALE) radiation hydrodynamics code (PINOCO). Those codes are sophisticated in each suitable plasma parameters, and boundaries conditions and initial conditions for them are imported/exported to each other by way of DCCP, a simple and compact communication tool which enable these codes to communicate each others under executing different machines. We show the feature of the FI3 code, and numerical results of whole process of fast ignition. Individual important physics behind the FI are explained with the numerical results also.

  10. Cluster Mechanism of Homogeneous Crystallization (Computer Study)

    NASA Astrophysics Data System (ADS)

    Belashchenko, D. K.

    2008-12-01

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

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

    PubMed

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

    2015-01-01

    Cefotaxime metal complexes of Cr(III), Mn(II), Fe(III), Co(II), Ni(II), Cu(II), Zn(II), Cd(II), Hg(II) and two mixed metals complexes of (Fe,Cu) and (Fe,Ni) were synthesized and characterized by elemental analysis, IR, electronic spectra, magnetic susceptibility and ESR spectra. The studies proved that cefotaxime may act as mono, bi, tri and tetra-dentate ligand through oxygen atoms of lactam carbonyl, carboxylic or amide carbonyl groups and nitrogen atom of thiazole ring. From the magnetic measurements and electronic spectral data, octahedral structures were proposed for all complexes. Quantum chemical methods have been performed for cefotaxime to calculate charges, bond lengths, bond angles, dihedral angles, electronegativity (χ), chemical potential (μ), global hardness (η), softness (σ) and the electrophilicity index (ω). The thermal decomposition of the prepared metals complexes was studied by TGA, DTA and DSC techniques. Thermogravimetric studies revealed the presence of lattice or coordinated water molecules in all the prepared complexes. The decomposition mechanisms were suggested. The thermal decomposition of the complexes ended with the formation of metal oxides and carbon residue as a final product except in case of Hg complex, sublimation occur at the temperature range 376.5-575.0 °C so, only carbon residue was produced during thermal decomposition. The orders of chemical reactions (n) were calculated via the peak symmetry method and the activation parameters were computed from the thermal decomposition data. The geometries of complexes may be converted from Oh to Td during the thermal decomposition steps. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. 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

  13. Combining H/D exchange mass spectroscopy and computational docking reveals extended DNA-binding surface on uracil-DNA glycosylase

    PubMed Central

    Roberts, Victoria A.; Pique, Michael E.; Hsu, Simon; Li, Sheng; Slupphaug, Geir; Rambo, Robert P.; Jamison, Jonathan W.; Liu, Tong; Lee, Jun H.; Tainer, John A.; Ten Eyck, Lynn F.; Woods, Virgil L.

    2012-01-01

    X-ray crystallography provides excellent structural data on protein–DNA interfaces, but crystallographic complexes typically contain only small fragments of large DNA molecules. We present a new approach that can use longer DNA substrates and reveal new protein–DNA interactions even in extensively studied systems. Our approach combines rigid-body computational docking with hydrogen/deuterium exchange mass spectrometry (DXMS). DXMS identifies solvent-exposed protein surfaces; docking is used to create a 3-dimensional model of the protein–DNA interaction. We investigated the enzyme uracil-DNA glycosylase (UNG), which detects and cleaves uracil from DNA. UNG was incubated with a 30 bp DNA fragment containing a single uracil, giving the complex with the abasic DNA product. Compared with free UNG, the UNG–DNA complex showed increased solvent protection at the UNG active site and at two regions outside the active site: residues 210–220 and 251–264. Computational docking also identified these two DNA-binding surfaces, but neither shows DNA contact in UNG–DNA crystallographic structures. Our results can be explained by separation of the two DNA strands on one side of the active site. These non-sequence-specific DNA-binding surfaces may aid local uracil search, contribute to binding the abasic DNA product and help present the DNA product to APE-1, the next enzyme on the DNA-repair pathway. PMID:22492624

  14. Feasibility Study of Computational Fluid Dynamics Simulation of Coronary Computed Tomography Angiography Based on Dual-Source Computed Tomography

    PubMed Central

    Lu, Jing; Yu, Jie; Shi, Heshui

    2017-01-01

    Background Adding functional features to morphological features offers a new method for non-invasive assessment of myocardial perfusion. This study aimed to explore technical routes of assessing the left coronary artery pressure gradient, wall shear stress distribution and blood flow velocity distribution, combining three-dimensional coronary model which was based on high resolution dual-source computed tomography (CT) with computational fluid dynamics (CFD) simulation. Methods Three cases of no obvious stenosis, mild stenosis and severe stenosis in left anterior descending (LAD) were enrolled. Images acquired on dual-source CT were input into software Mimics, ICEMCFD and FLUENT to simulate pressure gradient, wall shear stress distribution and blood flow velocity distribution. Measuring coronary enhancement ratio of coronary artery was to compare with pressure gradient. Results Results conformed to theoretical values and showed difference between normal and abnormal samples. Conclusions The study verified essential parameters and basic techniques in blood flow numerical simulation preliminarily. It was proved feasible. PMID:27924174

  15. Could offset cluster reveal strong earthquake pattern?——case study from Haiyuan Fault

    NASA Astrophysics Data System (ADS)

    Ren, Z.; Zhang, Z.; Chen, T.; Yin, J.; Zhang, P. Z.; Zheng, W.; Zhang, H.; Li, C.

    2016-12-01

    Since 1990s, researchers tried to use offset clusters to study strong earthquake patterns. However, due to the limitation of quantity of offset data, it was not widely used until recent years with the rapid development of high-resolution topographic data, such as remote sensing images, LiDAR. In this study, we use airborne LiDAR data to re-evaluate the cumulative offsets and co-seismic offset of the 1920 Haiyuan Ms 8.5 earthquake along the western and middle segments of the co-seismic surface rupture zone. Our LiDAR data indicate the offset observations along both the western and middle segments fall into five groups. The group with minimum slip amount is associated with the 1920 Haiyuan Ms 8.5 earthquake, which ruptured both the western and middle segments. Our research highlights two new interpretations: firstly, the previously reported maximum displacement of the 1920 Earthquake is likely to be produced by at least two earthquakes; secondly, Our results reveal that the Cumulative Offset Probability Density (COPD) peaks of same offset amount on western segment and middles segment did not corresponding to each other one by one. The ages of the paleoearthquakes indicate the offsets are not accumulated during same period. We suggest that any discussion of the rupture pattern of a certain fault based on the offset data should also consider fault segmentation and paleoseismological data; Therefore, using the COPD peaks for studying the number of palaeo-events and their rupture patterns, the COPD peaks should be computed and analyzed on fault sub-sections and not entire fault zones. Our results reveal that the rupture pattern on the western and middle segment of the Haiyuan Fault is different from each other, which provide new data for the regional seismic potential analysis.

  16. 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…

  17. 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…

  18. 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…

  19. 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…

  20. Computational Model Reveals Limited Correlation between Germinal Center B-Cell Subclone Abundancy and Affinity: Implications for Repertoire Sequencing

    PubMed Central

    Reshetova, Polina; van Schaik, Barbera D. C.; Klarenbeek, Paul L.; Doorenspleet, Marieke E.; Esveldt, Rebecca E. E.; Tak, Paul-Peter; Guikema, Jeroen E. J.; de Vries, Niek; van Kampen, Antoine H. C.

    2017-01-01

    Immunoglobulin repertoire sequencing has successfully been applied to identify expanded antigen-activated B-cell clones that play a role in the pathogenesis of immune disorders. One challenge is the selection of the Ag-specific B cells from the measured repertoire for downstream analyses. A general feature of an immune response is the expansion of specific clones resulting in a set of subclones with common ancestry varying in abundance and in the number of acquired somatic mutations. The expanded subclones are expected to have BCR affinities for the Ag higher than the affinities of the naive B cells in the background population. For these reasons, several groups successfully proceeded or suggested selecting highly abundant subclones from the repertoire to obtain the Ag-specific B cells. Given the nature of affinity maturation one would expect that abundant subclones are of high affinity but since repertoire sequencing only provides information about abundancies, this can only be verified with additional experiments, which are very labor intensive. Moreover, this would also require knowledge of the Ag, which is often not available for clinical samples. Consequently, in general we do not know if the selected highly abundant subclone(s) are also the high(est) affinity subclones. Such knowledge would likely improve the selection of relevant subclones for further characterization and Ag screening. Therefore, to gain insight in the relation between subclone abundancy and affinity, we developed a computational model that simulates affinity maturation in a single GC while tracking individual subclones in terms of abundancy and affinity. We show that the model correctly captures the overall GC dynamics, and that the amount of expansion is qualitatively comparable to expansion observed from B cells isolated from human lymph nodes. Analysis of the fraction of high- and low-affinity subclones among the unexpanded and expanded subclones reveals a limited correlation between

  1. 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…

  2. 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…

  3. Impact of Netbook Computers on One District's Social Studies Curriculum

    ERIC Educational Resources Information Center

    Schleicher, Joel L.

    2011-01-01

    The purpose of this study was to collect and analyze quantitative and qualitative data to determine the overall impact of a pilot netbook initiative in five social studies classrooms. The researcher explored the impact on teaching and learning social studies with the primary source of curriculum delivery through one-to-one netbook computer access…

  4. Computational Modeling of Allosteric Communication Reveals Organizing Principles of Mutation-Induced Signaling in ABL and EGFR Kinases

    PubMed Central

    Dixit, Anshuman; Verkhivker, Gennady M.

    2011-01-01

    The emerging structural information about allosteric kinase complexes and the growing number of allosteric inhibitors call for a systematic strategy to delineate and classify mechanisms of allosteric regulation and long-range communication that control kinase activity. In this work, we have investigated mechanistic aspects of long-range communications in ABL and EGFR kinases based on the results of multiscale simulations of regulatory complexes and computational modeling of signal propagation in proteins. These approaches have been systematically employed to elucidate organizing molecular principles of allosteric signaling in the ABL and EGFR multi-domain regulatory complexes and analyze allosteric signatures of the gate-keeper cancer mutations. We have presented evidence that mechanisms of allosteric activation may have universally evolved in the ABL and EGFR regulatory complexes as a product of a functional cross-talk between the organizing αF-helix and conformationally adaptive αI-helix and αC-helix. These structural elements form a dynamic network of efficiently communicated clusters that may control the long-range interdomain coupling and allosteric activation. The results of this study have unveiled a unifying effect of the gate-keeper cancer mutations as catalysts of kinase activation, leading to the enhanced long-range communication among allosterically coupled segments and stabilization of the active kinase form. The results of this study can reconcile recent experimental studies of allosteric inhibition and long-range cooperativity between binding sites in protein kinases. The presented study offers a novel molecular insight into mechanistic aspects of allosteric kinase signaling and provides a quantitative picture of activation mechanisms in protein kinases at the atomic level. PMID:21998569

  5. Computational analyses of intravascular tracer washout reveal altered capillary-level flow distributions in obese Zucker rats

    PubMed Central

    Wu, Fan; Beard, Daniel A; Frisbee, Jefferson C

    2011-01-01

    Abstract Intravascular tracer washout data obtained from gastrocnemius muscle of lean Zucker rats (LZRs) and obese Zucker rats (OZRs) were analysed to investigate flow distributions in the OZR, a model of non-atherosclerotic peripheral vascular disease. A computer model used to simulate the network washout curves was developed based on experimentally observed relative dispersions in large vessels and asymmetrical flow distributions at bifurcations in dichotomous microvascular networks. The model results of simulations were compared to experimental washout data of 125I-labelled albumin, an intravascular tracer, to uncover flow distributions on the arterial-network and capillary levels. The lean and obese Zucker rats demonstrated distinct capillary-level flow distributions, with higher dispersion and significantly more low-flow capillaries in the OZRs than in the LZRs. Targeted pharmacological treatments against identified sites of vascular dysfunction in OZRs (adrenoreceptor blockade with phentolamine, antioxidant treatment with Tempol and thromboxane receptor antagonism with SQ-29548) were shown to improve the capillary-level flow distributions in treated OZRs toward distributions determined in control LZRs. Combination therapy with multiple pharmacological interventions resulted in a greater degree of recovery. This study demonstrates that the enhanced perfusion heterogeneity at arteriole bifurcations is a potential mechanism underlying perfusion–demand mismatching in OZRs, and suggests that amelioration of this dysfunction must involve a multi-faceted interventional approach. PMID:21788350

  6. Contrast-Enhanced Chest Computed Tomography Reveals Treatable Causes of Cerebral Abscesses in Patients without Antecedent Surgery or Trauma.

    PubMed

    Cox, Mougnyan; Patel, Manisha; Deshmukh, Sandeep; Roth, Christopher G; Flanders, Adam E

    2017-05-01

    Brain abscesses cause substantial morbidity and mortality even after appropriate therapy, and no underlying cause is found in 25% of cases. We investigated the added utility of contrast-enhanced chest computed tomography (CT) in the diagnostic work-up of patients presenting with cerebral abscesses and no history or prior trauma or cranial surgery. All patients presenting to a single institution with a surgically proven brain abscess were reviewed. Concurrent contrast-enhanced chest CT imaging results were reviewed when available to identify treatable predisposing causes of intracranial suppuration. This study included 31 patients with biopsy-proven abscesses. Multiple abscesses were present in 8 patients (26%). Contrast-enhanced CT was performed in 15 patients (48%). Of these 15 patients, 2 had pulmonary arteriovenous malformations, 1 had an intrapulmonary shunt, and 3 had empyemas. Definitive therapy for the chest findings was provided to 6 of the 15 patients (40%). In the remaining 9 patients, 3 had pulmonary abscesses, for which diagnostic aspiration was requested. Another patient had an incidental pulmonary embolism, resulting in same-day placement of an inferior vena caval filter (not included in chest analysis, given that the finding was incidental). Contrast-enhanced chest CT is useful for identifying treatable causes of cerebral abscesses in patients with a cerebral abscess and no history of surgery or trauma. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. 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

  8. 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.

  9. 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

  10. 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)

  11. 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…

  12. 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…

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

    SciTech Connect

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

    1984-01-01

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

  14. 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,…

  15. Two Studies Examining Argumentation in Asynchronous Computer Mediated Communication

    ERIC Educational Resources Information Center

    Joiner, Richard; Jones, Sarah; Doherty, John

    2008-01-01

    Asynchronous computer mediated communication (CMC) would seem to be an ideal medium for supporting development in student argumentation. This paper investigates this assumption through two studies. The first study compared asynchronous CMC with face-to-face discussions. The transactional and strategic level of the argumentation (i.e. measures of…

  16. Combining computer and manual overlays—Willamette River Greenway Study

    Treesearch

    Asa Hanamoto; Lucille Biesbroeck

    1979-01-01

    We will present a method of combining computer mapping with manual overlays. An example of its use is the Willamette River Greenway Study produced for the State of Oregon Department of Transportation in 1974. This one year planning study included analysis of data relevant to a 286-mile river system. The product is a "wise use" plan which conserves the basic...

  17. 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.

  18. Insights into cellulase-lignin non-specific binding revealed by computational redesign of the surface of green fluorescent protein

    SciTech Connect

    Haarmeyer, Carolyn N.; Smith, Matthew D.; Chundawat, Shishir P. S.; Sammond, Deanne; Whitehead, Timothy A.

    2016-10-17

    Biological-mediated conversion of pretreated lignocellulosic biomass to biofuels and biochemicals is a promising avenue towards energy sustainability. However, a critical impediment to the commercialization of cellulosic biofuel production is the high cost of cellulase enzymes needed to deconstruct biomass into fermentable sugars. One major factor driving cost is cellulase adsorption and inactivation in the presence of lignin, yet we currently have a poor understanding of the protein structure-function relationships driving this adsorption. In this work, we have systematically investigated the role of protein surface potential on lignin adsorption using a model monomeric fluorescent protein. We have designed and experimentally characterized 16 model protein variants spanning the physiological range of net charge (-24 to +16 total charges) and total charge density (0.28 to 0.40 charges per sequence length) typical for natural proteins. Protein designs were expressed, purified, and subjected to in silico and in vitro biophysical measurements to evaluate the relationship between protein surface potential and lignin adsorption properties. The designs were comparable to model fluorescent protein in terms of thermostability and heterologous expression yield, although the majority of the designs unexpectedly formed homodimers. Protein adsorption to lignin was studied at two different temperatures using Quartz Crystal Microbalance with Dissipation Monitoring and a subtractive mass balance assay. We found a weak correlation between protein net charge and protein-binding capacity to lignin. No other single characteristic, including apparent melting temperature and 2nd virial coefficient, showed correlation with lignin binding. Analysis of an unrelated cellulase dataset with mutations localized to a family I carbohydrate-binding module showed a similar correlation between net charge and lignin binding capacity. Altogether, our study provides strategies to identify highly

  19. 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.

  20. Insights into cellulase-lignin non-specific binding revealed by computational redesign of the surface of green fluorescent protein.

    PubMed

    Haarmeyer, Carolyn N; Smith, Matthew D; Chundawat, Shishir P S; Sammond, Deanne; Whitehead, Timothy A

    2017-04-01

    Biological-mediated conversion of pretreated lignocellulosic biomass to biofuels and biochemicals is a promising avenue toward energy sustainability. However, a critical impediment to the commercialization of cellulosic biofuel production is the high cost of cellulase enzymes needed to deconstruct biomass into fermentable sugars. One major factor driving cost is cellulase adsorption and inactivation in the presence of lignin, yet we currently have a poor understanding of the protein structure-function relationships driving this adsorption. In this work, we have systematically investigated the role of protein surface potential on lignin adsorption using a model monomeric fluorescent protein. We have designed and experimentally characterized 16 model protein variants spanning the physiological range of net charge (-24 to +16 total charges) and total charge density (0.28-0.40 charges per sequence length) typical for natural proteins. Protein designs were expressed, purified, and subjected to in silico and in vitro biophysical measurements to evaluate the relationship between protein surface potential and lignin adsorption properties. The designs were comparable to model fluorescent protein in terms of thermostability and heterologous expression yield, although the majority of the designs unexpectedly formed homodimers. Protein adsorption to lignin was studied at two different temperatures using Quartz Crystal Microbalance with Dissipation Monitoring and a subtractive mass balance assay. We found a weak correlation between protein net charge and protein-binding capacity to lignin. No other single characteristic, including apparent melting temperature and 2nd virial coefficient, showed correlation with lignin binding. Analysis of an unrelated cellulase dataset with mutations localized to a family I carbohydrate-binding module showed a similar correlation between net charge and lignin binding capacity. Overall, our study provides strategies to identify highly active, low

  1. Insights into cellulase-lignin non-specific binding revealed by computational redesign of the surface of green fluorescent protein

    DOE PAGES

    Haarmeyer, Carolyn N.; Smith, Matthew D.; Chundawat, Shishir P. S.; ...

    2016-10-17

    Biological-mediated conversion of pretreated lignocellulosic biomass to biofuels and biochemicals is a promising avenue towards energy sustainability. However, a critical impediment to the commercialization of cellulosic biofuel production is the high cost of cellulase enzymes needed to deconstruct biomass into fermentable sugars. One major factor driving cost is cellulase adsorption and inactivation in the presence of lignin, yet we currently have a poor understanding of the protein structure-function relationships driving this adsorption. In this work, we have systematically investigated the role of protein surface potential on lignin adsorption using a model monomeric fluorescent protein. We have designed and experimentally characterizedmore » 16 model protein variants spanning the physiological range of net charge (-24 to +16 total charges) and total charge density (0.28 to 0.40 charges per sequence length) typical for natural proteins. Protein designs were expressed, purified, and subjected to in silico and in vitro biophysical measurements to evaluate the relationship between protein surface potential and lignin adsorption properties. The designs were comparable to model fluorescent protein in terms of thermostability and heterologous expression yield, although the majority of the designs unexpectedly formed homodimers. Protein adsorption to lignin was studied at two different temperatures using Quartz Crystal Microbalance with Dissipation Monitoring and a subtractive mass balance assay. We found a weak correlation between protein net charge and protein-binding capacity to lignin. No other single characteristic, including apparent melting temperature and 2nd virial coefficient, showed correlation with lignin binding. Analysis of an unrelated cellulase dataset with mutations localized to a family I carbohydrate-binding module showed a similar correlation between net charge and lignin binding capacity. Altogether, our study provides strategies to identify

  2. Doctors' experience with handheld computers in clinical practice: qualitative study

    PubMed Central

    McAlearney, Ann Scheck; Schweikhart, Sharon B; Medow, Mitchell A

    2004-01-01

    Objective To examine doctors' perspectives about their experiences with handheld computers in clinical practice. Design Qualitative study of eight focus groups consisting of doctors with diverse training and practice patterns. Setting Six practice settings across the United States and two additional focus group sessions held at a national meeting of general internists. Participants 54 doctors who did or did not use handheld computers. Results Doctors who used handheld computers in clinical practice seemed generally satisfied with them and reported diverse patterns of use. Users perceived that the devices helped them increase productivity and improve patient care. Barriers to use concerned the device itself and personal and perceptual constraints, with perceptual factors such as comfort with technology, preference for paper, and the impression that the devices are not easy to use somewhat difficult to overcome. Participants suggested that organisations can help promote handheld computers by providing advice on purchase, usage, training, and user support. Participants expressed concern about reliability and security of the device but were particularly concerned about dependency on the device and over-reliance as a substitute for clinical thinking. Conclusions Doctors expect handheld computers to become more useful, and most seem interested in leveraging (getting the most value from) their use. Key opportunities with handheld computers included their use as a stepping stone to build doctors' comfort with other information technology and ehealth initiatives and providing point of care support that helps improve patient care. PMID:15142920

  3. Experimental and Computational Study of Sonic and Supersonic Jet Plumes

    NASA Technical Reports Server (NTRS)

    Venkatapathy, E.; Naughton, J. W.; Fletcher, D. G.; Edwards, Thomas A. (Technical Monitor)

    1994-01-01

    Study of sonic and supersonic jet plumes are relevant to understanding such phenomenon as jet-noise, plume signatures, and rocket base-heating and radiation. Jet plumes are simple to simulate and yet, have complex flow structures such as Mach disks, triple points, shear-layers, barrel shocks, shock-shear-layer interaction, etc. Experimental and computational simulation of sonic and supersonic jet plumes have been performed for under- and over-expanded, axisymmetric plume conditions. The computational simulation compare very well with the experimental observations of schlieren pictures. Experimental data such as temperature measurements with hot-wire probes are yet to be measured and will be compared with computed values. Extensive analysis of the computational simulations presents a clear picture of how the complex flow structure develops and the conditions under which self-similar flow structures evolve. From the computations, the plume structure can be further classified into many sub-groups. In the proposed paper, detail results from the experimental and computational simulations for single, axisymmetric, under- and over-expanded, sonic and supersonic plumes will be compared and the fluid dynamic aspects of flow structures will be discussed.

  4. 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

  5. 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

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  8. Experiment and computation studies of high concentration pulverized coal combustion

    SciTech Connect

    Zhang, Z.; Qiu, J.; Chen, G.; Chen, C.; Li, F.; Sun, X.; Liu, S.

    1994-12-31

    This article gives out the studies of high concentration pulverized coal combustion. A series experiment and computation were done during research process. According to the result of the studies, if the authors increase the concentration of pulverized coal in primary air, some other method must be used to improve the mixture between primary and secondary air. Cross-flow of the two air jets is a way to get this effect. The importance of this technique is to determine the cross-angle and distance of two air jets. Through cold state two-phase and combustion experiment for a special coal they had chosen the cross-angle and distance between up and down secondary air as 30 and d/r as 8 (r is the relative diameter). In addition the mathematical computation was done to compare with experiment result. The comparison between experiment and computation shows agreement.

  9. 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.

  10. Computational analyses of transcriptomic data reveal the dynamic organization of the Escherichia coli chromosome under different conditions

    PubMed Central

    Ma, Qin; Yin, Yanbin; Schell, Mark A.; Zhang, Han; Li, Guojun; Xu, Ying

    2013-01-01

    The circular chromosome of Escherichia coli has been suggested to fold into a collection of sequentially consecutive domains, genes in each of which tend to be co-expressed. It has also been suggested that such domains, forming a partition of the genome, are dynamic with respect to the physiological conditions. However, little is known about which DNA segments of the E. coli genome form these domains and what determines the boundaries of these domain segments. We present a computational model here to partition the circular genome into consecutive segments, theoretically suggestive of the physically folded supercoiled domains, along with a method for predicting such domains under specified conditions. Our model is based on a hypothesis that the genome of E. coli is partitioned into a set of folding domains so that the total number of unfoldings of these domains in the folded chromosome is minimized, where a domain is unfolded when a biological pathway, consisting of genes encoded in this DNA segment, is being activated transcriptionally. Based on this hypothesis, we have predicted seven distinct sets of such domains along the E. coli genome for seven physiological conditions, namely exponential growth, stationary growth, anaerobiosis, heat shock, oxidative stress, nitrogen limitation and SOS responses. These predicted folding domains are highly stable statistically and are generally consistent with the experimental data of DNA binding sites of the nucleoid-associated proteins that assist the folding of these domains, as well as genome-scale protein occupancy profiles, hence supporting our proposed model. Our study established for the first time a strong link between a folded E. coli chromosomal structure and the encoded biological pathways and their activation frequencies. PMID:23599001

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

    PubMed

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

    2015-09-01

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

  12. 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

  13. Synthesis, crystal structure and computational studies of 4-nitrobenzylphosphonic acid

    NASA Astrophysics Data System (ADS)

    Wilk, Magdalena; Jarzembska, Katarzyna N.; Janczak, Jan; Hoffmann, Józef; Videnova-Adrabinska, Veneta

    2014-09-01

    4-Nitrobenzylphosphonic acid (1a) has been synthesized and structurally characterized by vibrational spectroscopy (IR and Raman) and single-crystal X-ray diffraction. Additionally, Hirshfeld surface analysis and computational methods have been used to compare the intermolecular interactions in the crystal structures of 1a and its carboxylic analogue, 4-nitrobenzylcarboxylic acid (4-NBCA). The crystal structure analysis of 1a has revealed that the acid molecules are extended into helical chains along the b axis using one of the hydrogen bonds established between phosphonic groups. The second (P)Osbnd H⋯O(P) hydrogen bond cross-links the inversion-related chains to form a thick monolayer with phosphonic groups arranged inwards and aromatic rings outwards. The nitro groups serve to link the neighbouring monolayers by weak Csbnd H⋯O(N) hydrogen bonds. Computations have confirmed the great contribution of electrostatic interactions for the crystal lattice stability. The cohesive energy, computed for the crystal structure of 1a exceeds 200 kJ mol-1 in magnitude and is nearly twice as large as that of 4-NBCA. The calculated cohesive energy values have been further related to the results of thermal analyses.

  14. 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.

  15. 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.

  16. A Study of Student-Teachers' Readiness to Use Computers in Teaching: An Empirical Study

    ERIC Educational Resources Information Center

    Padmavathi, M.

    2016-01-01

    This study attempts to analyze student-teachers' attitude towards the use of computers for classroom teaching. Four dimensions of computer attitude on a Likert-type five-point scale were used: Affect (liking), Perceived usefulness, Perceived Control, and Behaviour Intention to use computers. The effect of student-teachers' subject area, years of…

  17. A rare case of solitary subcutaneous scalp metastasis from follicular thyroid carcinoma revealed with positron emission tomography/computed tomography: a case report and review.

    PubMed

    Sager, Sait; Yilmaz, Sabire; Doner, Rana Kaya; Niyazoglu, Mutlu; Halac, Metin; Kanmaz, Bedii

    2014-01-01

    Differentiated thyroid cancer frequently metastasizes to regional cervical lymph nodes and in advanced cases metastases can be seen in the lungs and skeleton. Metastases to the skin or subcutaneous tissue are rare. Here we present a 49-year-old female patient with solitary scalp metastasis from follicular thyroid carcinoma FTC which was revealed with positron emission tomography (PET)/computed tomography (CT) imaging. PET showed flourodeoxiglucose avid lesion in the left vertex scalp. Scalp lesion was removed totally and histopathological examination revealed well-differentiated thyroid cancer metastasis.

  18. 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…

  19. AEDPS Computer Graphics Specification and Drawing Production Study.

    DTIC Science & Technology

    The purpose of this report is to present the results of the study of the current and planned Automated Engineering Document Preparation System ( AEDPS ...graphics subsystem as it would interface with AEDPS as currently operational. Since all computer systems have inputs, software and outputs - each of these

  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. Computer-Generated Geometry Instruction: A Preliminary Study

    ERIC Educational Resources Information Center

    Kang, Helen W.; Zentall, Sydney S.

    2011-01-01

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

  2. 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…

  3. Computerized Atlases: The Potential of Computers in Social Studies.

    ERIC Educational Resources Information Center

    de Leeuw, G.; Waters, N. M.

    1986-01-01

    Examines the use of computer atlases to see how they might contribute to the attainment of established social studies goals. Reviews advantages and disadvantages of existing software and hardware. Describes the potentials of computerized atlases and the hardware required to support such uses. (JDH)

  4. Merging Computers and Communication: A Case Study in Latin America.

    ERIC Educational Resources Information Center

    Oeffinger, John C.

    1987-01-01

    Discusses access to information through merging computers and new communications technology and its influence in developing nations. Highlights include a case study of InterNet/LACRIP (Latin American Cancer Research Information Project), a microcomputer-based international network involving institutions in the United States and Latin America that…

  5. 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…

  6. 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…

  7. 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.

  8. 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.

  9. 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.

  10. A Computer-Based System for Studies in Learning

    DTIC Science & Technology

    1974-09-01

    A D/A-000 102 A COMPUTER-BASED SYSTEM FOR STUDIES IN LEARNING Donald K. Centner, el al C a 1 i f o r n i a U n i v e nit v...DvlCUMENTATION PAGE I HEAD INSTRUCTIONS 1 1 Rf P;B’r S ^MBE R Tj GOVT ACCESSION NO 4 Ti T .. E ami f.itnlli- A Computer-Based System for...uuibisEinns D ams Th e views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily

  11. Language evolution as a Darwinian process: computational studies.

    PubMed

    Oudeyer, Pierre-Yves; Kaplan, Frédéric

    2007-03-01

    This paper presents computational experiments that illustrate how one can precisely conceptualize language evolution as a Darwinian process. We show that there is potentially a wide diversity of replicating units and replication mechanisms involved in language evolution. Computational experiments allow us to study systemic properties coming out of populations of linguistic replicators: linguistic replicators can adapt to specific external environments; they evolve under the pressure of the cognitive constraints of their hosts, as well as under the functional pressure of communication for which they are used; one can observe neutral drift; coalitions of replicators may appear, forming higher level groups which can themselves become subject to competition and selection.

  12. Computer models to study uterine activation at labour.

    PubMed

    Sharp, G C; Saunders, P T K; Norman, J E

    2013-11-01

    Improving our understanding of the initiation of labour is a major aim of modern obstetric research, in order to better diagnose and treat pregnant women in which the process occurs abnormally. In particular, increased knowledge will help us identify the mechanisms responsible for preterm labour, the single biggest cause of neonatal morbidity and mortality. Attempts to improve our understanding of the initiation of labour have been restricted by the inaccessibility of gestational tissues to study during pregnancy and at labour, and by the lack of fully informative animal models. However, computer modelling provides an exciting new approach to overcome these restrictions and offers new insights into uterine activation during term and preterm labour. Such models could be used to test hypotheses about drugs to treat or prevent preterm labour. With further development, an effective computer model could be used by healthcare practitioners to develop personalized medicine for patients on a pregnancy-by-pregnancy basis. Very promising work is already underway to build computer models of the physiology of uterine activation and contraction. These models aim to predict changes and patterns in uterine electrical excitation during term labour. There have been far fewer attempts to build computer models of the molecular pathways driving uterine activation and there is certainly scope for further work in this area. The integration of computer models of the physiological and molecular mechanisms that initiate labour will be particularly useful.

  13. 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

  14. 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.

  15. 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.

  16. Spectroscopic and Computational Investigations of a Mononuclear Manganese(IV)-Oxo Complex Reveal Electronic Structure Contributions to Reactivity

    DOE PAGES

    Leto, Domenick F.; Massie, Allyssa A.; Rice, Derek B.; ...

    2016-11-01

    The mononuclear Mn(IV)-oxo complex [MnIV(O)(N4py)]2+, where N4py is the pentadentate ligand N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)methylamine, we propose to attack C–H bonds by an excited-state reactivity pattern [Cho, K.-B.; Shaik, S.; Nam, W. J. Phys. Chem. Lett. 2012, 3, 2851-2856 (DOI: 10.1021/jz301241z)]. In this model, a 4E excited state is utilized to provide a lower-energy barrier for hydrogen-atom transfer. This proposal is intriguing, as it offers both a rationale for the relatively high hydrogen-atom-transfer reactivity of [MnIV(O)(N4py)]2+ and a guideline for creating more reactive complexes through ligand modification. Here we employ a combination of electronic absorption and variable-temperature magnetic circular dichroism (MCD) spectroscopy tomore » experimentally evaluate this excited-state reactivity model. Using these spectroscopic methods, in conjunction with time-dependent density functional theory (TD-DFT) and complete-active space self-consistent-field calculations (CASSCF), we define the ligand-field and charge-transfer excited states of [MnIV(O)(N4py)]2+. Through a graphical analysis of the signs of the experimental C-term MCD signals, we unambiguously assign a low-energy MCD feature of [MnIV(O)(N4py)]2+ as the 4E excited state predicted to be involved in hydrogen-atom-transfer reactivity. The CASSCF calculations predict enhanced MnIII-oxyl character on the excited-state 4E surface, consistent with previous DFT calculations. Potential-energy surfaces, developed using the CASSCF methods, are used to determine how the energies and wave functions of the ground and excited states evolved as a function of Mn=O distance. Furthermore, the unique insights into ground- and excited-state electronic structure offered by these spectroscopic and computational studies are harmonized with a thermodynamic model of hydrogen-atom-transfer reactivity, which predicts a correlation between transition-state barriers and driving force« less

  17. Computer Simulation for Pain Management Education: A Pilot Study.

    PubMed

    Allred, Kelly; Gerardi, Nicole

    2017-08-01

    Effective pain management is an elusive concept in acute care. Inadequate knowledge has been identified as a barrier to providing optimal pain management. This study aimed to determine student perceptions of an interactive computer simulation as a potential method for learning pain management, as a motivator to read and learn more about pain management, preference over traditional lecture, and its potential to change nursing practice. A post-computer simulation survey with a mixed-methods descriptive design was used in this study. A college of nursing in a large metropolitan university in the Southeast United States. A convenience sample of 30 nursing students in a Bachelor of Science nursing program. An interactive computer simulation was developed as a potential alternative method of teaching pain management to nursing students. Increases in educational gain as well as its potential to change practice were explored. Each participant was asked to complete a survey consisting of 10 standard 5-point Likert scale items and 5 open-ended questions. The survey was used to evaluate the students' perception of the simulation, specifically related to educational benefit, preference compared with traditional teaching methods, and perceived potential to change nursing practice. Data provided descriptive statistics for initial evaluation of the computer simulation. The responses on the survey suggest nursing students perceive the computer simulation to be entertaining, fun, educational, occasionally preferred over regular lecture, and with potential to change practice. Preliminary data support the use of computer simulation in educating nursing students about pain management. Copyright © 2017 American Society for Pain Management Nursing. Published by Elsevier Inc. All rights reserved.

  18. 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.

  19. Bedside computer access for an individual with severe and multiple disabilities: a case study.

    PubMed

    Blain, Stefanie; McKeever, Patricia; Chau, Tom

    2010-01-01

    This case study documents the process of designing a custom-tailored bedside computer access solution for a 20-year old individual with quadriplegia and reports the effects of computer access on her participation in life activities. We adopted a person-focused approach to match the individual to an access solution. Two months after the access solution's introduction, we measured its impact using a 2-dimensional Fitt's Law test and questionnaire from the ISO 9241-9 standards document, typing tests, a usage log and a semi-structured interview. The Canadian Occupational Performance Measure was also administered pre- and post- access, focusing on the client's perceived ability to use the computer. After 2 months, the individual was spending an average of 8.4 h per day on the computer, engaging in electronic communication, recreational, and educational activities. She learned single-switch typing with a throughput of 1.03 bits/s and targeting accuracy of 87.5%. The questionnaire revealed that the client was thoroughly satisfied with the interface. These results were interpreted as positive gains in the International Classification of Functioning, Disability and Health domains of communication and social interaction. By addressing individual goals, abilities and relevant environmental factors, a bedside computer access solution can be developed for individuals in long-term care. The introduction of a computer access solution augmented the participant's communication, leisure and educational activities, as well as perceived independence.

  20. Computational Study of Colloidal Droplet Interactions with Three Dimensional Structures

    DTIC Science & Technology

    2015-05-18

    SECURITY CLASSIFICATION OF: The colloidal droplet spreading on and sorption into a porous medium is important to 3D printing technology. In this study... colloidal fluid distribution in the porous structure after sorption of single/multiple droplets in powder beds. The spreading of the droplet on the surface...Feb-2015 Approved for Public Release; Distribution Unlimited Final Report: Computational Study of Colloidal Droplet Interactions with Three Dimensional

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. Computational aerodynamic study of a supersonic reference projectile

    NASA Astrophysics Data System (ADS)

    Zahir, S.; Gul, Waseem

    2017-04-01

    In the present paper results of computational aerodynamic study of a reference projectile in supersonic flow is presented. Pressure distribution along the projectiles nose in longitudinal and circumferential direction was studied using numerical simulations. Static aerodynamic coefficients in the freestream Mach numbers of 3 and 4 at an angle of incidence of -4 to 20 degrees were computed. For validation, the numerical solution was initially compared for the conic part with the experimental results and found to be in good agreement. Nose related aerodynamic features were initially studied in the first part of the study. Further complete projectile’s aerodynamic analysis is carried out. The present paper covers the results obtained in the study conducted for the projectile’s geometry. Significant flow features were investigated, including correct capturing of bow shock’s location, low pressure density/pressure variations in the low pressure regions along with its influence on the stagnation zone. Further evaluation of peak pressure values associated with the stagnation region on the nose was made. Also, static aerodynamic coefficients were computed to depict projectile’s static stability.

  6. Computational study of two possible intraplate earthquake triggering mechanisms

    SciTech Connect

    Kohsmann, J.J.

    1984-01-01

    The efficacy of two potential mechanisms for either triggering or causing seismicity is examined in this computational study. The conclusions reached are specifically applied to the seismicity of the new Madrid seismic zone, where they are found to have no demonstrable effect. The effect of water-loading in the Mississippi River is examined first. The modeling of river load by a finite length of rectangular load approximations results in a non-unique determination of the stress distribution which is dependent on the load geometry far outside of the region of interest. A statistical study of the relation between seismicity, river stage, and their tendency functions for 1976 in the northern Mississippi Embayment is also presented. As a prelude to the investigation of thermal stresses related to cylindrical plutonic intrusions, a detailed computational study of the thermal effects of such intrusions is also presented. The computational study of the thermal stresses associated with cylindrical plutonic intrusions is done using plots of the radial-dependence of the principal stresses associated with a given intrusion geometry at particular times after the initiation of intrusion and using focal mechanism plots based on the principal stress distribution. The results of these studies are discussed with relation to the seismicity and tectonic environment of the northern Mississippi Embayment.

  7. 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.

  8. 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.

  9. 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.

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

    NASA Astrophysics Data System (ADS)

    Jones, Peter M.; George, Anthony M.

    2016-03-01

    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.

  11. 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

  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

    2016-03-15

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

  13. Effects of septal perforation on nasal airflow: computer simulation study.

    PubMed

    Lee, H P; Garlapati, R R; Chong, V F H; Wang, D Y

    2010-01-01

    Nasal septal perforation is a structural or anatomical defect in the septum. The present study focused on the effects of septal perforation on nasal airflow and nasal patency, investigated using a computer simulation model. The effect of nasal septal perforation size on nasal airflow pattern was analysed using computer-generated, three-dimensional nasal models reconstructed using data from magnetic resonance imaging scans of a healthy human subject. Computer-based simulations using computational fluid dynamics were then conducted to determine nasal airflow patterns. The maximum velocity and wall shear stress were found always to occur in the downstream region of the septal perforation, and could potentially cause bleeding in that region, as previously reported. During the breathing process, there was flow exchange and flow reversal through the septal perforation, from the higher flow rate to the lower flow rate nostril side, especially for moderate and larger sized perforations. In the breathing process of patients with septal perforations, there is airflow exchange from the higher flow rate to the lower flow rate nostril side, especially for moderate and large sized perforations. For relatively small septal perforations, the amount of cross-flow is negligible. This cross-flow may cause the whistling sound typically experienced by patients.

  14. Computational Study of Scenarios Regarding Explosion Risk Mitigation

    NASA Astrophysics Data System (ADS)

    Vlasin, Nicolae-Ioan; Mihai Pasculescu, Vlad; Florea, Gheorghe-Daniel; Cornel Suvar, Marius

    2016-10-01

    Exploration in order to discover new deposits of natural gas, upgrading techniques to exploit these resources and new ways to convert the heat capacity of these gases into industrial usable energy is the research areas of great interest around the globe. But all activities involving the handling of natural gas (exploitation, transport, combustion) are subjected to the same type of risk: the risk to explosion. Experiments carried out physical scenarios to determine ways to reduce this risk can be extremely costly, requiring suitable premises, equipment and apparatus, manpower, time and, not least, presenting the risk of personnel injury. Taking in account the above mentioned, the present paper deals with the possibility of studying the scenarios of gas explosion type events in virtual domain, exemplifying by performing a computer simulation of a stoichiometric air - methane explosion (methane is the main component of natural gas). The advantages of computer-assisted imply are the possibility of using complex virtual geometries of any form as the area of deployment phenomenon, the use of the same geometry for an infinite number of settings of initial parameters as input, total elimination the risk of personnel injury, decrease the execution time etc. Although computer simulations are hardware resources consuming and require specialized personnel to use the CFD (Computational Fluid Dynamics) techniques, the costs and risks associated with these methods are greatly diminished, presenting, in the same time, a major benefit in terms of execution time.

  15. 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.

  16. 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.

  17. 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

  18. 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)

  19. 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)

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

    PubMed

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

    2008-06-07

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

  1. 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.

  2. [Comparison study between biological vision and computer vision].

    PubMed

    Liu, W; Yuan, X G; Yang, C X; Liu, Z Q; Wang, R

    2001-08-01

    The development and bearing of biology vision in structure and mechanism were discussed, especially on the aspects including anatomical structure of biological vision, tentative classification of reception field, parallel processing of visual information, feedback and conformity effect of visual cortical, and so on. The new advance in the field was introduced through the study of the morphology of biological vision. Besides, comparison between biological vision and computer vision was made, and their similarities and differences were pointed out.

  3. Contact angle hysteresis on randomly rough surfaces: a computational study.

    PubMed

    David, Robert; Neumann, A Wilhelm

    2013-04-09

    Wetting is important in many applications, and the solid surfaces being wet invariably feature some amount of surface roughness. A free energy-based computational simulation is used to study the effect of roughness on wetting and especially contact angle hysteresis. On randomly rough, self-affine surfaces, it is found that hysteresis depends primarily on the value of the Wenzel roughness parameter r, increasing in proportion with r - 1. Micrometer-level roughness causes hysteresis of a few degrees.

  4. 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.

  5. 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…

  6. 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,…

  7. 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,…

  8. 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…

  9. 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.

  10. 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.

  11. 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.

  12. Interfacing biological macromolecules with carbon nanotubes and silicon surfaces: a computer modelling and dynamic simulation study

    NASA Astrophysics Data System (ADS)

    Tatke, S. S.; Renugopalakrishnan, V.; Prabhakaran, M.

    2004-10-01

    Proteins are naturally occurring nanosystems, optimized by the process of evolution. Biotechnology of protein based nanostructures offers vast opportunities to re-engineer and combine them with other nanomaterials for technological applications. Our primary interest is to interface proteins like bacteriorhodopsin (bR) with carbon nanotubes and silicon surfaces for application in storage devices and biosensors. We have carried out extensive computer simulations to study the dynamics of carbon nanotubes and their interaction with proteins. The immobilization of the protein on the carbon nanotubes is carried out by either covalent bonding or aromatic pgr stacking. Our simulation studies reveal the difference between the pgr stacking and covalent bonding.

  13. 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.

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

    PubMed

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

    2016-08-04

    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.

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

    PubMed

    Neuman, Yair; Turney, Peter; Cohen, Yohai

    2012-06-01

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

  16. Computational Studies of Protein-Protein Interface Designs

    NASA Astrophysics Data System (ADS)

    Gaines, Jennifer; O'Hern, Corey; Regan, Lynne

    We implement a hard-sphere model for amino acid structure to study natural and designed protein-protein interfaces. Current computational methods have found limited success in designing novel interfaces and resorted to implementing several rounds of experimental mutation and selection to achieve successful designs. Here, we show that the hard-sphere model can recapitulate the side chain dihedral angle distributions for amino acids at natural protein-protein interfaces. In addition, we calculate the packing fraction in naturally occurring interfaces and find that it is comparable to dense random packing in protein cores. We then evaluate a number of successful and unsuccessful prior computational designs in terms of the number of allowed side chain dihedral angle conformations and the packing fraction of residues at the interface.

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

    PubMed

    Reggia, James A

    2013-08-01

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

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

    PubMed Central

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

    2013-01-01

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

  19. Computer simulation study of hexokinase II from Ehrlich ascites cells.

    PubMed

    Garfinkel, L

    1975-02-21

    A study of the mechanism of hexokinase II from ascites cells the effects of its binding to mitochondrial membranes has been carried out by computer simulation. This is based on experimental data of Kosow and Rose and of Gumaa and McLean, and the theoretical methods of cleveland. For the soluble enzyme the mechanism is random with ternary produce-inhibition complexes; when bound to mitochondria, the mechanism becomes ordered-on, random-off, as the binding of ATP to the free enzymes becomes negligibly slow. The requirements of experimental data for mechanistic studies are discussed.

  20. [Ebstein's anomaly revealed by fetal-placental anasarca. Original case study].

    PubMed

    Hadraoui, Hanaa El; Barkat, Amina

    2016-01-01

    Ebstein's anomaly is a congenital heart defect rarely revealed by fetal-placental anasarca. Our study reports an original case of Ebstein's anomaly diagnosed during fetal-placental anasarca assessment, revealed by antenatal ultrasound, objectifying hydramnios, ascites and pericardial effusion. Echocardiography allowed the identification of Ebstein's disease with significant tricuspid insufficiency, mitral regurgitation (grade 3) and patent ductus arteriosus. The closure of the ductus arteriosus associated with the decrease of pulmonary resistance using optimal ventilation allowed hemodynamic improvement and patient survival.

  1. Terahertz spectra of DNA nucleobase crystals: A joint experimental and computational study.

    PubMed

    Wang, Fang; Zhao, Dongbo; Dong, Hao; Jiang, Ling; Liu, Yunfei; Li, Shuhua

    2017-02-21

    Terahertz (THz) spectra of DNA nucleobase crystals were experimentally studied by terahertz time domain spectroscopy (THz-TDS), Fourier transform infrared spectroscopy (FTIR), and computationally studied by the generalized energy-based fragmentation approach under periodic boundary conditions (denoted as PBC-GEBF). We analyzed the vibrational spectra of solid-state DNA nucleobases and assigned the corresponding vibrational modes to the main peaks in the experimental spectra with the PBC-GEBF results. The computational results were verified to be in good accordance with the experimental data. Harmonic vibrational frequency results revealed that all the vibrational modes belong to collective vibrational modes, which involve complicated mixtures of inter- and intramolecular displacements, somewhere in the vicinity of 0.5-9THz.

  2. Terahertz spectra of DNA nucleobase crystals: A joint experimental and computational study

    NASA Astrophysics Data System (ADS)

    Wang, Fang; Zhao, Dongbo; Dong, Hao; Jiang, Ling; Liu, Yunfei; Li, Shuhua

    2017-05-01

    Terahertz (THz) spectra of DNA nucleobase crystals were experimentally studied by terahertz time domain spectroscopy (THz-TDS), Fourier transform infrared spectroscopy (FTIR), and computationally studied by the generalized energy-based fragmentation approach under periodic boundary conditions (denoted as PBC-GEBF). We analyzed the vibrational spectra of solid-state DNA nucleobases and assigned the corresponding vibrational modes to the main peaks in the experimental spectra with the PBC-GEBF results. The computational results were verified to be in good accordance with the experimental data. Harmonic vibrational frequency results revealed that all the vibrational modes belong to collective vibrational modes, which involve complicated mixtures of inter- and intramolecular displacements, somewhere in the vicinity of 0.5-9 THz.

  3. Pd-Catalyzed N-Arylation of Secondary Acyclic Amides: Catalyst Development, Scope, and Computational Study

    PubMed Central

    Hicks, Jacqueline D.; Hyde, Alan M.; Cuezva, Alberto Martinez; Buchwald, Stephen L.

    2009-01-01

    We report the efficient N-arylation of acyclic secondary amides and related nucleophiles with aryl nonaflates, triflates, and chlorides. This method allows for easy variation of the aromatic component in tertiary aryl amides. A new biaryl phosphine with P-bound 3,5-(bis)trifluoromethylphenyl groups was found to be uniquely effective for this amidation. The critical aspects of the ligand were explored through synthetic, mechanistic, and computational studies. Systematic variation of the ligand revealed the importance of (1) a methoxy group on the aromatic carbon of the “top ring” ortho to the phosphorus and (2) two highly electron-withdrawing P-bound 3,5-(bis)trifluoromethylphenyl groups. Computational studies suggest the electron-deficient nature of the ligand is important in facilitating amide binding to the LPd(II)(Ph)(X) intermediate. PMID:19886610

  4. 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

    2015-01-30

    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.

  5. The mystery of a missing bone: revealing the orbitosphenoid in basal Epicynodontia (Cynodontia, Therapsida) through computed tomography

    NASA Astrophysics Data System (ADS)

    Benoit, Julien; Jasinoski, Sandra C.; Fernandez, Vincent; Abdala, Fernando

    2017-08-01

    The basal non-mammaliaform cynodonts from the late Permian (Lopingian) and Early Triassic are a major source of information for the understanding of the evolutionary origin of mammals. Detailed knowledge of their anatomy is critical for understanding the phylogenetic transition toward mammalness and the paleobiological reconstruction of mammalian precursors. Using micro-computed tomography (μCT), we describe the internal morphology of the interorbital region that includes the rarely fossilized orbitosphenoid elements in four basal cynodonts. These paired bones, which are positioned relatively dorsally in the skull, contribute to the wall of the anterior part of the braincase and form the floor for the olfactory lobes. Unlike procynosuchids and the more basal therapsids in which the orbitosphenoids are well developed, dense, and bear a ventral keel, the basal epicynodonts Cynosaurus, Galesaurus, and Thrinaxodon display cancellous, reduced, and loosely articulated orbitosphenoids, a condition shared with many eucynodonts. The hemi-cylindrical orbitosphenoid from which the mammalian condition is derived re-evolved convergently in traversodontid and some probainognathian cynodonts.

  6. Trends in chemical ecology revealed with a personal computer program for searching data bases of scientific references and abstracts.

    PubMed

    Byers, J A

    1992-09-01

    A compiled program, JCE-REFS.EXE (coded in the QuickBASIC language), for use on IBM-compatible personal computers is described. The program converts a DOS text file of current B-I-T-S (BIOSIS Information Transfer System) or BIOSIS Previews references into a DOS file of citations, including abstracts, in a general style used by scientific journals. The latter file can be imported directly into a word processor or the program can convert the file into a random access data base of the references. The program can search the data base for up to 40 text strings with Boolean logic. Selected references in the data base can be exported as a DOS text file of citations. Using the search facility, articles in theJournal of Chemical Ecology from 1975 to 1991 were searched for certain key words in regard to semiochemicals, taxa, methods, chemical classes, and biological terms to determine trends in usage over the period. Positive trends were statistically significant in the use of the words: semiochemical, allomone, allelochemic, deterrent, repellent, plants, angiosperms, dicots, wind tunnel, olfactometer, electrophysiology, mass spectrometry, ketone, evolution, physiology, herbivore, defense, and receptor. Significant negative trends were found for: pheromone, vertebrates, mammals, Coleoptera, Scolytidae,Dendroctonus, lactone, isomer, and calling.

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

    PubMed

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

    2014-11-11

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

  8. 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

  9. Implications of Ubiquitous Computing for the Social Studies Curriculum

    ERIC Educational Resources Information Center

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

    2004-01-01

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

  10. NMR and computational studies of chiral discrimination by amylose tris(3,5-dimethylphenylcarbamate).

    PubMed

    Ye, Yun K; Bai, Shi; Vyas, Shyam; Wirth, Mary J

    2007-02-08

    Proton NMR and simulations were combined to study the origin of chiral selectivity by a polysaccharide used in a commercial chromatographic stationary phase: amylose tris(3,5-dimethylphenylcarbamate). This material has unusually high enantioselectivity for p-O-tert-butyltyrosine allyl ester, which is activated by the presence of an acid. Proton NMR spectra agreed with the HPLC in showing that the l-enantiomer interacts much more strongly with the polysaccharide and that acidity switches on the selectivity. 2D NOESY spectra revealed which protons of each enantiomer and the polysaccharide were in proximity, and these spectra revealed folding of the l-enantiomer. Computations generated energy-minimized structures for the polysaccharide-enantiomer complexes, independently predicting folding of the l-enantiomer. Molecular dynamics simulations 2 ns in duration, repeated for three different energy-minimized structures, generated pair distribution functions that are in excellent agreement with the 2D NOESY spectra. The modeling studies revealed why acidity switches on chiral selectivity and minimally affects the chromatographic retention time of the unfavored d-enantiomer. The results comprise the first case of a chiral separation by a commercial polysaccharide stationary phase being explained using a combination of 2D NOESY and simulations, providing excellent agreement between experiment and computation and lending detailed molecular insight into enantioselectivity for this system.

  11. Computational study on the properties and structure of methyl lactate.

    PubMed

    Aparicio, Santiago

    2007-05-31

    A theoretical study on the properties and molecular level structure of the very important green solvent methyl lactate is carried out in the gas phase and methanol and water solutions, with the solvent treated both explicitly and as a continuum. Torsional barriers giving rise to different conformers by rotation of the hydroxyl and methyl groups were analyzed using density functional theory (DFT) to establish the most stable conformer both in gas phase and solution. DFT computations on lactate dimers were also done to study short-range features, and the effect of the surrounding solvent on intra- and intermolecular hydrogen bonding was analyzed according to the polarizable continuum model approach. We have also studied lactate/water and lactate/methanol small clusters together with the corresponding binding energies. Moreover, classical molecular dynamics simulations (MD) were carried out to study medium- and large-range effects at lower computational cost. MD simulations at different pressure and temperature conditions on pure lactate were carried out, and mixtures with water and methanol of different compositions were also studied. Structural information, analyzed through the radial distribution functions, together with dynamic aspects of pure and mixed fluids were considered. The intramolecular hydrogen bonding ability of methyl lactate together with the possibility of homo- and hetero-intermolecular association determines the behavior of this molecule in pure fluids or in mixed.

  12. Mechanism of Consistent Gyrus Formation: an Experimental and Computational Study

    NASA Astrophysics Data System (ADS)

    Zhang, Tuo; Razavi, Mir Jalil; Li, Xiao; Chen, Hanbo; Liu, Tianming; Wang, Xianqiao

    2016-11-01

    As a significant type of cerebral cortical convolution pattern, the gyrus is widely preserved across species. Although many hypotheses have been proposed to study the underlying mechanisms of gyrus formation, it is currently still far from clear which factors contribute to the regulation of consistent gyrus formation. In this paper, we employ a joint analysis scheme of experimental data and computational modeling to investigate the fundamental mechanism of gyrus formation. Experimental data on mature human brains and fetal brains show that thicker cortices are consistently found in gyral regions and gyral cortices have higher growth rates. We hypothesize that gyral convolution patterns might stem from heterogeneous regional growth in the cortex. Our computational simulations show that gyral convex patterns may occur in locations where the cortical plate grows faster than the cortex of the brain. Global differential growth can only produce a random gyrification pattern, but it cannot guarantee gyrus formation at certain locations. Based on extensive computational modeling and simulations, it is suggested that a special area in the cerebral cortex with a relatively faster growth speed could consistently engender gyri.

  13. Mechanism of Consistent Gyrus Formation: an Experimental and Computational Study

    PubMed Central

    Zhang, Tuo; Razavi, Mir Jalil; Li, Xiao; Chen, Hanbo; Liu, Tianming; Wang, Xianqiao

    2016-01-01

    As a significant type of cerebral cortical convolution pattern, the gyrus is widely preserved across species. Although many hypotheses have been proposed to study the underlying mechanisms of gyrus formation, it is currently still far from clear which factors contribute to the regulation of consistent gyrus formation. In this paper, we employ a joint analysis scheme of experimental data and computational modeling to investigate the fundamental mechanism of gyrus formation. Experimental data on mature human brains and fetal brains show that thicker cortices are consistently found in gyral regions and gyral cortices have higher growth rates. We hypothesize that gyral convolution patterns might stem from heterogeneous regional growth in the cortex. Our computational simulations show that gyral convex patterns may occur in locations where the cortical plate grows faster than the cortex of the brain. Global differential growth can only produce a random gyrification pattern, but it cannot guarantee gyrus formation at certain locations. Based on extensive computational modeling and simulations, it is suggested that a special area in the cerebral cortex with a relatively faster growth speed could consistently engender gyri. PMID:27853245

  14. Fragmentation of 3-hydroxyflavone; a computational and mass spectrometric study.

    PubMed

    Lewars, Errol G; March, Raymond E

    2007-01-01

    In a recent study of the collision-induced dissociation of protonated and deprotonated molecules of 3-, 5-, 6-, 7-, 2'-, 3'- and 4'-hydroxyflavone, it was observed that the ratio, gamma, of the propensities for cross-ring cleavage (CRC) to ring opening (RO) varied by a factor of 660, i.e., from 0.014:1 (for deprotonated 3-hydroxyflavone) to 9.27:1 (for deprotonated 5-hydroxyflavone). An explanation for the variation of gamma was presented in terms of experimental NMR (13)C and (1)H spectra modified by computation. Deprotonated 3-hydroxyflavone exhibited the highest ion signal intensity for fragmentation following RO relative to that for CRC in that gamma = 0.014:1. Because no chemical computations of the fragmentation of protonated and deprotonated monohydroxyflavone molecules have been carried out thus far, the basis on which fragmentation mechanisms for deprotonated 3-hydroxyflavone have been proposed is principally chemical intuition. The energy states of product ions formed in the fragmentation of deprotonated 3-hydroxyflavone molecules were computed by the CBS-4M method implemented in Gaussian 03. The overly demanding calculations needed to handle diradicals reliably and directly were circumvented by a process in which each of the bond-breaking reactions was approximated by a process that gave two monoradicals. Bond energies were calculated, with one exception, from the approximation reactions as the energy of products minus the energy of reactants.

  15. [Study of dietary habits and its relation with cardiovascular disease risk factors with help of specialization computers programme].

    PubMed

    Kontsevaia, A V; Eganian, R A; Kalinina, A M; Romanenko, T S; Omel'ianenko, M G

    2008-01-01

    Specialization computers programme investigation of dietary risk factors in organized population of universities employers revealed high abundance of this behavior chronic disease risk factors: disturbances of dietary regimen, high salt intake, high intake of saturated fats (butter) and eggs. The study showed significant relationship between abdominal obesity and high blood pressure, total plasma cholesterol also was significantly higher in persons with abdominal obesity.

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

    DOE PAGES

    Lin, Yen -Lin; Meng, Yilin; Huang, Lei; ...

    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

  17. 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.

  18. Tensor Analysis Reveals Distinct Population Structure that Parallels the Different Computational Roles of Areas M1 and V1.

    PubMed

    Seely, Jeffrey S; Kaufman, Matthew T; Ryu, Stephen I; Shenoy, Krishna V; Cunningham, John P; Churchland, Mark M

    2016-11-01

    Cortical firing rates frequently display elaborate and heterogeneous temporal structure. One often wishes to compute quantitative summaries of such structure-a basic example is the frequency spectrum-and compare with model-based predictions. The advent of large-scale population recordings affords the opportunity to do so in new ways, with the hope of distinguishing between potential explanations for why responses vary with time. We introduce a method that assesses a basic but previously unexplored form of population-level structure: when data contain responses across multiple neurons, conditions, and times, they are naturally expressed as a third-order tensor. We examined tensor structure for multiple datasets from primary visual cortex (V1) and primary motor cortex (M1). All V1 datasets were 'simplest' (there were relatively few degrees of freedom) along the neuron mode, while all M1 datasets were simplest along the condition mode. These differences could not be inferred from surface-level response features. Formal considerations suggest why tensor structure might differ across modes. For idealized linear models, structure is simplest across the neuron mode when responses reflect external variables, and simplest across the condition mode when responses reflect population dynamics. This same pattern was present for existing models that seek to explain motor cortex responses. Critically, only dynamical models displayed tensor structure that agreed with the empirical M1 data. These results illustrate that tensor structure is a basic feature of the data. For M1 the tensor structure was compatible with only a subset of existing models.

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

    PubMed

    Tan, Rui Zhen; Chiam, Keng-Hwee

    2014-01-01

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

  20. Tensor Analysis Reveals Distinct Population Structure that Parallels the Different Computational Roles of Areas M1 and V1

    PubMed Central

    Ryu, Stephen I.; Shenoy, Krishna V.; Cunningham, John P.; Churchland, Mark M.

    2016-01-01

    Cortical firing rates frequently display elaborate and heterogeneous temporal structure. One often wishes to compute quantitative summaries of such structure—a basic example is the frequency spectrum—and compare with model-based predictions. The advent of large-scale population recordings affords the opportunity to do so in new ways, with the hope of distinguishing between potential explanations for why responses vary with time. We introduce a method that assesses a basic but previously unexplored form of population-level structure: when data contain responses across multiple neurons, conditions, and times, they are naturally expressed as a third-order tensor. We examined tensor structure for multiple datasets from primary visual cortex (V1) and primary motor cortex (M1). All V1 datasets were ‘simplest’ (there were relatively few degrees of freedom) along the neuron mode, while all M1 datasets were simplest along the condition mode. These differences could not be inferred from surface-level response features. Formal considerations suggest why tensor structure might differ across modes. For idealized linear models, structure is simplest across the neuron mode when responses reflect external variables, and simplest across the condition mode when responses reflect population dynamics. This same pattern was present for existing models that seek to explain motor cortex responses. Critically, only dynamical models displayed tensor structure that agreed with the empirical M1 data. These results illustrate that tensor structure is a basic feature of the data. For M1 the tensor structure was compatible with only a subset of existing models. PMID:27814353

  1. 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

  2. 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.

  3. 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.

  4. Pentazole-Based Energetic Ionic Liquids: A Computational Study (Postprint)

    DTIC Science & Technology

    2007-01-09

    Postprint) 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Ian S.O. Pimienta , Sherrie Elzey, Mark S. Gordon (Iowa State University...A Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std. 239.18 Pentazole-Based Energetic Ionic Liquids: A Computational Study Ian S. O. Pimienta ...2007 Pimienta et al. fully optimized with second-order Møller-Plesset perturbation theory (MP2),32,33 using the restricted Hartree-Fock (RHF)34

  5. 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.

  6. Computational Fluid Dynamics Study for Optimization of a Fin Design

    DTIC Science & Technology

    2005-09-28

    Computational Fluid Dynamics Study for Optimization of a Fin Design 5b. GRANT NUMBER 64-6093-A-5 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR( S ) 5d. PROJECT...NUMBER Ravi Ramamurti and William C. Sandberg 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME( S ) AND ADDRESS(ES) 8. PERFORMING...MONITORING AGENCY NAME( S ) AND ADDRESS(ES) 10. SPONSOR / MONITOR’S ACRONYM( S ) 11. SPONSOR I MONITOR’S REPORT NUMBER( S ) 12. DISTRIBUTION / AVAILABILITY

  7. 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…

  8. 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…

  9. 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…

  10. 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'…

  11. 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.

  12. 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.

  13. Advances in the computational study of language acquisition.

    PubMed

    Brent, M R

    1996-01-01

    This paper provides a tutorial introduction to computational studies of how children learn their native languages. Its aim is to make recent advances accessible to the broader research community, and to place them in the context of current theoretical issues. The first section locates computational studies and behavioral studies within a common theoretical framework. The next two sections review two papers that appear in this volume: one on learning the meanings of words and one or learning the sounds of words. The following section highlights an idea which emerges independently in these two papers and which I have dubbed autonomous bootstrapping. Classical bootstrapping hypotheses propose that children begin to get a toc-hold in a particular linguistic domain, such as syntax, by exploiting information from another domain, such as semantics. Autonomous bootstrapping complements the cross-domain acquisition strategies of classical bootstrapping with strategies that apply within a single domain. Autonomous bootstrapping strategies work by representing partial and/or uncertain linguistic knowledge and using it to analyze the input. The next two sections review two more more contributions to this special issue: one on learning word meanings via selectional preferences and one on algorithms for setting grammatical parameters. The final section suggests directions for future research.

  14. 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.

  15. 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.

  16. 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…

  17. 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…

  18. 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…

  19. 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…

  20. Computed tomographic study of hormone-secreting microadenomas

    SciTech Connect

    Hemminghytt, S.; Kalkhoff, R.K.; Daniels, D.L.; Williams, A.L.; Grogan, J.P.; Haughton, V.M.

    1983-01-01

    A review was made of the computed tomographic (CT) studies of 33 patients with hormone-secreting microadenomas that had been verified by transsphenoidal surgery and endocrinologic evaluation. In previous studies in small series of patients, the CT appearance of pituitary microadenomas has been reported as hypodense, isodense, and hyperdense. In this study, CT showed a region of diminished enhancement and ususally an enlarged pituitary gland in cases of prolactin-secreting adenomas. HGH- or ACTH-secreting adenomas were less consistently hypodense. It is concluded that hypodensity and enlargement in the pituitary gland are the most useful criteria for identification of microadenomas. Some technical factors that may affect the CT appearance of microadenomas and lead to conflicting reports are discussed.

  1. Using computer simulations to study relativistic heavy ion collisions

    NASA Astrophysics Data System (ADS)

    Murray, Joelle Lynn

    1998-12-01

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

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

    ERIC Educational Resources Information Center

    Acikalin, Mehmet

    2010-01-01

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

  3. 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…

  4. 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…

  5. 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.

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

    PubMed

    Liu, H; Aono, H

    2009-03-01

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

  7. 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.

  8. The electronic structure of pyracene: a spectroscopic and computational study.

    PubMed

    Auerswald, Johannes; Engels, Bernd; Fischer, Ingo; Gerbich, Thiemo; Herterich, Jörg; Krueger, Anke; Lang, Melanie; Schmitt, Hans-Christian; Schon, Christof; Walter, Christof

    2013-06-07

    We report a synthetic, spectroscopic and computational study of the polycyclic aromatic molecule pyracene, which contains aliphatic five-membered rings annealed to a naphthalene chromophore. An improved route to synthesize the compound is described. Gas-phase IR and solid-state Raman spectra agree with a ground-state D2h structure. The electronically excited S1 A(1)B3u state has been studied by resonance-enhanced multiphoton ionisation. An adiabatic excitation energy T0 = 30,798 cm(-1) (3.818 eV) was determined. SCS-ADC(2) calculations found a D2h minimum energy structure of the S1 state and yielded an excitation energy of +3.98 eV, including correction for zero point vibrational energy. The spectrum shows a rich low-frequency vibrational structure that can be assigned to the overtones of out-of-plane deformation modes of the five-membered rings by comparison with computations. The appearance of these modes as well as the frequency reduction in the excited state indicate that the potential in the S1 state is very flat. At higher excess energies most bands can be assigned to fundamentals, overtones and combination bands of either totally symmetric ag modes or of b2g modes that appear due to vibronic coupling. Lifetimes between 43 ns and 76 ns were measured for a number of vibronic bands. For the S2 state an equilibrium geometry with a non-planar carbon framework was computed. In addition a signal from the pyracene dimer was present. The spectrum shows several broad and structureless transitions. The origin band has a maximum at around 329 nm (30,400 cm(-1)). Again lifetimes between 60 ns and 70 ns were found. The dimer ion signal rises within less than 10 ps. Computations show that a crossed geometry with the long axis of one unit aligned with the short axis of the second constitutes the most stable structure. The broadening of the bands is most likely caused by excimer formation.

  9. 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)

  10. 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…

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

    PubMed

    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.

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

    PubMed Central

    Schultheiss, Oliver C.

    2013-01-01

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

  13. Computational and experimental studies on large scale solar heating

    NASA Astrophysics Data System (ADS)

    Peltola, S.

    The experimental part of the work deals mainly with the experiences gained from the Kerava Solar Village (KSV) but some additional remarks are presented from international studies. The measured thermal performance of the KSV heating system indicates considerably poorer performance than original design values. Reasons for this are studied by means of computational analyses. Fundamental problems with KSV systems was too small storage size with respect both to installed collector area and connected load. From an operational point of view, the frequent heat pump failures were the most severe problem. Computational tools for large solar heating system design and analyses are presented. Numerical models developed in this work, the KERCONT and SUPERSOL, are validated with measured performance from the KSV indicating reasonably good accuracy. The tools have been applied for detecting KSV heating system problems and for finding solutions for them as well as for re-design of the system. More general analyses are presented on the applicability of the KSV system principle in other load sizes and locations. A new approach for preliminary studies on Central Solar Heating Plants with Seasonal Storage (CSHPSS) is described. The analytical model, SOLCHIPS, is shown to be a very effective tool for pre-design studies. The validity of SOLCHIPS approach is studied by comparing the results against results from validated numerical model, MINSUN. In the last part of the work, preliminary results from numerical simulations of summer time district solar heating with short term storage are presented. According to the analyses, these systems should provide heat at or below the cost achievable with seasonal storage systems.

  14. Assessing stapes piston position using computed tomography: a cadaveric study.

    PubMed

    Hahn, Yoav; Diaz, Rodney; Hartman, Jonathan; Bobinski, Matthew; Brodie, Hilary

    2009-02-01

    Temporal bone computed tomographic (CT) scanning in the postoperative stapedotomy patient is inaccurate in assessing stapes piston position within the vestibule. Poststapedotomy patients that have persistent vertigo may undergo CT scanning to assess the position of the stapes piston within the vestibule to rule out overly deep insertion. Vertigo is a recognized complication of the deep piston, and CT evaluation is often recommended. The accuracy of CT scan in this setting is unestablished. Stapedotomy was performed on 12 cadaver ears, and stainless steel McGee pistons were placed. The cadaver heads were then scanned using a fine-cut temporal bone protocol. Temporal bone dissection was performed with microscopic measurement of the piston depth in the vestibule. These values were compared with depth of intravestibular penetration measured on CT scan by 4 independent measurements. The intravestibular penetration as assessed by computed tomography was consistently greater than the value found on cadaveric anatomic dissection. The radiographic bias was greater when piston location within the vestibule was shallower. The axial CT scan measurement was 0.53 mm greater, on average, than the anatomic measurement. On average, the coronal CT measurement was 0.68 mm greater than the anatomic measurement. The degree of overestimation of penetration, however, was highly inconsistent. Standard temporal bone CT scan is neither an accurate nor precise examination of stapes piston depth within the vestibule. We found that CT measurement consistently overstated intravestibular piston depth. Computed tomography is not a useful study in the evaluation of piston depth for poststapedectomy vertigo and is of limited value in this setting.

  15. 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.

  16. 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.

  17. 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…

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

    ERIC Educational Resources Information Center

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

    2016-01-01

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

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

    ERIC Educational Resources Information Center

    Eignor, Daniel R.; And Others

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

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

    ERIC Educational Resources Information Center

    Ben-Jacob, Marion G.

    2005-01-01

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

  1. 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…

  2. 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…

  3. Cysteamine supplementation revealed detrimental effect on cryosurvival of buffalo sperm based on computer-assisted semen analysis and oxidative parameters.

    PubMed

    Swami, Dheer Singh; Kumar, Pradeep; Malik, R K; Saini, Monika; Kumar, Dharmendra; Jan, M H

    2017-02-01

    The aim of this study was to investigate the effect of addition of cysteamine to the semen extender on post-thaw semen quality. A total of 30 ejaculates were collected from six bulls. Each ejaculate was divided into five equal parts and diluted to final concentration of 80 million sperms/mL using Optixcell(®)(IMV, France) semen extender supplemented with different concentrations of cysteamine (0, 0.75, 1.25, 2.5 and 5mM) and cryopreserved. In the frozen-thawed samples, the VAP, VSL, VCL ALH and sperm motility of control samples was greater (P<0.05) than cysteamine treated samples. The sperm abnormality and malondialdehyde (MDA) concentration were found highest in 5mM cysteamine treated samples. The cysteamine treated samples travelled significantly less distance in cervical mucus as compared to control. Further, cysteamine decreased acrosomal integrity of sperm. In incubation test, control samples showed better sperm motility as compared to treatment groups. Further, cysteamine supplementation decreased the total antioxidants and increased the MDA concentration of sperm. From the study, we hypothesized that cysteamine cannot stimulate synthesis of glutathione (GSH) intracellularly in sperm to combat free radicals because during the maturation, sperm lost its cytoplasm which is necessary for biochemical reaction in which cysteamine reacts with cystine to form a mixed disulfide which taken up by cells and split into cysteine in the cytoplasm. Synthesis of GSH depends on the availability of cysteine. In conclusion, the results of our study strongly emphasize that cysteamine would not be a suitable additive in extender for freezing buffalo bull semen.

  4. 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.

  5. Conversion of eugenol to methyleugenol: Computational study and experimental

    NASA Astrophysics Data System (ADS)

    Kurniawan, Muhammad Arsyik; Matsjeh, Sabirin; Triono, Sugeng

    2017-03-01

    This study provides comprehensive benchmark calculations for the computational study and experimental research on conversion of eugenol to methyleugenol with different pathway of the transition state compounds. First-principle calculation (DFT) were used to generate the structure optimization, energies of species. The calculation parameter are used to predict reactant, product and transition state species as guide to predict the experimental development of chemical characterization method including NMR and IR. The calculation showed significant effect of NaOH in formation of transition state in reaction. Experimentally, the step was nucleophilic substitution reaction of eugenolate ion to dimethylsulfate compound, it was obtained methyleugenol compound with purity of 90.73 %, which analyzed by Infrared and H-NMR spectrometer.

  6. Photoelectron spectroscopic and computational study of hydrated pyrimidine anions.

    PubMed

    Kelly, John T; Xu, Shoujun; Graham, Jacob; Nilles, J Michael; Radisic, Dunja; Buonaugurio, Angela M; Bowen, Kit H; Hammer, Nathan I; Tschumper, Gregory S

    2014-12-26

    The stabilization of the pyrimidine anion by the addition of water molecules is studied experimentally using photoelectron spectroscopy of mass-selected hydrated pyrimidine clusters and computationally using quantum-mechanical electronic structure theory. Although the pyrimidine molecular anion is not observed experimentally, the addition of a single water molecule is sufficient to impart a positive electron affinity. The sequential hydration data have been used to extrapolate to -0.22 eV for the electron affinity of neutral pyrimidine, which agrees very well with previous observations. These results for pyrimidine are consistent with previous studies of the hydrated cluster anions of uridine, cytidine, thymine, adenine, uracil, and naphthalene. This commonality suggests a universal effect of sequential hydration on the electron affinity of similar molecules.

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

    PubMed

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

    2008-01-01

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

  8. Alcohol assessment using wireless handheld computers: a pilot study.

    PubMed

    Bernhardt, Jay M; Usdan, Stuart; Mays, Darren; Arriola, Kimberly Jacob; Martin, Ryan J; Cremeens, Jennifer; McGill, Tia; Weitzel, Jessica Aungst

    2007-12-01

    The present study sought to test the feasibility of measuring quantity and frequency of self-reported alcohol consumption among college students using the Handheld Assisted Network Diary (HAND) by comparing results to a retrospective Timeline Followback (TLFB). A total of 40 undergraduate college students completed a HAND assessment during the two-week study period and completed a TLFB at follow-up. The HAND recorded similar levels of alcohol consumption compared to the TLFB. There were no significant differences in overall alcohol consumption, drinks per drinking day, or heavy drinking days between the two methods of assessment. Handheld computers may represent a useful tool for assessing daily alcohol use among college students.

  9. Theoretical and computational studies of organometallic reactions: successful or not?

    PubMed

    Sakaki, Shigeyoshi; Ohnishi, Yu-Ya; Sato, Hirofumi

    2010-03-01

    Theoretical and computational methods are powerful in studying transition metal complexes. Our theoretical studies of C-H sigma-bond activation of benzene by Pd(II)-formate complex and that of methane by Ti(IV)-imido complex successfully disclosed that these reactions are understood to undergo heterolytic sigma-bond activation and the driving force is the formation of strong O-H and N-H bonds in the former and the latter, respectively. Orbital interactions are considerably different from those of sigma-bond activation by oxidative addition. The transmetallation, which is a key process in the cross-coupling reaction, is understood to be heterolytic sigma-bond activation. Our theoretical study clarified how to accelerate this transmetallation. Also, we wish to discuss weak points in theoretical and computational studies of large systems including transition metal elements, such as the necessity to incorporate solvation effect and to present quantitatively correct numerical results. The importance of solvation effects is discussed in the oxidative addition of methyliodide to Pt(II) complex which occurs in a way similar to an S(N)2 substitution. To apply the CCSD(T) (coupled cluster singles and doubles with perturbative triples correction) method, which is the gold standard of electronic structure theory, to large system, we need to reduce the size of the system by employing a small model. But, such modeling induces neglects of electronic and steric effects of substituents which are replaced in the small model. Frontier-orbital-consistent quantum-capping potential (FOC-QCP) was recently proposed by our group to incorporate the electronic effects of the substituents neglected in the modeling. The CCSD(T) calculation with the FOC-QCP was successfully applied to large systems including transition metal elements.

  10. 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

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

    PubMed

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

    2013-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  13. Payload/orbiter contamination control requirement study: Computer interface

    NASA Technical Reports Server (NTRS)

    Bareiss, L. E.; Hooper, V. W.; Ress, E. B.; Strange, D. A.

    1976-01-01

    A preliminary assessment of the computer interface requirements of the Spacelab configuration contamination computer model was conducted to determine the compatibility of the program, as presently formatted, with the computer facilities at MSFC. The necessary Spacelab model modifications are pointed out. The MSFC computer facilities and their future plans are described, and characteristics of the various computers as to availability and suitability for processing the contamination program are discussed. A listing of the CDC 6000 series and UNIVAC 1108 characteristics is presented so that programming requirements can be compared directly and differences noted.

  14. Space Shuttle flight crew/computer interface simulation studies.

    NASA Technical Reports Server (NTRS)

    Callihan, J. C.; Rybarczyk, D. T.

    1972-01-01

    An approach to achieving an optimized set of crew/computer interface requirements on the Space Shuttle program is described. It consists of defining the mission phases and crew timelines, developing a functional description of the crew/computer interface displays and controls software, conducting real-time simulations using pilot evaluation of the interface displays and controls, and developing a set of crew/computer functional requirements specifications. The simulator is a two-man crew station which includes three CRTs with keyboards for simulating the crew/computer interface. The programs simulate the mission phases and the flight hardware, including the flight computer and CRT displays.

  15. 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

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

    PubMed

    Timmins, Amy; de Visser, Sam P

    2015-01-01

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

  17. Computational micromagnetic study of particulate media hysteresis and recording

    NASA Astrophysics Data System (ADS)

    Seberino, Christian

    2000-11-01

    A description of the micromagnetic theory, algorithms, computer software and computer hardware built and used to study particulate media particles, hysteresis and recording is first provided. This includes a derivation and analysis of the modified version of the Fast Multipole Method used in this dissertation. Results will then be presented on particulate media particle nucleation field dependence on particle shape, particle aspect ratio, ferromagnetic exchange energy and external magnetic field angle. Results on the discretization necessary to accurately model a particle will also be provided. The reversal mode of a particle will be simulated and analyzed. Simulated longitudinal and transverse hysteresis loops will be presented. Results will also be presented on particulate media coercivity and squareness dependence on volumetric packing fraction. Simulated recorded transition results will be given as well as total power spectra results for AC and DC erased particulate media. Numerical results will be compared to experimental data and analytical theories. Advice is provided on how to build a personal supercomputer like the one used in the numerical experiments of this dissertation.

  18. 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

  19. 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.

  20. Host immunity and pathogen diversity: A computational study.

    PubMed

    Aquino, Tomás; Nunes, Ana

    2016-01-01

    The distinctive features of human influenza A phylogeny have inspired many mathematical and computational studies of viral infections spreading in a host population, but our understanding of the mechanisms that shape the coupled evolution of host immunity, disease incidence and viral antigenic properties is far from complete. In this paper we explore the epidemiology and the phylogeny of a rapidly mutating pathogen in a host population with a weak immune response, that allows re-infection by the same strain and provides little cross-immunity. We find that mutation generates explosive diversity and that, as diversity grows, the system is driven to a very high prevalence level. This is in stark contrast with the behavior of similar models where mutation gives rise to a large epidemic followed by disease extinction, under the assumption that infection with a strain provides lifelong immunity. For low mutation rates, the behavior of the system shows the main qualitative features of influenza evolution. Our results highlight the importance of heterogeneity in the human immune response for understanding influenza A phenomenology. They are meant as a first step toward computationally affordable, individual based models including more complex host-pathogen interactions.

  1. A computational study of Al/Si ordering in cordierite

    NASA Astrophysics Data System (ADS)

    Thayaparam, S.; Heine, V.; Dove, M. T.; Hammonds, K. D.

    1996-03-01

    The ordering of Al and Si in Mg cordierite Mg2Al4Si5O18 is considered using computer simulation. First the enthalpy of interaction J ij between sites is derived by computer modelling 101 different Al/Si configurations and analysing their energies. They are compared with similar results for three other minerals and with ab initio calculations to assess the whole approach. Secondly the ordering process is studied using Monte Carlo simulation applied to the J ij . The ordering phase transition temperature T c is found as 1800°C in reasonable agreement with the experimental estimate of 1450° C. These are much lower than the estimate T c(ABW)≈7600°C obtained from Bragg-Williams theory. Strong short-range order sets in below T c(ABW), and the reasons for much lower temperature T c of long-range ordering are discussed. Strong short-range also sets in very rapidly in a simulated anneal, in agreement with experiment. Thirdly an attempt is made to compare our calculated enthalpies directly with the results of NMR and calorimetry experiments, not completely successfully. A free energy ΔG≈4.6 eV for the activation barrier for ordering is suggested.

  2. 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.

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

    PubMed

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

    2014-06-14

    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.

  4. 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.

  5. Host immunity and pathogen diversity: A computational study

    PubMed Central

    Aquino, Tomás; Nunes, Ana

    2016-01-01

    ABSTRACT The distinctive features of human influenza A phylogeny have inspired many mathematical and computational studies of viral infections spreading in a host population, but our understanding of the mechanisms that shape the coupled evolution of host immunity, disease incidence and viral antigenic properties is far from complete. In this paper we explore the epidemiology and the phylogeny of a rapidly mutating pathogen in a host population with a weak immune response, that allows re-infection by the same strain and provides little cross-immunity. We find that mutation generates explosive diversity and that, as diversity grows, the system is driven to a very high prevalence level. This is in stark contrast with the behavior of similar models where mutation gives rise to a large epidemic followed by disease extinction, under the assumption that infection with a strain provides lifelong immunity. For low mutation rates, the behavior of the system shows the main qualitative features of influenza evolution. Our results highlight the importance of heterogeneity in the human immune response for understanding influenza A phenomenology. They are meant as a first step toward computationally affordable, individual based models including more complex host-pathogen interactions. PMID:26836775

  6. Gastric flow and mixing studied using computer simulation.

    PubMed Central

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

    2004-01-01

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

  7. A study of kinematic cues and anticipatory performance in tennis using computational manipulation and computer graphics.

    PubMed

    Ida, Hirofumi; Fukuhara, Kazunobu; Kusubori, Seiji; Ishii, Motonobu

    2011-09-01

    Computer graphics of digital human models can be used to display human motions as visual stimuli. This study presents our technique for manipulating human motion with a forward kinematics calculation without violating anatomical constraints. A motion modulation of the upper extremity was conducted by proportionally modulating the anatomical joint angular velocity calculated by motion analysis. The effect of this manipulation was examined in a tennis situation--that is, the receiver's performance of predicting ball direction when viewing a digital model of the server's motion derived by modulating the angular velocities of the forearm or that of the elbow during the forward swing. The results showed that the faster the server's forearm pronated, the more the receiver's anticipation of the ball direction tended to the left side of the serve box. In contrast, the faster the server's elbow extended, the more the receiver's anticipation of the ball direction tended to the right. This suggests that tennis players are sensitive to the motion modulation of their opponent's racket-arm.

  8. Revealing the electrophilicity of N-Ac indoles with FeCl3: a mechanistic study.

    PubMed

    Beaud, Rodolphe; Nandi, Raj Kumar; Perez-Luna, Alejandro; Guillot, Régis; Gori, Didier; Kouklovsky, Cyrille; Ghermani, Nour-Eddine; Gandon, Vincent; Vincent, Guillaume

    2017-05-30

    Herein, we report a mechanistic exploration of the unusual FeCl3-mediated hydroarylation of N-Ac indoles. Electron density topology analysis of a crystal, in situ IR monitoring, Hammett and Taft studies as well as DFT computations allowed us to determine that activation of acetyl with FeCl3 and of the C2[double bond, length as m-dash]C3 bond with a proton is involved.

  9. 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

  10. 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.

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

    PubMed Central

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

    2015-01-01

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

  12. Computational study of missense mutations in phenylalanine hydroxylase.

    PubMed

    Réblová, Kamila; Kulhánek, Petr; Fajkusová, Lenka

    2015-04-01

    Hyperphenylalaninemia (HPA) is one of the most common metabolic disorders. HPA, which is transmitted by an autosomal recessive mode of inheritance, is caused by mutations of the phenylalanine hydroxylase gene. Most mutations are missense and lead to reduced protein stability and/or impaired catalytic function. The impact of such mutations varies, ranging from classical phenylketonuria (PKU), mild PKU, to non-PKU HPA phenotypes. Despite the fact that HPA is a monogenic disease, clinical data show that one PKU genotype can be associated with more in vivo phenotypes, which indicates the role of other (still unknown) factors. To better understand the phenotype-genotype relationships, we analyzed computationally the impact of missense mutations in homozygotes stored in the BIOPKU database. A total of 34 selected homozygous genotypes was divided into two main groups according to their phenotypes: (A) genotypes leading to non-PKU HPA or combined phenotype non-PKU HPA/mild PKU and (B) genotypes leading to classical PKU, mild PKU or combined phenotype mild PKU/classical PKU. Combining in silico analysis and molecular dynamics simulations (in total 3 μs) we described the structural impact of the mutations, which allowed us to separate 32 out of 34 mutations between groups A and B. Testing the simulation conditions revealed that the outcome of mutant simulations can be modulated by the ionic strength. We also employed programs SNPs3D, Polyphen-2, and SIFT but based on the predictions performed we were not able to discriminate mutations with mild and severe PKU phenotypes.

  13. 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…

  14. Attitudes toward Computers: A Study of Post-Secondary Students in Singapore

    ERIC Educational Resources Information Center

    Teo, Timothy

    2006-01-01

    Research has found that computer attitudes not only play an influential role in determining the extent to which students accept the computer as a learning tool but also future behaviours towards the computer such as using it for further study and vocational purposes. A sample of 183 post-secondary students was assessed for their computer attitudes…

  15. A Comparative Study of Teacher Candidates Attitudes Towards Computing and IT in North Cyprus

    ERIC Educational Resources Information Center

    Bekirogullari, Zaferi; Paralik, Ceren; Huseyin, Gulsen

    2007-01-01

    This study aims to measure the attitudes of the freshman year students at Pre-School Teaching, Primary School, Psychological Consulting and Computing and Computing and Education Technologies Teaching Departments in Near East University, Ataturk Education Faculty towards computers. Usage of computing and IT is an essential factor in human life…

  16. 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.

  17. 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.

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

    NASA Astrophysics Data System (ADS)

    Newby, Josh; Nesheiwat, Jackleen

    2016-06-01

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

  19. 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

  20. A computational study of carbon dioxide adsorption on solid boron.

    PubMed

    Sun, Qiao; Wang, Meng; Li, Zhen; Du, Aijun; Searles, Debra J

    2014-07-07

    Capturing and sequestering carbon dioxide (CO2) can provide a route to partial mitigation of climate change associated with anthropogenic CO2 emissions. Here we report a comprehensive theoretical study of CO2 adsorption on two phases of boron, α-B12 and γ-B28. The theoretical results demonstrate that the electron deficient boron materials, such as α-B12 and γ-B28, can bond strongly with CO2 due to Lewis acid-base interactions because the electron density is higher on their surfaces. In order to evaluate the capacity of these boron materials for CO2 capture, we also performed calculations with various degrees of CO2 coverage. The computational results indicate CO2 capture on the boron phases is a kinetically and thermodynamically feasible process, and therefore from this perspective these boron materials are predicted to be good candidates for CO2 capture.

  1. Computational study of radiation doses at UNLV accelerator facility

    NASA Astrophysics Data System (ADS)

    Hodges, Matthew; Barzilov, Alexander; Chen, Yi-Tung; Lowe, Daniel

    2017-09-01

    A Varian K15 electron linear accelerator (linac) has been considered for installation at University of Nevada, Las Vegas (UNLV). Before experiments can be performed, it is necessary to evaluate the photon and neutron spectra as generated by the linac, as well as the resulting dose rates within the accelerator facility. A computational study using MCNPX was performed to characterize the source terms for the bremsstrahlung converter. The 15 MeV electron beam available in the linac is above the photoneutron threshold energy for several materials in the linac assembly, and as a result, neutrons must be accounted for. The angular and energy distributions for bremsstrahlung flux generated by the interaction of the 15 MeV electron beam with the linac target were determined. This source term was used in conjunction with the K15 collimators to determine the dose rates within the facility.

  2. 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.

  3. A Computational Study of the Growth of Hexagonal Ice

    NASA Astrophysics Data System (ADS)

    Fulford, Maxwell; Salvalaglio, Matteo; Parrinello, Michele; Molteni, Carla

    Hexagonal ice (Ih) has two distinct crystallographic surfaces; a basal and prism surface. At low vapour pressures, Ih forms thin plates and elongated prisms, depending on the temperature. The macroscopic shape depends on the relative rate of growth of the basal and prism surfaces. The aim of our research is to estimate the relative rate of growth of the two surfaces for a range of temperatures and ultimately predict the shape of Ih, using computer simulations. Our simulations show the well-know phenomenon that the surface of ice lowers its interfacial free energy by forming a stable quasi-liquid layer (QLL). The QLL mediates crystal growth and has a thickness which varies with temperature and crystallographic surface. We use a combination of Molecular Dynamics and Metadynamics to study how the interfacial structure at the ice/quasi-liquid and quasi-liquid/vapour interfaces influence the adsorption potential, surface transport properties and growth shape..

  4. 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.

  5. 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.

  6. Patterned corneal collagen crosslinking for astigmatism: Computational modeling study

    PubMed Central

    Seven, Ibrahim; Roy, Abhijit Sinha; Dupps, William J.

    2014-01-01

    PURPOSE To test the hypothesis that spatially selective corneal stromal stiffening can alter corneal astigmatism and assess the effects of treatment orientation, pattern, and material model complexity in computational models using patient-specific geometries. SETTING Cornea and Refractive Surgery Service, Academic Eye Institute, Cleveland, Ohio, USA. DESIGN Computational modeling study. METHODS Three-dimensional corneal geometries from 10 patients with corneal astigmatism were exported from a clinical tomography system (Pentacam). Corneoscleral finite element models of each eye were generated. Four candidate treatment patterns were simulated, and the effects of treatment orientation and magnitude of stiffening on anterior curvature and aberrations were studied. The effect of material model complexity on simulated outcomes was also assessed. RESULTS Pretreatment anterior corneal astigmatism ranged from 1.22 to 3.92 diopters (D) in a series that included regular and irregular astigmatic patterns. All simulated treatment patterns oriented on the flat axis resulted in mean reductions in corneal astigmatism and depended on the pattern geometry. The linear bow-tie pattern produced a greater mean reduction in astigmatism (1.08 D ± 0.13 [SD]; range 0.74 to 1.23 D) than other patterns tested under an assumed 2-times increase in corneal stiffness, and it had a nonlinear relationship to the degree of stiffening. The mean astigmatic effect did not change significantly with a fiber- or depth-dependent model, but it did affect the coupling ratio. CONCLUSIONS In silico simulations based on patient-specific geometries suggest that clinically significant reductions in astigmatism are possible with patterned collagen crosslinking. Effect magnitude was dependent on patient-specific geometry, effective stiffening pattern, and treatment orientation. PMID:24767795

  7. Feasibility study on Generalized-Aurora Computed Tomography

    NASA Astrophysics Data System (ADS)

    Tanaka, Y.-M.; Aso, T.; Gustavsson, B.; Tanabe, K.; Ogawa, Y.; Kadokura, A.; Miyaoka, H.; Sergienko, T.; Brändström, U.; Sandahl, I.

    2011-03-01

    Aurora Computed Tomography (ACT) is a method for retrieving the three-dimensional (3-D) distribution of the volume emission rate from monochromatic auroral images obtained simultaneously by a multi-point camera network. We extend this method to a Generalized-Aurora Computed Tomography (G-ACT) that reconstructs the energy and spatial distributions of precipitating electrons from multi-instrument data, such as ionospheric electron density from incoherent scatter radar, cosmic noise absorption (CNA) from imaging riometers, as well as the auroral images. The purpose of this paper is to describe the reconstruction algorithm involved in this method and to test its feasibility by numerical simulation. Based on a Bayesian model with prior information as the smoothness of the electron energy spectra, the inverse problem is formulated as a maximization of posterior probability. The relative weighting of each instrument data is determined by the cross-validation method. We apply this method to the simulated data from real instruments, the Auroral Large Imaging System (ALIS), the European Incoherent Scatter (EISCAT) radar at Tromsø, and the Imaging Riometer for Ionospheric Study (IRIS) at Kilpisjärvi. The results indicate that the differential flux of the precipitating electrons is well reconstructed from the ALIS images for the low-noise cases. Furthermore, we demonstrate in a case study that the ionospheric electron density from the EISCAT radar is useful for improving the reconstructed electron flux. On the other hand, the incorporation of CNA data into this method is difficult at this stage, because the extension of energy range to higher energy causes a difficulty in the reconstruction of the low-energy electron flux. Nevertheless, we expect that this method may be useful in analyzing multi-instrument data and, in particular, 3-D data, which will be obtained in the upcoming EISCAT_3D.

  8. Genome-wide association study reveals sex-specific selection signals against autosomal nucleotide variants.

    PubMed

    Ryu, Dongchan; Ryu, Jihye; Lee, Chaeyoung

    2016-05-01

    A genome-wide association study (GWAS) was conducted to examine genetic associations of common autosomal nucleotide variants with sex in a Korean population with 4183 males and 4659 females. Nine genetic association signals were identified in four intragenic and five intergenic regions (P<5 × 10(-8)). Further analysis with an independent data set confirmed two intragenic association signals in the genes encoding protein phosphatase 1, regulatory subunit 12B (PPP1R12B, intron 12, rs1819043) and dynein, axonemal, heavy chain 11 (DNAH11, intron 61, rs10255013), which are directly involved in the reproductive system. This study revealed autosomal genetic variants associated with sex ratio by GWAS for the first time. This implies that genetic variants in proximity to the association signals may influence sex-specific selection and contribute to sex ratio variation. Further studies are required to reveal the mechanisms underlying sex-specific selection.

  9. 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

  10. The consequences of misinterpreting dive computers: three case studies.

    PubMed

    Sayer, Martin Dj; Wilson, Colin M; Laden, Gerard; Lonsdale, Phillip

    2008-03-01

    Three cases are presented where there is a direct link between how the divers used their dive computers and the eventual requirement for their therapeutic recompression. The first case involves a diver with a previous history of decompression incidents making adjustments to their dive computer without understanding the outcomes of those alterations. The second case involves two divers running out of air and surfacing having missed significant amounts of decompression, caused by the dive computer not reducing their decompression obligation in actual time. This effect and performance differences between three models of computers were demonstrated in subsequent compression chamber trials reported here. The final case involves a diver who completed their dive within the indicated limits of their dive computer but subsequently developed serious neurological decompression sickness that left severe permanent residua. Compression chamber trials suggested that a combination of poor measurement accuracy and outdated decompression management in the computer used could have contributed to the diver's eventual poor outcome.

  11. 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

  12. A computational approach to studying ageing at the individual level

    PubMed Central

    Mourão, Márcio A.; Schnell, Santiago; Pletcher, Scott D.

    2016-01-01

    The ageing process is actively regulated throughout an organism's life, but studying the rate of ageing in individuals is difficult with conventional methods. Consequently, ageing studies typically make biological inference based on population mortality rates, which often do not accurately reflect the probabilities of death at the individual level. To study the relationship between individual and population mortality rates, we integrated in vivo switch experiments with in silico stochastic simulations to elucidate how carefully designed experiments allow key aspects of individual ageing to be deduced from group mortality measurements. As our case study, we used the recent report demonstrating that pheromones of the opposite sex decrease lifespan in Drosophila melanogaster by reversibly increasing population mortality rates. We showed that the population mortality reversal following pheromone removal was almost surely occurring in individuals, albeit more slowly than suggested by population measures. Furthermore, heterogeneity among individuals due to the inherent stochasticity of behavioural interactions skewed population mortality rates in middle-age away from the individual-level trajectories of which they are comprised. This article exemplifies how computational models function as important predictive tools for designing wet-laboratory experiments to use population mortality rates to understand how genetic and environmental manipulations affect ageing in the individual. PMID:26865300

  13. 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.

  14. 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.

  15. X-ray luminescence computed tomography: a sensitivity study

    NASA Astrophysics Data System (ADS)

    Lun, Michael C.; Zhang, Wei; Li, Changqing

    2017-03-01

    X-ray luminescence computed tomography (XLCT) is a hybrid molecular imaging modality that uses high energy x-ray photons to excite nanophosphors (e.g. Europium doped Gadolinium Oxysulfide - GOS: Eu3+) emitting optical photons to be measured by a sensitive detector for image reconstruction. XLCT has potentials to combine both the merits of x-ray imaging (high spatial resolution) and optical imaging (high sensitivity), which makes XLCT an attractive imaging modality to image nanophosphor targets deeply embedded in turbid media. In this study, we have evaluated the sensitivity of XLCT with phantom experiments by scanning targets of different phosphor concentrations at different depths. Cylindrical phantoms embedded with a cylindrical target with varying concentrations of GOS: Eu3+ (27.6 mM, 2.76 mM, 276 μM, and 27.6 μM) were scanned inside our lab made XLCT imaging system for varying scanning depths (6, 11, 16, and 21 mm). We found that XLCT is capable of imaging targets of very low concentrations (27.6 μM or 0.01 mg/mL) at significant depths, such as 21 mm. Our results demonstrate that there is also little variation in the reconstructed target size for different imaging depths for XLCT. We have for the first time, compared the sensitivity of XLCT with that of traditional computed tomography (CT) for phosphor targets. We found that XLCT's use of x-ray induced photons provides much higher measurement sensitivity and contrast compared to CT which provides image contrast solely based on x-ray attenuation.

  16. 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

  17. 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

  18. 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.

  19. Computational studies of methane adsorption in nanoporous carbon

    NASA Astrophysics Data System (ADS)

    Ortiz, Lindsey

    In this thesis we have completed computational studies on the adsorption of methane into nanoporous carbon. We identified multi-layer adsorption at supercritical temperatures with excess amount even at large distances from the pore walls. We also determined that results could be used successfully to model methane adsorption from PSD’s coming from N 2. This works for both the adsorption isotherms and isosteric heats. A future direction would be to analyze lower temperature adsorption. Simulations at 195 K, the temperature of dry ice, would be of interest since dry ice is deemed of possible importance for storage. Another future direction is to study more varied pore geometries. In this thesis, we have only studied slit shaped pores. As can be seen in Figure 36, AC contains more varied pore geometries. Analysis of more varied pore geometries would offer a greater understanding of adsorption in AC and is therefore of interest. Figure 37 shows a possible model that may be used to run simulations on multiple pore sizes at the same time.

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

    NASA Astrophysics Data System (ADS)

    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 α, β or γ). 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 βCD 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.

  1. Computational fluid dynamics (CFD) studies of a miniaturized dissolution system.

    PubMed

    Frenning, G; Ahnfelt, E; Sjögren, E; Lennernäs, H

    2017-04-15

    Dissolution testing is an important tool that has applications ranging from fundamental studies of drug-release mechanisms to quality control of the final product. The rate of release of the drug from the delivery system is known to be affected by hydrodynamics. In this study we used computational fluid dynamics to simulate and investigate the hydrodynamics in a novel miniaturized dissolution method for parenteral formulations. The dissolution method is based on a rotating disc system and uses a rotating sample reservoir which is separated from the remaining dissolution medium by a nylon screen. Sample reservoirs of two sizes were investigated (SR6 and SR8) and the hydrodynamic studies were performed at rotation rates of 100, 200 and 400rpm. The overall fluid flow was similar for all investigated cases, with a lateral upward spiraling motion and central downward motion in the form of a vortex to and through the screen. The simulations indicated that the exchange of dissolution medium between the sample reservoir and the remaining release medium was rapid for typical screens, for which almost complete mixing would be expected to occur within less than one minute at 400rpm. The local hydrodynamic conditions in the sample reservoirs depended on their size; SR8 appeared to be relatively more affected than SR6 by the resistance to liquid flow resulting from the screen. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. High Performance Computer Cluster for Theoretical Studies of Roaming in Chemical Reactions

    DTIC Science & Technology

    2016-08-30

    High-performance Computer Cluster for Theoretical Studies of Roaming in Chemical Reactions A dedicated high-performance computer cluster was...purchased in order to carry out extensive and state-of-the art computations of chemical reaction dynamics. The specific aim of this computational research...SPONSORING/MONITORING AGENCY NAME(S) AND ADDRESS (ES) U.S. Army Research Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 Computer cluster

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

    PubMed

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

    2014-12-08

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

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

    PubMed Central

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

    2014-01-01

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

  5. 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.

  6. 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…

  7. 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…

  8. 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.

  9. Computer Controlled Spelling Instruction: A Case Study in Courseware Design.

    ERIC Educational Resources Information Center

    Assink, Egbert; van der Linden, Jan

    The research project "Feedback Processes in Computer Managed Spelling Instruction" is aimed at developing and testing an instructional software program for teaching the orthography of Dutch verbs. The main focus of this paper is on how to design an optimal educational environment. The design of the man-computer interaction is highlighted…

  10. Computer model for economic study of unbleached kraft paperboard production

    Treesearch

    Peter J. Ince

    1984-01-01

    Unbleached kraft paperboard is produced from wood fiber in an industrial papermaking process. A highly specific and detailed model of the process is presented. The model is also presented as a working computer program. A user of the computer program will provide data on physical parameters of the process and on prices of material inputs and outputs. The program is then...

  11. 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…

  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. 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…

  14. Payload/orbiter contamination control requirement study: Computer interface

    NASA Technical Reports Server (NTRS)

    Bareiss, L. E.; Hooper, V. W.; Ress, E. B.

    1976-01-01

    The MSFC computer facilities, and future plans for them are described relative to characteristics of the various computers as to availability and suitability for processing the contamination program. A listing of the CDC 6000 series and UNIVAC 1108 characteristics is presented so that programming requirements can be compared directly and differences noted.

  15. A preliminary study on the short-term efficacy of chairside computer-aided design/computer-assisted manufacturing- generated posterior lithium disilicate crowns.

    PubMed

    Reich, Sven; Fischer, Sören; Sobotta, Bernhard; Klapper, Horst-Uwe; Gozdowski, Stephan

    2010-01-01

    The purpose of this preliminary study was to evaluate the clinical performance of chairside-generated crowns over a preliminary time period of 24 months. Forty-one posterior crowns made of a machinable lithium disilicate ceramic for full-contour crowns were inserted in 34 patients using a chairside computer-aided design/computer-assisted manufacturing technique. The crowns were evaluated at baseline and after 6, 12, and 24 months according to modified United States Public Health Service criteria. After 2 years, all reexamined crowns (n = 39) were in situ; one abutment exhibited secondary caries and two abutments received root canal treatment. Within the limited observation period, the crowns revealed clinically satisfying results.

  16. 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…

  17. 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…

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

    PubMed Central

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

    2010-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  20. 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.