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Sample records for computational studies reveal

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

    PubMed

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

    2016-01-15

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

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. Extreme Scale Computing Studies

    DTIC Science & Technology

    2010-12-01

    SUPPLEMENTARY NOTES DISTAR case 17642; Clearance Date: 18 July 2011. This report contains color. 14 . ABSTRACT Four studies were conducted to...Embedded Computing Applications................................................. 14 4.2.3 Low Power Computational Algorithms... 14 4.2.4 High Performance Libraries for Advanced Graphics Processing Units ................ 15 4.2.5 Metrics

  9. 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.

  10. 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…

  11. Pupillary dynamics reveal computational cost in sentence planning.

    PubMed

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

    2014-01-01

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

  12. 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).

  13. 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…

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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

  1. 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

  2. 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.

  3. 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.

  4. 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…

  5. 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.

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

    PubMed Central

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

    2015-01-01

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

  7. Flight Trainer Digital Computer Study

    DTIC Science & Technology

    1951-03-21

    digital I*? computation. By programming, is: meant the process of breaMhg down ail complex algebraic formulae» and numerical iiategnatioli formulae...instructiveTir~sTtö~ enumerate. the^r^heiföt^Fop^tipis" which constitute the computation, and solution of the ERCO, equations. From tie algebraic .point of view...pösTte routines •Ehe algebraic notion of ^operation^cpmpl’exity is aliiiost immediate- ly applicable ,t,o digital computation. On. the other’ hand

  8. 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)…

  9. 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

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

    ERIC Educational Resources Information Center

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

    2006-01-01

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

  11. Computer technology forecast study for general aviation

    NASA Technical Reports Server (NTRS)

    Seacord, C. L.; Vaughn, D.

    1976-01-01

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

  12. 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…

  13. 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.

  14. 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…

  15. 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…

  16. 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,…

  17. 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…

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. 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.

  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. 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.

  8. 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.

  9. 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

  10. 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,…

  11. 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.

  12. 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

  13. 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.

  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. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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…

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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,…

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

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

    SciTech Connect

    Not Available

    2012-07-01

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

  2. 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.

  3. 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

  4. 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…

  5. 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)

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. [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.

  15. 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

  16. 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

  17. 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.

  18. A study of pipelining in computing arrays

    NASA Technical Reports Server (NTRS)

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

    1986-01-01

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

  19. A Study on Use of Computer among Higher Secondary Students as Related with Their Computer Anxiety, Internet Attitude and Self-Efficacy in Computer

    ERIC Educational Resources Information Center

    Vinaitheerthan, V.; Johnson, Jomy

    2009-01-01

    The present attempt is to study the use of computer and its possible relationship to Internet attitude, self-efficacy in computer and computer anxiety among higher secondary students. The present study aims at finding the levels of use of computer, Internet attitude, Self-efficacy in computer and computer anxiety among higher secondary students.…

  20. 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

  1. 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.

  2. 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

  3. 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.

  4. 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…

  5. 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.

  6. 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…

  7. 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)

  8. 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…

  9. Where Computer Science and Cultural Studies Collide

    ERIC Educational Resources Information Center

    Kirschenbaum, Matthew

    2009-01-01

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

  10. 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.

  11. 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

  12. 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.

  13. 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.

  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. 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.

  16. 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.

  17. 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

  18. 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.

  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. 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…

  1. 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

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

    NASA Astrophysics Data System (ADS)

    Falkner, Katrina; Vivian, Rebecca

    2015-10-01

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

  3. 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.

  4. 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.

  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. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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

  15. 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.

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

    NASA Technical Reports Server (NTRS)

    Simpson, David G.

    2012-01-01

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

  17. 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…

  18. 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…

  19. 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,…

  20. 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.…

  1. 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.'

  2. 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…

  3. 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

  4. 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

  5. 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

  6. 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

  7. Computational Studies of Strongly Interacting Ultracold Atoms

    DTIC Science & Technology

    2010-01-01

    are studied synergistically. We quantified effects of many-body correlations in trapped atomic Bose gases; developed auxiliary-field quantum Monte...are studied synergistically. We quantified effects of many-body correlations in trapped atomic Bose gases; developed auxiliary-field quantum Monte...in the following categories: Wirawan Purwanto, Shiwei Zhang, "Correlation effects in the ground state of trapped atomic Bose gases," Phys. Rev. A 72

  8. 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.

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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.

  17. 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

  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 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.

  20. Advanced Computational Techniques in Regional Wave Studies

    DTIC Science & Technology

    1990-01-03

    the new GERESS data. The dissertation work emphasized the development and use of advanced computa- tional techniques for studying regional seismic...hand, the possibility of new data sources at regional distances permits using previously ignored signals. Unfortunately, these regional signals will...the Green’s function around this new reference point is containing the propagation effects, and V is the source Gnk(x,t;r,t) - (2) volume where fJk

  1. 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

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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..

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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.

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

    ERIC Educational Resources Information Center

    Perez-Marin, Diana; Pascual-Nieto, Ismael

    2012-01-01

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

  13. 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

  14. 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…

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

    ERIC Educational Resources Information Center

    Allsop, Yasemin

    2016-01-01

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

  16. 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…

  17. 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

  18. 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.

  19. 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…

  20. 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…

  1. 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

  2. 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

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  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. 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…

  17. 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…

  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. 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…

  20. 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

  1. Computational fluid dynamics studies of nuclear rocket performance

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

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

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. Study of the TRAC Airfoil Table Computational System

    NASA Technical Reports Server (NTRS)

    Hu, Hong

    1999-01-01

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

  7. A Computational and Experimental Study of Slit Resonators

    NASA Technical Reports Server (NTRS)

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

    2003-01-01

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

  8. 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.

  9. 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

  10. High Performance Computing Innovation Service Portal Study (HPC-ISP)

    DTIC Science & Technology

    2009-04-01

    develop technical and business concepts that could help enable these “desktop-only” users to employ more advanced computing solutions in their...Card", a case study of Woodward, a supplier of P&W, “Woodward FST: Software Costs and Finding Experts Are Stalling HPC Adoption”, and a business and...Dynamics ...................................................................... 3  2.2.2  Task 2: Business and Technical Concept Study

  11. 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.

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

    SciTech Connect

    Agha, F.P.

    1983-07-01

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

  13. 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.

  14. 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.

  15. 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.

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

    PubMed Central

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

    2015-01-01

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

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. [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.

  7. 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)

  8. [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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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,…

  17. 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…

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

    PubMed

    Reggia, James A

    2013-08-01

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

  19. 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

  20. 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.

  1. 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

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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

  18. 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.

  19. Pediatric Computed Tomography. Radiation Dose in Abdominal Studies

    SciTech Connect

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

    2008-08-11

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

  20. 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.

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

    SciTech Connect

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

    2014-06-16

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

  2. 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. 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…

  4. 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…

  5. 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'…

  6. 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.

  7. Using computer simulations to study relativistic heavy ion collisions

    NASA Astrophysics Data System (ADS)

    Murray, Joelle Lynn

    1998-12-01

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

  8. 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…

  9. 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…

  10. 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.

  11. 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.

  12. 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.

  13. 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…

  14. 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…

  15. 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.

  16. Gliomatosis cerebri with formation of a glioblastoma multiform. Study and follow-up by magnetic resonance and computed tomography.

    PubMed

    Romero, F J; Ortega, A; Titus, F; Ibarra, B; Navarro, C; Rovira, M

    1988-10-01

    A case of gliomatosis cerebri studied by computed tomography (CT) and magnetic resonance imaging (MRI) is reported. Follow-up by serial CT revealed a right parieto-occipital glioblastoma. Gliomatosis cerebri and multiform glioblastoma were demonstrated by histologic study. Anatomic and CT data were correlated. The role of CT and MRI in the diagnosis of this disease was evaluated and case studies of CT published in the literature were reviewed.

  17. 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)

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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…

  5. 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…

  6. 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…

  7. 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…

  8. 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…

  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. 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.

  11. 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.

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  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. 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.

  2. 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.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2013-01-01

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

  5. 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

  6. 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.

  7. 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

  8. 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.

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

    ERIC Educational Resources Information Center

    Belon, Barbara; Wright, Marie

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

  10. 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.

  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. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  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. 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…

  20. 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…

  1. 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.

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

    PubMed

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

    2016-06-21

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

  3. 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

  4. 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

  5. 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.

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

    PubMed

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

    2017-02-08

    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.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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…

  15. 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…

  16. 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.

  17. 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.

  18. Computational and Experimental Study of Spherocylinder Particles in Fluidized Beds

    NASA Astrophysics Data System (ADS)

    Mahajan, Vinay; Kuipers, Hans; Padding, Johan; Multiphase Reactors Group, TU Eindhoven Team

    2016-11-01

    Non-spherical particle flows are often encountered in fluidized process equipment. A coupled computational fluid dynamics (CFD) and discrete element method(DEM) approach has been extensively applied in recent years to study these flows at the particle scale. However, most of these studies focus on spherical particles while in reality, the constituent particles are seldom spherical. Particle shape can significantly affect the hydrodynamical response in fluidized beds. The drag force acting on a non-spherical particle can vary considerably with particle shape, orientation of the particle, Reynolds number and packing fraction. In this work, a CFD-DEM approach has been extended to model a lab scale quasi-2D fluidized bed of spherocylinder (rod-like) particles. These particles can be classified as Geldart D particles and have an aspect ratio of 4. Numerical results for the pressure drop, bed height and solid circulation patterns are compared with results from a complementary laboratory experiment. We also present results on particle orientations close to the confining walls, which provides interesting insight regarding the particle alignment. Thus the capability of the CFD-DEM approach to efficiently account for global bed dynamics in fluidized bed of rod-like particle is demonstrated. This research work is funded by ERC Grant.

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

    PubMed

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

    2015-10-01

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

  20. A computational study of flashover voltage of iced insulators

    SciTech Connect

    Sundarajan, R.

    1996-11-01

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

  1. 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.

  2. 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…

  3. Computational Studies on Optoelectronic and Nonlinear Properties of Octaphyrin Derivatives

    PubMed Central

    Islam, Nasarul; Lone, Irfan H.

    2017-01-01

    The electronic and nonlinear optical (NLO) properties of octaphyrin derivatives were studied by employing the DFT/TDFT at CAM-B3LYP/6-311++G (2d, 2p) level of the theory. Thiophene, phenyl, methyl and cyano moieties were substituted on the molecular framework of octaphyrin core, in order to observe the change in optoelectronic and nonlinear response of these systems. The frontier molecular orbital studies and values of electron affinity reveals that the studied compounds are stable against the oxygen and moisture present in air. The calculated ionization energies, adiabatic electron affinity and reorganization energy values indicate that octaphyrin derivatives can be employed as effective n-type material for Organic Light Emitting Diodes (OLEDs). This character shows an enhancement with the introduction of an electron withdrawing group in the octaphyrin framework. The polarizability and hyperpolarizability values of octaphyrin derivatives demonstrate that they are good candidates for NLO devices. The nonlinear response of these systems shows enhancement on the introduction of electron donating groups on octaphyrin moiety. However, these claims needs further experimental verification. PMID:28321394

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

    NASA Technical Reports Server (NTRS)

    1989-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Rowinski, David H.; Pope, Stephen B.

    2013-08-01

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

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

    NASA Technical Reports Server (NTRS)

    Olson, J. R.

    1978-01-01

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

  7. Pilot study of bovine interdigital cassetteless computed radiography.

    PubMed

    El-Shafaey, El-Sayed Ahmed Awad; Aoki, Takahiro; Ishii, Mitsuo; Yamada, Kazutaka

    2013-11-01

    Twenty-one limbs of bovine cadavers (42 digits) were exposed to interdigital cassetteless imaging plate using computed radiography. The radiographic findings included exostosis, a rough planta surface, osteolysis of the apex of the distal phalanx and widening of the laminar zone between the distal phalanx and the hoof wall. All these findings were confirmed by computed tomography. The hindlimbs (19 digits) showed more changes than the forelimbs (10 digits), particularly in the lateral distal phalanx. The cassetteless computed radiography technique is expected to be an easily applicable method for the distal phalanx rather than a conventional cassette-plate and/or the film-screen cassetteless methods.

  8. Study of Alzheimer family case reveals hemochromotosis-associated HFE mutation

    PubMed Central

    Artemov, Artem V; Boulygina, Eugenia S; Tsygankova, Svetlana V; Nedoluzhko, Artem V; Chekanov, Nikolay N; Gruzdeva, Natalia M; Selezneva, Natalia D; Roshchina, Irina F; Gavrilova, Svetlana I; Velichkovsky, Boris B; Skryabin, Konstantin G; Prokhortchouk, Egor B

    2014-01-01

    We report a family case of type II early-onset Alzheimer’s disease (AD) inherited over three generations. None of the patients in the family had mutations in the genes believed to be the major risk factors for AD, such as APP, presenilin 1 or 2. Targeted exome sequencing of 249 genes that were previously reported to be associated with AD revealed a rare mutation in hemochromatosis (HFE) gene known to be associated with hemochromotosis. Compared to previous studies, we show that HFE mutation can possess the risk of AD in transferrin-, APOE- and APP-normal patients. PMID:27081498

  9. Study of Alzheimer family case reveals hemochromotosis-associated HFE mutation.

    PubMed

    Artemov, Artem V; Boulygina, Eugenia S; Tsygankova, Svetlana V; Nedoluzhko, Artem V; Chekanov, Nikolay N; Gruzdeva, Natalia M; Selezneva, Natalia D; Roshchina, Irina F; Gavrilova, Svetlana I; Velichkovsky, Boris B; Skryabin, Konstantin G; Prokhortchouk, Egor B

    2014-01-01

    We report a family case of type II early-onset Alzheimer's disease (AD) inherited over three generations. None of the patients in the family had mutations in the genes believed to be the major risk factors for AD, such as APP, presenilin 1 or 2. Targeted exome sequencing of 249 genes that were previously reported to be associated with AD revealed a rare mutation in hemochromatosis (HFE) gene known to be associated with hemochromotosis. Compared to previous studies, we show that HFE mutation can possess the risk of AD in transferrin-, APOE- and APP-normal patients.

  10. A Longitudinal Study of the Use of Student-Owned Portable Computers in a Secondary School.

    ERIC Educational Resources Information Center

    Newhouse, Paul; Rennie, Leonie

    2001-01-01

    Presents findings from a three-year evaluative study, plus a follow-up study four years later, into the implementation of a student-owned portable computer program in a secondary school in Perth, Western Australia. Discusses computer use, student computer attitudes, teacher attitudes, the role of teachers in curriculum integration, and…

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

    PubMed

    Gallo Vallejo, Francisco Javier; Giner Ruiz, Vicente

    2014-01-01

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

  12. Computational and Experimental Study of Neuroglobin and Mutants

    NASA Astrophysics Data System (ADS)

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

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

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

    NASA Astrophysics Data System (ADS)

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

    2006-11-01

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

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

    PubMed

    Khayyeri, Hanifeh; Barreto, Sara; Lacroix, Damien

    2015-08-21

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

  15. A computational study of λ-lac mutants

    NASA Astrophysics Data System (ADS)

    Werner, Maria; Aurell, Erik

    2009-12-01

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

  16. Computational study of the risk of restenosis in coronary bypasses.

    PubMed

    Guerciotti, Bruno; Vergara, Christian; Ippolito, Sonia; Quarteroni, Alfio; Antona, Carlo; Scrofani, Roberto

    2017-02-01

    Coronary artery disease, caused by the buildup of atherosclerotic plaques in the coronary vessel wall, is one of the leading causes of death in the world. For high-risk patients, coronary artery bypass graft is the preferred treatment. Despite overall excellent patency rates, bypasses may fail due to restenosis. In this context, the purpose of this work was to perform a parametric computational study of the fluid dynamics in patient-specific geometries with the aim of investigating a possible relationship between coronary stenosis degree and risk of graft failure. Firstly, we propose a strategy to prescribe realistic boundary conditions in the absence of measured data, based on an extension of Murray's law to provide the flow division at bifurcations in case of stenotic vessels and non-Newtonian blood rheology. Then, we carry out numerical simulations in three patients affected by severe coronary stenosis and treated with a graft, in which the stenosis degree is virtually varied in order to compare the resulting fluid dynamics in terms of hemodynamic indices potentially involved in restenosis development. Our findings suggest that low degrees of coronary stenosis produce a more disturbed fluid dynamics in the graft, resulting in hemodynamic conditions that may promote a higher risk of graft failure.

  17. Thermochemical properties for isooctane and carbon radicals: computational study.

    PubMed

    Snitsiriwat, Suarwee; Bozzelli, Joseph W

    2013-01-17

    Thermochemical properties for isooctane, its internal rotation conformers, and radicals with corresponding bond energies are determined by use of computational chemistry. Enthalpies of formation are determined using isodesmic reactions with B3LYP density function theory and composite CBS-QB3 methods. Application of group additivity with comparison to calculated values is illustrated. Entropy and heat capacities are determined using geometric parameters, internal rotor potentials, and frequencies from B3LYP/6-31G(d,p) calculations for the lowest energy conformer. Internal rotor potentials are determined for the isooctane parent and for the primary, secondary, and tertiary radicals in order to identify isomer energies. Intramolecular interactions are shown to have a significant effect on the enthalpy of formation of the isooctane parent and its radicals. The computed standard enthalpy of formation for the lowest energy conformers of isooctane from this study is -54.40 ± 1.60 kcal mol(-1), which is 0.8 kcal mol(-1) lower than the evaluated experimental value -53.54 ± 0.36 kcal mol(-1). The standard enthalpy of formation for the primary radical for a methyl on the quaternary carbon is -5.00 ± 1.69 kcal mol(-1), for the primary radical on the tertiary carbon is -5.18 ± 1.69 kcal mol(-1), for the secondary isooctane radical is -9.03 ± 1.84 kcal mol(-1), and for the tertiary isooctane radical is -12.30 ± 2.02 kcal mol(-1). Bond energy values for the isooctane radicals are 100.64 ± 1.73, 100.46 ± 1.73, 96.41 ± 1.88 and 93.14 ± 2.05 kcal mol(-1) for C3•CCCC2, C3CCCC2•, C3CC•CC2, and C3CCC•C2, respectively. Entropy and heat capacity values are reported for the lowest energy homologues.

  18. A Study into Advanced Guidance Laws Using Computational Methods

    DTIC Science & Technology

    2011-12-01

    computing aerodynamic forces % and moments. Except where noted, all dimensions in % MKS system. % Inputs...9] R. L. Shaw, Fighter Combat: Tactics and Maneuvering. Annapolis, MD: Naval Institute Press, 1988. [10] U. S. Shukla and P. R. Mahapatra

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

    NASA Astrophysics Data System (ADS)

    Johri, Sonika

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

  20. Computing and information sciences preliminary engineering design study

    SciTech Connect

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

    1991-04-01

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

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

    PubMed

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

    2015-07-16

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

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

    PubMed

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

    2009-02-15

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

  3. A computed tomography phantom study of foam earplugs

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

    Siekmeier, Peter J; vanMaanen, David P

    2014-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  6. Revealing pathologies in the liquid crystalline structures of the brain by polarimetric studies (Presentation Recording)

    NASA Astrophysics Data System (ADS)

    Bakhshetyan, Karen; Melkonyan, Gurgen G.; Galstian, Tigran V.; Saghatelyan, Armen

    2015-10-01

    Natural or "self" alignment of molecular complexes in living tissue represents many similarities with liquid crystals (LC), which are anisotropic liquids. The orientational characteristics of those complexes may be related to many important functional parameters and their study may reveal important pathologies. The know-how, accumulated thanks to the study of LC materials, may thus be used to this end. One of the traditionally used methods, to characterize those materials, is the polarized light imaging (PLI) that allows for label-free analysis of anisotropic structures in the brain tissue and can be used, for example, for the analysis of myelinated fiber bundles. In the current work, we first attempted to apply the PLI on the mouse histological brain sections to create a map of anisotropic structures using cross-polarizer transmission light. Then we implemented the PLI for comparative study of histological sections of human postmortem brain samples under normal and pathological conditions, such as Parkinson's disease (PD). Imaging the coronal, sagittal and horizontal sections of mouse brain allowed us to create a false color-coded fiber orientation map under polarized light. In human brain datasets for both control and PD groups we measured the pixel intensities in myelin-rich subregions of internal capsule and normalized these to non-myelinated background signal from putamen and caudate nucleus. Quantification of intensities revealed a statistically significant reduction of fiber intensity of PD compared to control subjects (2.801 +/- 0.303 and 3.724 +/- 0.07 respectively; *p < 0.05). Our study confirms the validity of PLI method for visualizing myelinated axonal fibers. This relatively simple technique can become a promising tool for study of neurodegenerative diseases where labeling-free imaging is an important benefit.

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

    PubMed

    Biglino, Giovanni; Cosentino, Daria; Steeden, Jennifer A; De Nova, Lorenzo; Castelli, Matteo; Ntsinjana, Hopewell; Pennati, Giancarlo; Taylor, Andrew M; Schievano, Silvia

    2015-01-01

    Computational fluid dynamics (CFD) can have a complementary predictive role alongside the exquisite visualization capabilities of 4D cardiovascular magnetic resonance (CMR) imaging. In order to exploit these capabilities (e.g., for decision-making), it is necessary to validate computational models against real world data. In this study, we sought to acquire 4D CMR flow data in a controllable, experimental setup and use these data to validate a corresponding computational model. We applied this paradigm to a case of congenital heart disease, namely, transposition of the great arteries (TGA) repaired with arterial switch operation. For this purpose, a mock circulatory loop compatible with the CMR environment was constructed and two detailed aortic 3D models (i.e., one TGA case and one normal aortic anatomy) were tested under realistic hemodynamic conditions, acquiring 4D CMR flow. The same 3D domains were used for multi-scale CFD simulations, whereby the remainder of the mock circulatory system was appropriately summarized with a lumped parameter network. Boundary conditions of the simulations mirrored those measured in vitro. Results showed a very good quantitative agreement between experimental and computational models in terms of pressure (overall maximum % error = 4.4% aortic pressure in the control anatomy) and flow distribution data (overall maximum % error = 3.6% at the subclavian artery outlet of the TGA model). Very good qualitative agreement could also be appreciated in terms of streamlines, throughout the cardiac cycle. Additionally, velocity vectors in the ascending aorta revealed less symmetrical flow in the TGA model, which also exhibited higher wall shear stress in the anterior ascending aorta.

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

    PubMed Central

    Biglino, Giovanni; Cosentino, Daria; Steeden, Jennifer A.; De Nova, Lorenzo; Castelli, Matteo; Ntsinjana, Hopewell; Pennati, Giancarlo; Taylor, Andrew M.; Schievano, Silvia

    2015-01-01

    Computational fluid dynamics (CFD) can have a complementary predictive role alongside the exquisite visualization capabilities of 4D cardiovascular magnetic resonance (CMR) imaging. In order to exploit these capabilities (e.g., for decision-making), it is necessary to validate computational models against real world data. In this study, we sought to acquire 4D CMR flow data in a controllable, experimental setup and use these data to validate a corresponding computational model. We applied this paradigm to a case of congenital heart disease, namely, transposition of the great arteries (TGA) repaired with arterial switch operation. For this purpose, a mock circulatory loop compatible with the CMR environment was constructed and two detailed aortic 3D models (i.e., one TGA case and one normal aortic anatomy) were tested under realistic hemodynamic conditions, acquiring 4D CMR flow. The same 3D domains were used for multi-scale CFD simulations, whereby the remainder of the mock circulatory system was appropriately summarized with a lumped parameter network. Boundary conditions of the simulations mirrored those measured in vitro. Results showed a very good quantitative agreement between experimental and computational models in terms of pressure (overall maximum % error = 4.4% aortic pressure in the control anatomy) and flow distribution data (overall maximum % error = 3.6% at the subclavian artery outlet of the TGA model). Very good qualitative agreement could also be appreciated in terms of streamlines, throughout the cardiac cycle. Additionally, velocity vectors in the ascending aorta revealed less symmetrical flow in the TGA model, which also exhibited higher wall shear stress in the anterior ascending aorta. PMID:26697416

  9. Rotating Detonation Combustion: A Computational Study for Stationary Power Generation

    NASA Astrophysics Data System (ADS)

    Escobar, Sergio

    The increased availability of gaseous fossil fuels in The US has led to the substantial growth of stationary Gas Turbine (GT) usage for electrical power generation. In fact, from 2013 to 2104, out of the 11 Tera Watts-hour per day produced from fossil fuels, approximately 27% was generated through the combustion of natural gas in stationary GT. The thermodynamic efficiency for simple-cycle GT has increased from 20% to 40% during the last six decades, mainly due to research and development in the fields of combustion science, material science and machine design. However, additional improvements have become more costly and more difficult to obtain as technology is further refined. An alternative to improve GT thermal efficiency is the implementation of a combustion regime leading to pressure-gain; rather than pressure loss across the combustor. One concept being considered for such purpose is Rotating Detonation Combustion (RDC). RDC refers to a combustion regime in which a detonation wave propagates continuously in the azimuthal direction of a cylindrical annular chamber. In RDC, the fuel and oxidizer, injected from separated streams, are mixed near the injection plane and are then consumed by the detonation front traveling inside the annular gap of the combustion chamber. The detonation products then expand in the azimuthal and axial direction away from the detonation front and exit through the combustion chamber outlet. In the present study Computational Fluid Dynamics (CFD) is used to predict the performance of Rotating Detonation Combustion (RDC) at operating conditions relevant to GT applications. As part of this study, a modeling strategy for RDC simulations was developed. The validation of the model was performed using benchmark cases with different levels of complexity. First, 2D simulations of non-reactive shock tube and detonation tubes were performed. The numerical predictions that were obtained using different modeling parameters were compared with

  10. Temperature dependence of the colloidal agglomeration inhibition: computer simulation study.

    PubMed

    Barcenas, Mariana; Douda, Janna; Duda, Yurko

    2007-09-21

    There exist experimental evidences that the structure and extension of colloidal aggregates in suspensions change dramatically with temperature. This results in an associated change in the suspension rheology. Experimental studies of the inhibitor applications to control the particle clustering have revealed some unexpected tendencies. Namely, the heating of colloidal suspensions has provoked either extension or reduction of the colloidal aggregates. To elucidate the origin of this behavior, we investigate the influence of temperature on the stabilizing effect of the inhibitor, applying an associative two-component fluid model. Our results of the canonical Monte Carlo simulations indicate that the anomalous effect of the temperature may not be necessarily explained by the temperature dependent changes in the inhibitor tail conformation, as has been suggested recently by Won et al. [Langmuir 21, 924 (2005)]. We show that the competition between colloid-colloid and colloid-inhibitor associations, which, in turn, depends on the temperature and the relative concentrations, may be one of the main reasons for the unexpected temperature dependence of inhibitor efficacy.

  11. Computational Studies of Physical Properties of Boron Carbide

    SciTech Connect

    Lizhi Ouyang

    2011-09-30

    The overall goal is to provide valuable insight in to the mechanisms and processes that could lead to better engineering the widely used boron carbide which could play an important role in current plight towards greener energy. Carbon distribution in boron carbide, which has been difficult to retrieve from experimental methods, is critical to our understanding of its structure-properties relation. For modeling disorders in boron carbide, we implemented a first principles method based on supercell approach within our G(P,T) package. The supercell approach was applied to boron carbide to determine its carbon distribution. Our results reveal that carbon prefers to occupy the end sites of the 3-atom chain in boron carbide and further carbon atoms will distribute mainly on the equatorial sites with a small percentage on the 3-atom chains and the apex sites. Supercell approach was also applied to study mechanical properties of boron carbide under uniaxial load. We found that uniaxial load can lead to amorphization. Other physical properties of boron carbide were calculated using the G(P,T) package.

  12. Thermoelectric properties of isoelectronically substituted bismuth compounds: a computational study

    NASA Astrophysics Data System (ADS)

    Liangruksa, Monrudee

    2017-03-01

    This work focuses on using isoelectronic substitution to modify electronic density of states (DOS) of bismuth (Bi) compounds for thermoelectric property modification. The calculations include first-principle density functional theory (DFT) and analytical calculations based on Mott formula. The thermoelectric materials selected in the present study are Bi compounds, i.e. Bi2Te3, Bi2Se3, Bi2Se2Te, Bi2Te2Se, Bi2O2Te, and Bi2O2Se. The results reveal that isoelectronic substitution of Se and Te atoms with O atoms (Bi2O2Te and Bi2O2Se) introduces changes in DOS around the valence band maximum and the conduction band minimum, exhibiting the figure of merit (ZT) approaching the values 0.004 and 0.03 at room temperature, for Bi2O2Se and Bi2O2Te, respectively. Though the ZT of these oxide compounds are inferior to conventional thermoelectric materials, it is known that they show better stability and less toxicity which could be the alternative materials.

  13. First Principles Computational Study of the Active Site of Arginase

    SciTech Connect

    Ivanov, Ivaylo; Klien, Micheal

    2004-01-14

    Ab initio density functional theory (DFT) methods were used to investigate the structural features of the active site of the binuclear enzyme rat liver arginase. Special emphasis was placed on the crucial role of the second shell ligand interactions. These interactions were systematically studied by performing calculations on models of varying size. It was determined that a water molecule, and not hydroxide, is the bridging exogenous ligand. The carboxylate ligands facilitate the close approach of the Mn (II) ions by attenuating the metal-metal electrostatic repulsion. Of the two metals, MnA was shown to carry a larger positive charge. Analysis of the electronic properties of the active site revealed that orbitals involving the terminal Asp234 residue, as well as the flexible -1,1 bridging Asp232, lie at high energies, suggesting weaker coordination. This is reflected in certain structural variability present in our models and is also consistent with recent experimental findings. Finally, implications of our findings for the biological function of the enzyme are delineated.

  14. A genome-wide association study reveals a QTL influencing caudal supernumerary teats in Holstein cattle.

    PubMed

    Joerg, H; Meili, C; Ruprecht, O; Bangerter, E; Burren, A; Bigler, A

    2014-12-01

    Supernumerary teats represent a common abnormality of the bovine udder. A genome-wide association study was performed based on the proportion of the occurrence of supernumerary teats in the daughters of 1097 Holstein bulls. The heritability of caudal supernumerary teats without mammary gland in this study was 0.604. The largest proportion of the heritability was attributable to BTA 20. The strongest evidence for association was with five SNPs on chromosome 20, referred to as a QTL. The mode of inheritance at this QTL was dominant. These findings reveal that the occurrence of caudal supernumerary teats without mammary gland in Holstein cattle is influenced by a QTL on chromosome 20 and a polygenic part. The data support the high potential of the SNPs in the QTL region as markers for breeding against caudal supernumerary teats.

  15. A computational study of an atomizing liquid sheet

    SciTech Connect

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

    2015-08-15

    Linear instability predictions of liquid sheets injected into a gas medium are well established in the literature. These analyses are often used in Lagrangian-Eulerian spray simulations, a prominent simulation method, to model the dynamics occurring in the near-nozzle region. In the present work, these instability predictions are re-examined by first generalizing the treatment of interfacial conditions and related assumptions with a two-phase Orr-Sommerfeld (OS) system, and second, by employing highly resolved-Volume-of-Fluid (VoF) simulations. After presenting some validation exercises for both the VoF and OS solvers, the OS predictions are compared to earlier studies from the literature leading to reasonable agreement in the limit as the boundary layer thickness tends to zero. Results from VoF simulations of liquid sheet injection are used to characterize the range of scales of the liquid structures immediately before atomization. The mean value in this range is found to be approximately two to three orders of magnitude larger than the corresponding predictions from previous studies. A two-phase mixing layer under the same physical conditions is used to examine this disparity, revealing that within the linear regime, relatively good agreement exists between the VoF and OS predicted instability mechanisms. However, the most unstable mode in the linear regime is too small to cause a fracture or atomization of the liquid sheet and hence cannot be directly responsible for the atomization. The generation of a much larger mode, which emerges well beyond the linear regime, is the one causing breakup.

  16. Time-dependent computational studies of flames in microgravity

    NASA Technical Reports Server (NTRS)

    Oran, Elaine S.; Kailasanath, K.

    1989-01-01

    The research performed at the Center for Reactive Flow and Dynamical Systems in the Laboratory for Computational Physics and Fluid Dynamics, at the Naval Research Laboratory, in support of the NASA Microgravity Science and Applications Program is described. The primary focus was on investigating fundamental questions concerning the propagation and extinction of premixed flames in Earth gravity and in microgravity environments. The approach was to use detailed time-dependent, multispecies, numerical models as tools to simulate flames in different gravity environments. The models include a detailed chemical kinetics mechanism consisting of elementary reactions among the eight reactive species involved in hydrogen combustion, coupled to algorithms for convection, thermal conduction, viscosity, molecular and thermal diffusion, and external forces. The external force, gravity, can be put in any direction relative to flame propagation and can have a range of values. A combination of one-dimensional and two-dimensional simulations was used to investigate the effects of curvature and dilution on ignition and propagation of flames, to help resolve fundamental questions on the existence of flammability limits when there are no external losses or buoyancy forces in the system, to understand the mechanism leading to cellular instability, and to study the effects of gravity on the transition to cellular structure. A flame in a microgravity environment can be extinguished without external losses, and the mechanism leading to cellular structure is not preferential diffusion but a thermo-diffusive instability. The simulations have also lead to a better understanding of the interactions between buoyancy forces and the processes leading to thermo-diffusive instability.

  17. Time-dependent Computational Studies of Premixed Flames in Microgravity

    NASA Technical Reports Server (NTRS)

    Kailasanath, K.; Patnaik, Gopal; Oran, Elaine S.

    1993-01-01

    This report describes the research performed at the Center for Reactive Flow and Dynamical Systems in the Laboratory for Computational Physics and Fluid Dynamics, at the Naval Research Laboratory, in support of NASA Microgravity Science and Applications Program. The primary focus of this research is on investigating fundamental questions concerning the propagation and extinction of premixed flames in earth gravity and in microgravity environments. Our approach is to use detailed time-dependent, multispecies, numerical models as tools to simulate flames in different gravity environments. The models include a detailed chemical kinetics mechanism consisting of elementary reactions among the eight reactive species involved in hydrogen combustion, coupled to algorithms for convection, thermal conduction, viscosity, molecular and thermal diffusion, and external forces. The external force, gravity, can be put in any direction relative to flame propagation and can have a range of values. Recently more advanced wall boundary conditions such as isothermal and no-slip have been added to the model. This enables the simulation of flames propagating in more practical systems than before. We have used the numerical simulations to investigate the effects of heat losses and buoyancy forces on the structure and stability of flames, to help resolve fundamental questions on the existence of flammability limits when there are no external losses or buoyancy forces in the system, to understand the interaction between the various processes leading to flame instabilities and extinguishment, and to study the dynamics of cell formation and splitting. Our studies have been able to bring out the differences between upward- and downward-propagating flames and predict the zero-gravity behavior of these flames. The simulations have also highlighted the dominant role of wall heat losses in the case of downward-propagating flames. The simulations have been able to qualitatively predict the

  18. Performance studies of four-dimensional cone beam computed tomography

    NASA Astrophysics Data System (ADS)

    Qi, Zhihua; Chen, Guang-Hong

    2011-10-01

    Four-dimensional cone beam computed tomography (4DCBCT) has been proposed to characterize the breathing motion of tumors before radiotherapy treatment. However, when the acquired cone beam projection data are retrospectively gated into several respiratory phases, the available data to reconstruct each phase is under-sampled and thus causes streaking artifacts in the reconstructed images. To solve the under-sampling problem and improve image quality in 4DCBCT, various methods have been developed. This paper presents performance studies of three different 4DCBCT methods based on different reconstruction algorithms. The aims of this paper are to study (1) the relationship between the accuracy of the extracted motion trajectories and the data acquisition time of a 4DCBCT scan and (2) the relationship between the accuracy of the extracted motion trajectories and the number of phase bins used to sort projection data. These aims will be applied to three different 4DCBCT methods: conventional filtered backprojection reconstruction (FBP), FBP with McKinnon-Bates correction (MB) and prior image constrained compressed sensing (PICCS) reconstruction. A hybrid phantom consisting of realistic chest anatomy and a moving elliptical object with known 3D motion trajectories was constructed by superimposing the analytical projection data of the moving object to the simulated projection data from a chest CT volume dataset. CBCT scans with gantry rotation times from 1 to 4 min were simulated, and the generated projection data were sorted into 5, 10 and 20 phase bins before different methods were used to reconstruct 4D images. The motion trajectories of the moving object were extracted using a fast free-form deformable registration algorithm. The root mean square errors (RMSE) of the extracted motion trajectories were evaluated for all simulated cases to quantitatively study the performance. The results demonstrate (1) longer acquisition times result in more accurate motion delineation

  19. A computational study of surface adsorption and desorption

    NASA Astrophysics Data System (ADS)

    Wang, Lin-Lin

    In this work, the phenomena of surface adsorption and desorption have been studied by various computational methods. Large-scale density functional calculations with the local density approximation have been applied to investigate the energetics and electronic structure of a C60 monolayer adsorbed on noble metal (111) surfaces. In all cases, the most energetically preferred adsorption configuration corresponds to a hexagon of C60 adsorbing on an hcp site. A small amount of electronic charge transfer of 0.8, 0.5 and 0.2 electrons per molecule from the Cu(111), Ag(111) and Au(111) surfaces to C60 has been found. We also find that the work function decreases by 0.1 eV on Cu(111) surface, increases by 0.1 eV on Ag(111) surface and decreases by 0.6 eV on Au(111) surface upon the adsorption of a C60 monolayer. The puzzling work function change is well explained by a close examination of the surface dipole formation due to electron density redistribution in the interface region. Potential sputtering on the lithium fluoride (LiF) (100) surface by slow highly charged ions has been studied via molecular dynamics (MD) simulations. A model that is different from the conventional MD is formulated to allow electrons to be in the ground state as well as the low-lying excited states. The interatomic potential energy functions are obtained by a high-level quantum chemistry method. The results from MD simulations demonstrate that the so-called defect-mediated sputtering model provides a qualitatively correct picture. The simulations provide quantitative descriptions in which neutral particles dominate the sputtering yield by 99%, in agreement with experiments. An embedding atom-jellium model has been formulated into a multiscale simulation scheme to treat only the top metal surface layers in atomistic pseudopotential and the rest of the surface in a jellium model. The calculated work functions of Al and Cu clean surfaces agree well with the all-atomistic calculations. The multiscale

  20. Computer analysis of lighting style in fine art: steps towards inter-artist studies

    NASA Astrophysics Data System (ADS)

    Stork, David G.

    2011-03-01

    Stylometry in visual art-the mathematical description of artists' styles - has been based on a number of properties of works, such as color, brush stroke shape, visual texture, and measures of contours' curvatures. We introduce the concept of quantitative measures of lighting, such as statistical descriptions of spatial coherence, diuseness, and so forth, as properties of artistic style. Some artists of the high Renaissance, such as Leonardo, worked from nature and strove to render illumination "faithfully" photorealists, such as Richard Estes, worked from photographs and duplicated the "physics based" lighting accurately. As such, each had dierent motivations, methodologies, stagings, and "accuracies" in rendering lighting clues. Perceptual studies show that observers are poor judges of properties of lighting in photographs such as consistency (and thus by extension in paintings as well); computer methods such as rigorous cast-shadow analysis, occluding-contour analysis and spherical harmonic based estimation of light fields can be quite accurate. For this reasons, computer lighting analysis can provide a new tools for art historical studies. We review lighting analysis in paintings such as Vermeer's Girl with a pearl earring, de la Tour's Christ in the carpenter's studio, Caravaggio's Magdalen with the smoking flame and Calling of St. Matthew) and extend our corpus to works where lighting coherence is of interest to art historians, such as Caravaggio's Adoration of the Shepherds or Nativity (1609) in the Capuchin church of Santa Maria degli Angeli. Our measure of lighting coherence may help reveal the working methods of some artists and in diachronic studies of individual artists. We speculate on artists and art historical questions that may ultimately profit from future renements to these new computational tools.

  1. Comparative study of ultrasound and computed tomography for incidentally detecting diffuse thyroid disease.

    PubMed

    Kim, Dong Wook; Jung, Soo Jin; Ha, Tae Kwun; Park, Ha Kyoung; Kang, Taewoo

    2014-08-01

    The aim of this study was to compare the diagnostic values of thyroid ultrasound (US) and neck computed tomography (CT) in incidentally detecting diffuse thyroid disease (DTD). A single radiologist made US and CT diagnoses of incidentally detected DTD in 130 consecutive patients before thyroidectomy for various malignancies. Histopathologic examinations confirmed normal thyroid (n = 80), Hashimoto thyroiditis (n = 20), non-Hashimoto lymphocytic thyroiditis (n = 28) and diffuse hyperplasia (n = 2). Receiver operating characteristic curves revealed that the best diagnostic indices of both imaging methods were achieved on the basis of two or more abnormal imaging findings. The sensitivity, specificity and accuracy of US and CT in incidentally detecting DTD by this classification were 72% and 72%, 87.5% and 91.3% and 81.5% and 83.8%, respectively. Thyroid US and neck CT have similar diagnostic values for differentiating incidental DTD from normal thyroid.

  2. Transcription closed and open complex dynamics studies reveal balance between genetic determinants and co-factors.

    PubMed

    Sala, Adrien; Shoaib, Muhammad; Anufrieva, Olga; Mutharasu, Gnanavel; Jahan Hoque, Rawnak; Yli-Harja, Olli; Kandhavelu, Meenakshisundaram

    2015-05-19

    In E. coli, promoter closed and open complexes are key steps in transcription initiation, where magnesium-dependent RNA polymerase catalyzes RNA synthesis. However, the exact mechanism of initiation remains to be fully elucidated. Here, using single mRNA detection and dual reporter studies, we show that increased intracellular magnesium concentration affects Plac initiation complex formation resulting in a highly dynamic process over the cell growth phases. Mg2+ regulates transcription transition, which modulates bimodality of mRNA distribution in the exponential phase. We reveal that Mg2+ regulates the size and frequency of the mRNA burst by changing the open complex duration. Moreover, increasing magnesium concentration leads to higher intrinsic and extrinsic noise in the exponential phase. RNAP-Mg2+ interaction simulation reveals critical movements creating a shorter contact distance between aspartic acid residues and Nucleotide Triphosphate residues and increasing electrostatic charges in the active site. Our findings provide unique biophysical insights into the balanced mechanism of genetic determinants and magnesium ion in transcription initiation regulation during cell growth.

  3. Transcription closed and open complex dynamics studies reveal balance between genetic determinants and co-factors

    NASA Astrophysics Data System (ADS)

    Sala, Adrien; Shoaib, Muhammad; Anufrieva, Olga; Mutharasu, Gnanavel; Jahan Hoque, Rawnak; Yli-Harja, Olli; Kandhavelu, Meenakshisundaram

    2015-05-01

    In E. coli, promoter closed and open complexes are key steps in transcription initiation, where magnesium-dependent RNA polymerase catalyzes RNA synthesis. However, the exact mechanism of initiation remains to be fully elucidated. Here, using single mRNA detection and dual reporter studies, we show that increased intracellular magnesium concentration affects Plac initiation complex formation resulting in a highly dynamic process over the cell growth phases. Mg2+ regulates transcription transition, which modulates bimodality of mRNA distribution in the exponential phase. We reveal that Mg2+ regulates the size and frequency of the mRNA burst by changing the open complex duration. Moreover, increasing magnesium concentration leads to higher intrinsic and extrinsic noise in the exponential phase. RNAP-Mg2+ interaction simulation reveals critical movements creating a shorter contact distance between aspartic acid residues and Nucleotide Triphosphate residues and increasing electrostatic charges in the active site. Our findings provide unique biophysical insights into the balanced mechanism of genetic determinants and magnesium ion in transcription initiation regulation during cell growth.

  4. Comparative study of the human ficolins reveals unique features of Ficolin-3 (Hakata antigen).

    PubMed

    Hummelshoj, Tina; Fog, Lea Munthe; Madsen, Hans O; Sim, Robert B; Garred, Peter

    2008-03-01

    The ficolins and mannose-binding lectin (MBL) are collagen-like defence proteins that serve as recognition molecules in lectin complement pathway. Differential features that may indicate diverse functions of these proteins are poorly understood. In this study we compared important biological features of the ficolins and MBL. We investigated the tissue distribution of the FCN1-3 and the MBL2 genes encoding the ficolins and MBL by quantitative PCR. Recombinant proteins were produced and structural and biological characteristics were investigated and compared. Our main findings were that FCN3 mRNA was highly expressed in the liver and lung compared with the other genes revealing the lung as the tissue with the highest FCN3 expression pattern. Ficolin-3 revealed higher complement activating capacity compared with Ficolin-2, MBL and Ficolin-1 and was highly resistant to bacterial collagenase treatment, which is different from the other ficolins and MBL. We discovered several unique properties of Ficolin-3 showing that FCN3 is the most highly expressed gene in liver and lung among the lectin complement pathway initiators. Moreover, Ficolin-3 has a high complement activating potential and is the only collagenase proteolytic resistant molecule among the lectin complement pathway initiators.

  5. Health behavior changes after genetic risk assessment for Alzheimer disease: The REVEAL Study.

    PubMed

    Chao, Serena; Roberts, J Scott; Marteau, Theresa M; Silliman, Rebecca; Cupples, L Adrienne; Green, Robert C

    2008-01-01

    Risk information for Alzheimer disease (AD) may be communicated through susceptibility gene disclosure, even though this is not currently in clinical use. The REVEAL Study is the first randomized clinical trial of risk assessment for AD with apolipoprotein E (APOE) genotype and numerical risk estimate disclosure. We examined whether APOE genotype and numerical risk disclosure to asymptomatic individuals at high risk for AD alters health behaviors. One hundred sixty-two participants were randomized to either intervention (APOE disclosure) or control (no genotype disclosure) groups. Subjects in both groups received numerical lifetime risk estimates of future AD development based on sex and family history of AD. The intervention group received their APOE genotype. Subjects were informed that no proven preventive measures for AD existed and given an information sheet on preventative therapies under investigation. Participants who learned they were epsilon 4 positive were significantly more likely than epsilon 4 negative participants to report AD-specific health behavior change 1 year after disclosure (adjusted odds ratio: 2.73; 95% confidence interval: 1.14, 6.54; P=0.02). Post hoc analyses revealed similar significant associations between numerical lifetime risk estimates and self-report of AD-specific health behavior change. Despite lack of preventive measures for AD, knowledge of APOE genotype, numerical lifetime risk, or both, influences health behavior.

  6. Fault-tolerant building-block computer study

    NASA Technical Reports Server (NTRS)

    Rennels, D. A.

    1978-01-01

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

  7. Significant changes in combined consistent biomarkers and computed tomography angiography revealed during an interval of 6months before abdominal aortic aneurysm rupture.

    PubMed

    Szumilowicz, Pawel; Wiernicki, Ireneusz; Kazimierczak, Arkadiusz; Golubinska-Szemitko, Elzbieta; Zurkowska, Joanna; Kasprzak, Piotr

    2017-02-28

    The most commonly used predictor of rupture of abdominal aortic aneurysm (AAA) is the diameter, but this does not correlate well with the risk of rupture. Therefore, in order to make further improvements in clinical decisions regarding AAA patients, the development of additional predictive tools other than aneurysm size alone is needed. We herein report a case of a 72-year-old man with AAA that underwent rupture transformation during six months. We review the morphological features changes detected by computed tomography and also observe several alters circulating biomarkers at the same time. In the study presented essentially an association of those combined parameters with the risk of AAA impending rupture.

  8. Mind the gap: an attempt to bridge computational and neuroscientific approaches to study creativity

    PubMed Central

    Wiggins, Geraint A.; Bhattacharya, Joydeep

    2014-01-01

    Creativity is the hallmark of human cognition and is behind every innovation, scientific discovery, piece of music, artwork, and idea that have shaped our lives, from ancient times till today. Yet scientific understanding of creative processes is quite limited, mostly due to the traditional belief that considers creativity as a mysterious puzzle, a paradox, defying empirical enquiry. Recently, there has been an increasing interest in revealing the neural correlates of human creativity. Though many of these studies, pioneering in nature, help demystification of creativity, but the field is still dominated by popular beliefs in associating creativity with “right brain thinking”, “divergent thinking”, “altered states” and so on (Dietrich and Kanso, 2010). In this article, we discuss a computational framework for creativity based on Baars’ Global Workspace Theory (GWT; Baars, 1988) enhanced with mechanisms based on information theory. Next we propose a neurocognitive architecture of creativity with a strong focus on various facets (i.e., unconscious thought theory, mind wandering, spontaneous brain states) of un/pre-conscious brain responses. Our principal argument is that pre-conscious creativity happens prior to conscious creativity and the proposed computational model may provide a mechanism by which this transition is managed. This integrative approach, albeit unconventional, will hopefully stimulate future neuroscientific studies of the inscrutable phenomenon of creativity. PMID:25104930

  9. Mind the gap: an attempt to bridge computational and neuroscientific approaches to study creativity.

    PubMed

    Wiggins, Geraint A; Bhattacharya, Joydeep

    2014-01-01

    Creativity is the hallmark of human cognition and is behind every innovation, scientific discovery, piece of music, artwork, and idea that have shaped our lives, from ancient times till today. Yet scientific understanding of creative processes is quite limited, mostly due to the traditional belief that considers creativity as a mysterious puzzle, a paradox, defying empirical enquiry. Recently, there has been an increasing interest in revealing the neural correlates of human creativity. Though many of these studies, pioneering in nature, help demystification of creativity, but the field is still dominated by popular beliefs in associating creativity with "right brain thinking", "divergent thinking", "altered states" and so on (Dietrich and Kanso, 2010). In this article, we discuss a computational framework for creativity based on Baars' Global Workspace Theory (GWT; Baars, 1988) enhanced with mechanisms based on information theory. Next we propose a neurocognitive architecture of creativity with a strong focus on various facets (i.e., unconscious thought theory, mind wandering, spontaneous brain states) of un/pre-conscious brain responses. Our principal argument is that pre-conscious creativity happens prior to conscious creativity and the proposed computational model may provide a mechanism by which this transition is managed. This integrative approach, albeit unconventional, will hopefully stimulate future neuroscientific studies of the inscrutable phenomenon of creativity.

  10. A computational study of the TiO2 molecule

    NASA Technical Reports Server (NTRS)

    Ramana, M. V.; Phillips, D. H.

    1988-01-01

    A computational investigation of the ground 1A1 and lowest energy B2 states of the titanium dioxide molecule has been carried out. The treatment utilized SCF calculations in an extended basis followed by a CI treatment for each geometry. The ground state geometry agrees well with experiment, while the agreement between the computed vibrational frequency nu1 and the experimental value for a matrix isolated TiO2 is less satisfactory. Population analysis for the ground state indicates less than one excess electron on each oxygen atom. The first excited state has a linear geometry and the singlet and triplet are essentially degenerate.

  11. Computational Study of Nonequilibrium Chemistry in High Temperature Flows

    NASA Astrophysics Data System (ADS)

    Doraiswamy, Sriram

    Recent experimental measurements in the reflected shock tunnel CUBRC LENS-I facility raise questions about our ability to correctly model the recombination processes in high enthalpy flows. In the carbon dioxide flow, the computed shock standoff distance over the Mars Science Laboratory (MSL) shape was less than half of the experimental result. For the oxygen flows, both pressure and heat transfer data on the double cone geometry were not correctly predicted. The objective of this work is to investigate possible reasons for these discrepancies. This process involves systematically addressing different factors that could possibly explain the differences. These factors include vibrational modeling, role of electronic states and chemistry-vibrational coupling in high enthalpy flows. A state-specific vibrational model for CO2, CO, O2 and O system is devised by taking into account the first few vibrational states of each species. All vibrational states with energies at or below 1 eV are included in the present work. Of the three modes of vibration in CO2 , the antisymmetric mode is considered separately from the symmetric stretching mode and the doubly degenerate bending modes. The symmetric and the bending modes are grouped together since the energy transfer rates between the two modes are very large due to Fermi resonance. The symmetric and bending modes are assumed to be in equilibrium with the translational and rotational modes. The kinetic rates for the vibrational-translation energy exchange reactions, and the intermolecular and intramolecular vibrational-vibrational energy exchange reactions are based on experimental data to the maximum extent possible. Extrapolation methods are employed when necessary. This vibrational model is then coupled with an axisymmetric computational fluid dynamics code to study the expansion of CO2 in a nozzle. The potential role of low lying electronic states is also investigated. Carbon dioxide has a single excited state just below

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

    ERIC Educational Resources Information Center

    Haworth, Ian S.; And Others

    1997-01-01

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

  13. The Study of Surface Computer Supported Cooperative Work and Its Design, Efficiency, and Challenges

    ERIC Educational Resources Information Center

    Hwang, Wu-Yuin; Su, Jia-Han

    2012-01-01

    In this study, a Surface Computer Supported Cooperative Work paradigm is proposed. Recently, multitouch technology has become widely available for human-computer interaction. We found it has great potential to facilitate more awareness of human-to-human interaction than personal computers (PCs) in colocated collaborative work. However, other…

  14. The Role and Design of Computer Studies in a Research-Oriented Translation Program.

    ERIC Educational Resources Information Center

    Meyer, Ingrid

    1991-01-01

    Notes the increasing use of computers by professional translators. Argues that instruction in translation systems should prepare students for both the receiving and production ends of machine translation systems. Discusses considerations for the design of computer translation studies. Includes a course outline from a computer translation seminar.…

  15. Educational Computer Use in Leisure Contexts: A Phenomenological Study of Adolescents' Experiences at Internet Cafes

    ERIC Educational Resources Information Center

    Cilesiz, Sebnem

    2009-01-01

    Computer use is a widespread leisure activity for adolescents. Leisure contexts, such as Internet cafes, constitute specific social environments for computer use and may hold significant educational potential. This article reports a phenomenological study of adolescents' experiences of educational computer use at Internet cafes in Turkey. The…

  16. The Effects of Integrating Service Learning into Computer Science: An Inter-Institutional Longitudinal Study

    ERIC Educational Resources Information Center

    Payton, Jamie; Barnes, Tiffany; Buch, Kim; Rorrer, Audrey; Zuo, Huifang

    2015-01-01

    This study is a follow-up to one published in computer science education in 2010 that reported preliminary results showing a positive impact of service learning on student attitudes associated with success and retention in computer science. That paper described how service learning was incorporated into a computer science course in the context of…

  17. Case Studies of Auditing in a Computer-Based Systems Environment.

    ERIC Educational Resources Information Center

    General Accounting Office, Washington, DC.

    In response to a growing need for effective and efficient means for auditing computer-based systems, a number of studies dealing primarily with batch-processing type computer operations have been conducted to explore the impact of computers on auditing activities in the Federal Government. This report first presents some statistical data on…

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

    ERIC Educational Resources Information Center

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

    2012-01-01

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

  19. A study of standard building blocks for the design of fault-tolerant distributed computer systems

    NASA Technical Reports Server (NTRS)

    Rennels, D. A.; Avizienis, A.; Ercegovac, M.

    1978-01-01

    This paper presents the results of a study that has established a standard set of four semiconductor VLSI building-block circuits. These circuits can be assembled with off-the-shelf microprocessors and semiconductor memory modules into fault-tolerant distributed computer configurations. The resulting multi-computer architecture uses self-checking computer modules backed up by a limited number of spares. A redundant bus system is employed for communication between computer modules.

  20. Revealing Nature’s Synthetic Potential Through the Study of Ribosomal Natural Product Biosynthesis

    PubMed Central

    Dunbar, Kyle L.; Mitchell, Douglas A.

    2013-01-01

    Ribosomally synthesized posttranslationally modified peptides (RiPPs) are a rapidly growing class of natural products with diverse structures and activities. In recent years, a great deal of progress has been made in elucidating the biosynthesis of various RiPP family members. As with the study of nonribosomal peptide and polyketide biosynthetic enzymes, these investigations have led to the discovery of entirely new biological chemistry. With each unique enzyme investigated, a more complex picture of Nature’s synthetic potential is revealed. This review focuses on recent reports (since 2008) that have changed the way that we think about ribosomal natural product biosynthesis and the enzymology of complex bond-forming reactions. PMID:23286465

  1. Computational Study of Axisymmetric Off-Design Nozzle Flows

    NASA Technical Reports Server (NTRS)

    DalBello, Teryn; Georgiadis, Nicholas; Yoder, Dennis; Keith, Theo

    2003-01-01

    Computational Fluid Dynamics (CFD) analyses of axisymmetric circular-arc boattail nozzles operating off-design at transonic Mach numbers have been completed. These computations span the very difficult transonic flight regime with shock-induced separations and strong adverse pressure gradients. External afterbody and internal nozzle pressure distributions computed with the Wind code are compared with experimental data. A range of turbulence models were examined, including the Explicit Algebraic Stress model. Computations have been completed at freestream Mach numbers of 0.9 and 1.2, and nozzle pressure ratios (NPR) of 4 and 6. Calculations completed with variable time-stepping (steady-state) did not converge to a true steady-state solution. Calculations obtained using constant timestepping (timeaccurate) indicate less variations in flow properties compared with steady-state solutions. This failure to converge to a steady-state solution was the result of using variable time-stepping with large-scale separations present in the flow. Nevertheless, time-averaged boattail surface pressure coefficient and internal nozzle pressures show reasonable agreement with experimental data. The SST turbulence model demonstrates the best overall agreement with experimental data.

  2. Efficiency of Computer Literacy Course in Communication Studies

    ERIC Educational Resources Information Center

    Gümüs, Agah; Özad, Bahire Efe

    2004-01-01

    Following the exponential increase in the global usage of the Internet as one of the main tools for communication, the Internet established itself as the fourth most powerful media. In a similar vein, computer literacy education and related courses established themselves as the essential components of the Faculty of Communication and Media…

  3. Case Study of a Computer Based Examination System

    ERIC Educational Resources Information Center

    Fluck, Andrew; Pullen, Darren; Harper, Colleen

    2009-01-01

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

  4. "It's Boring": Female Students' Experience of Studying ICT and Computing

    ERIC Educational Resources Information Center

    Pau, Reena; Hall, Wendy; Grace, Marcus

    2011-01-01

    The declining number of women in computing is a cause for concern for those in education and the IT industry. A diverse workforce is necessary for there to be a creative balance in the IT industry. The reasons for this decline are varied and can be attributed to factors such as schooling, parental influences and the media. This article focuses on…

  5. Elementary School Computer Literacy: A Case Study of Success.

    ERIC Educational Resources Information Center

    Lanza, Leonard G.

    1983-01-01

    Describes the preparation and successful introduction into an elementary school of a computer literacy program for pupils and parents. Preparation involved setting up a steering committee, purchase of 18 microcomputers and one disk drive unit, providing inservice training for class teachers, and production of a fifth-grade teaching manual. (EAO)

  6. Framework for Computer Assisted Instruction Courseware: A Case Study.

    ERIC Educational Resources Information Center

    Betlach, Judith A.

    1987-01-01

    Systematically investigates, defines, and organizes variables related to production of internally designed and implemented computer assisted instruction (CAI) courseware: special needs of users; costs; identification and definition of realistic training needs; CAI definition and design methodology; hardware and software requirements; and general…

  7. Beowulf Cluster for Computational Corrosion and Catalysis Studies

    DTIC Science & Technology

    2007-11-02

    This DURIP-funded Beowulf cluster will enhance our AFOSR-funded research in several areas. Large-scale modeling of complex systems in the areas of...high accuracy on real-world systems requires significant computational cost. This grant, by funding a Beowulf cluster supercomputing environment, has

  8. Structural Studies of FlaA1 from Helicobacter Pylori Reveal the Mechanism for Inverting 4,6-dehydratase Activity

    SciTech Connect

    Ishiyama,N.; Creuzenet, C.; Miller, W.; Demendi, M.; Anderson, E.; Harauz, G.; Lam, J.; Berghuis, A.

    2006-01-01

    FlaA1 from the human pathogen Helicobacter pylori is an enzyme involved in saccharide biosynthesis that has been shown to be essential for pathogenicity. Here we present five crystal structures of FlaA1 in the presence of substrate, inhibitors, and bound cofactor, with resolutions ranging from 2.8 to 1.9 {angstrom}. These structures reveal that the enzyme is a novel member of the short-chain dehydrogenase/reductase superfamily. Additional electron microscopy studies show the enzyme to possess a hexameric doughnut-shaped quaternary structure. NMR analyses of 'real time' enzyme-substrate reactions indicate that FlaA1 is a UDP-GlcNAc-inverting 4,6-dehydratase, suggesting that the enzyme catalyzes the first step in the biosynthetic pathway of a pseudaminic acid derivative, which is implicated in protein glycosylation. Guided by evidence from site-directed mutagenesis and computational simulations, a three-step reaction mechanism is proposed that involves Lys-133 functioning as both a catalytic acid and base.

  9. Surface phenomena revealed by in situ imaging: studies from adhesion, wear and cutting

    NASA Astrophysics Data System (ADS)

    Viswanathan, Koushik; Mahato, Anirban; Yeung, Ho; Chandrasekar, Srinivasan

    2017-03-01

    Surface deformation and flow phenomena are ubiquitous in mechanical processes. In this work we present an in situ imaging framework for studying a range of surface mechanical phenomena at high spatial resolution and across a range of time scales. The in situ framework is capable of resolving deformation and flow fields quantitatively in terms of surface displacements, velocities, strains and strain rates. Three case studies are presented demonstrating the power of this framework for studying surface deformation. In the first, the origin of stick-slip motion in adhesive polymer interfaces is investigated, revealing a intimate link between stick-slip and surface wave propagation. Second, the role of flow in mediating formation of surface defects and wear particles in metals is analyzed using a prototypical sliding process. It is shown that conventional post-mortem observation and inference can lead to erroneous conclusions with regard to formation of surface cracks and wear particles. The in situ framework is shown to unambiguously capture delamination wear in sliding. Third, material flow and surface deformation in a typical cutting process is analyzed. It is shown that a long-standing problem in the cutting of annealed metals is resolved by the imaging, with other benefits such as estimation of energy dissipation and power from the flow fields. In closure, guidelines are provided for profitably exploiting in situ observations to study large-strain deformation, flow and friction phenomena at surfaces that display a variety of time-scales.

  10. Seed metabolomic study reveals significant metabolite variations and correlations among different soybean cultivars.

    PubMed

    Lin, Hong; Rao, Jun; Shi, Jianxin; Hu, Chaoyang; Cheng, Fang; Wilson, Zoe A; Zhang, Dabing; Quan, Sheng

    2014-09-01

    Soybean [Glycine max (L.) Merr.] is one of the world's major crops, and soybean seeds are a rich and important resource for proteins and oils. While "omics" studies, such as genomics, transcriptomics, and proteomics, have been widely applied in soybean molecular research, fewer metabolomic studies have been conducted for large-scale detection of low molecular weight metabolites, especially in soybean seeds. In this study, we investigated the seed metabolomes of 29 common soybean cultivars through combined gas chromatography-mass spectrometry and ultra-performance liquid chromatography-tandem mass spectrometry. One hundred sixty-nine named metabolites were identified and subsequently used to construct a metabolic network of mature soybean seed. Among the 169 detected metabolites, 104 were found to be significantly variable in their levels across tested cultivars. Metabolite markers that could be used to distinguish genetically related soybean cultivars were also identified, and metabolite-metabolite correlation analysis revealed some significant associations within the same or among different metabolite groups. Findings from this work may potentially provide the basis for further studies on both soybean seed metabolism and metabolic engineering to improve soybean seed quality and yield.

  11. Neurobiology of mood, anxiety, and emotions as revealed by studies of a unique antidepressant: tianeptine.

    PubMed

    McEwen, B S; Olié, J P

    2005-06-01

    Recent studies have provided evidence that structural remodeling of certain brain regions is a feature of depressive illness, and the postulated underlying mechanisms contribute to the idea that there is more to antidepressant actions that can be explained exclusively by a monoaminergic hypothesis. This review summarizes recent neurobiological studies on the antidepressant, tianeptine (S-1574, [3-chloro-6-methyl-5,5-dioxo-6,11-dihydro-(c,f)-dibenzo-(1,2-thiazepine)-11-yl) amino]-7 heptanoic acid, sodium salt), a compound with structural similarities to the tricyclic antidepressant agents, the efficacy and good tolerance of which have been clearly established. These studies have revealed that the neurobiological properties of tianeptine involve the dynamic interplay between numerous neurotransmitter systems, as well as a critical role of structural and functional plasticity in the brain regions that permit the full expression of emotional learning. Although the story is far from complete, the schema underlying the effect of tianeptine on central plasticity is the most thoroughly studied of any antidepressants. Effects of tianeptine on neuronal excitability, neuroprotection, anxiety, and memory have also been found. Together with clinical data on the efficacy of tianeptine as an antidepressant, these actions offer insights into how compounds like tianeptine may be useful in the treatment of neurobiological features of depressive disorders.

  12. HIGH-PERFORMANCE COMPUTING FOR THE STUDY OF EARTH AND ENVIRONMENTAL SCIENCE MATERIALS USING SYNCHROTRON X-RAY COMPUTED MICROTOMOGRAPHY.

    SciTech Connect

    FENG,H.; JONES,K.W.; MCGUIGAN,M.; SMITH,G.J.; SPILETIC,J.

    2001-10-12

    Synchrotron x-ray computed microtomography (CMT) is a non-destructive method for examination of rock, soil, and other types of samples studied in the earth and environmental sciences. The high x-ray intensities of the synchrotron source make possible the acquisition of tomographic volumes at a high rate that requires the application of high-performance computing techniques for data reconstruction to produce the three-dimensional volumes, for their visualization, and for data analysis. These problems are exacerbated by the need to share information between collaborators at widely separated locations over both local and tide-area networks. A summary of the CMT technique and examples of applications are given here together with a discussion of the applications of high-performance computing methods to improve the experimental techniques and analysis of the data.

  13. Computational studies of competing phases in model Hamiltonians

    NASA Astrophysics Data System (ADS)

    Jiang, Mi

    Model Hamiltonians play an important role in our understanding of both quantum and classical systems, such as strongly correlated unconventional superconductivity, quantum magnetism, non-fermi liquid heavy fermion materials and classical magnetic phase transitions. The central problem is how models with many degrees of freedom choose between competing ground states, e.g. magnetic, superconducting, metallic, insulating as the degree of thermal and quantum fluctuations is varied. This dissertation focuses on the numerical investigation of several important model Hamiltonians. Specifically, we used the determinant Quantum Monte Carlo (DQMC) to study three Hubbard-like models: the Fermi-Hubbard model with two regions of different interaction strength, the Fermi-Hubbard model with a spin-dependent band structure, and the related periodic Anderson model (PAM). The first model used was to explore inter-penetration of metallic and Mott insulator physics across a Metal-Mott Insulator interface by computing the magnetic properties and spectral functions. As a minimal model of a half metallic magnet, the second model was used to explore the impact of on-site Hubbard interaction U, finite temperature, and an external (Zeeman) magnetic field on a bilayer tight-binding model with spin-dependent hybridization. We use PAM to study the Knight shift anomaly in heavy fermion materials found in Nuclear magnetic resonance (NMR) experiments and confirm several predictions of the two-fluid theory accounting for the anomaly. Another application of the Hubbard model described in this dissertation is the investigation on the effects of spin-dependent disorder on s-wave superconductors based on the attractive Hubbard model. Here we used the Bogoliubov-de Gennes (BdG) self-consistent approach instead of quantum simulations. The spin-dependent random potential was shown to induce distinct transitions at which the energy gap and average order parameter vanish, generating an intermediate gapless

  14. Markov models of the apo-MDM2 lid region reveal diffuse yet two-state binding dynamics and receptor poses for computational docking

    NASA Astrophysics Data System (ADS)

    Mukherjee, Sudipto; Pantelopulos, George A.; Voelz, Vincent A.

    2016-08-01

    MDM2 is a negative regulator of p53 activity and an important target for cancer therapeutics. The N-terminal lid region of MDM2 modulates interactions with p53 via competition for its binding cleft, exchanging slowly between docked and undocked conformations in the absence of p53. To better understand these dynamics, we constructed Markov State Models (MSMs) from large collections of unbiased simulation trajectories of apo-MDM2, and find strong evidence for diffuse, yet two-state folding and binding of the N-terminal region to the p53 receptor site. The MSM also identifies holo-like receptor conformations highly suitable for computational docking, despite initiating trajectories from closed-cleft receptor structures unsuitable for docking. Fixed-anchor docking studies using a test set of high-affinity small molecules and peptides show simulated receptor ensembles achieve docking successes comparable to cross-docking studies using crystal structures of receptors bound by alternative ligands. For p53, the best-scoring receptor structures have the N-terminal region lid region bound in a helical conformation mimicking the bound structure of p53, suggesting lid region association induces receptor conformations suitable for binding. These results suggest that MD + MSM approaches can sample binding-competent receptor conformations suitable for computational peptidomimetic design, and that inclusion of disordered regions may be essential to capturing the correct receptor dynamics.

  15. Markov models of the apo-MDM2 lid region reveal diffuse yet two-state binding dynamics and receptor poses for computational docking

    PubMed Central

    Mukherjee, Sudipto; Pantelopulos, George A.; Voelz, Vincent A.

    2016-01-01

    MDM2 is a negative regulator of p53 activity and an important target for cancer therapeutics. The N-terminal lid region of MDM2 modulates interactions with p53 via competition for its binding cleft, exchanging slowly between docked and undocked conformations in the absence of p53. To better understand these dynamics, we constructed Markov State Models (MSMs) from large collections of unbiased simulation trajectories of apo-MDM2, and find strong evidence for diffuse, yet two-state folding and binding of the N-terminal region to the p53 receptor site. The MSM also identifies holo-like receptor conformations highly suitable for computational docking, despite initiating trajectories from closed-cleft receptor structures unsuitable for docking. Fixed-anchor docking studies using a test set of high-affinity small molecules and peptides show simulated receptor ensembles achieve docking successes comparable to cross-docking studies using crystal structures of receptors bound by alternative ligands. For p53, the best-scoring receptor structures have the N-terminal region lid region bound in a helical conformation mimicking the bound structure of p53, suggesting lid region association induces receptor conformations suitable for binding. These results suggest that MD + MSM approaches can sample binding-competent receptor conformations suitable for computational peptidomimetic design, and that inclusion of disordered regions may be essential to capturing the correct receptor dynamics. PMID:27538695

  16. Markov models of the apo-MDM2 lid region reveal diffuse yet two-state binding dynamics and receptor poses for computational docking.

    PubMed

    Mukherjee, Sudipto; Pantelopulos, George A; Voelz, Vincent A

    2016-08-19

    MDM2 is a negative regulator of p53 activity and an important target for cancer therapeutics. The N-terminal lid region of MDM2 modulates interactions with p53 via competition for its binding cleft, exchanging slowly between docked and undocked conformations in the absence of p53. To better understand these dynamics, we constructed Markov State Models (MSMs) from large collections of unbiased simulation trajectories of apo-MDM2, and find strong evidence for diffuse, yet two-state folding and binding of the N-terminal region to the p53 receptor site. The MSM also identifies holo-like receptor conformations highly suitable for computational docking, despite initiating trajectories from closed-cleft receptor structures unsuitable for docking. Fixed-anchor docking studies using a test set of high-affinity small molecules and peptides show simulated receptor ensembles achieve docking successes comparable to cross-docking studies using crystal structures of receptors bound by alternative ligands. For p53, the best-scoring receptor structures have the N-terminal region lid region bound in a helical conformation mimicking the bound structure of p53, suggesting lid region association induces receptor conformations suitable for binding. These results suggest that MD + MSM approaches can sample binding-competent receptor conformations suitable for computational peptidomimetic design, and that inclusion of disordered regions may be essential to capturing the correct receptor dynamics.

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

    PubMed

    Lo, Rabindranath; Ganguly, Bishwajit

    2015-02-01

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

  18. Computer Simulation Studies of Ion Channels at High Temperatures

    NASA Astrophysics Data System (ADS)

    Song, Hyun Deok

    The gramicidin channel is the smallest known biological ion channel, and it exhibits cation selectivity. Recently, Dr. John Cuppoletti's group at the University of Cincinnati showed that the gramicidin channel can function at high temperatures (360 ˜ 380K) with significant currents. This finding may have significant implications for fuel cell technology. In this thesis, we have examined the gramicidin channel at 300K, 330K, and 360K by computer simulation. We have investigated how the temperature affects the current and differences in magnitude of free energy between the two gramicidin forms, the helical dimer (HD) and the double helix (DH). A slight decrease of the free energy barrier inside the gramicidin channel and increased diffusion at high temperatures result in an increase of current. An applied external field of 0.2V/nm along the membrane normal results in directly observable ion transport across the channels at high temperatures for both HD and DH forms. We found that higher temperatures also affect the probability distribution of hydrogen bonds, the bending angle, the distance between dimers, and the size of the pore radius for the helical dimer structure. These findings may be related to the gating of the gramicidin channel. Methanococcus jannaschii (MJ) is a methane-producing thermophile, which was discovered at a depth of 2600m in a Pacific Ocean vent in 1983. It has the ability to thrive at high temperatures and high pressures, which are unfavorable for most life forms. There have been some experiments to study its stability under extreme conditions, but still the origin of the stability of MJ is not exactly known. MJ0305 is the chloride channel protein from the thermophile MJ. After generating a structure of MJ0305 by homology modeling based on the Ecoli ClC templates, we examined the thermal stability, and the network stability from the change of network entropy calculated from the adjacency matrices of the protein. High temperatures increase the

  19. Products and mechanism of acene dimerization. A computational study.

    PubMed

    Zade, Sanjio S; Zamoshchik, Natalia; Reddy, A Ravikumar; Fridman-Marueli, Galit; Sheberla, Dennis; Bendikov, Michael

    2011-07-20

    The high reactivity of acenes can reduce their potential applications in the field of molecular electronics. Although pentacene is an important material for use in organic field-effect transistors because of its high charge mobility, its reactivity is a major disadvantage hindering the development of pentacene applications. In this study, several reaction pathways for the thermal dimerization of acenes were considered computationally. The formation of acene dimers via a central benzene ring and the formation of acene-based polymers were found to be the preferred pathways, depending on the length of the monomer. Interestingly, starting from hexacene, acene dimers are thermodynamically disfavored products, and the reaction pathway is predicted to proceed instead via a double cycloaddition reaction (polymerization) to yield acene-based polymers. A concerted asynchronous reaction mechanism was found for benzene and naphthalene dimerization, while a stepwise biradical mechanism was predicted for the dimerization of anthracene, pentacene, and heptacene. The biradical mechanism for dimerization of anthracene and pentacene proceeds via syn or anti transition states and biradical minima through stepwise biradical pathways, while dimerization of heptacene proceeds via asynchronous ring closure of the complex formed by two heptacene molecules. The activation barriers for thermal dimerization decrease rapidly with increasing acene chain length and are calculated (at M06-2X/6-31G(d)+ZPVE) to be 77.9, 57.1, 33.3, -0.3, and -12.1 kcal/mol vs two isolated acene molecules for benzene, naphthalene, anthracene, pentacene, and heptacene, respectively. If activation energy is calculated vs the initially formed complex of two acene molecules, then the calculated barriers are 80.5, 63.2, 43.7, 16.7, and 12.3 kcal/mol. Dimerization is exothermic from anthracene onward, but it is endothermic at the terminal rings, even for heptacene. Phenyl substitution at the most reactive meso

  20. A study revealing the key aroma compounds of steamed bread made by Chinese traditional sourdough.

    PubMed

    Zhang, Guo-Hua; Wu, Tao; Sadiq, Faizan A; Yang, Huan-Yi; Liu, Tong-Jie; Ruan, Hui; He, Guo-Qing

    Aroma of Chinese steamed bread (CSB) is one of the important parameters that determines the overall quality attributes and consumer acceptance. However, the aroma profile of CSB still remains poorly understood, mainly because of relying on only a single method for aroma extraction in previous studies. Therefore, the objective of this study was to determine the volatile aroma compounds of five different samples of CSB using three different aroma extraction methods, namely solid-phase microextraction (SPME), simultaneous distillation-extraction (SDE), and purge and trap (P&T). All samples showed a unique aroma profile, which could be attributed to their unique microbial consortia. (E)-2-Nonenal and (E,E)-2,4-decadienal were the most prevalent aromatic compounds revealed by SDE, which have not been reported previously, while ethanol and acetic acid proved to be the most dominant compounds by both SPME and P&T. Our approach of combining three different aroma extraction methods provided better insights into the aroma profile of CSB, which had remained largely unknown in previous studies.

  1. A study revealing the key aroma compounds of steamed bread made by Chinese traditional sourdough*

    PubMed Central

    Zhang, Guo-hua; Wu, Tao; Sadiq, Faizan A.; Yang, Huan-yi; Liu, Tong-jie; Ruan, Hui; He, Guo-qing

    2016-01-01

    Aroma of Chinese steamed bread (CSB) is one of the important parameters that determines the overall quality attributes and consumer acceptance. However, the aroma profile of CSB still remains poorly understood, mainly because of relying on only a single method for aroma extraction in previous studies. Therefore, the objective of this study was to determine the volatile aroma compounds of five different samples of CSB using three different aroma extraction methods, namely solid-phase microextraction (SPME), simultaneous distillation–extraction (SDE), and purge and trap (P&T). All samples showed a unique aroma profile, which could be attributed to their unique microbial consortia. (E)-2-Nonenal and (E,E)-2,4-decadienal were the most prevalent aromatic compounds revealed by SDE, which have not been reported previously, while ethanol and acetic acid proved to be the most dominant compounds by both SPME and P&T. Our approach of combining three different aroma extraction methods provided better insights into the aroma profile of CSB, which had remained largely unknown in previous studies. PMID:27704748

  2. The effects of integrating service learning into computer science: an inter-institutional longitudinal study

    NASA Astrophysics Data System (ADS)

    Payton, Jamie; Barnes, Tiffany; Buch, Kim; Rorrer, Audrey; Zuo, Huifang

    2015-07-01

    This study is a follow-up to one published in computer science education in 2010 that reported preliminary results showing a positive impact of service learning on student attitudes associated with success and retention in computer science. That paper described how service learning was incorporated into a computer science course in the context of the Students & Technology in Academia, Research, and Service (STARS) Alliance, an NSF-supported broadening participation in computing initiative that aims to diversify the computer science pipeline through innovative pedagogy and inter-institutional partnerships. The current paper describes how the STARS Alliance has expanded to diverse institutions, all using service learning as a vehicle for broadening participation in computing and enhancing attitudes and behaviors associated with student success. Results supported the STARS model of service learning for enhancing computing efficacy and computing commitment and for providing diverse students with many personal and professional development benefits.

  3. Revealed social preference for potable groundwater: An Eastern Iowa case study

    NASA Astrophysics Data System (ADS)

    Raunikar, R. P.; Bernknopf, R. L.; Forney, W.; Mishra, S.

    2011-12-01

    The spatially explicit land use and land cover information provided by Landsat moderate-resolution land imagery (MRLI) is needed to more efficiently balance the production of goods and services over landscapes. For example, economic trade-offs are needed to provide both clean groundwater resources and other non-environmental goods and services produced by activities that affect the vadose zone and thus contribute to contamination of groundwater. These trade-off choices are made by numerous economic agents and are constrained by many social institutions including governmental regulations at many levels, contractual obligations and traditions. In effect, on a social level, society acts as if it values groundwater by foregoing other goods to protect these resources. The result of the protection afforded to groundwater resources is observable by measuring contamination in well samples. This observed level of groundwater contamination risk is the revealed preference of society as a whole for clean groundwater. We observed the risk of groundwater contamination in a sampling of well data from our study area (35 counties of Eastern Iowa.) We used a proportional hazard model to quantify the nitrate contamination survival implied by the panel of 19,873 well data, where remaining below a 10 mg/ml maximum contamination level (MCL) is defined as survival. We tested the data for evidence that the levels of protection provided to these resources is correlated with aquifer and vadose zone characteristics and geographic location and whether it changed over time and with economic and other conditions. We demonstrate the use of a nitrate conditioned hazard function for projecting the survival of wells based on nitrate exposure information over the 1940 to 2010 time period. We discuss results of simulations of the survival process that demonstrate the economic significance of this approach. We find that aquifer survival has been significantly improving over time. The principle of

  4. Computational study of developing high-quality decision trees

    NASA Astrophysics Data System (ADS)

    Fu, Zhiwei

    2002-03-01

    Recently, decision tree algorithms have been widely used in dealing with data mining problems to find out valuable rules and patterns. However, scalability, accuracy and efficiency are significant concerns regarding how to effectively deal with large and complex data sets in the implementation. In this paper, we propose an innovative machine learning approach (we call our approach GAIT), combining genetic algorithm, statistical sampling, and decision tree, to develop intelligent decision trees that can alleviate some of these problems. We design our computational experiments and run GAIT on three different data sets (namely Socio- Olympic data, Westinghouse data, and FAA data) to test its performance against standard decision tree algorithm, neural network classifier, and statistical discriminant technique, respectively. The computational results show that our approach outperforms standard decision tree algorithm profoundly at lower sampling levels, and achieves significantly better results with less effort than both neural network and discriminant classifiers.

  5. Mathematical Analysis and Computer Program Development for Electromagnetic Science Studies.

    DTIC Science & Technology

    1981-11-01

    interest that needed to be computed was the far-field power pattern of a planar array of electrodes . The derivation of it is carried out belnw. Fig. 3...shows, for a double- electrode array and relevant geometry. As several inve3tigators have shown, radiation into an isotropic medium is often a reasonable...physical approximation to make. and certainly makes the analysis simpler. For the double- electrode array shown in Fig. 3 , we note that Y" + L -1 2. (2

  6. Using Wearable Computers in Shuttle Processing: A Feasibility Study

    NASA Technical Reports Server (NTRS)

    Centeno, Martha A.; Correa, Daisy; Groh-Hammond, Marcia

    2001-01-01

    Shuttle processing operations are performed following prescribed instructions compiled in a Work Authorization Document (WAD). Until very recently, WADs were printed so that they could be properly executed, including the buy off of each and every step by the appropriate authorizing agent. However, with the development of EPICs, Maximo, and PeopleSoft applications, some of these documents are now available in electronic format; hence, it is possible for technicians and engineers to access them on line and buy off the steps electronically. To take full advantage of these developments, technicians need access to such documents at the point of job execution. Body wearable computers present an opportunity to develop a WAD delivery system that enables access while preserving technician's mobility, safety levels, and quality of work done. The primary objectives of this project were to determine if body wearable computers are a feasible delivery system for WADs. More specifically, identify and recommend specific brands of body wearable computers readily available on the market. Thus, this effort has field-tested this technology in two areas of shuttle processing, and it has examined the usability of the technology. Results of two field tests and a Human Factors Usability Test are presented. Section 2 provides a description of the body wearable computer technology. Section 3 presents the test at the Space Shuttle Main Engine (SSME) Shop. Section 4 presents the results of the integration test at the Solid Rocket Boosters Assembly and Refurbishing Facility (SRBARF). Section 5 presents the results of the usability test done at the Operations Support Building (OSB).

  7. Cogeneration computer model assessment: Advanced cogeneration research study

    NASA Technical Reports Server (NTRS)

    Rosenberg, L.

    1983-01-01

    Cogeneration computer simulation models to recommend the most desirable models or their components for use by the Southern California Edison Company (SCE) in evaluating potential cogeneration projects was assessed. Existing cogeneration modeling capabilities are described, preferred models are identified, and an approach to the development of a code which will best satisfy SCE requirements is recommended. Five models (CELCAP, COGEN 2, CPA, DEUS, and OASIS) are recommended for further consideration.

  8. Computational Study of Flow Interactions in Coaxial Rotors

    NASA Technical Reports Server (NTRS)

    Yoon, Seokkwan; Lee, Henry C.; Pulliam, Thomas H.

    2016-01-01

    account for multiple real-world constraints up front in design nor possible to know what performance is possible with a given design. Since unmanned vehicles are sized and optimized for the particular mission, a modern low-fidelity conceptual design and sizing tool that has been used for the design of large helicopters can be used for design of small coaxial rotorcraft. However, unlike most helicopters with single main rotor, the interactions between the upper and lower rotors emerge as an important factor to consider in design because an increase in performance of a multi-rotor system is not proportional to the number of rotors. Interference losses and differences in thrusts between the upper and lower rotors were investigated by theoretical methods as well as a computational fluid dynamics (CFD) method using the Reynolds-Averaged Navier-Stokes (RANS) equations. In this work, hybrid turbulence models are used to investigate the physics of interactions between coaxial rotors and a fuselage that are not well understood. Present study covers not only small-scale drones but also large-scale coaxial rotors for heavy-lifting missions. Considering the recently proposed FAA drone rules that require the flight only in visual line-of-sight, a large multirotor might be used as an airborne carrier for launch and recovery of unmanned aircraft systems with a human operator onboard. For applications to civil operations, their aerodynamic performance and noise levels need to be assessed. Noise is one of the largest limiting factors to rotorcraft operations in urban area. Since the high-frequency noise of multi-rotors may increase the annoyance, noise may turn out to be a key issue that must be addressed for market acceptability. One of the objectives of the present work is to study the effects of inter-rotor spacing and collectives on the performance, efficiency, and acoustics of coaxial rotor systems.

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

    NASA Astrophysics Data System (ADS)

    Soto Valle, Fernando Antonio

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

  10. A study on strategic provisioning of cloud computing services.

    PubMed

    Whaiduzzaman, Md; Haque, Mohammad Nazmul; Rejaul Karim Chowdhury, Md; Gani, Abdullah

    2014-01-01

    Cloud computing is currently emerging as an ever-changing, growing paradigm that models "everything-as-a-service." Virtualised physical resources, infrastructure, and applications are supplied by service provisioning in the cloud. The evolution in the adoption of cloud computing is driven by clear and distinct promising features for both cloud users and cloud providers. However, the increasing number of cloud providers and the variety of service offerings have made it difficult for the customers to choose the best services. By employing successful service provisioning, the essential services required by customers, such as agility and availability, pricing, security and trust, and user metrics can be guaranteed by service provisioning. Hence, continuous service provisioning that satisfies the user requirements is a mandatory feature for the cloud user and vitally important in cloud computing service offerings. Therefore, we aim to review the state-of-the-art service provisioning objectives, essential services, topologies, user requirements, necessary metrics, and pricing mechanisms. We synthesize and summarize different provision techniques, approaches, and models through a comprehensive literature review. A thematic taxonomy of cloud service provisioning is presented after the systematic review. Finally, future research directions and open research issues are identified.

  11. A Study on Strategic Provisioning of Cloud Computing Services

    PubMed Central

    Rejaul Karim Chowdhury, Md

    2014-01-01

    Cloud computing is currently emerging as an ever-changing, growing paradigm that models “everything-as-a-service.” Virtualised physical resources, infrastructure, and applications are supplied by service provisioning in the cloud. The evolution in the adoption of cloud computing is driven by clear and distinct promising features for both cloud users and cloud providers. However, the increasing number of cloud providers and the variety of service offerings have made it difficult for the customers to choose the best services. By employing successful service provisioning, the essential services required by customers, such as agility and availability, pricing, security and trust, and user metrics can be guaranteed by service provisioning. Hence, continuous service provisioning that satisfies the user requirements is a mandatory feature for the cloud user and vitally important in cloud computing service offerings. Therefore, we aim to review the state-of-the-art service provisioning objectives, essential services, topologies, user requirements, necessary metrics, and pricing mechanisms. We synthesize and summarize different provision techniques, approaches, and models through a comprehensive literature review. A thematic taxonomy of cloud service provisioning is presented after the systematic review. Finally, future research directions and open research issues are identified. PMID:25032243

  12. Computational diagnosis of protein conformational diseases: short molecular dynamics simulations reveal a fast unfolding of r-LDL mutants that cause familial hypercholesterolemia.

    PubMed

    Cuesta-López, S; Falo, F; Sancho, J

    2007-01-01

    The molecular basis of conformational diseases frequently resides in mutant proteins constituting a subset of the vast mutational space. While the subtleties of protein structure point to molecular dynamics (MD) techniques as promising tools for an efficient exploration of such a space, the average size of proteins and the time scale of unfolding events make this goal difficult with present computational capabilities. We show here, nevertheless, that an efficient approach is already feasible for modular proteins. Familial hypercholesterolemia (FH) is a conformational disease linked to mutations in the gene encoding the low density lipoprotein receptor. A high percentage of these mutations has been found in the seven small modular binding repeats of the receptor. Taking advantage of its small size, we have performed an in depth MD study of the fifth binding repeat. Fast unfolding dynamics have been observed in the absence of a structural bound calcium ion, which agrees with its reported essential role in the stability of the module. In addition, several mutations detected in FH patients have been analyzed, starting from the native conformation. Our results indicate that in contrast with the wild type protein and an innocuous control mutant, disease-related mutants experience, in short simulation times (2-8 ns), gross departures from the native state that lead to unfolded conformations and, in some cases, to binding site desorganization deriving in calcium release. Computational diagnosis of mutations leading to conformational diseases seems thus feasible, at least for small or modular pathogenic proteins.

  13. A comprehensive immunoinformatics and target site study revealed the corner-stone toward Chikungunya virus treatment.

    PubMed

    Hasan, Md Anayet; Khan, Md Arif; Datta, Amit; Mazumder, Md Habibul Hasan; Hossain, Mohammad Uzzal

    2015-05-01

    Recent concerning facts of Chikungunya virus (CHIKV); a Togaviridae family alphavirus has proved this as a worldwide emerging threat which causes Chikungunya fever and devitalizing arthritis. Despite severe outbreaks and lack of antiviral drug, a mere progress has been made regarding to an epitope-based vaccine designed for CHIKV. In this study, we aimed to design an epitope-based vaccine that can trigger a significant immune response as well as to prognosticate inhibitor that can bind with potential drug target sites by using various immunoinformatics and docking simulation tools. Initially, whole proteome of CHIKV was retrieved from database and perused to identify the most immunogenic protein. Structural properties of the selected protein were analyzed. The capacity to induce both humoral and cell-mediated immunity by T cell and B cell were checked for the selected protein. The peptide region spanning 9 amino acids from 397 to 405 and the sequence YYYELYPTM were found as the most potential B cell and T cell epitopes respectively. This peptide could interact with as many as 19 HLAs and showed high population coverage ranging from 69.50% to 84.94%. By using in silico docking techniques the epitope was further assessed for binding against HLA molecules to verify the binding cleft interaction. In addition with this, the allergenicity of the epitopes was also evaluated. In the post therapeutic strategy, three dimensional structure was predicted along with validation and verification that resulted in molecular docking study to identify the potential drug binding sites and suitable therapeutic inhibitor against targeted protein. Finally, pharmacophore study was also performed in quest of seeing potent drug activity. However, this computational epitope-based peptide vaccine designing and target site prediction against CHIKV opens up a new horizon which may be the prospective way in Chikungunya virus research; the results require validation by in vitro and in vivo

  14. Body dynamics and hydrodynamics of swimming fish larvae: a computational study.

    PubMed

    Li, Gen; Müller, Ulrike K; van Leeuwen, Johan L; Liu, Hao

    2012-11-15

    To understand the mechanics of fish swimming, we need to know the forces exerted by the fluid and how these forces affect the motion of the fish. To this end, we developed a 3-D computational approach that integrates hydrodynamics and body dynamics. This study quantifies the flow around a swimming zebrafish (Danio rerio) larva. We used morphological and kinematics data from actual fish larvae aged 3 and 5 days post fertilization as input for a computational model that predicted free-swimming dynamics from prescribed changes in body shape. We simulated cyclic swimming and a spontaneous C-start. A rigorous comparison with 2-D particle image velocimetry and kinematics data revealed that the computational model accurately predicted the motion of the fish's centre of mass as well as the spatial and temporal characteristics of the flow. The distribution of pressure and shear forces along the body showed that thrust is mainly produced in the posterior half of the body. We also explored the effect of the body wave amplitude on swimming performance by considering wave amplitudes that were up to 40% larger or smaller than the experimentally observed value. Increasing the body wave amplitude increased forward swimming speed from 7 to 21 body lengths per second, which is consistent with experimental observations. The model also predicted a non-linear increase in propulsive efficiency from 0.22 to 0.32 while the required mechanical power quadrupled. The efficiency increase was only minor for wave amplitudes above the experimental reference value, whereas the cost of transport rose significantly.

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

    PubMed

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

    2013-08-01

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

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

    PubMed Central

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

    2009-01-01

    We carried out a test sample study to try to identify errors leading to irreproducibility, including incompleteness of peptide sampling, in LC-MS-based proteomics. We distributed a test sample consisting of an equimolar mix of 20 highly purified recombinant human proteins, to 27 laboratories for identification. Each protein contained one or more unique tryptic peptides of 1250 Da to also test for ion selection and sampling in the mass spectrometer. Of the 27 labs, initially only 7 labs reported all 20 proteins correctly, and only 1 lab reported all the tryptic peptides of 1250 Da. Nevertheless, a subsequent centralized analysis of the raw data revealed that all 20 proteins and most of the 1250 Da peptides had in fact been detected by all 27 labs. The centralized analysis allowed us to determine sources of problems encountered in the study, which include missed identifications (false negatives), environmental contamination, database matching, and curation of protein identifications. Improved search engines and databases are likely to increase the fidelity of mass spectrometry-based proteomics. PMID:19448641

  17. Fish gut-liver immunity during homeostasis or inflammation revealed by integrative transcriptome and proteome studies.

    PubMed

    Wu, Nan; Song, Yu-Long; Wang, Bei; Zhang, Xiang-Yang; Zhang, Xu-Jie; Wang, Ya-Li; Cheng, Ying-Yin; Chen, Dan-Dan; Xia, Xiao-Qin; Lu, Yi-Shan; Zhang, Yong-An

    2016-11-03

    The gut-associated lymphoid tissue, connected with liver via bile and blood, constructs a local immune environment of both defense and tolerance. The gut-liver immunity has been well-studied in mammals, yet in fish remains largely unknown, even though enteritis as well as liver and gallbladder syndrome emerged as a limitation in aquaculture. In this study, we performed integrative bioinformatic analysis for both transcriptomic (gut and liver) and proteomic (intestinal mucus and bile) data, in both healthy and infected tilapias. We found more categories of immune transcripts in gut than liver, as well as more adaptive immune in gut meanwhile more innate in liver. Interestingly reduced differential immune transcripts between gut and liver upon inflammation were also revealed. In addition, more immune proteins in bile than intestinal mucus were identified. And bile probably providing immune effectors to intestinal mucus upon inflammation was deduced. Specifically, many key immune transcripts in gut or liver as well as key immune proteins in mucus or bile were demonstrated. Accordingly, we proposed a hypothesized profile of fish gut-liver immunity, during either homeostasis or inflammation. Current data suggested that fish gut and liver may collaborate immunologically while keep homeostasis using own strategies, including potential unique mechanisms.

  18. Single exosome study reveals subpopulations distributed among cell lines with variability related to membrane content

    PubMed Central

    Smith, Zachary J.; Lee, Changwon; Rojalin, Tatu; Carney, Randy P.; Hazari, Sidhartha; Knudson, Alisha; Lam, Kit; Saari, Heikki; Ibañez, Elisa Lazaro; Viitala, Tapani; Laaksonen, Timo; Yliperttula, Marjo; Wachsmann-Hogiu, Sebastian

    2015-01-01

    Current analysis of exosomes focuses primarily on bulk analysis, where exosome-to-exosome variability cannot be assessed. In this study, we used Raman spectroscopy to study the chemical composition of single exosomes. We measured spectra of individual exosomes from 8 cell lines. Cell-line-averaged spectra varied considerably, reflecting the variation in total exosomal protein, lipid, genetic, and cytosolic content. Unexpectedly, single exosomes isolated from the same cell type also exhibited high spectral variability. Subsequent spectral analysis revealed clustering of single exosomes into 4 distinct groups that were not cell-line specific. Each group contained exosomes from multiple cell lines, and most cell lines had exosomes in multiple groups. The differences between these groups are related to chemical differences primarily due to differing membrane composition. Through a principal components analysis, we identified that the major sources of spectral variation among the exosomes were in cholesterol content, relative expression of phospholipids to cholesterol, and surface protein expression. For example, exosomes derived from cancerous versus non-cancerous cell lines can be largely separated based on their relative expression of cholesterol and phospholipids. We are the first to indicate that exosome subpopulations are shared among cell types, suggesting distributed exosome functionality. The origins of these differences are likely related to the specific role of extracellular vesicle subpopulations in both normal cell function and carcinogenesis, and they may provide diagnostic potential at the single exosome level. PMID:26649679

  19. Fish gut-liver immunity during homeostasis or inflammation revealed by integrative transcriptome and proteome studies

    PubMed Central

    Wu, Nan; Song, Yu-Long; Wang, Bei; Zhang, Xiang-Yang; Zhang, Xu-Jie; Wang, Ya-Li; Cheng, Ying-Yin; Chen, Dan-Dan; Xia, Xiao-Qin; Lu, Yi-Shan; Zhang, Yong-An

    2016-01-01

    The gut-associated lymphoid tissue, connected with liver via bile and blood, constructs a local immune environment of both defense and tolerance. The gut-liver immunity has been well-studied in mammals, yet in fish remains largely unknown, even though enteritis as well as liver and gallbladder syndrome emerged as a limitation in aquaculture. In this study, we performed integrative bioinformatic analysis for both transcriptomic (gut and liver) and proteomic (intestinal mucus and bile) data, in both healthy and infected tilapias. We found more categories of immune transcripts in gut than liver, as well as more adaptive immune in gut meanwhile more innate in liver. Interestingly reduced differential immune transcripts between gut and liver upon inflammation were also revealed. In addition, more immune proteins in bile than intestinal mucus were identified. And bile probably providing immune effectors to intestinal mucus upon inflammation was deduced. Specifically, many key immune transcripts in gut or liver as well as key immune proteins in mucus or bile were demonstrated. Accordingly, we proposed a hypothesized profile of fish gut-liver immunity, during either homeostasis or inflammation. Current data suggested that fish gut and liver may collaborate immunologically while keep homeostasis using own strategies, including potential unique mechanisms. PMID:27808112

  20. New insights into sulfur metabolism in yeasts as revealed by studies of Yarrowia lipolytica.

    PubMed

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

    2013-02-01

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

  1. Fish gut-liver immunity during homeostasis or inflammation revealed by integrative transcriptome and proteome studies

    NASA Astrophysics Data System (ADS)

    Wu, Nan; Song, Yu-Long; Wang, Bei; Zhang, Xiang-Yang; Zhang, Xu-Jie; Wang, Ya-Li; Cheng, Ying-Yin; Chen, Dan-Dan; Xia, Xiao-Qin; Lu, Yi-Shan; Zhang, Yong-An

    2016-11-01

    The gut-associated lymphoid tissue, connected with liver via bile and blood, constructs a local immune environment of both defense and tolerance. The gut-liver immunity has been well-studied in mammals, yet in fish remains largely unknown, even though enteritis as well as liver and gallbladder syndrome emerged as a limitation in aquaculture. In this study, we performed integrative bioinformatic analysis for both transcriptomic (gut and liver) and proteomic (intestinal mucus and bile) data, in both healthy and infected tilapias. We found more categories of immune transcripts in gut than liver, as well as more adaptive immune in gut meanwhile more innate in liver. Interestingly reduced differential immune transcripts between gut and liver upon inflammation were also revealed. In addition, more immune proteins in bile than intestinal mucus were identified. And bile probably providing immune effectors to intestinal mucus upon inflammation was deduced. Specifically, many key immune transcripts in gut or liver as well as key immune proteins in mucus or bile were demonstrated. Accordingly, we proposed a hypothesized profile of fish gut-liver immunity, during either homeostasis or inflammation. Current data suggested that fish gut and liver may collaborate immunologically while keep homeostasis using own strategies, including potential unique mechanisms.

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

    PubMed Central

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

    2013-01-01

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

  3. Interaction studies reveal specific recognition of an anti-inflammatory polyphosphorhydrazone dendrimer by human monocytes.

    PubMed

    Ledall, Jérémy; Fruchon, Séverine; Garzoni, Matteo; Pavan, Giovanni M; Caminade, Anne-Marie; Turrin, Cédric-Olivier; Blanzat, Muriel; Poupot, Rémy

    2015-11-14

    Dendrimers are nano-materials with perfectly defined structure and size, and multivalency properties that confer substantial advantages for biomedical applications. Previous work has shown that phosphorus-based polyphosphorhydrazone (PPH) dendrimers capped with azabisphosphonate (ABP) end groups have immuno-modulatory and anti-inflammatory properties leading to efficient therapeutic control of inflammatory diseases in animal models. These properties are mainly prompted through activation of monocytes. Here, we disclose new insights into the molecular mechanisms underlying the anti-inflammatory activation of human monocytes by ABP-capped PPH dendrimers. Following an interdisciplinary approach, we have characterized the physicochemical and biological behavior of the lead ABP dendrimer with model and cell membranes, and compared this experimental set of data to predictive computational modelling studies. The behavior of the ABP dendrimer was compared to the one of an isosteric analog dendrimer capped with twelve azabiscarboxylate (ABC) end groups instead of twelve ABP end groups. The ABC dendrimer displayed no biological activity on human monocytes, therefore it was considered as a negative control. In detail, we show that the ABP dendrimer can bind both non-specifically and specifically to the membrane of human monocytes. The specific binding leads to the internalization of the ABP dendrimer by human monocytes. On the contrary, the ABC dendrimer only interacts non-specifically with human monocytes and is not internalized. These data indicate that the bioactive ABP dendrimer is recognized by specific receptor(s) at the surface of human monocytes.

  4. Computer Game Theories for Designing Motivating Educational Software: A Survey Study

    ERIC Educational Resources Information Center

    Ang, Chee Siang; Rao, G. S. V. Radha Krishna

    2008-01-01

    The purpose of this study is to evaluate computer game theories for educational software. We propose a framework for designing engaging educational games based on contemporary game studies which includes ludology and narratology. Ludology focuses on the study of computer games as play and game activities, while narratology revolves around the…

  5. An Exploratory Study of the Implementation of Computer Technology in an American Islamic Private School

    ERIC Educational Resources Information Center

    Saleem, Mohammed M.

    2009-01-01

    This exploratory study of the implementation of computer technology in an American Islamic private school leveraged the case study methodology and ethnographic methods informed by symbolic interactionism and the framework of the Muslim Diaspora. The study focused on describing the implementation of computer technology and identifying the…

  6. A Computer-Assisted 3D Model for Analyzing the Aggregation of Tumorigenic Cells Reveals Specialized Behaviors and Unique Cell Types that Facilitate Aggregate Coalescence

    PubMed Central

    Scherer, Amanda; Kuhl, Spencer; Wessels, Deborah; Lusche, Daniel F.; Hanson, Brett; Ambrose, Joseph; Voss, Edward; Fletcher, Emily; Goldman, Charles; Soll, David R.

    2015-01-01

    We have developed a 4D computer-assisted reconstruction and motion analysis system, J3D-DIAS 4.1, and applied it to the reconstruction and motion analysis of tumorigenic cells in a 3D matrix. The system is unique in that it is fast, high-resolution, acquires optical sections using DIC microscopy (hence there is no associated photoxicity), and is capable of long-term 4D reconstruction. Specifically, a z-series at 5 μm increments can be acquired in less than a minute on tissue samples embedded in a 1.5 mm thick 3D Matrigel matrix. Reconstruction can be repeated at intervals as short as every minute and continued for 30 days or longer. Images are converted to mathematical representations from which quantitative parameters can be derived. Application of this system to cancer cells from established lines and fresh tumor tissue has revealed unique behaviors and cell types not present in non-tumorigenic lines. We report here that cells from tumorigenic lines and tumors undergo rapid coalescence in 3D, mediated by specific cell types that we have named “facilitators” and “probes.” A third cell type, the “dervish”, is capable of rapid movement through the gel and does not adhere to it. These cell types have never before been described. Our data suggest that tumorigenesis in vitro is a developmental process involving coalescence facilitated by specialized cells that culminates in large hollow spheres with complex architecture. The unique effects of select monoclonal antibodies on these processes demonstrate the usefulness of the model for analyzing the mechanisms of anti-cancer drugs. PMID:25790299

  7. Space station Simulation Computer System (SCS) study for NASA/MSFC. Volume 5: Study analysis report

    NASA Technical Reports Server (NTRS)

    1989-01-01

    The Simulation Computer System (SCS) is the computer hardware, software, and workstations that will support the Payload Training Complex (PTC) at the Marshall Space Flight Center (MSFC). The PTC will train the space station payload scientists, station scientists, and ground controllers to operate the wide variety of experiments that will be on-board the Freedom Space Station. The further analysis performed on the SCS study as part of task 2-Perform Studies and Parametric Analysis-of the SCS study contract is summarized. These analyses were performed to resolve open issues remaining after the completion of task 1, and the publishing of the SCS study issues report. The results of these studies provide inputs into SCS task 3-Develop and present SCS requirements, and SCS task 4-develop SCS conceptual designs. The purpose of these studies is to resolve the issues into usable requirements given the best available information at the time of the study. A list of all the SCS study issues is given.

  8. Computer Simulation Study of Human Locomotion with a Three-Dimensional Entire-Body Neuro-Musculo-Skeletal Model

    NASA Astrophysics Data System (ADS)

    Hase, Kazunori; Obinata, Goro

    It is essential for the biomechanical study of human walking motion to consider not only in vivo mechanical load and energy efficiency but also aspects of motor control such as walking stability. In this study, walking stability was investigated using a three-dimensional entire-body neuro-musculo-skeletal model in the computer simulation. In the computational experiments, imaginary constraints, such as no muscular system, were set in the neuro-musculo-skeletal model to investigate their influence on walking stability. The neuronal parameters were adjusted using numerical search techniques in order to adapt walking patterns to constraints on the neuro-musculo-skeletal system. Simulation results revealed that the model of the normal neuro-musculo-skeletal system yielded a higher stability than the imaginary models. Unstable walking by a model with a time delay in the neuronal system suggested significant unknown mechanisms which stabilized walking patterns that have been neglected in previous studies.

  9. Computational studies on small wind turbine performance characteristics

    NASA Astrophysics Data System (ADS)

    Karthikeyan, N.; Suthakar, T.

    2016-10-01

    To optimize the selection of suitable airfoils for small wind turbine applications, computational investigation on aerodynamic characteristics of low Re airfoils MID321a, MID321d, SG6040, SG6041, SG6042 and SG6043 are carried out for the Reynolds number range of (0.5- 2)×105. The BEM method is used to determine the power coefficient of the rotor from the airfoil characteristics; in addition, the blade parameters like chord and twist are also determined. The newly designed MID321a airfoil shows better aerodynamic performance and maximum power coefficient as compared with other investigated airfoils for wider operating ranges.

  10. Computer studies of multiple-quantum spin dynamics

    SciTech Connect

    Murdoch, J.B.

    1982-11-01

    The excitation and detection of multiple-quantum (MQ) transitions in Fourier transform NMR spectroscopy is an interesting problem in the quantum mechanical dynamics of spin systems as well as an important new technique for investigation of molecular structure. In particular, multiple-quantum spectroscopy can be used to simplify overly complex spectra or to separate the various interactions between a nucleus and its environment. The emphasis of this work is on computer simulation of spin-system evolution to better relate theory and experiment.

  11. Computational approach to the study of thermal spin crossover phenomena

    SciTech Connect

    Rudavskyi, Andrii; Broer, Ria; Sousa, Carmen

    2014-05-14

    The key parameters associated to the thermally induced spin crossover process have been calculated for a series of Fe(II) complexes with mono-, bi-, and tridentate ligands. Combination of density functional theory calculations for the geometries and for normal vibrational modes, and highly correlated wave function methods for the energies, allows us to accurately compute the entropy variation associated to the spin transition and the zero-point corrected energy difference between the low- and high-spin states. From these values, the transition temperature, T{sub 1/2}, is estimated for different compounds.

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

    PubMed Central

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

    2013-01-01

    The future spread and impact of an introduced species will depend on how it adapts to the abiotic and biotic conditions encountered in its new range, so the potential for rapid evolution subsequent to species introduction is a critical, evolutionary dimension of invasion biology. Using a resurrection approach, we provide a direct test for change over time within populations in a species' introduced range, in the Asian shade annual Polygonum cespitosum. We document, over an 11-year period, the evolution of increased reproductive output as well as greater physiological and root-allocational plasticity in response to the more open, sunny conditions found in the North American range in which the species has become invasive. These findings show that extremely rapid adaptive modifications to ecologically-important traits and plastic expression patterns can evolve subsequent to a species' introduction, within populations established in its introduced range. This study is one of the first to directly document evolutionary change in adaptive plasticity. Such rapid evolutionary changes can facilitate the spread of introduced species into novel habitats and hence contribute to their invasive success in a new range. The data also reveal how evolutionary trajectories can differ among populations in ways that can influence invasion dynamics. PMID:23798976

  13. Gender and population history: sex bias revealed by studying genetic admixture of Ngazidja population (Comoro Archipelago).

    PubMed

    Gourjon, Géraud; Boëtsch, Gilles; Degioanni, Anna

    2011-04-01

    The peopling of Comoro Archipelago is defined by successive waves of migration from three main areas: the East African Coast (Bantu-speaking populations), the Persia and Arabian Peninsula, and Southeast Asia (especially Indonesia). It follows an apparent classic trihybrid admixture model. To better understand the Comorian population admixture dynamics, we analyzed the contributions of these three historical parental components to its genetic pool. To enhance accuracy and reliability, we used both classical and molecular markers. Samples consist of published data: blood group frequencies, 14 KIR genes, 19 mitochondrial DNA SNPs (to highlight female migrations), 14 Y chromosome SNPs (male migrations). We revealed distinct admixture patterns for autosomal and uniparental markers. KIR gene frequencies had never been used to estimate admixture rates, this being a first assessment of their informative power in admixture studies. To avoid major methodological and statistical bias, we determined admixture coefficients through nine well-tried estimators and their associated software programs (ADMIX95, ADMIX, admix 2.0, LEA, LEADMIX, and Mistura). Results from mtDNA and Y chromosome markers point to an important sex-bias in the admixture event. The original Bantu gene pool received a predominant male-mediated contribution from the Arabian Peninsula and Persia, and a female-mediated contribution from Southeast Asia. Admixture rates estimated from autosomal KIR gene markers point also to an unexpected elevated Austronesian contribution.

  14. Metagenomic study of red biofilms from Diamante Lake reveals ancient arsenic bioenergetics in haloarchaea.

    PubMed

    Rascovan, Nicolás; Maldonado, Javier; Vazquez, Martín P; Eugenia Farías, María

    2016-02-01

    Arsenic metabolism is proposed to be an ancient mechanism in microbial life. Different bacteria and archaea use detoxification processes to grow under high arsenic concentration. Some of them are also able to use arsenic as a bioenergetic substrate in either anaerobic arsenate respiration or chemolithotrophic growth on arsenite. However, among the archaea, bioenergetic arsenic metabolism has only been found in the Crenarchaeota phylum. Here we report the discovery of haloarchaea (Euryarchaeota phylum) biofilms forming under the extreme environmental conditions such as high salinity, pH and arsenic concentration at 4589 m above sea level inside a volcano crater in Diamante Lake, Argentina. Metagenomic analyses revealed a surprisingly high abundance of genes used for arsenite oxidation (aioBA) and respiratory arsenate reduction (arrCBA) suggesting that these haloarchaea use arsenic compounds as bioenergetics substrates. We showed that several haloarchaea species, not only from this study, have all genes required for these bioenergetic processes. The phylogenetic analysis of aioA showed that haloarchaea sequences cluster in a novel and monophyletic group, suggesting that the origin of arsenic metabolism in haloarchaea is ancient. Our results also suggest that arsenite chemolithotrophy likely emerged within the archaeal lineage. Our results give a broad new perspective on the haloarchaea metabolism and shed light on the evolutionary history of arsenic bioenergetics.

  15. Metagenomic study of red biofilms from Diamante Lake reveals ancient arsenic bioenergetics in haloarchaea

    PubMed Central

    Rascovan, Nicolás; Maldonado, Javier; Vazquez, Martín P; Eugenia Farías, María

    2016-01-01

    Arsenic metabolism is proposed to be an ancient mechanism in microbial life. Different bacteria and archaea use detoxification processes to grow under high arsenic concentration. Some of them are also able to use arsenic as a bioenergetic substrate in either anaerobic arsenate respiration or chemolithotrophic growth on arsenite. However, among the archaea, bioenergetic arsenic metabolism has only been found in the Crenarchaeota phylum. Here we report the discovery of haloarchaea (Euryarchaeota phylum) biofilms forming under the extreme environmental conditions such as high salinity, pH and arsenic concentration at 4589 m above sea level inside a volcano crater in Diamante Lake, Argentina. Metagenomic analyses revealed a surprisingly high abundance of genes used for arsenite oxidation (aioBA) and respiratory arsenate reduction (arrCBA) suggesting that these haloarchaea use arsenic compounds as bioenergetics substrates. We showed that several haloarchaea species, not only from this study, have all genes required for these bioenergetic processes. The phylogenetic analysis of aioA showed that haloarchaea sequences cluster in a novel and monophyletic group, suggesting that the origin of arsenic metabolism in haloarchaea is ancient. Our results also suggest that arsenite chemolithotrophy likely emerged within the archaeal lineage. Our results give a broad new perspective on the haloarchaea metabolism and shed light on the evolutionary history of arsenic bioenergetics. PMID:26140530

  16. Structural Studies of AAV2 Rep68 Reveal a Partially Structured Linker and Compact Domain Conformation

    PubMed Central

    Musayev, Faik N.; Zarate-Perez, Francisco; Bardelli, Martino; Bishop, Clayton; Saniev, Emil F.; Linden, R. Michael; Henckaerts, Els; Escalante, Carlos R.

    2015-01-01

    Adeno-associated virus (AAV) nonstructural proteins Rep78 and Rep68 carry out all DNA transactions that regulate the AAV life cycle. They share two multifunctional domains: an N-terminal origin binding/nicking domain (OBD) from the HUH superfamily and a SF3 helicase domain. A short linker of ~20 amino acids that is critical for oligomerization and function connects the two domains. Although X-ray structures of the AAV5 OBD and AAV2 helicase domains have been determined, information about the full-length protein and linker conformation is not known. This article presents the solution structure of AAV2 Rep68 using small-angle X-ray scattering (SAXS). We first determined the X-ray structures of the minimal AAV2 Rep68 OBD and of the OBD with the linker region. These X-ray structures reveal novel features that include a long C-terminal α-helix that protrudes from the core of the protein at a 45° angle and a partially structured linker. SAXS studies corroborate that the linker is not extended, and we show that a proline residue in the linker is critical for Rep68 oligomerization and function. SAXS-based rigid-body modeling of Rep68 confirms these observations, showing a compact arrangement of the two domains in which they acquire a conformation that positions key residues in all domains on one face of the protein, poised to interact with DNA. PMID:26314310

  17. Structural Studies of AAV2 Rep68 Reveal a Partially Structured Linker and Compact Domain Conformation.

    PubMed

    Musayev, Faik N; Zarate-Perez, Francisco; Bardelli, Martino; Bishop, Clayton; Saniev, Emil F; Linden, R Michael; Henckaerts, Els; Escalante, Carlos R

    2015-09-29

    Adeno-associated virus (AAV) nonstructural proteins Rep78 and Rep68 carry out all DNA transactions that regulate the AAV life cycle. They share two multifunctional domains: an N-terminal origin binding/nicking domain (OBD) from the HUH superfamily and a SF3 helicase domain. A short linker of ∼20 amino acids that is critical for oligomerization and function connects the two domains. Although X-ray structures of the AAV5 OBD and AAV2 helicase domains have been determined, information about the full-length protein and linker conformation is not known. This article presents the solution structure of AAV2 Rep68 using small-angle X-ray scattering (SAXS). We first determined the X-ray structures of the minimal AAV2 Rep68 OBD and of the OBD with the linker region. These X-ray structures reveal novel features that include a long C-terminal α-helix that protrudes from the core of the protein at a 45° angle and a partially structured linker. SAXS studies corroborate that the linker is not extended, and we show that a proline residue in the linker is critical for Rep68 oligomerization and function. SAXS-based rigid-body modeling of Rep68 confirms these observations, showing a compact arrangement of the two domains in which they acquire a conformation that positions key residues in all domains on one face of the protein, poised to interact with DNA.

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

    PubMed

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

    2013-02-01

    The future spread and impact of an introduced species will depend on how it adapts to the abiotic and biotic conditions encountered in its new range, so the potential for rapid evolution subsequent to species introduction is a critical, evolutionary dimension of invasion biology. Using a resurrection approach, we provide a direct test for change over time within populations in a species' introduced range, in the Asian shade annual Polygonum cespitosum. We document, over an 11-year period, the evolution of increased reproductive output as well as greater physiological and root-allocational plasticity in response to the more open, sunny conditions found in the North American range in which the species has become invasive. These findings show that extremely rapid adaptive modifications to ecologically-important traits and plastic expression patterns can evolve subsequent to a species' introduction, within populations established in its introduced range. This study is one of the first to directly document evolutionary change in adaptive plasticity. Such rapid evolutionary changes can facilitate the spread of introduced species into novel habitats and hence contribute to their invasive success in a new range. The data also reveal how evolutionary trajectories can differ among populations in ways that can influence invasion dynamics.

  19. Proteomics study reveals that the dysregulation of focal adhesion and ribosome contribute to early pregnancy loss

    PubMed Central

    Xin, Lingli; Xu, Benhong; Ma, Li; Hou, Qingxiang; Ye, Mei; Meng, Shu; Ge, Wei

    2016-01-01

    Purpose Early pregnancy loss (EPL) affects 50–70% pregnant women in first trimester. The precise molecular mechanisms underlying EPL are far from being fully understood. Therefore, we aim to identify the molecular signaling pathways relating to EPL. Experimental design We performed proteomics and bioinformatics analysis of the placental villi in women who have undergone EPL and in normal pregnant women. The proteomics data were validated by Western blot analysis. Results We identified a total of 5952 proteins in placental villi, of which 588 proteins were differentially expressed in the EPL women. Bioinformatics analysis revealed that these differentially expressed proteins participated in a variety of signaling pathways, including the focal adhesion pathway and ribosome pathway. Moreover, results of the Western blot confirmed that Desmin, Lamin A/C, MMP‐9, and histone H4 were upregulated in EPL and the Lamin C/ Lamin A ratio decreased obviously in EPL. These proteins could be associated with the pathophysiology of EPL. The data have been deposited to the ProteomeXchange with identifier PXD002391. Conclusion and clinical relevance Our study demonstrated that the focal adhesion pathway and ribosome pathway are involved in EPL, and these findings might contribute to unveil the pathophysiology of EPL. PMID:26947931

  20. Computer-Related Success and Failure: A Longitudinal Field Study of the Factors Influencing Computer-Related Performance.

    ERIC Educational Resources Information Center

    Rozell, E. J.; Gardner, W. L., III

    1999-01-01

    A model of the intrapersonal processes impacting computer-related performance was tested using data from 75 manufacturing employees in a computer training course. Gender, computer experience, and attributional style were predictive of computer attitudes, which were in turn related to computer efficacy, task-specific performance expectations, and…

  1. A Computational Study of Systemic Hydration in Vocal Fold Collision

    PubMed Central

    Bhattacharya, Pinaki; Siegmund, Thomas

    2013-01-01

    Mechanical stresses develop within vocal fold (VF) soft tissues, due to phonation-associated vibration and collision. These stresses in turn affect the hydration of VF tissue and thus influence voice health. In this paper, high-fidelty numerical computations are described taking into account fully three-dimensional geometry, realistic tissue and air properties, and high-amplitude vibration and collision. A segregated solver approach is employed, using sophisticated commercial solvers for both the VF tissue and glottal airflow domains. The tissue viscoelastic properties were derived from a biphasic formulation. Two cases were considered, whereby the tissue viscoelastic properties corresponded to two different volume fractions of the fluid phase of the VF tissue. For each case, hydrostatic stresses occurring as a result of vibration and collision were investigated. Assuming the VF tissue to be poroelastic, interstitial fluid movement within VF tissue was estimated from the hydrostatic stress gradient. Computed measures of overall VF dynamics (peak air-flow velocity, magnitude of VF deformation, frequency of vibration and contact pressure) were well within the range of experimentally observed values. The VF motion leading to mechanical stresses within the VFs and their effect on the interstitial fluid flux is detailed. It is found that average deformation and vibration of VFs tends to increase the state of hydration of the VF tissue whereas VF collision works to reduce hydration. PMID:23531170

  2. Computer models for designing hypertension experiments and studying concepts.

    PubMed

    Guyton, A C; Montani, J P; Hall, J E; Manning, R D

    1988-04-01

    This paper demonstrates how computer models along with animal experiments have been used to work out the conceptual bases of hypertensive mechanisms, especially the following: (1) The renal-fluid volume pressure control mechanism has a feed-back gain for pressure control of infinity. Therefore, the chronic level to which the arterial pressure is controlled can be changed only by altering this pressure control mechanism. (2) An increase in total peripheral resistance is not sufficient by itself to cause hypertension. The only resistances in the circulatory system that, when increased, will cause hypertension are those along a restricted axis from the root of the aorta to Bowman's capsule in the kidneys. (3) Autoregulation in the peripheral vascular beds does not increase the arterial pressure in hypertension. However, autoregulation can convert high cardiac output hypertension into high peripheral resistance hypertension. (4) In a computer simulation that cannot yet be performed in animals, a simulated hypertension caused by a combination of increased renal afferent and efferent arteriolar resistances has characteristics that match almost exactly those of essential hypertension.

  3. Computational meta'omics for microbial community studies

    PubMed Central

    Segata, Nicola; Boernigen, Daniela; Tickle, Timothy L; Morgan, Xochitl C; Garrett, Wendy S; Huttenhower, Curtis

    2013-01-01

    Complex microbial communities are an integral part of the Earth's ecosystem and of our bodies in health and disease. In the last two decades, culture-independent approaches have provided new insights into their structure and function, with the exponentially decreasing cost of high-throughput sequencing resulting in broadly available tools for microbial surveys. However, the field remains far from reaching a technological plateau, as both computational techniques and nucleotide sequencing platforms for microbial genomic and transcriptional content continue to improve. Current microbiome analyses are thus starting to adopt multiple and complementary meta'omic approaches, leading to unprecedented opportunities to comprehensively and accurately characterize microbial communities and their interactions with their environments and hosts. This diversity of available assays, analysis methods, and public data is in turn beginning to enable microbiome-based predictive and modeling tools. We thus review here the technological and computational meta'omics approaches that are already available, those that are under active development, their success in biological discovery, and several outstanding challenges. PMID:23670539

  4. Computer Studies Of The Isleworth And Louvre Mona Lisas

    NASA Astrophysics Data System (ADS)

    Asmus, John F.

    1989-07-01

    One of the most pervasive problems in the scholarship of classical paintings is that of authenticity. Traditionally, the attribution of a work of art rests on the subjective opinion of an art historian bolstered by scientific data pertaining to the types and possibly the ages of the materials of the artwork. To expand the range of technical information that may be applied to the painting authentication problem, the methods of computer image processing (IP) have been employed to compare the techniques in two paintings. One is the Mona Lisa del Gioconda by Leonardo da Vinci. The other is known as the Isleworth Mona Lisa and has also been attributed to Leonardo by a few scholars. Computer IP was used to compare statistical and geometrical features of the two paintings. It emerged that the Isleworth work is not a copy of the Louvre painting but does have numerous similarities in composition and execution. These findings lend support to the theory that the Louvre Mona Lisa may be a portrait of Costanza by Leonardo that had been thought lost.

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

    PubMed

    Bhattacharya, Pinaki; Siegmund, Thomas

    2014-01-01

    Mechanical stresses develop within vocal fold (VF) soft tissues due to phonation-associated vibration and collision. These stresses in turn affect the hydration of VF tissue and thus influence voice health. In this paper, high-fidelity numerical computations are described, taking into account fully 3D geometry, realistic tissue and air properties, and high-amplitude vibration and collision. A segregated solver approach is employed, using sophisticated commercial solvers for both the VF tissue and glottal airflow domains. The tissue viscoelastic properties were derived from a biphasic formulation. Two cases were considered, whereby the tissue viscoelastic properties corresponded to two different volume fractions of the fluid phase of the VF tissue. For each case, hydrostatic stresses occurring as a result of vibration and collision were investigated. Assuming the VF tissue to be poroelastic, interstitial fluid movement within VF tissue was estimated from the hydrostatic stress gradient. Computed measures of overall VF dynamics (peak airflow velocity, magnitude of VF deformation, frequency of vibration and contact pressure) were well within the range of experimentally observed values. The VF motion leading to mechanical stresses within the VFs and their effect on the interstitial fluid flux is detailed. It is found that average deformation and vibration of VFs tend to increase the state of hydration of the VF tissue, whereas VF collision works to reduce hydration.

  6. AN IMAGING AND SPECTROSCOPIC STUDY OF FOUR STRONG Mg II ABSORBERS REVEALED BY GRB 060418

    SciTech Connect

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

    2009-08-20

    We present results from an imaging and spectroscopic study of four strong Mg II absorbers of W(2796) {approx}> 1 A revealed by the afterglow of GRB 060418 at z{sub GRB} = 1.491. These absorbers, at z = 0.603, 0.656, 1.107, and z {sub GRB}, exhibit large ion abundances that suggest neutral gas columns characteristic of damped Ly{alpha} systems. The imaging data include optical images obtained using Low-Resolution Imaging Spectrometer (LRIS) on the Keck I telescope and using Advanced Camera for Surveys on board Hubble Space Telescope, and near-infrared H-band images obtained using Persson's Auxiliary Nasmyth Infrared Camera on the Magellan Baade Telescope and K'-band images obtained using NIRC2 with laser guide star adaptive optics on the Keck II telescope. These images reveal six distinct objects at {delta} {theta} {approx}< 3.''5 of the afterglow's position, two of which exhibit well-resolved mature disk morphology, one shows red colors, and three are blue compact sources. Follow-up spectroscopic observations using LRIS confirm that one of the disk galaxies coincides with the Mg II absorber at z = 0.656. The observed broadband spectral energy distributions of the second disk galaxy and the red source indicate that they are associated with the absorbers at z = 0.603 and z = 1.107, respectively. These results show that strong Mg II absorbers identified in gamma-ray burst (GRB) afterglow spectra are associated with typical galaxies of luminosity {approx}0.1 - 1 L{sub *} at impact parameter of {rho} {approx}< 10 h {sup -1} kpc. The close angular separation would preclude easy detections toward a bright quasar. Finally, we associate the remaining three blue compact sources with the GRB host galaxy, noting that they are likely star-forming knots located at projected distances of {rho} = 2 - 12 h {sup -1} kpc from the afterglow. At the afterglow's position, we derive a 2{sigma} upper limit to the underlying star-formation rate intensity of 0.0074 M{sub sun} yr{sup -1} kpc

  7. Interaction studies reveal specific recognition of an anti-inflammatory polyphosphorhydrazone dendrimer by human monocytes

    NASA Astrophysics Data System (ADS)

    Ledall, Jérémy; Fruchon, Séverine; Garzoni, Matteo; Pavan, Giovanni M.; Caminade, Anne-Marie; Turrin, Cédric-Olivier; Blanzat, Muriel; Poupot, Rémy

    2015-10-01

    Dendrimers are nano-materials with perfectly defined structure and size, and multivalency properties that confer substantial advantages for biomedical applications. Previous work has shown that phosphorus-based polyphosphorhydrazone (PPH) dendrimers capped with azabisphosphonate (ABP) end groups have immuno-modulatory and anti-inflammatory properties leading to efficient therapeutic control of inflammatory diseases in animal models. These properties are mainly prompted through activation of monocytes. Here, we disclose new insights into the molecular mechanisms underlying the anti-inflammatory activation of human monocytes by ABP-capped PPH dendrimers. Following an interdisciplinary approach, we have characterized the physicochemical and biological behavior of the lead ABP dendrimer with model and cell membranes, and compared this experimental set of data to predictive computational modelling studies. The behavior of the ABP dendrimer was compared to the one of an isosteric analog dendrimer capped with twelve azabiscarboxylate (ABC) end groups instead of twelve ABP end groups. The ABC dendrimer displayed no biological activity on human monocytes, therefore it was considered as a negative control. In detail, we show that the ABP dendrimer can bind both non-specifically and specifically to the membrane of human monocytes. The specific binding leads to the internalization of the ABP dendrimer by human monocytes. On the contrary, the ABC dendrimer only interacts non-specifically with human monocytes and is not internalized. These data indicate that the bioactive ABP dendrimer is recognized by specific receptor(s) at the surface of human monocytes.Dendrimers are nano-materials with perfectly defined structure and size, and multivalency properties that confer substantial advantages for biomedical applications. Previous work has shown that phosphorus-based polyphosphorhydrazone (PPH) dendrimers capped with azabisphosphonate (ABP) end groups have immuno-modulatory and anti

  8. Thermal decomposition of 2-phenylethanol: A computational study on mechanism

    NASA Astrophysics Data System (ADS)

    Sakai, Yasuyuki; Ando, Hiromitsu; Oguchi, Tatsuo; Murakami, Yoshinori

    2013-01-01

    Quantum mechanical calculations for the thermal decomposition of 2-phenylethanol have been performed using the CBS-QB3 method. Based on the potential energy surfaces at the CBS-QB3 level of theory, the preferred reaction channel for the thermal decomposition of 2-phenylethanol was the six-membered cyclic rearrangement reaction and the dehydration reaction to form styrene and H2O. Further quantum chemical calculations of the subsequent reactions followed by the six-membered cyclic rearrange reaction of 2-phenylethanol were carried out and it was revealed that the barrier height for the ring opening reaction was the lowest among all of the other subsequent reactions.

  9. A Study of Effectiveness of Computer Assisted Instruction (CAI) over Classroom Lecture (CRL) at ICS Level

    ERIC Educational Resources Information Center

    Kaousar, Tayyeba; Choudhry, Bushra Naoreen; Gujjar, Aijaz Ahmed

    2008-01-01

    This study was aimed to evaluate the effectiveness of CAI vs. classroom lecture for computer science at ICS level. The objectives were to compare the learning effects of two groups with classroom lecture and computer-assisted instruction studying the same curriculum and the effects of CAI and CRL in terms of cognitive development. Hypotheses of…

  10. Short Stories via Computers in EFL Classrooms: An Empirical Study for Reading and Writing Skills

    ERIC Educational Resources Information Center

    Yilmaz, Adnan

    2015-01-01

    The present empirical study scrutinizes the use of short stories via computer technologies in teaching and learning English language. The objective of the study is two-fold: to examine how short stories could be used through computer programs in teaching and learning English and to collect data about students' perceptions of this technique via…

  11. International Computer and Information Literacy Study: ICILS 2013 User Guide for the International Database

    ERIC Educational Resources Information Center

    Jung, Michael, Ed.; Carstens, Ralph, Ed.

    2015-01-01

    The International Computer and Information Literacy Study (ICILS) 2013, conducted by the International Association for the Evaluation of Educational Achievement (IEA), studied how students in different countries develop the knowledge, understanding, attitudes, dispositions, and skills that comprise computer and information literacy (CIL). The aim…

  12. Effectiveness of Computer Based Education: The UNC Phoenix System. Staff Study.

    ERIC Educational Resources Information Center

    Jelden, D. L.

    The purpose of this study was to evaluate college student attitudes toward the PHOENIX computer-based education system and to gauge the instructional effectiveness of computer-assisted instruction (CAI) achievement and testing in a variety of disciplines in a university setting. Data for the study were obtained from 400 students enrolled in five…

  13. Effectiveness of Computer-Assisted Mathematics Education (CAME) over Academic Achievement: A Meta-Analysis Study

    ERIC Educational Resources Information Center

    Demir, Seda; Basol, Gülsah

    2014-01-01

    The aim of the current study is to determine the overall effects of Computer-Assisted Mathematics Education (CAME) on academic achievement. After an extensive review of the literature, studies using Turkish samples and observing the effects of Computer-Assisted Education (CAE) on mathematics achievement were examined. As a result of this…

  14. Effect of Computer-Based Video Games on Children: An Experimental Study

    ERIC Educational Resources Information Center

    Chuang, Tsung-Yen; Chen, Wei-Fan

    2009-01-01

    This experimental study investigated whether computer-based video games facilitate children's cognitive learning. In comparison to traditional computer-assisted instruction (CAI), this study explored the impact of the varied types of instructional delivery strategies on children's learning achievement. One major research null hypothesis was…

  15. Dropping Out of Computer Science: A Phenomenological Study of Student Lived Experiences in Community College Computer Science

    NASA Astrophysics Data System (ADS)

    Gilbert-Valencia, Daniel H.

    California community colleges contribute alarmingly few computer science degree or certificate earners. While the literature shows clear K-12 impediments to CS matriculation in higher education, very little is known about the experiences of those who overcome initial impediments to CS yet do not persist through to program completion. This phenomenological study explores insights into that specific experience by interviewing underrepresented, low income, first-generation college students who began community college intending to transfer to 4-year institutions majoring in CS but switched to another field and remain enrolled or graduated. This study explores the lived experiences of students facing barriers, their avenues for developing interest in CS, and the persistence support systems they encountered, specifically looking at how students constructed their academic choice from these experiences. The growing diversity within California's population necessitates that experiences specific to underrepresented students be considered as part of this exploration. Ten semi-structured interviews and observations were conducted, transcribed and coded. Artifacts supporting student experiences were also collected. Data was analyzed through a social-constructivist lens to provide insight into experiences and how they can be navigated to create actionable strategies for community college computer science departments wishing to increase student success. Three major themes emerged from this research: (1) students shared pre-college characteristics; (2) faced similar challenges in college CS courses; and (3) shared similar reactions to the "work" of computer science. Results of the study included (1) CS interest development hinged on computer ownership in the home; (2) participants shared characteristics that were ideal for college success but not CS success; and (3) encounters in CS departments produced unique challenges for participants. Though CS interest was and remains

  16. Study of USGS/NASA land use classification system. [computer analysis from LANDSAT data

    NASA Technical Reports Server (NTRS)

    Spann, G. W.

    1975-01-01

    The results of a computer mapping project using LANDSAT data and the USGS/NASA land use classification system are summarized. During the computer mapping portion of the project, accuracies of 67 percent to 79 percent were achieved using Level II of the classification system and a 4,000 acre test site centered on Douglasville, Georgia. Analysis of response to a questionaire circulated to actual and potential LANDSAT data users reveals several important findings: (1) there is a substantial desire for additional information related to LANDSAT capabilities; (2) a majority of the respondents feel computer mapping from LANDSAT data could aid present or future projects; and (3) the costs of computer mapping are substantially less than those of other methods.

  17. Carbonyl mediated conductance through metal bound peptides: a computational study

    NASA Astrophysics Data System (ADS)

    Perrine, Trilisa M.; Dunietz, Barry D.

    2007-10-01

    Large increases in the conductance of peptides upon binding to metal ions have recently been reported experimentally. The mechanism of the conductance switching is examined computationally. It is suggested that oxidation of the metal ion occurs after binding to the peptide. This is caused by the bias potential placed across the metal-peptide complex. A combination of configurational changes, metal ion involvement and interactions between carbonyl group oxygen atoms and the gold leads are all shown to be necessary for the large improvement in the conductance seen experimentally. Differences in the molecular orbitals of the nickel and copper complexes are noted and serve to explain the variation of the improvement in conductance upon binding to either a nickel or copper ion.

  18. Computational study of ion beam extraction phenomena through multiple apertures

    SciTech Connect

    Hu, Wanpeng; Sang, Chaofeng; Tang, Tengfei; Wang, Dezhen; Li, Ming; Jin, Dazhi; Tan, Xiaohua

    2014-03-15

    The process of ion extraction through multiple apertures is investigated using a two-dimensional particle-in-cell code. We consider apertures with a fixed diameter with a hydrogen plasma background, and the trajectories of electrons, H{sup +} and H{sub 2}{sup +} ions in the self-consistently calculated electric field are traced. The focus of this work is the fundamental physics of the ion extraction, and not particular to a specific device. The computed convergence and divergence of the extracted ion beam are analyzed. We find that the extracted ion flux reaching the extraction electrode is non-uniform, and the peak flux positions change according to operational parameters, and do not necessarily match the positions of the apertures in the y-direction. The profile of the ion flux reaching the electrode is mainly affected by the bias voltage and the distance between grid wall and extraction electrode.

  19. Breast computed tomography with the PICASSO detector: A feasibility study

    NASA Astrophysics Data System (ADS)

    Rigon, Luigi; Tapete, Federica; Dreossi, Diego; Arfelli, Fulvia; Bergamaschi, Anna; Chen, Rong-Chang; Longo, Renata; Menk, Ralf-Hendrik; Schmitt, Bernd; Vallazza, Erik; Castelli, Edoardo

    2011-02-01

    The SYRMEP (Synchrotron Radiation for Medical Physics) collaboration has performed, for the first time in the world, a clinical program of mammography with synchrotron radiation. This program provided excellent results, although utilizing a commercial screen-film system as a detector. The PICASSO (Phase Imaging for Clinical Application with Silicon detector and Synchrotron radiation) project has developed a detector prototype capable of fully exploiting the peculiar characteristics of the synchrotron source, utilizing silicon microstrip sensors illuminated in the edge-on geometry and operated in single-photon counting. In this paper the potential of the PICASSO detector in breast computed tomography was evaluated by means of custom phantoms. Very encouraging results have been obtained with severe dose constrains as far as both spatial and contrast resolution are concerned. Moreover, the capability of detecting phase contrast effects was demonstrated, albeit with a higher delivered dose.

  20. Computational study of protein secondary structure elements: Ramachandran plots revisited.

    PubMed

    Carrascoza, Francisco; Zaric, Snezana; Silaghi-Dumitrescu, Radu

    2014-05-01

    Potential energy surface (PES) were built for nineteen amino acids using density functional theory (PW91 and DFT M062X/6-311**). Examining the energy as a function of the φ/ψ dihedral angles in the allowed regions of the Ramachandran plot, amino acid groups that share common patterns on their PES plots and global minima were identified. These patterns show partial correlation with their structural and pharmacophoric features. Differences between these computational results and the experimentally noted permitted conformations of each amino acid are rationalized on the basis of attractive intra- and inter-molecular non-covalent interactions. The present data are focused on the intrinsic properties of an amino acid - an element which to our knowledge is typically ignored, as larger models are always used for the sake of similarity to real biological polypeptides.

  1. A comparative study of computational methods in cosmic gas dynamics

    NASA Technical Reports Server (NTRS)

    Van Albada, G. D.; Van Leer, B.; Roberts, W. W., Jr.

    1982-01-01

    Many theoretical investigations of fluid flows in astrophysics require extensive numerical calculations. The selection of an appropriate computational method is, therefore, important for the astronomer who has to solve an astrophysical flow problem. The present investigation has the objective to provide an informational basis for such a selection by comparing a variety of numerical methods with the aid of a test problem. The test problem involves a simple, one-dimensional model of the gas flow in a spiral galaxy. The numerical methods considered include the beam scheme, Godunov's method (G), the second-order flux-splitting method (FS2), MacCormack's method, and the flux corrected transport methods of Boris and Book (1973). It is found that the best second-order method (FS2) outperforms the best first-order method (G) by a huge margin.

  2. Computer programs for eddy-current defect studies

    SciTech Connect

    Pate, J. R.; Dodd, C. V.

    1990-06-01

    Several computer programs to aid in the design of eddy-current tests and probes have been written. The programs, written in Fortran, deal in various ways with the response to defects exhibited by four types of probes: the pancake probe, the reflection probe, the circumferential boreside probe, and the circumferential encircling probe. Programs are included which calculate the impedance or voltage change in a coil due to a defect, which calculate and plot the defect sensitivity factor of a coil, and which invert calculated or experimental readings to obtain the size of a defect. The theory upon which the programs are based is the Burrows point defect theory, and thus the calculations of the programs will be more accurate for small defects. 6 refs., 21 figs.

  3. Hybrid Epidemics—A Case Study on Computer Worm Conficker

    PubMed Central

    Zhang, Changwang; Zhou, Shi; Chain, Benjamin M.

    2015-01-01

    Conficker is a computer worm that erupted on the Internet in 2008. It is unique in combining three different spreading strategies: local probing, neighbourhood probing, and global probing. We propose a mathematical model that combines three modes of spreading: local, neighbourhood, and global, to capture the worm’s spreading behaviour. The parameters of the model are inferred directly from network data obtained during the first day of the Conficker epidemic. The model is then used to explore the tradeoff between spreading modes in determining the worm’s effectiveness. Our results show that the Conficker epidemic is an example of a critically hybrid epidemic, in which the different modes of spreading in isolation do not lead to successful epidemics. Such hybrid spreading strategies may be used beneficially to provide the most effective strategies for promulgating information across a large population. When used maliciously, however, they can present a dangerous challenge to current internet security protocols. PMID:25978309

  4. Attitudes of dental students towards using computers in education--a mixed design study.

    PubMed

    El Tantawi, M M A; Saleh, S M

    2008-01-01

    This mixed design study explored attitudes of dental students towards use of computers. It employed quantitative analyses of a questionnaire answered by 979 students and qualitative analysis of suggestions by a subgroup of 339. Positive attitudes towards computers were predicted by "computer use for > 1 year" and "year of study". Qualitative analysis of students' suggestions confirmed these findings and brought up new issues such as the need for establishing a website for the faculty. The results indicate that careful planning is needed to improve students' skills and incorporate computer applications in educational curricula.

  5. A computational study of highly viscous impinging jets

    SciTech Connect

    Silva, M.W.

    1998-11-01

    Two commercially-available computational fluid dynamics codes, FIDAP (Fluent, Inc., Lebanon, NH) and FLOW-3D (Flow Science, Inc., Los Alamos, NM), were used to simulate the landing region of jets of highly viscous fluids impinging on flat surfaces. The volume-of-fluid method was combined with finite difference and finite element approaches to predict the jet behavior. Several computational models with varying degrees of physical realism were developed, and the results were compared with experimental observations. In experiments, the jet exhibited several complex behaviors. As soon as it exited the nozzle, the jet began to neck down and become narrower. When it impacted the solid surface, the jet developed an instability near the impact point and buckled to the side. This buckling became a spiraling motion, and the jet spiraled about the impact point. As the jet spiraled around, a cone-shaped pile was build up which eventually became unstable and slumped to the side. While all of these behaviors were occurring, air bubbles, or voids, were being entrapped in the fluid pool. The results obtained from the FLOW-3D models more closely matched the behavior of real jets than the results obtained from /the FIDAP models. Most of the FLOW-3D models predicted all of the significant jet behaviors observed in experiments: necking, buckling, spiraling, slumping, and void entrapment. All of the FIDAP models predicted that the jet would buckle relatively far from the point of impact, whereas the experimentally observed jet behavior indicates that the jets buckle much nearer the impact point. Furthermore, it was shown that FIDAP is incapable of incorporating heat transfer effects into the model, making it unsuitable for this work.

  6. Genome-wide association study of toxic metals and trace elements reveals novel associations.

    PubMed

    Ng, Esther; Lind, P Monica; Lindgren, Cecilia; Ingelsson, Erik; Mahajan, Anubha; Morris, Andrew; Lind, Lars

    2015-08-15

    The accumulation of toxic metals in the human body is influenced by exposure and mechanisms involved in metabolism, some of which may be under genetic control. This is the first genome-wide association study to investigate variants associated with whole blood levels of a range of toxic metals. Eleven toxic metals and trace elements (aluminium, cadmium, cobalt, copper, chromium, mercury, manganese, molybdenum, nickel, lead and zinc) were assayed in a cohort of 949 individuals using mass spectrometry. DNA samples were genotyped on the Infinium Omni Express bead microarray and imputed up to reference panels from the 1000 Genomes Project. Analyses revealed two regions associated with manganese level at genome-wide significance, mapping to 4q24 and 1q41. The lead single nucleotide polymorphism (SNP) in the 4q24 locus was rs13107325 (P-value = 5.1 × 10(-11), β = -0.77), located in an exon of SLC39A8, which encodes a protein involved in manganese and zinc transport. The lead SNP in the 1q41 locus is rs1776029 (P-value = 2.2 × 10(-14), β = -0.46). The SNP lies within the intronic region of SLC30A10, another transporter protein. Among other metals, the loci 6q14.1 and 3q26.32 were associated with cadmium and mercury levels (P = 1.4 × 10(-10), β = -1.2 and P = 1.8 × 10(-9), β = -1.8, respectively). Whole blood measurements of toxic metals are associated with genetic variants in metal transporter genes and others. This is relevant in inferring metabolic pathways of metals and identifying subsets of individuals who may be more susceptible to metal toxicity.

  7. Revealing fibrinogen monolayer conformations at different pHs: electrokinetic and colloid deposition studies.

    PubMed

    Nattich-Rak, Małgorzata; Adamczyk, Zbigniew; Wasilewska, Monika; Sadowska, Marta

    2015-07-01

    Adsorption mechanism of human fibrinogen on mica at different pHs is studied using the streaming potential and colloid deposition measurements. The fibrinogen monolayers are produced by a controlled adsorption under diffusion transport at pH of 3.5 and 7.4. Initially, the electrokinetic properties of these monolayers and their stability for various ionic strength are determined. It is shown that at pH 3.5 fibrinogen adsorbs irreversibly on mica for ionic strength range of 4×10(-4) to 0.15 M. At pH 7.4, a partial desorption is observed for ionic strength below 10(-2) M. This is attributed to the desorption of the end-on oriented molecules whereas the side-on adsorbed molecules remain irreversibly bound at all ionic strengths. The orientation of molecules and monolayer structure is evaluated by the colloid deposition measurements involving negatively charged polystyrene latex microspheres, 820 nm in diameter. An anomalous deposition of negative latex particles on substrates exhibiting a negative zeta potential is observed. At pH 3.5 measurable deposition of latex is observed even at low ionic strength where the approach distance of latex particles exceeded 70 nm. At pH 7.4 this critical distance is 23 nm. This confirms that fibrinogen monolayers formed at both pHs are characterized by the presence of the side-on and end-on oriented molecules that prevail at higher coverage range. It is also shown that positive charge is located at the end parts of the αA chains of the adsorbed fibrinogen molecules. Therefore, it is concluded that the colloid deposition method is an efficient tool for revealing protein adsorption mechanisms at solid/electrolyte interfaces.

  8. Comparative study of human mitochondrial proteome reveals extensive protein subcellular relocalization after gene duplications

    PubMed Central

    2009-01-01

    Background Gene and genome duplication is the principle creative force in evolution. Recently, protein subcellular relocalization, or neolocalization was proposed as one of the mechanisms responsible for the retention of duplicated genes. This hypothesis received support from the analysis of yeast genomes, but has not been tested thoroughly on animal genomes. In order to evaluate the importance of subcellular relocalizations for retention of duplicated genes in animal genomes, we systematically analyzed nuclear encoded mitochondrial proteins in the human genome by reconstructing phylogenies of mitochondrial multigene families. Results The 456 human mitochondrial proteins selected for this study were clustered into 305 gene families including 92 multigene families. Among the multigene families, 59 (64%) consisted of both mitochondrial and cytosolic (non-mitochondrial) proteins (mt-cy families) while the remaining 33 (36%) were composed of mitochondrial proteins (mt-mt families). Phylogenetic analyses of mt-cy families revealed three different scenarios of their neolocalization following gene duplication: 1) relocalization from mitochondria to cytosol, 2) from cytosol to mitochondria and 3) multiple subcellular relocalizations. The neolocalizations were most commonly enabled by the gain or loss of N-terminal mitochondrial targeting signals. The majority of detected subcellular relocalization events occurred early in animal evolution, preceding the evolution of tetrapods. Mt-mt protein families showed a somewhat different pattern, where gene duplication occurred more evenly in time. However, for both types of protein families, most duplication events appear to roughly coincide with two rounds of genome duplications early in vertebrate evolution. Finally, we evaluated the effects of inaccurate and incomplete annotation of mitochondrial proteins and found that our conclusion of the importance of subcellular relocalization after gene duplication on the genomic scale was

  9. Genome-wide association study of toxic metals and trace elements reveals novel associations

    PubMed Central

    Ng, Esther; Lind, P. Monica; Lindgren, Cecilia; Ingelsson, Erik; Mahajan, Anubha; Morris, Andrew; Lind, Lars

    2015-01-01

    The accumulation of toxic metals in the human body is influenced by exposure and mechanisms involved in metabolism, some of which may be under genetic control. This is the first genome-wide association study to investigate variants associated with whole blood levels of a range of toxic metals. Eleven toxic metals and trace elements (aluminium, cadmium, cobalt, copper, chromium, mercury, manganese, molybdenum, nickel, lead and zinc) were assayed in a cohort of 949 individuals using mass spectrometry. DNA samples were genotyped on the Infinium Omni Express bead microarray and imputed up to reference panels from the 1000 Genomes Project. Analyses revealed two regions associated with manganese level at genome-wide significance, mapping to 4q24 and 1q41. The lead single nucleotide polymorphism (SNP) in the 4q24 locus was rs13107325 (P-value = 5.1 × 10−11, β = −0.77), located in an exon of SLC39A8, which encodes a protein involved in manganese and zinc transport. The lead SNP in the 1q41 locus is rs1776029 (P-value = 2.2 × 10−14, β = −0.46). The SNP lies within the intronic region of SLC30A10, another transporter protein. Among other metals, the loci 6q14.1 and 3q26.32 were associated with cadmium and mercury levels (P = 1.4 × 10−10, β = −1.2 and P = 1.8 × 10−9, β = −1.8, respectively). Whole blood measurements of toxic metals are associated with genetic variants in metal transporter genes and others. This is relevant in inferring metabolic pathways of metals and identifying subsets of individuals who may be more susceptible to metal toxicity. PMID:26025379

  10. Probing the simulant behavior of PNPDPP toward parathion and paraoxon: a computational study.

    PubMed

    Khan, Abdul Shafeeuulla; Bandyopadhyay, Tusar; Ganguly, Bishwajit

    2012-04-01

    The extreme toxicity of organophosphorus nerve agents and pesticides mandates to employ models or simulants in place of the actual compounds in the laboratory. The importance of simulants is known, however, their efficacy for direct comparison with the toxic organophosphorus compounds is not well documented. We have examined the potential energy surfaces (PES) for the alkaline hydrolysis of pesticides like paraoxon (diethyl 4-nitrophenyl phosphate), parathion (O,O-diethyl O-4-nitrophenyl phosphorothioate) and PNPDPP (4-nitrophenyl diphenyl phosphate), a simulant with MP2/6-311+G*//B3LYP/6-311+G*+ΔG(solv) (HF/6-31+G*) level of theory. The effect of aqueous solvation was considered with the Integral Equation Formalism Polarizable Continuum Model (IEF-PCM). The alkaline hydrolysis of these organophosphorus compounds reveals that the reaction proceeds through the attack of hydroxide ion at the phosphorus center to form a pentacoordinate intermediate. The calculated free energies of activation for the alkaline hydrolysis of paraoxon and parathion are in good agreement with the available experimental activation free energies. The computed results show that the reaction profiles for the alkaline hydrolysis of paraoxon, parathion and PNPDPP are largely similar; however, the rate of hydrolysis of parathion may be higher than that of paraxon and PNPDPP. Such difference arises due to the less electrophilic nature of the phosphorus atom of parathion molecule as observed in the charge analysis study. The conceptual DFT analysis also showed the similar trend for the alkaline hydrolysis of paraoxon, parathion and PNPDPP with hydroxide anion. This computational study provides a quantitative support toward the use of PNPDPP as a simulant for organophosphorus compounds, which cannot be used directly for the laboratory purposes.

  11. Learning support assessment study of a computer simulation for the development of microbial identification strategies.

    PubMed

    Johnson, T E; Gedney, C

    2001-05-01

    This paper describes a study that examined how microbiology students construct knowledge of bacterial identification while using a computer simulation. The purpose of this study was to understand how the simulation affects the cognitive processing of students during thinking, problem solving, and learning about bacterial identification and to determine how the simulation facilitates the learning of a domain-specific problem-solving strategy. As part of an upper-division microbiology course, five students participated in several simulation assignments. The data were collected using think-aloud protocol and video action logs as the students used the simulation. The analysis revealed two major themes that determined the performance of the students: Simulation Usage-how the students used the software features and Problem-Solving Strategy Development-the strategy level students started with and the skill level they achieved when they completed their use of the simulation. SEVERAL CONCLUSIONS EMERGED FROM THE ANALYSIS OF THE DATA: (i) The simulation affects various aspects of cognitive processing by creating an environment that makes it possible to practice the application of a problem-solving strategy. The simulation was used as an environment that allowed students to practice the cognitive skills required to solve an unknown. (ii) Identibacter (the computer simulation) may be considered to be a cognitive tool to facilitate the learning of a bacterial identification problem-solving strategy. (iii) The simulation characteristics did support student learning of a problem-solving strategy. (iv) Students demonstrated problem-solving strategy development specific to bacterial identification. (v) Participants demonstrated an improved performance from their repeated use of the simulation.

  12. A 3-D Computational Study of a Variable Camber Continuous Trailing Edge Flap (VCCTEF) Spanwise Segment

    NASA Technical Reports Server (NTRS)

    Kaul, Upender K.; Nguyen, Nhan T.

    2015-01-01

    Results of a computational study carried out to explore the effects of various elastomer configurations joining spanwise contiguous Variable Camber Continuous Trailing Edge Flap (VCCTEF) segments are reported here. This research is carried out as a proof-of-concept study that will seek to push the flight envelope in cruise with drag optimization as the objective. The cruise conditions can be well off design such as caused by environmental conditions, maneuvering, etc. To handle these off-design conditions, flap deflection is used so when the flap is deflected in a given direction, the aircraft angle of attack changes accordingly to maintain a given lift. The angle of attack is also a design parameter along with the flap deflection. In a previous 2D study,1 the effect of camber was investigated and the results revealed some insight into the relative merit of various camber settings of the VCCTEF. The present state of the art has not advanced sufficiently to do a full 3-D viscous analysis of the whole NASA Generic Transport Model (GTM) wing with VCCTEF deployed with elastomers. Therefore, this study seeks to explore the local effects of three contiguous flap segments on lift and drag of a model devised here to determine possible trades among various flap deflections to achieve desired lift and drag results. Although this approach is an approximation, it provides new insights into the "local" effects of the relative deflections of the contiguous spanwise flap systems and various elastomer segment configurations. The present study is a natural extension of the 2-D study to assess these local 3-D effects. Design cruise condition at 36,000 feet at free stream Mach number of 0.797 and a mean aerodynamic chord (MAC) based Reynolds number of 30.734x10(exp 6) is simulated for an angle of attack (AoA) range of 0 to 6 deg. In the previous 2-D study, the calculations revealed that the parabolic arc camber (1x2x3) and circular arc camber (VCCTEF222) offered the best L

  13. Computational Studies of Molecular Permeation through Connexin26 Channels.

    PubMed

    Luo, Yun; Rossi, Angelo R; Harris, Andrew L

    2016-02-02

    A signal property of connexin channels is the ability to mediate selective diffusive movement of molecules through plasma membrane(s), but the energetics and determinants of molecular movement through these channels have yet to be understood. Different connexin channels have distinct molecular selectivities that cannot be explained simply on the basis of size or charge of the permeants. To gain insight into the forces and interactions that underlie selective molecular permeation, we investigated the energetics of two uncharged derivatized sugars, one permeable and one impermeable, through a validated connexin26 (Cx26) channel structural model, using molecular dynamics and associated analytic tools. The system is a Cx26 channel equilibrated in explicit membrane/solvent, shown by Brownian dynamics to reproduce key conductance characteristics of the native channel. The results are consistent with the known difference in permeability to each molecule. The energetic barriers extend through most of the pore length, rather than being highly localized as in ion-specific channels. There is little evidence for binding within the pore. Force decomposition reveals how, for each tested molecule, interactions with water and the Cx26 protein vary over the length of the pore and reveals a significant contribution from hydrogen bonding and interaction with K(+). The flexibility of the pore width varies along its length, and the tested molecules have differential effects on pore width as they pass through. Potential sites of interaction within the pore are defined for each molecule. The results suggest that for the tested molecules, differences in hydrogen bonding and entropic factors arising from permeant flexibility substantially contribute to the energetics of permeation. This work highlights factors involved in selective molecular permeation that differ from those that define selectivity among atomic ions.

  14. Photocatalytic Water Splitting with the Acridine Chromophore: A Computational Study.

    PubMed

    Liu, Xiaojun; Karsili, Tolga N V; Sobolewski, Andrzej L; Domcke, Wolfgang

    2015-08-20

    The hydrogen-bonded acridine-water complex is considered as a model system for the exploration of photochemical reactions which can lead to the splitting of water into H(•) and OH(•) radicals. The vertical excitation energies of the lowest singlet and triplet excited states of the complex were calculated with the CASSCF/CASPT2 and ADC(2) ab initio electronic-structure methods. In addition to the well-known excited states of the acridine chromophore, excited states of charge-transfer character were identified, in which an electron is transferred from the p orbital of the H2O molecule to the π* orbital of acridine. The low-energy barriers which separate these reactive charge-transfer states from the spectroscopic states of the acridine-water complex have been characterized by the calculation of two-dimensional relaxed potential-energy surfaces as functions of the H atom-transfer coordinate and the donor (O)-acceptor (N) distance. When populated, these charge-transfer states drive the transfer of a proton from the water molecule to acridine, which results in the acridinyl-hydroxyl biradical. The same computational methods were employed to explore the photochemistry of the (N-hydrogenated) acridinyl radical. The latter possesses low-lying (about 3.0 eV) ππ* excited states with appreciable oscillator strengths in addition to a low-lying dark ππ* excited state. The bound potential-energy functions of the ππ* excited states are predissociated by the potential-energy function of an excited state of πσ* character which is repulsive with respect to the NH stretching coordinate. The dissociation threshold of the πσ* state is about 2.7 eV and thus below the excitation energies of the bright ππ* states. The conical intersections of the πσ* state with the ππ* excited states and with the electronic ground state provide a mechanism for the direct and fast photodetachment of the H atom from the acridinyl radical. These computational results indicate that the H2

  15. Mt. Etna plumbing system revealed by combined textural, compositional, and thermobarometric studies in clinopyroxenes

    NASA Astrophysics Data System (ADS)

    Giacomoni, P. P.; Coltorti, M.; Bryce, J. G.; Fahnestock, M. F.; Guitreau, M.

    2016-04-01

    Coupled textural and in situ geochemical studies of clinopyroxene (cpx) phenocrysts, from both historical and recent eruptions of Mt. Etna volcano, provide a means to investigate the processes occurring in the deepest portion of the feeding system (>10 km depth). Five distinct textures were recognized: (1) normal oscillatory zoning, (2) normal zoning with Fe-rich rim, (3) sieve-textured core, (4) reverse oscillatory zoning, and (5) dusty rim. Electron microprobe analyses indicate an almost constant diopside-augite composition, with a slight enrichment in the enstatite for more recent erupted cpx. Core-to-rim compositional profiles, performed along the cpx, reveal distinct compositional characteristics. Normal oscillatory zoning is often characterized by a sharp increase in FeO (Δ ~ 2 wt%) accompanied by a drop in Al2O3 on the outermost 30 μm. Reverse oscillatory zoning, by contrast, exhibits a drop in FeO, Al2O3 (Δ ~ 2 wt%), and a remarkable crystal rim increase in MgO (up to 5 wt%). Similar compositional changes are evident in dusty-textured rims, which are characterized by dissolution edges and overgrowth containing glass pockets and channels. No significant compositional variations have been observed across crystals with sieve-textured cores. Trace element concentrations show enrichments in Sr, La, Zr, and REE, together with a decreasing La/Yb ratio (from ~7 to ~4) in rims of normally zoned crystals. Cpx with reverse zoning and dusty rims has low Sr, La, Zr, and REE contents toward crystal rims. Thermometers and barometers, based on equilibrium cpx-melt pairs, suggest that cpx cores start nucleating at 720 MPa, with the majority of them forming between 600 and 400 MPa but continuing to crystallize until very shallow depths (<100 MPa). Normal oscillatory-zoned phenocrysts surrounded by rims form at pressures shallower than 400 MPa, while reverse zoning and dusty rims occur between 400 and 500 MPa. Coupled petrologic and thermobarometric studies on both

  16. Serial computed tomography scanning in acute pancreatitis: a prospective study.

    PubMed Central

    London, N J; Neoptolemos, J P; Lavelle, J; Bailey, I; James, D

    1989-01-01

    One hundred and two patients with acute pancreatitis had abdominal computed tomography (CT) scans within 72 hours of admission, at one week and at six weeks. Twenty eight attacks were clinically severe, 74 clinically mild. Ninety three (91%) admission scans, 85 (84%) one week scans, and 52 (51%) six week scans were abnormal. The aetiology of the pancreatitis could be inferred from 28 (27%) of admission scans, the CT sign of fatty liver having a sensitivity of 21% and specificity of 100% for alcoholic aetiology. The sensitivity of CT for gall stone aetiology was 34%, specificity 100%. The pancreatic size indices (max anteroposterior measurement of head x max anteroposterior measurement of body) of those patients with severe attacks were significantly greater than those with mild attacks on admission, at one week and at six weeks (p less than 0.004). Fourteen pseudocysts were detected by CT, five (36%) of which were clinically apparent. The pseudocyst size indices (max anteroposterior x max transverse measurement) of the pseudocysts which were clinically apparent were significantly greater than those which were not apparent (p less than 0.01) and only those pseudocysts with a size index greater than or equal to 15 cm2 required treatment. PMID:2651228

  17. Control of neural synchrony using channelrhodopsin-2: a computational study.

    PubMed

    Talathi, Sachin S; Carney, Paul R; Khargonekar, Pramod P

    2011-08-01

    In this paper, we present an optical stimulation based approach to induce 1:1 in-phase synchrony in a network of coupled interneurons wherein each interneuron expresses the light sensitive protein channelrhodopsin-2 (ChR2). We begin with a transition rate model for the channel kinetics of ChR2 in response to light stimulation. We then define "functional optical time response curve (fOTRC)" as a measure of the response of a periodically firing interneuron (transfected with ChR2 ion channel) to a periodic light pulse stimulation. We specifically consider the case of unidirectionally coupled (UCI) network and propose an open loop control architecture that uses light as an actuation signal to induce 1:1 in-phase synchrony in the UCI network. Using general properties of the spike time response curves (STRCs) for Type-1 neuron model (Ermentrout, Neural Comput 8:979-1001, 1996) and fOTRC, we estimate the (open loop) optimal actuation signal parameters required to induce 1:1 in-phase synchrony. We then propose a closed loop controller architecture and a controller algorithm to robustly sustain stable 1:1 in-phase synchrony in the presence of unknown deviations in the network parameters. Finally, we test the performance of this closed-loop controller in a network of mutually coupled (MCI) interneurons.

  18. Specificity in lipases: A computational study of transesterification of sucrose

    PubMed Central

    Fuentes, Gloria; Ballesteros, Anthonio; Verma, Chandra S.

    2004-01-01

    Computational conformational searches of putative transition states of the reaction of sucrose with vinyl laurate catalyzed by lipases from Candida antarctica B and Thermomyces lanuginosus have been carried out. The dielectric of the media have been varied to understand the role of protein plasticity in modulating the observed regioselective transesterification. The binding pocket of lipase from Candida adapts to the conformational variability of the various substates of the substrates by small, local adjustments within the binding pocket. In contrast, the more constrained pocket of the lipase from Thermomyces adapts by adjusting through concerted global motions between subdomains. This leads to the identification of one large pocket in Candida that accommodates both the sucrose and the lauroyl moieties of the transition state, whereas in Thermomyces the binding pocket is smaller, leading to the localization of the two moieties in two distinct pockets; this partly rationalizes the broader specificity of the former relative to the latter. Mutations have been suggested to exploit the differences towards changing the observed selectivities. PMID:15557256

  19. Computational Study of Shock-Associated Noise Characteristics Using LES

    NASA Astrophysics Data System (ADS)

    Liu, J.; Corrigan, A.; Kailasanath, K.; Heeb, N.; Munday, D.; Gutmark, E.

    2013-11-01

    Shock-associated noise generation has been investigated by using large-eddy simulations to compute jet flows at an underexpanded jet condition with three jet temperatures. To better understand shock-associated noise generation, shock-free jets with the same fully expanded jet conditions have also been simulated. The predictions agree well with the available experimental data in both the near and far field. It is found that shock cells at this underexpanded jet condition have little impact on the jet core length and the turbulence kinetic energy distribution, whereas the heating effect has a much larger impact by increasing the initial shear-layer spreading and shortening the jet core length. Shock-associated noise dominates in the upstream direction, and the broadband peak frequencies move to higher values in downstream direction. This frequency increase is initially small in the upstream direction, but becomes much larger in the downstream direction. In addition, it is found that the heating effect increases the broadband peak frequency. Overall the heating effect increases the mixing noise and slightly reduces the shock-associated noise. This reduces the difference between the shock-containing jets and the shock-free jets as the temperature increases. This research has been sponsored by the Office of Naval Research (ONR).

  20. A preliminary study of molecular dynamics on reconfigurable computers

    SciTech Connect

    Wolinski, C.; Trouw, F. R.; Gokhale, M.

    2003-01-01

    In this paper we investigate the performance of platform FPGAs on a compute-intensive, floating-point-intensive supercomputing application, Molecular Dynamics (MD). MD is a popular simulation technique to track interacting particles through time by integrating their equations of motion. One part of the MD algorithm was implemented using the Fabric Generator (FG)[l I ] and mapped onto several reconfigurable logic arrays. FG is a Java-based toolset that greatly accelerates construction of the fabrics from an abstract technology independent representation. Our experiments used technology-independent IEEE 32-bit floating point operators so that the design could be easily re-targeted. Experiments were performed using both non-pipelined and pipelined floating point modules. We present results for the Altera Excalibur ARM System on a Programmable Chip (SoPC), the Altera Strath EPlS80, and the Xilinx Virtex-N Pro 2VP.50. The best results obtained were 5.69 GFlops at 8OMHz(Altera Strath EPlS80), and 4.47 GFlops at 82 MHz (Xilinx Virtex-II Pro 2VF50). Assuming a lOWpower budget, these results compare very favorably to a 4Gjlop/40Wprocessing/power rate for a modern Pentium, suggesting that reconfigurable logic can achieve high performance at low power on jloating-point-intensivea pplications.