Science.gov

Sample records for accurate theoretical predictions

  1. A survey of factors contributing to accurate theoretical predictions of atomization energies and molecular structures

    NASA Astrophysics Data System (ADS)

    Feller, David; Peterson, Kirk A.; Dixon, David A.

    2008-11-01

    High level electronic structure predictions of thermochemical properties and molecular structure are capable of accuracy rivaling the very best experimental measurements as a result of rapid advances in hardware, software, and methodology. Despite the progress, real world limitations require practical approaches designed for handling general chemical systems that rely on composite strategies in which a single, intractable calculation is replaced by a series of smaller calculations. As typically implemented, these approaches produce a final, or "best," estimate that is constructed from one major component, fine-tuned by multiple corrections that are assumed to be additive. Though individually much smaller than the original, unmanageable computational problem, these corrections are nonetheless extremely costly. This study presents a survey of the widely varying magnitude of the most important components contributing to the atomization energies and structures of 106 small molecules. It combines large Gaussian basis sets and coupled cluster theory up to quadruple excitations for all systems. In selected cases, the effects of quintuple excitations and/or full configuration interaction were also considered. The availability of reliable experimental data for most of the molecules permits an expanded statistical analysis of the accuracy of the approach. In cases where reliable experimental information is currently unavailable, the present results are expected to provide some of the most accurate benchmark values available.

  2. Accurate theoretical chemistry with coupled pair models.

    PubMed

    Neese, Frank; Hansen, Andreas; Wennmohs, Frank; Grimme, Stefan

    2009-05-19

    Quantum chemistry has found its way into the everyday work of many experimental chemists. Calculations can predict the outcome of chemical reactions, afford insight into reaction mechanisms, and be used to interpret structure and bonding in molecules. Thus, contemporary theory offers tremendous opportunities in experimental chemical research. However, even with present-day computers and algorithms, we cannot solve the many particle Schrodinger equation exactly; inevitably some error is introduced in approximating the solutions of this equation. Thus, the accuracy of quantum chemical calculations is of critical importance. The affordable accuracy depends on molecular size and particularly on the total number of atoms: for orientation, ethanol has 9 atoms, aspirin 21 atoms, morphine 40 atoms, sildenafil 63 atoms, paclitaxel 113 atoms, insulin nearly 800 atoms, and quaternary hemoglobin almost 12,000 atoms. Currently, molecules with up to approximately 10 atoms can be very accurately studied by coupled cluster (CC) theory, approximately 100 atoms with second-order Møller-Plesset perturbation theory (MP2), approximately 1000 atoms with density functional theory (DFT), and beyond that number with semiempirical quantum chemistry and force-field methods. The overwhelming majority of present-day calculations in the 100-atom range use DFT. Although these methods have been very successful in quantum chemistry, they do not offer a well-defined hierarchy of calculations that allows one to systematically converge to the correct answer. Recently a number of rather spectacular failures of DFT methods have been found-even for seemingly simple systems such as hydrocarbons, fueling renewed interest in wave function-based methods that incorporate the relevant physics of electron correlation in a more systematic way. Thus, it would be highly desirable to fill the gap between 10 and 100 atoms with highly correlated ab initio methods. We have found that one of the earliest (and now

  3. On the Accurate Prediction of CME Arrival At the Earth

    NASA Astrophysics Data System (ADS)

    Zhang, Jie; Hess, Phillip

    2016-07-01

    We will discuss relevant issues regarding the accurate prediction of CME arrival at the Earth, from both observational and theoretical points of view. In particular, we clarify the importance of separating the study of CME ejecta from the ejecta-driven shock in interplanetary CMEs (ICMEs). For a number of CME-ICME events well observed by SOHO/LASCO, STEREO-A and STEREO-B, we carry out the 3-D measurements by superimposing geometries onto both the ejecta and sheath separately. These measurements are then used to constrain a Drag-Based Model, which is improved through a modification of including height dependence of the drag coefficient into the model. Combining all these factors allows us to create predictions for both fronts at 1 AU and compare with actual in-situ observations. We show an ability to predict the sheath arrival with an average error of under 4 hours, with an RMS error of about 1.5 hours. For the CME ejecta, the error is less than two hours with an RMS error within an hour. Through using the best observations of CMEs, we show the power of our method in accurately predicting CME arrival times. The limitation and implications of our accurate prediction method will be discussed.

  4. Hounsfield unit density accurately predicts ESWL success.

    PubMed

    Magnuson, William J; Tomera, Kevin M; Lance, Raymond S

    2005-01-01

    Extracorporeal shockwave lithotripsy (ESWL) is a commonly used non-invasive treatment for urolithiasis. Helical CT scans provide much better and detailed imaging of the patient with urolithiasis including the ability to measure density of urinary stones. In this study we tested the hypothesis that density of urinary calculi as measured by CT can predict successful ESWL treatment. 198 patients were treated at Alaska Urological Associates with ESWL between January 2002 and April 2004. Of these 101 met study inclusion with accessible CT scans and stones ranging from 5-15 mm. Follow-up imaging demonstrated stone freedom in 74.2%. The overall mean Houndsfield density value for stone-free compared to residual stone groups were significantly different ( 93.61 vs 122.80 p < 0.0001). We determined by receiver operator curve (ROC) that HDV of 93 or less carries a 90% or better chance of stone freedom following ESWL for upper tract calculi between 5-15mm.

  5. Theoretical predictions for exotic hadrons

    SciTech Connect

    Barnes, T. |

    1996-12-31

    In this contribution the authors discuss current theoretical expectations for the properties of light meson exotica, which are meson resonances outside the q{anti q} quark model. Specifically they discuss expectations for gluonic hadrons (glueballs and hybrids) and multiquark systems (molecules). Experimental candidates for these states are summarized, and the relevance of a TCF to these studies is stressed.

  6. Theoretical prediction of crystal structures of rubrene

    NASA Astrophysics Data System (ADS)

    Obata, Shigeaki; Miura, Toshiaki; Shimoi, Yukihiro

    2014-01-01

    We theoretically predict crystal structures and molecular arrangements for rubrene molecule using CONFLEX program and compare them with the experimental ones. The most, second-most, and fourth-most stable predicted crystal structures show good agreement with the triclinic, orthorhombic, and monoclinic polymorphs of rubrene, respectively. The change in molecular conformation is also predicted between crystalline and gas phases: the tetracene backbone takes flat conformation in crystalline phase as in the observed structure. Meanwhile, it is twisted in gas phase. The theoretical prediction method used in this work provides the successful results on the determination of the three kinds of crystal structures and molecular arrangements for rubrene molecule.

  7. Isodesmic reaction for accurate theoretical pKa calculations of amino acids and peptides.

    PubMed

    Sastre, S; Casasnovas, R; Muñoz, F; Frau, J

    2016-04-28

    Theoretical and quantitative prediction of pKa values at low computational cost is a current challenge in computational chemistry. We report that the isodesmic reaction scheme provides semi-quantitative predictions (i.e. mean absolute errors of 0.5-1.0 pKa unit) for the pKa1 (α-carboxyl), pKa2 (α-amino) and pKa3 (sidechain groups) of a broad set of amino acids and peptides. This method fills the gaps of thermodynamic cycles for the computational pKa calculation of molecules that are unstable in the gas phase or undergo proton transfer reactions or large conformational changes from solution to the gas phase. We also report the key criteria to choose a reference species to make accurate predictions. This method is computationally inexpensive and makes use of standard density functional theory (DFT) and continuum solvent models. It is also conceptually simple and easy to use for researchers not specialized in theoretical chemistry methods. PMID:27052591

  8. Passive samplers accurately predict PAH levels in resident crayfish.

    PubMed

    Paulik, L Blair; Smith, Brian W; Bergmann, Alan J; Sower, Greg J; Forsberg, Norman D; Teeguarden, Justin G; Anderson, Kim A

    2016-02-15

    Contamination of resident aquatic organisms is a major concern for environmental risk assessors. However, collecting organisms to estimate risk is often prohibitively time and resource-intensive. Passive sampling accurately estimates resident organism contamination, and it saves time and resources. This study used low density polyethylene (LDPE) passive water samplers to predict polycyclic aromatic hydrocarbon (PAH) levels in signal crayfish, Pacifastacus leniusculus. Resident crayfish were collected at 5 sites within and outside of the Portland Harbor Superfund Megasite (PHSM) in the Willamette River in Portland, Oregon. LDPE deployment was spatially and temporally paired with crayfish collection. Crayfish visceral and tail tissue, as well as water-deployed LDPE, were extracted and analyzed for 62 PAHs using GC-MS/MS. Freely-dissolved concentrations (Cfree) of PAHs in water were calculated from concentrations in LDPE. Carcinogenic risks were estimated for all crayfish tissues, using benzo[a]pyrene equivalent concentrations (BaPeq). ∑PAH were 5-20 times higher in viscera than in tails, and ∑BaPeq were 6-70 times higher in viscera than in tails. Eating only tail tissue of crayfish would therefore significantly reduce carcinogenic risk compared to also eating viscera. Additionally, PAH levels in crayfish were compared to levels in crayfish collected 10 years earlier. PAH levels in crayfish were higher upriver of the PHSM and unchanged within the PHSM after the 10-year period. Finally, a linear regression model predicted levels of 34 PAHs in crayfish viscera with an associated R-squared value of 0.52 (and a correlation coefficient of 0.72), using only the Cfree PAHs in water. On average, the model predicted PAH concentrations in crayfish tissue within a factor of 2.4 ± 1.8 of measured concentrations. This affirms that passive water sampling accurately estimates PAH contamination in crayfish. Furthermore, the strong predictive ability of this simple model suggests

  9. Plant diversity accurately predicts insect diversity in two tropical landscapes.

    PubMed

    Zhang, Kai; Lin, Siliang; Ji, Yinqiu; Yang, Chenxue; Wang, Xiaoyang; Yang, Chunyan; Wang, Hesheng; Jiang, Haisheng; Harrison, Rhett D; Yu, Douglas W

    2016-09-01

    Plant diversity surely determines arthropod diversity, but only moderate correlations between arthropod and plant species richness had been observed until Basset et al. (Science, 338, 2012 and 1481) finally undertook an unprecedentedly comprehensive sampling of a tropical forest and demonstrated that plant species richness could indeed accurately predict arthropod species richness. We now require a high-throughput pipeline to operationalize this result so that we can (i) test competing explanations for tropical arthropod megadiversity, (ii) improve estimates of global eukaryotic species diversity, and (iii) use plant and arthropod communities as efficient proxies for each other, thus improving the efficiency of conservation planning and of detecting forest degradation and recovery. We therefore applied metabarcoding to Malaise-trap samples across two tropical landscapes in China. We demonstrate that plant species richness can accurately predict arthropod (mostly insect) species richness and that plant and insect community compositions are highly correlated, even in landscapes that are large, heterogeneous and anthropogenically modified. Finally, we review how metabarcoding makes feasible highly replicated tests of the major competing explanations for tropical megadiversity. PMID:27474399

  10. Basophile: Accurate Fragment Charge State Prediction Improves Peptide Identification Rates

    DOE PAGES

    Wang, Dong; Dasari, Surendra; Chambers, Matthew C.; Holman, Jerry D.; Chen, Kan; Liebler, Daniel; Orton, Daniel J.; Purvine, Samuel O.; Monroe, Matthew E.; Chung, Chang Y.; et al

    2013-03-07

    In shotgun proteomics, database search algorithms rely on fragmentation models to predict fragment ions that should be observed for a given peptide sequence. The most widely used strategy (Naive model) is oversimplified, cleaving all peptide bonds with equal probability to produce fragments of all charges below that of the precursor ion. More accurate models, based on fragmentation simulation, are too computationally intensive for on-the-fly use in database search algorithms. We have created an ordinal-regression-based model called Basophile that takes fragment size and basic residue distribution into account when determining the charge retention during CID/higher-energy collision induced dissociation (HCD) of chargedmore » peptides. This model improves the accuracy of predictions by reducing the number of unnecessary fragments that are routinely predicted for highly-charged precursors. Basophile increased the identification rates by 26% (on average) over the Naive model, when analyzing triply-charged precursors from ion trap data. Basophile achieves simplicity and speed by solving the prediction problem with an ordinal regression equation, which can be incorporated into any database search software for shotgun proteomic identification.« less

  11. Basophile: Accurate Fragment Charge State Prediction Improves Peptide Identification Rates

    SciTech Connect

    Wang, Dong; Dasari, Surendra; Chambers, Matthew C.; Holman, Jerry D.; Chen, Kan; Liebler, Daniel; Orton, Daniel J.; Purvine, Samuel O.; Monroe, Matthew E.; Chung, Chang Y.; Rose, Kristie L.; Tabb, David L.

    2013-03-07

    In shotgun proteomics, database search algorithms rely on fragmentation models to predict fragment ions that should be observed for a given peptide sequence. The most widely used strategy (Naive model) is oversimplified, cleaving all peptide bonds with equal probability to produce fragments of all charges below that of the precursor ion. More accurate models, based on fragmentation simulation, are too computationally intensive for on-the-fly use in database search algorithms. We have created an ordinal-regression-based model called Basophile that takes fragment size and basic residue distribution into account when determining the charge retention during CID/higher-energy collision induced dissociation (HCD) of charged peptides. This model improves the accuracy of predictions by reducing the number of unnecessary fragments that are routinely predicted for highly-charged precursors. Basophile increased the identification rates by 26% (on average) over the Naive model, when analyzing triply-charged precursors from ion trap data. Basophile achieves simplicity and speed by solving the prediction problem with an ordinal regression equation, which can be incorporated into any database search software for shotgun proteomic identification.

  12. Passive samplers accurately predict PAH levels in resident crayfish.

    PubMed

    Paulik, L Blair; Smith, Brian W; Bergmann, Alan J; Sower, Greg J; Forsberg, Norman D; Teeguarden, Justin G; Anderson, Kim A

    2016-02-15

    Contamination of resident aquatic organisms is a major concern for environmental risk assessors. However, collecting organisms to estimate risk is often prohibitively time and resource-intensive. Passive sampling accurately estimates resident organism contamination, and it saves time and resources. This study used low density polyethylene (LDPE) passive water samplers to predict polycyclic aromatic hydrocarbon (PAH) levels in signal crayfish, Pacifastacus leniusculus. Resident crayfish were collected at 5 sites within and outside of the Portland Harbor Superfund Megasite (PHSM) in the Willamette River in Portland, Oregon. LDPE deployment was spatially and temporally paired with crayfish collection. Crayfish visceral and tail tissue, as well as water-deployed LDPE, were extracted and analyzed for 62 PAHs using GC-MS/MS. Freely-dissolved concentrations (Cfree) of PAHs in water were calculated from concentrations in LDPE. Carcinogenic risks were estimated for all crayfish tissues, using benzo[a]pyrene equivalent concentrations (BaPeq). ∑PAH were 5-20 times higher in viscera than in tails, and ∑BaPeq were 6-70 times higher in viscera than in tails. Eating only tail tissue of crayfish would therefore significantly reduce carcinogenic risk compared to also eating viscera. Additionally, PAH levels in crayfish were compared to levels in crayfish collected 10 years earlier. PAH levels in crayfish were higher upriver of the PHSM and unchanged within the PHSM after the 10-year period. Finally, a linear regression model predicted levels of 34 PAHs in crayfish viscera with an associated R-squared value of 0.52 (and a correlation coefficient of 0.72), using only the Cfree PAHs in water. On average, the model predicted PAH concentrations in crayfish tissue within a factor of 2.4 ± 1.8 of measured concentrations. This affirms that passive water sampling accurately estimates PAH contamination in crayfish. Furthermore, the strong predictive ability of this simple model suggests

  13. Mouse models of human AML accurately predict chemotherapy response

    PubMed Central

    Zuber, Johannes; Radtke, Ina; Pardee, Timothy S.; Zhao, Zhen; Rappaport, Amy R.; Luo, Weijun; McCurrach, Mila E.; Yang, Miao-Miao; Dolan, M. Eileen; Kogan, Scott C.; Downing, James R.; Lowe, Scott W.

    2009-01-01

    The genetic heterogeneity of cancer influences the trajectory of tumor progression and may underlie clinical variation in therapy response. To model such heterogeneity, we produced genetically and pathologically accurate mouse models of common forms of human acute myeloid leukemia (AML) and developed methods to mimic standard induction chemotherapy and efficiently monitor therapy response. We see that murine AMLs harboring two common human AML genotypes show remarkably diverse responses to conventional therapy that mirror clinical experience. Specifically, murine leukemias expressing the AML1/ETO fusion oncoprotein, associated with a favorable prognosis in patients, show a dramatic response to induction chemotherapy owing to robust activation of the p53 tumor suppressor network. Conversely, murine leukemias expressing MLL fusion proteins, associated with a dismal prognosis in patients, are drug-resistant due to an attenuated p53 response. Our studies highlight the importance of genetic information in guiding the treatment of human AML, functionally establish the p53 network as a central determinant of chemotherapy response in AML, and demonstrate that genetically engineered mouse models of human cancer can accurately predict therapy response in patients. PMID:19339691

  14. Fast and accurate predictions of covalent bonds in chemical space.

    PubMed

    Chang, K Y Samuel; Fias, Stijn; Ramakrishnan, Raghunathan; von Lilienfeld, O Anatole

    2016-05-01

    We assess the predictive accuracy of perturbation theory based estimates of changes in covalent bonding due to linear alchemical interpolations among molecules. We have investigated σ bonding to hydrogen, as well as σ and π bonding between main-group elements, occurring in small sets of iso-valence-electronic molecules with elements drawn from second to fourth rows in the p-block of the periodic table. Numerical evidence suggests that first order Taylor expansions of covalent bonding potentials can achieve high accuracy if (i) the alchemical interpolation is vertical (fixed geometry), (ii) it involves elements from the third and fourth rows of the periodic table, and (iii) an optimal reference geometry is used. This leads to near linear changes in the bonding potential, resulting in analytical predictions with chemical accuracy (∼1 kcal/mol). Second order estimates deteriorate the prediction. If initial and final molecules differ not only in composition but also in geometry, all estimates become substantially worse, with second order being slightly more accurate than first order. The independent particle approximation based second order perturbation theory performs poorly when compared to the coupled perturbed or finite difference approach. Taylor series expansions up to fourth order of the potential energy curve of highly symmetric systems indicate a finite radius of convergence, as illustrated for the alchemical stretching of H2 (+). Results are presented for (i) covalent bonds to hydrogen in 12 molecules with 8 valence electrons (CH4, NH3, H2O, HF, SiH4, PH3, H2S, HCl, GeH4, AsH3, H2Se, HBr); (ii) main-group single bonds in 9 molecules with 14 valence electrons (CH3F, CH3Cl, CH3Br, SiH3F, SiH3Cl, SiH3Br, GeH3F, GeH3Cl, GeH3Br); (iii) main-group double bonds in 9 molecules with 12 valence electrons (CH2O, CH2S, CH2Se, SiH2O, SiH2S, SiH2Se, GeH2O, GeH2S, GeH2Se); (iv) main-group triple bonds in 9 molecules with 10 valence electrons (HCN, HCP, HCAs, HSiN, HSi

  15. Fast and accurate predictions of covalent bonds in chemical space

    NASA Astrophysics Data System (ADS)

    Chang, K. Y. Samuel; Fias, Stijn; Ramakrishnan, Raghunathan; von Lilienfeld, O. Anatole

    2016-05-01

    We assess the predictive accuracy of perturbation theory based estimates of changes in covalent bonding due to linear alchemical interpolations among molecules. We have investigated σ bonding to hydrogen, as well as σ and π bonding between main-group elements, occurring in small sets of iso-valence-electronic molecules with elements drawn from second to fourth rows in the p-block of the periodic table. Numerical evidence suggests that first order Taylor expansions of covalent bonding potentials can achieve high accuracy if (i) the alchemical interpolation is vertical (fixed geometry), (ii) it involves elements from the third and fourth rows of the periodic table, and (iii) an optimal reference geometry is used. This leads to near linear changes in the bonding potential, resulting in analytical predictions with chemical accuracy (˜1 kcal/mol). Second order estimates deteriorate the prediction. If initial and final molecules differ not only in composition but also in geometry, all estimates become substantially worse, with second order being slightly more accurate than first order. The independent particle approximation based second order perturbation theory performs poorly when compared to the coupled perturbed or finite difference approach. Taylor series expansions up to fourth order of the potential energy curve of highly symmetric systems indicate a finite radius of convergence, as illustrated for the alchemical stretching of H 2+ . Results are presented for (i) covalent bonds to hydrogen in 12 molecules with 8 valence electrons (CH4, NH3, H2O, HF, SiH4, PH3, H2S, HCl, GeH4, AsH3, H2Se, HBr); (ii) main-group single bonds in 9 molecules with 14 valence electrons (CH3F, CH3Cl, CH3Br, SiH3F, SiH3Cl, SiH3Br, GeH3F, GeH3Cl, GeH3Br); (iii) main-group double bonds in 9 molecules with 12 valence electrons (CH2O, CH2S, CH2Se, SiH2O, SiH2S, SiH2Se, GeH2O, GeH2S, GeH2Se); (iv) main-group triple bonds in 9 molecules with 10 valence electrons (HCN, HCP, HCAs, HSiN, HSi

  16. Fast and accurate predictions of covalent bonds in chemical space.

    PubMed

    Chang, K Y Samuel; Fias, Stijn; Ramakrishnan, Raghunathan; von Lilienfeld, O Anatole

    2016-05-01

    We assess the predictive accuracy of perturbation theory based estimates of changes in covalent bonding due to linear alchemical interpolations among molecules. We have investigated σ bonding to hydrogen, as well as σ and π bonding between main-group elements, occurring in small sets of iso-valence-electronic molecules with elements drawn from second to fourth rows in the p-block of the periodic table. Numerical evidence suggests that first order Taylor expansions of covalent bonding potentials can achieve high accuracy if (i) the alchemical interpolation is vertical (fixed geometry), (ii) it involves elements from the third and fourth rows of the periodic table, and (iii) an optimal reference geometry is used. This leads to near linear changes in the bonding potential, resulting in analytical predictions with chemical accuracy (∼1 kcal/mol). Second order estimates deteriorate the prediction. If initial and final molecules differ not only in composition but also in geometry, all estimates become substantially worse, with second order being slightly more accurate than first order. The independent particle approximation based second order perturbation theory performs poorly when compared to the coupled perturbed or finite difference approach. Taylor series expansions up to fourth order of the potential energy curve of highly symmetric systems indicate a finite radius of convergence, as illustrated for the alchemical stretching of H2 (+). Results are presented for (i) covalent bonds to hydrogen in 12 molecules with 8 valence electrons (CH4, NH3, H2O, HF, SiH4, PH3, H2S, HCl, GeH4, AsH3, H2Se, HBr); (ii) main-group single bonds in 9 molecules with 14 valence electrons (CH3F, CH3Cl, CH3Br, SiH3F, SiH3Cl, SiH3Br, GeH3F, GeH3Cl, GeH3Br); (iii) main-group double bonds in 9 molecules with 12 valence electrons (CH2O, CH2S, CH2Se, SiH2O, SiH2S, SiH2Se, GeH2O, GeH2S, GeH2Se); (iv) main-group triple bonds in 9 molecules with 10 valence electrons (HCN, HCP, HCAs, HSiN, HSi

  17. An Overview of Practical Applications of Protein Disorder Prediction and Drive for Faster, More Accurate Predictions

    PubMed Central

    Deng, Xin; Gumm, Jordan; Karki, Suman; Eickholt, Jesse; Cheng, Jianlin

    2015-01-01

    Protein disordered regions are segments of a protein chain that do not adopt a stable structure. Thus far, a variety of protein disorder prediction methods have been developed and have been widely used, not only in traditional bioinformatics domains, including protein structure prediction, protein structure determination and function annotation, but also in many other biomedical fields. The relationship between intrinsically-disordered proteins and some human diseases has played a significant role in disorder prediction in disease identification and epidemiological investigations. Disordered proteins can also serve as potential targets for drug discovery with an emphasis on the disordered-to-ordered transition in the disordered binding regions, and this has led to substantial research in drug discovery or design based on protein disordered region prediction. Furthermore, protein disorder prediction has also been applied to healthcare by predicting the disease risk of mutations in patients and studying the mechanistic basis of diseases. As the applications of disorder prediction increase, so too does the need to make quick and accurate predictions. To fill this need, we also present a new approach to predict protein residue disorder using wide sequence windows that is applicable on the genomic scale. PMID:26198229

  18. Theoretical Ecology: Beginnings of a Predictive Science

    ERIC Educational Resources Information Center

    Kolata, Gina Bari

    1974-01-01

    Examines new directions in ecological research in which ecologists are analyzing systems with theoretical models and are using descriptive studies to confirm and extend their studies. The development of a model relating to species equilibriums on islands is now being applied to problems of conservation of wildlife in national parks. (JR)

  19. PredictSNP: robust and accurate consensus classifier for prediction of disease-related mutations.

    PubMed

    Bendl, Jaroslav; Stourac, Jan; Salanda, Ondrej; Pavelka, Antonin; Wieben, Eric D; Zendulka, Jaroslav; Brezovsky, Jan; Damborsky, Jiri

    2014-01-01

    Single nucleotide variants represent a prevalent form of genetic variation. Mutations in the coding regions are frequently associated with the development of various genetic diseases. Computational tools for the prediction of the effects of mutations on protein function are very important for analysis of single nucleotide variants and their prioritization for experimental characterization. Many computational tools are already widely employed for this purpose. Unfortunately, their comparison and further improvement is hindered by large overlaps between the training datasets and benchmark datasets, which lead to biased and overly optimistic reported performances. In this study, we have constructed three independent datasets by removing all duplicities, inconsistencies and mutations previously used in the training of evaluated tools. The benchmark dataset containing over 43,000 mutations was employed for the unbiased evaluation of eight established prediction tools: MAPP, nsSNPAnalyzer, PANTHER, PhD-SNP, PolyPhen-1, PolyPhen-2, SIFT and SNAP. The six best performing tools were combined into a consensus classifier PredictSNP, resulting into significantly improved prediction performance, and at the same time returned results for all mutations, confirming that consensus prediction represents an accurate and robust alternative to the predictions delivered by individual tools. A user-friendly web interface enables easy access to all eight prediction tools, the consensus classifier PredictSNP and annotations from the Protein Mutant Database and the UniProt database. The web server and the datasets are freely available to the academic community at http://loschmidt.chemi.muni.cz/predictsnp.

  20. Accurately Predicting Complex Reaction Kinetics from First Principles

    NASA Astrophysics Data System (ADS)

    Green, William

    Many important systems contain a multitude of reactive chemical species, some of which react on a timescale faster than collisional thermalization, i.e. they never achieve a Boltzmann energy distribution. Usually it is impossible to fully elucidate the processes by experiments alone. Here we report recent progress toward predicting the time-evolving composition of these systems a priori: how unexpected reactions can be discovered on the computer, how reaction rates are computed from first principles, and how the many individual reactions are efficiently combined into a predictive simulation for the whole system. Some experimental tests of the a priori predictions are also presented.

  1. Does more accurate exposure prediction necessarily improve health effect estimates?

    PubMed

    Szpiro, Adam A; Paciorek, Christopher J; Sheppard, Lianne

    2011-09-01

    A unique challenge in air pollution cohort studies and similar applications in environmental epidemiology is that exposure is not measured directly at subjects' locations. Instead, pollution data from monitoring stations at some distance from the study subjects are used to predict exposures, and these predicted exposures are used to estimate the health effect parameter of interest. It is usually assumed that minimizing the error in predicting the true exposure will improve health effect estimation. We show in a simulation study that this is not always the case. We interpret our results in light of recently developed statistical theory for measurement error, and we discuss implications for the design and analysis of epidemiologic research.

  2. Microstructure-Dependent Gas Adsorption: Accurate Predictions of Methane Uptake in Nanoporous Carbons

    SciTech Connect

    Ihm, Yungok; Cooper, Valentino R; Gallego, Nidia C; Contescu, Cristian I; Morris, James R

    2014-01-01

    We demonstrate a successful, efficient framework for predicting gas adsorption properties in real materials based on first-principles calculations, with a specific comparison of experiment and theory for methane adsorption in activated carbons. These carbon materials have different pore size distributions, leading to a variety of uptake characteristics. Utilizing these distributions, we accurately predict experimental uptakes and heats of adsorption without empirical potentials or lengthy simulations. We demonstrate that materials with smaller pores have higher heats of adsorption, leading to a higher gas density in these pores. This pore-size dependence must be accounted for, in order to predict and understand the adsorption behavior. The theoretical approach combines: (1) ab initio calculations with a van der Waals density functional to determine adsorbent-adsorbate interactions, and (2) a thermodynamic method that predicts equilibrium adsorption densities by directly incorporating the calculated potential energy surface in a slit pore model. The predicted uptake at P=20 bar and T=298 K is in excellent agreement for all five activated carbon materials used. This approach uses only the pore-size distribution as an input, with no fitting parameters or empirical adsorbent-adsorbate interactions, and thus can be easily applied to other adsorbent-adsorbate combinations.

  3. Is Three-Dimensional Soft Tissue Prediction by Software Accurate?

    PubMed

    Nam, Ki-Uk; Hong, Jongrak

    2015-11-01

    The authors assessed whether virtual surgery, performed with a soft tissue prediction program, could correctly simulate the actual surgical outcome, focusing on soft tissue movement. Preoperative and postoperative computed tomography (CT) data for 29 patients, who had undergone orthognathic surgery, were obtained and analyzed using the Simplant Pro software. The program made a predicted soft tissue image (A) based on presurgical CT data. After the operation, we obtained actual postoperative CT data and an actual soft tissue image (B) was generated. Finally, the 2 images (A and B) were superimposed and analyzed differences between the A and B. Results were grouped in 2 classes: absolute values and vector values. In the absolute values, the left mouth corner was the most significant error point (2.36 mm). The right mouth corner (2.28 mm), labrale inferius (2.08 mm), and the pogonion (2.03 mm) also had significant errors. In vector values, prediction of the right-left side had a left-sided tendency, the superior-inferior had a superior tendency, and the anterior-posterior showed an anterior tendency. As a result, with this program, the position of points tended to be located more left, anterior, and superior than the "real" situation. There is a need to improve the prediction accuracy for soft tissue images. Such software is particularly valuable in predicting craniofacial soft tissues landmarks, such as the pronasale. With this software, landmark positions were most inaccurate in terms of anterior-posterior predictions.

  4. Towards Accurate Ab Initio Predictions of the Spectrum of Methane

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.; Kwak, Dochan (Technical Monitor)

    2001-01-01

    We have carried out extensive ab initio calculations of the electronic structure of methane, and these results are used to compute vibrational energy levels. We include basis set extrapolations, core-valence correlation, relativistic effects, and Born- Oppenheimer breakdown terms in our calculations. Our ab initio predictions of the lowest lying levels are superb.

  5. Standardized EEG interpretation accurately predicts prognosis after cardiac arrest

    PubMed Central

    Rossetti, Andrea O.; van Rootselaar, Anne-Fleur; Wesenberg Kjaer, Troels; Horn, Janneke; Ullén, Susann; Friberg, Hans; Nielsen, Niklas; Rosén, Ingmar; Åneman, Anders; Erlinge, David; Gasche, Yvan; Hassager, Christian; Hovdenes, Jan; Kjaergaard, Jesper; Kuiper, Michael; Pellis, Tommaso; Stammet, Pascal; Wanscher, Michael; Wetterslev, Jørn; Wise, Matt P.; Cronberg, Tobias

    2016-01-01

    Objective: To identify reliable predictors of outcome in comatose patients after cardiac arrest using a single routine EEG and standardized interpretation according to the terminology proposed by the American Clinical Neurophysiology Society. Methods: In this cohort study, 4 EEG specialists, blinded to outcome, evaluated prospectively recorded EEGs in the Target Temperature Management trial (TTM trial) that randomized patients to 33°C vs 36°C. Routine EEG was performed in patients still comatose after rewarming. EEGs were classified into highly malignant (suppression, suppression with periodic discharges, burst-suppression), malignant (periodic or rhythmic patterns, pathological or nonreactive background), and benign EEG (absence of malignant features). Poor outcome was defined as best Cerebral Performance Category score 3–5 until 180 days. Results: Eight TTM sites randomized 202 patients. EEGs were recorded in 103 patients at a median 77 hours after cardiac arrest; 37% had a highly malignant EEG and all had a poor outcome (specificity 100%, sensitivity 50%). Any malignant EEG feature had a low specificity to predict poor prognosis (48%) but if 2 malignant EEG features were present specificity increased to 96% (p < 0.001). Specificity and sensitivity were not significantly affected by targeted temperature or sedation. A benign EEG was found in 1% of the patients with a poor outcome. Conclusions: Highly malignant EEG after rewarming reliably predicted poor outcome in half of patients without false predictions. An isolated finding of a single malignant feature did not predict poor outcome whereas a benign EEG was highly predictive of a good outcome. PMID:26865516

  6. PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations

    PubMed Central

    Bendl, Jaroslav; Stourac, Jan; Salanda, Ondrej; Pavelka, Antonin; Wieben, Eric D.; Zendulka, Jaroslav; Brezovsky, Jan; Damborsky, Jiri

    2014-01-01

    Single nucleotide variants represent a prevalent form of genetic variation. Mutations in the coding regions are frequently associated with the development of various genetic diseases. Computational tools for the prediction of the effects of mutations on protein function are very important for analysis of single nucleotide variants and their prioritization for experimental characterization. Many computational tools are already widely employed for this purpose. Unfortunately, their comparison and further improvement is hindered by large overlaps between the training datasets and benchmark datasets, which lead to biased and overly optimistic reported performances. In this study, we have constructed three independent datasets by removing all duplicities, inconsistencies and mutations previously used in the training of evaluated tools. The benchmark dataset containing over 43,000 mutations was employed for the unbiased evaluation of eight established prediction tools: MAPP, nsSNPAnalyzer, PANTHER, PhD-SNP, PolyPhen-1, PolyPhen-2, SIFT and SNAP. The six best performing tools were combined into a consensus classifier PredictSNP, resulting into significantly improved prediction performance, and at the same time returned results for all mutations, confirming that consensus prediction represents an accurate and robust alternative to the predictions delivered by individual tools. A user-friendly web interface enables easy access to all eight prediction tools, the consensus classifier PredictSNP and annotations from the Protein Mutant Database and the UniProt database. The web server and the datasets are freely available to the academic community at http://loschmidt.chemi.muni.cz/predictsnp. PMID:24453961

  7. Accurate contact predictions using covariation techniques and machine learning

    PubMed Central

    Kosciolek, Tomasz

    2015-01-01

    ABSTRACT Here we present the results of residue–residue contact predictions achieved in CASP11 by the CONSIP2 server, which is based around our MetaPSICOV contact prediction method. On a set of 40 target domains with a median family size of around 40 effective sequences, our server achieved an average top‐L/5 long‐range contact precision of 27%. MetaPSICOV method bases on a combination of classical contact prediction features, enhanced with three distinct covariation methods embedded in a two‐stage neural network predictor. Some unique features of our approach are (1) the tuning between the classical and covariation features depending on the depth of the input alignment and (2) a hybrid approach to generate deepest possible multiple‐sequence alignments by combining jackHMMer and HHblits. We discuss the CONSIP2 pipeline, our results and show that where the method underperformed, the major factor was relying on a fixed set of parameters for the initial sequence alignments and not attempting to perform domain splitting as a preprocessing step. Proteins 2016; 84(Suppl 1):145–151. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc. PMID:26205532

  8. How Accurately Can We Predict Eclipses for Algol? (Poster abstract)

    NASA Astrophysics Data System (ADS)

    Turner, D.

    2016-06-01

    (Abstract only) beta Persei, or Algol, is a very well known eclipsing binary system consisting of a late B-type dwarf that is regularly eclipsed by a GK subgiant every 2.867 days. Eclipses, which last about 8 hours, are regular enough that predictions for times of minima are published in various places, Sky & Telescope magazine and The Observer's Handbook, for example. But eclipse minimum lasts for less than a half hour, whereas subtle mistakes in the current ephemeris for the star can result in predictions that are off by a few hours or more. The Algol system is fairly complex, with the Algol A and Algol B eclipsing system also orbited by Algol C with an orbital period of nearly 2 years. Added to that are complex long-term O-C variations with a periodicity of almost two centuries that, although suggested by Hoffmeister to be spurious, fit the type of light travel time variations expected for a fourth star also belonging to the system. The AB sub-system also undergoes mass transfer events that add complexities to its O-C behavior. Is it actually possible to predict precise times of eclipse minima for Algol months in advance given such complications, or is it better to encourage ongoing observations of the star so that O-C variations can be tracked in real time?

  9. Theoretical prediction of 'optimal' freezing programmes.

    PubMed

    Woelders, H; Chaveiro, A

    2004-12-01

    We have developed a quantitative description of the osmotic behaviour of cells during freezing without a presupposed value of the cooling rate. Instead, at all times the intracellular supercooling is maximised provided that it does not exceed a predetermined value 'p' (e.g., 2 degrees C). This should preclude intracellular ice formation, but also ensures that the osmotic gradient and the CPA concentration gradient are limited, as well as the gradient driven transmembrane fluxes of water and CPA. Using the condition of a constant level of supercooling of p degrees C, equations can be derived to generate non-linear cooling curves in which at all times the cooling rate is maximised (to minimise slow cooling damage), while preventing conditions that could lead to fast cooling damage. Simulations of the osmotic events during freezing, and prediction of the 'optimal' freezing curve can be performed provided that values are available for the membrane permeability coefficients for water (L(p)) and cryoprotectant (P(s)), and their respective activation energies, the initial intracellular osmotically active aqueous volume, and the membrane surface area. Simulations are shown, both with and without permeant solute, to demonstrate how the predicted 'optimal' freezing curve is affected by medium composition, and by membrane permeability and osmotic cell characteristics.

  10. Theoretical prediction of new carbon allotropes

    NASA Astrophysics Data System (ADS)

    Yang, L.; He, H. Y.; Pan, B. C.

    2013-01-01

    Novel carbon allotropes are predicted by optionally substituting carbon atoms in diamond with carbon tetrahedrons. All these allotropes exhibit semiconducting properties, with bandgaps ranging from 3.2 to 4.7 eV. The calculated cohesive energy, mass density, and the bulk modulus are essentially related with the component of the tetrahedron units in these allotropes. In particular, we reveal the evolution of mechanical and electronic properties with the component of tetrahedrons for this family of crystalline carbon allotropes. This sheds a new light of tuning electronic and elastic properties of new allotropes by controlling the composition of carbon tetrahedrons. In addition, the calculated Raman spectra for these allotropes exhibit different features, and Raman characteristic modes for the tetrahedron units are addressed, which are available for identifying these allotropes in experiment.

  11. Database of theoretical thermosphere/ionosphere predictions

    SciTech Connect

    Fesen, C.G.; Roble, R.G. |

    1994-11-01

    The National Center for Atmospheric Research (NCAR) thermosphere-ionosphere general circulation model has performed a series of self-consistent calculations of the thermosphere/ionosphere structure for a variety of geophysical conditions. The model simulates March, June, and December periods for solar cycle minimum and maximum for three levels of geomagnetic activity representing quiet, moderate, and disturbed conditions. The calculations include predictions of N2, O2, O, N(sup 4)S, N(sup 2)D, NO, N2(+), O2(+), O(+), NO(+), and N(+), along with the ion, electron, and neutral temperatures and three components of the neutral winds. The model simulations are available from the authors or through the Coupling, Energetic, and Dynamics of Atmospheric Regions database at NCAR.

  12. Accurate and predictive antibody repertoire profiling by molecular amplification fingerprinting

    PubMed Central

    Khan, Tarik A.; Friedensohn, Simon; de Vries, Arthur R. Gorter; Straszewski, Jakub; Ruscheweyh, Hans-Joachim; Reddy, Sai T.

    2016-01-01

    High-throughput antibody repertoire sequencing (Ig-seq) provides quantitative molecular information on humoral immunity. However, Ig-seq is compromised by biases and errors introduced during library preparation and sequencing. By using synthetic antibody spike-in genes, we determined that primer bias from multiplex polymerase chain reaction (PCR) library preparation resulted in antibody frequencies with only 42 to 62% accuracy. Additionally, Ig-seq errors resulted in antibody diversity measurements being overestimated by up to 5000-fold. To rectify this, we developed molecular amplification fingerprinting (MAF), which uses unique molecular identifier (UID) tagging before and during multiplex PCR amplification, which enabled tagging of transcripts while accounting for PCR efficiency. Combined with a bioinformatic pipeline, MAF bias correction led to measurements of antibody frequencies with up to 99% accuracy. We also used MAF to correct PCR and sequencing errors, resulting in enhanced accuracy of full-length antibody diversity measurements, achieving 98 to 100% error correction. Using murine MAF-corrected data, we established a quantitative metric of recent clonal expansion—the intraclonal diversity index—which measures the number of unique transcripts associated with an antibody clone. We used this intraclonal diversity index along with antibody frequencies and somatic hypermutation to build a logistic regression model for prediction of the immunological status of clones. The model was able to predict clonal status with high confidence but only when using MAF error and bias corrected Ig-seq data. Improved accuracy by MAF provides the potential to greatly advance Ig-seq and its utility in immunology and biotechnology. PMID:26998518

  13. Accurate predictions for the production of vaporized water

    SciTech Connect

    Morin, E.; Montel, F.

    1995-12-31

    The production of water vaporized in the gas phase is controlled by the local conditions around the wellbore. The pressure gradient applied to the formation creates a sharp increase of the molar water content in the hydrocarbon phase approaching the well; this leads to a drop in the pore water saturation around the wellbore. The extent of the dehydrated zone which is formed is the key controlling the bottom-hole content of vaporized water. The maximum water content in the hydrocarbon phase at a given pressure, temperature and salinity is corrected by capillarity or adsorption phenomena depending on the actual water saturation. Describing the mass transfer of the water between the hydrocarbon phases and the aqueous phase into the tubing gives a clear idea of vaporization effects on the formation of scales. Field example are presented for gas fields with temperatures ranging between 140{degrees}C and 180{degrees}C, where water vaporization effects are significant. Conditions for salt plugging in the tubing are predicted.

  14. Predicting accurate fluorescent spectra for high molecular weight polycyclic aromatic hydrocarbons using density functional theory

    NASA Astrophysics Data System (ADS)

    Powell, Jacob; Heider, Emily C.; Campiglia, Andres; Harper, James K.

    2016-10-01

    The ability of density functional theory (DFT) methods to predict accurate fluorescence spectra for polycyclic aromatic hydrocarbons (PAHs) is explored. Two methods, PBE0 and CAM-B3LYP, are evaluated both in the gas phase and in solution. Spectra for several of the most toxic PAHs are predicted and compared to experiment, including three isomers of C24H14 and a PAH containing heteroatoms. Unusually high-resolution experimental spectra are obtained for comparison by analyzing each PAH at 4.2 K in an n-alkane matrix. All theoretical spectra visually conform to the profiles of the experimental data but are systematically offset by a small amount. Specifically, when solvent is included the PBE0 functional overestimates peaks by 16.1 ± 6.6 nm while CAM-B3LYP underestimates the same transitions by 14.5 ± 7.6 nm. These calculated spectra can be empirically corrected to decrease the uncertainties to 6.5 ± 5.1 and 5.7 ± 5.1 nm for the PBE0 and CAM-B3LYP methods, respectively. A comparison of computed spectra in the gas phase indicates that the inclusion of n-octane shifts peaks by +11 nm on average and this change is roughly equivalent for PBE0 and CAM-B3LYP. An automated approach for comparing spectra is also described that minimizes residuals between a given theoretical spectrum and all available experimental spectra. This approach identifies the correct spectrum in all cases and excludes approximately 80% of the incorrect spectra, demonstrating that an automated search of theoretical libraries of spectra may eventually become feasible.

  15. Change in BMI accurately predicted by social exposure to acquaintances.

    PubMed

    Oloritun, Rahman O; Ouarda, Taha B M J; Moturu, Sai; Madan, Anmol; Pentland, Alex Sandy; Khayal, Inas

    2013-01-01

    Research has mostly focused on obesity and not on processes of BMI change more generally, although these may be key factors that lead to obesity. Studies have suggested that obesity is affected by social ties. However these studies used survey based data collection techniques that may be biased toward select only close friends and relatives. In this study, mobile phone sensing techniques were used to routinely capture social interaction data in an undergraduate dorm. By automating the capture of social interaction data, the limitations of self-reported social exposure data are avoided. This study attempts to understand and develop a model that best describes the change in BMI using social interaction data. We evaluated a cohort of 42 college students in a co-located university dorm, automatically captured via mobile phones and survey based health-related information. We determined the most predictive variables for change in BMI using the least absolute shrinkage and selection operator (LASSO) method. The selected variables, with gender, healthy diet category, and ability to manage stress, were used to build multiple linear regression models that estimate the effect of exposure and individual factors on change in BMI. We identified the best model using Akaike Information Criterion (AIC) and R(2). This study found a model that explains 68% (p<0.0001) of the variation in change in BMI. The model combined social interaction data, especially from acquaintances, and personal health-related information to explain change in BMI. This is the first study taking into account both interactions with different levels of social interaction and personal health-related information. Social interactions with acquaintances accounted for more than half the variation in change in BMI. This suggests the importance of not only individual health information but also the significance of social interactions with people we are exposed to, even people we may not consider as close friends.

  16. Accurate First-Principles Spectra Predictions for Planetological and Astrophysical Applications at Various T-Conditions

    NASA Astrophysics Data System (ADS)

    Rey, M.; Nikitin, A. V.; Tyuterev, V.

    2014-06-01

    Knowledge of near infrared intensities of rovibrational transitions of polyatomic molecules is essential for the modeling of various planetary atmospheres, brown dwarfs and for other astrophysical applications 1,2,3. For example, to analyze exoplanets, atmospheric models have been developed, thus making the need to provide accurate spectroscopic data. Consequently, the spectral characterization of such planetary objects relies on the necessity of having adequate and reliable molecular data in extreme conditions (temperature, optical path length, pressure). On the other hand, in the modeling of astrophysical opacities, millions of lines are generally involved and the line-by-line extraction is clearly not feasible in laboratory measurements. It is thus suggested that this large amount of data could be interpreted only by reliable theoretical predictions. There exists essentially two theoretical approaches for the computation and prediction of spectra. The first one is based on empirically-fitted effective spectroscopic models. Another way for computing energies, line positions and intensities is based on global variational calculations using ab initio surfaces. They do not yet reach the spectroscopic accuracy stricto sensu but implicitly account for all intramolecular interactions including resonance couplings in a wide spectral range. The final aim of this work is to provide reliable predictions which could be quantitatively accurate with respect to the precision of available observations and as complete as possible. All this thus requires extensive first-principles quantum mechanical calculations essentially based on three necessary ingredients which are (i) accurate intramolecular potential energy surface and dipole moment surface components well-defined in a large range of vibrational displacements and (ii) efficient computational methods combined with suitable choices of coordinates to account for molecular symmetry properties and to achieve a good numerical

  17. An information-theoretic look at branch-prediction

    SciTech Connect

    Ponder, C.G. ); Shebanow, M.C. )

    1990-09-11

    Accurate branch-prediction is necessary to utilize deeply pipelined and Very Long Instruction-Word (VLIW) architectures. For a set of program traces we show the upper limits on branch predictability, and hence machine utilization, for important classes of branch-predictors using static (compiletime) and dynamic (runtime) program information. A set of optimal superpredictors'' is derived from these program traces. These optimal predictors compare favorably with other proposed methods of branch-prediction. 3 refs., 5 figs., 12 tabs.

  18. A Game Theoretic Approach to Cyber Attack Prediction

    SciTech Connect

    Peng Liu

    2005-11-28

    The area investigated by this project is cyber attack prediction. With a focus on correlation-based prediction, current attack prediction methodologies overlook the strategic nature of cyber attack-defense scenarios. As a result, current cyber attack prediction methodologies are very limited in predicting strategic behaviors of attackers in enforcing nontrivial cyber attacks such as DDoS attacks, and may result in low accuracy in correlation-based predictions. This project develops a game theoretic framework for cyber attack prediction, where an automatic game-theory-based attack prediction method is proposed. Being able to quantitatively predict the likelihood of (sequences of) attack actions, our attack prediction methodology can predict fine-grained strategic behaviors of attackers and may greatly improve the accuracy of correlation-based prediction. To our best knowledge, this project develops the first comprehensive framework for incentive-based modeling and inference of attack intent, objectives, and strategies; and this project develops the first method that can predict fine-grained strategic behaviors of attackers. The significance of this research and the benefit to the public can be demonstrated to certain extent by (a) the severe threat of cyber attacks to the critical infrastructures of the nation, including many infrastructures overseen by the Department of Energy, (b) the importance of cyber security to critical infrastructure protection, and (c) the importance of cyber attack prediction to achieving cyber security.

  19. Using theoretical descriptors in structure activity relationships: Validating toxicity predictions

    SciTech Connect

    Famini, G.R.; Wilson, L.Y.; Chester, N.A.; Sterling, P.A.

    1995-12-01

    Quantitative Structure Activity Relationships (QSAR) and Linear Free Energy Relationships (LFER) are very useful for correlating toxicological data, and in characterizating trends in terms of structural and electronic effects. Several years ago, we developed a series of equations correlating a number of toxicity tests with theoretically determined descriptors. One of these tests was the Microtox test, using the degradation in light from Photobacteriurn phosphoreum. Recently, several new compounds have been tested in our laboratory using the Microtox test, and compared against the predicted values. The agreement between experimental and theoretical results will be discussed, as will reasons for {open_quotes}good{close_quotes} or {open_quotes}poor{close_quotes} predictions.

  20. Theoretical Foundation for Mechanical Products Service Life Prediction

    NASA Astrophysics Data System (ADS)

    Konovodov, V. V.; Valentov, A. V.; Lafetova, T. V.; Basalaev, M. N.

    2016-04-01

    The article presents theoretical foundations for prediction of service life of mechanical products, based on the fatigue theory and fatigue limit. Ultimate amplitude and ultimate stress diagrams are presented. Wohler curve, characterizing material durability, is constructed on the results of the tests.

  1. Accurate prediction of band gaps and optical properties of HfO2

    NASA Astrophysics Data System (ADS)

    Ondračka, Pavel; Holec, David; Nečas, David; Zajíčková, Lenka

    2016-10-01

    We report on optical properties of various polymorphs of hafnia predicted within the framework of density functional theory. The full potential linearised augmented plane wave method was employed together with the Tran-Blaha modified Becke-Johnson potential (TB-mBJ) for exchange and local density approximation for correlation. Unit cells of monoclinic, cubic and tetragonal crystalline, and a simulated annealing-based model of amorphous hafnia were fully relaxed with respect to internal positions and lattice parameters. Electronic structures and band gaps for monoclinic, cubic, tetragonal and amorphous hafnia were calculated using three different TB-mBJ parametrisations and the results were critically compared with the available experimental and theoretical reports. Conceptual differences between a straightforward comparison of experimental measurements to a calculated band gap on the one hand and to a whole electronic structure (density of electronic states) on the other hand, were pointed out, suggesting the latter should be used whenever possible. Finally, dielectric functions were calculated at two levels, using the random phase approximation without local field effects and with a more accurate Bethe-Salpether equation (BSE) to account for excitonic effects. We conclude that a satisfactory agreement with experimental data for HfO2 was obtained only in the latter case.

  2. Theoretical study and prediction of BVI noise including close interactions

    NASA Astrophysics Data System (ADS)

    Spiegel, Pierre; Rahier, Gilles

    1991-05-01

    The following study deals with the highly impulsive blade-vortex interaction (BVI) noise which is generated by helicopter main rotors in descent flight. Two computer codes have been especially designed to predict it at reduced computing costs, starting from given vortices. The aerodynamic code, called MAIR, predicts the unsteady airloads, even for head-on collisions, by using a singularity method and modeling the vortices as cloud vortices with viscous cores. The acoustic code, called PARIS, computes the resulting radiated loading noise and is based on the Ffowcs Williams and Hawkings equation. These two codes are ready to perform noise prediction in the flight cases but the vortex prediction required for input data still needs to be improved. While waiting for better wake data, the two codes have been used for a theoretical parametric study of arbitrary single blade-vortex interactions. This study gives a physical insight of the phenomenon and its predicted tendencies could help designing quieter blades.

  3. A comparison of SAR ATR performance with information theoretic predictions

    NASA Astrophysics Data System (ADS)

    Blacknell, David

    2003-09-01

    Performance assessment of automatic target detection and recognition algorithms for SAR systems (or indeed any other sensors) is essential if the military utility of the system / algorithm mix is to be quantified. This is a relatively straightforward task if extensive trials data from an existing system is used. However, a crucial requirement is to assess the potential performance of novel systems as a guide to procurement decisions. This task is no longer straightforward since a hypothetical system cannot provide experimental trials data. QinetiQ has previously developed a theoretical technique for classification algorithm performance assessment based on information theory. The purpose of the study presented here has been to validate this approach. To this end, experimental SAR imagery of targets has been collected using the QinetiQ Enhanced Surveillance Radar to allow algorithm performance assessments as a number of parameters are varied. In particular, performance comparisons can be made for (i) resolutions up to 0.1m, (ii) single channel versus polarimetric (iii) targets in the open versus targets in scrubland and (iv) use versus non-use of camouflage. The change in performance as these parameters are varied has been quantified from the experimental imagery whilst the information theoretic approach has been used to predict the expected variation of performance with parameter value. A comparison of these measured and predicted assessments has revealed the strengths and weaknesses of the theoretical technique as will be discussed in the paper.

  4. Theoretical prediction of airplane stability derivatives at subcritical speeds

    NASA Technical Reports Server (NTRS)

    Tulinius, J.; Clever, W.; Nieman, A.; Dunn, K.; Gaither, B.

    1973-01-01

    The theoretical development and application is described of an analysis for predicting the major static and rotary stability derivatives for a complete airplane. The analysis utilizes potential flow theory to compute the surface flow fields and pressures on any configuration that can be synthesized from arbitrary lifting bodies and nonplanar thick lifting panels. The pressures are integrated to obtain section and total configuration loads and moments due side slip, angle of attack, pitching motion, rolling motion, yawing motion, and control surface deflection. Subcritical compressibility is accounted for by means of the Gothert similarity rule.

  5. Mind-set and close relationships: when bias leads to (In)accurate predictions.

    PubMed

    Gagné, F M; Lydon, J E

    2001-07-01

    The authors investigated whether mind-set influences the accuracy of relationship predictions. Because people are more biased in their information processing when thinking about implementing an important goal, relationship predictions made in an implemental mind-set were expected to be less accurate than those made in a more impartial deliberative mind-set. In Study 1, open-ended thoughts of students about to leave for university were coded for mind-set. In Study 2, mind-set about a major life goal was assessed using a self-report measure. In Study 3, mind-set was experimentally manipulated. Overall, mind-set interacted with forecasts to predict relationship survival. Forecasts were more accurate in a deliberative mind-set than in an implemental mind-set. This effect was more pronounced for long-term than for short-term relationship survival. Finally, deliberatives were not pessimistic; implementals were unduly optimistic.

  6. Theoretical and numerical predictions of hypervelocity impact-generated plasma

    SciTech Connect

    Li, Jianqiao; Song, Weidong Ning, Jianguo

    2014-08-15

    The hypervelocity impact generated plasmas (HVIGP) in thermodynamic non-equilibrium state were theoretically analyzed, and a physical model was presented to explore the relationship between plasma ionization degree and internal energy of the system by a group of equations including a chemical reaction equilibrium equation, a chemical reaction rate equation, and an energy conservation equation. A series of AUTODYN 3D (a widely used software in dynamic numerical simulations and developed by Century Dynamic Inc.) numerical simulations of the impacts of hypervelocity Al projectile on its targets at different incident angles were performed. The internal energy and the material density obtained from the numerical simulations were then used to calculate the ionization degree and the electron temperature. Based on a self-developed 2D smooth particle hydrodynamic (SPH) code and the theoretical model, the plasmas generated by 6 hypervelocity impacts were directly simulated and their total charges were calculated. The numerical results are in good agreements with the experimental results as well as the empirical formulas, demonstrating that the theoretical model is justified by the AUTODYN 3D and self-developed 2D SPH simulations and applicable to predict HVIGPs. The study is of significance for astrophysical and cosmonautic researches and safety.

  7. Modeling methodology for the accurate and prompt prediction of symptomatic events in chronic diseases.

    PubMed

    Pagán, Josué; Risco-Martín, José L; Moya, José M; Ayala, José L

    2016-08-01

    Prediction of symptomatic crises in chronic diseases allows to take decisions before the symptoms occur, such as the intake of drugs to avoid the symptoms or the activation of medical alarms. The prediction horizon is in this case an important parameter in order to fulfill the pharmacokinetics of medications, or the time response of medical services. This paper presents a study about the prediction limits of a chronic disease with symptomatic crises: the migraine. For that purpose, this work develops a methodology to build predictive migraine models and to improve these predictions beyond the limits of the initial models. The maximum prediction horizon is analyzed, and its dependency on the selected features is studied. A strategy for model selection is proposed to tackle the trade off between conservative but robust predictive models, with respect to less accurate predictions with higher horizons. The obtained results show a prediction horizon close to 40min, which is in the time range of the drug pharmacokinetics. Experiments have been performed in a realistic scenario where input data have been acquired in an ambulatory clinical study by the deployment of a non-intrusive Wireless Body Sensor Network. Our results provide an effective methodology for the selection of the future horizon in the development of prediction algorithms for diseases experiencing symptomatic crises. PMID:27260782

  8. SIFTER search: a web server for accurate phylogeny-based protein function prediction.

    PubMed

    Sahraeian, Sayed M; Luo, Kevin R; Brenner, Steven E

    2015-07-01

    We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access to precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. The SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded.

  9. Theoretical predictions of structures in dispersions containing charged colloidal particles and non-adsorbing polymers.

    PubMed

    Xie, Fei; Turesson, Martin; Woodward, Clifford E; van Gruijthuijsen, Kitty; Stradner, Anna; Forsman, Jan

    2016-04-28

    We develop a theoretical model to describe structural effects on a specific system of charged colloidal polystyrene particles, upon the addition of non-adsorbing PEG polymers. This system has previously been investigated experimentally, by scattering methods, so we are able to quantitatively compare predicted structure factors with corresponding experimental data. Our aim is to construct a model that is coarse-grained enough to be computationally manageable, yet detailed enough to capture the important physics. To this end, we utilize classical polymer density functional theory, wherein all possible polymer configurations are accounted for, subject to a mean-field Boltzmann weight. We make efforts to counteract drawbacks with this mean-field approach, resulting in structural predictions that agree very well with computationally more demanding simulations. Electrostatic interactions are handled at the fully non-linear Poisson-Boltzmann level, and we demonstrate that a linearization leads to less accurate predictions. The particle charge is an experimentally unknown parameter. We define the surface charge such that the experimental and theoretical gel point at equal polymer concentration coincide. Assuming a fixed surface charge for a certain salt concentration, we find very good agreements between measured and predicted structure factors across a wide range of polymer concentrations. We also present predictions for other structural quantities, such as radial distribution functions, and cluster size distributions. Finally, we demonstrate that our model predicts the occurrence of equilibrium clusters at high polymer concentrations, but low particle volume fractions and salt levels. PMID:27056112

  10. Aircraft noise prediction program theoretical manual: Rotorcraft System Noise Prediction System (ROTONET), part 4

    NASA Technical Reports Server (NTRS)

    Weir, Donald S.; Jumper, Stephen J.; Burley, Casey L.; Golub, Robert A.

    1995-01-01

    This document describes the theoretical methods used in the rotorcraft noise prediction system (ROTONET), which is a part of the NASA Aircraft Noise Prediction Program (ANOPP). The ANOPP code consists of an executive, database manager, and prediction modules for jet engine, propeller, and rotor noise. The ROTONET subsystem contains modules for the prediction of rotor airloads and performance with momentum theory and prescribed wake aerodynamics, rotor tone noise with compact chordwise and full-surface solutions to the Ffowcs-Williams-Hawkings equations, semiempirical airfoil broadband noise, and turbulence ingestion broadband noise. Flight dynamics, atmosphere propagation, and noise metric calculations are covered in NASA TM-83199, Parts 1, 2, and 3.

  11. A Single Linear Prediction Filter that Accurately Predicts the AL Index

    NASA Astrophysics Data System (ADS)

    McPherron, R. L.; Chu, X.

    2015-12-01

    The AL index is a measure of the strength of the westward electrojet flowing along the auroral oval. It has two components: one from the global DP-2 current system and a second from the DP-1 current that is more localized near midnight. It is generally believed that the index a very poor measure of these currents because of its dependence on the distance of stations from the source of the two currents. In fact over season and solar cycle the coupling strength defined as the steady state ratio of the output AL to the input coupling function varies by a factor of four. There are four factors that lead to this variation. First is the equinoctial effect that modulates coupling strength with peaks (strongest coupling) at the equinoxes. Second is the saturation of the polar cap potential which decreases coupling strength as the strength of the driver increases. Since saturation occurs more frequently at solar maximum we obtain the result that maximum coupling strength occurs at equinox at solar minimum. A third factor is ionospheric conductivity with stronger coupling at summer solstice as compared to winter. The fourth factor is the definition of a solar wind coupling function appropriate to a given index. We have developed an optimum coupling function depending on solar wind speed, density, transverse magnetic field, and IMF clock angle which is better than previous functions. Using this we have determined the seasonal variation of coupling strength and developed an inverse function that modulates the optimum coupling function so that all seasonal variation is removed. In a similar manner we have determined the dependence of coupling strength on solar wind driver strength. The inverse of this function is used to scale a linear prediction filter thus eliminating the dependence on driver strength. Our result is a single linear filter that is adjusted in a nonlinear manner by driver strength and an optimum coupling function that is seasonal modulated. Together this

  12. A review of the kinetic detail required for accurate predictions of normal shock waves

    NASA Technical Reports Server (NTRS)

    Muntz, E. P.; Erwin, Daniel A.; Pham-Van-diep, Gerald C.

    1991-01-01

    Several aspects of the kinetic models used in the collision phase of Monte Carlo direct simulations have been studied. Accurate molecular velocity distribution function predictions require a significantly increased number of computational cells in one maximum slope shock thickness, compared to predictions of macroscopic properties. The shape of the highly repulsive portion of the interatomic potential for argon is not well modeled by conventional interatomic potentials; this portion of the potential controls high Mach number shock thickness predictions, indicating that the specification of the energetic repulsive portion of interatomic or intermolecular potentials must be chosen with care for correct modeling of nonequilibrium flows at high temperatures. It has been shown for inverse power potentials that the assumption of variable hard sphere scattering provides accurate predictions of the macroscopic properties in shock waves, by comparison with simulations in which differential scattering is employed in the collision phase. On the other hand, velocity distribution functions are not well predicted by the variable hard sphere scattering model for softer potentials at higher Mach numbers.

  13. Can phenological models predict tree phenology accurately under climate change conditions?

    NASA Astrophysics Data System (ADS)

    Chuine, Isabelle; Bonhomme, Marc; Legave, Jean Michel; García de Cortázar-Atauri, Inaki; Charrier, Guillaume; Lacointe, André; Améglio, Thierry

    2014-05-01

    The onset of the growing season of trees has been globally earlier by 2.3 days/decade during the last 50 years because of global warming and this trend is predicted to continue according to climate forecast. The effect of temperature on plant phenology is however not linear because temperature has a dual effect on bud development. On one hand, low temperatures are necessary to break bud dormancy, and on the other hand higher temperatures are necessary to promote bud cells growth afterwards. Increasing phenological changes in temperate woody species have strong impacts on forest trees distribution and productivity, as well as crops cultivation areas. Accurate predictions of trees phenology are therefore a prerequisite to understand and foresee the impacts of climate change on forests and agrosystems. Different process-based models have been developed in the last two decades to predict the date of budburst or flowering of woody species. They are two main families: (1) one-phase models which consider only the ecodormancy phase and make the assumption that endodormancy is always broken before adequate climatic conditions for cell growth occur; and (2) two-phase models which consider both the endodormancy and ecodormancy phases and predict a date of dormancy break which varies from year to year. So far, one-phase models have been able to predict accurately tree bud break and flowering under historical climate. However, because they do not consider what happens prior to ecodormancy, and especially the possible negative effect of winter temperature warming on dormancy break, it seems unlikely that they can provide accurate predictions in future climate conditions. It is indeed well known that a lack of low temperature results in abnormal pattern of bud break and development in temperate fruit trees. An accurate modelling of the dormancy break date has thus become a major issue in phenology modelling. Two-phases phenological models predict that global warming should delay

  14. The effect of stress concentration on bone remodeling: theoretical predictions.

    PubMed

    Firoozbakhsh, K; Aleyaasin, M

    1989-11-01

    Theoretical predictions of internal bone remodeling around an elliptical hole are studied. The internal remodeling theory due to Cowin and Hegedus is employed. The bone is modeled as an initially homogeneous adaptive elastic plate with an elliptical hole under a superposed steady compressive load. It is shown that there will exist a final inhomogeneous remodeling distribution around the hole that will disappear away from the hole. The remodeling is such that the compressive stress concentration causes the bone structure to evolve to one of greater density and stiffer elastic coefficients. The speed of remodeling around the hole and its variation with respect to distance is investigated and discussed. It is shown that the rate of bone reinforcement in the area of compressive stress concentration is much higher than the rate of bone resorption in the area of existing tensile stress. Special cases of a circular hole and vertical and horizontal slots are studied and discussed.

  15. STM fingerprints of point defects in graphene: a theoretical prediction

    SciTech Connect

    Amara, Hakim; Latil, Sylvain; Meunier, Vincent; Lambin, Philippe; Charlier, Jean Christophe

    2007-01-01

    Scanning tunneling microscopy (STM) is one of the most appropriate techniques to investigate the atomic structure of carbon nanomaterials. However, the experimental identification of topological and nontopological modifications of the hexagonal network of sp{sup 2} carbon nanostructures remains a great challenge. The goal of the present theoretical work is to predict the typical electronic features of a few defects that are likely to occur in sp{sup 2} carbon nanostructures, such as atomic vacancy, divacancy, adatom, and Stone-Wales defect. The modifications induced by those defects in the electronic properties of the graphene sheet are investigated using first-principles calculations. In addition, computed constant-current STM images of these defects are calculated within a tight-binding approach in order to facilitate the interpretation of STM images of defected carbon nanostructures.

  16. Can phenological models predict tree phenology accurately in the future? The unrevealed hurdle of endodormancy break.

    PubMed

    Chuine, Isabelle; Bonhomme, Marc; Legave, Jean-Michel; García de Cortázar-Atauri, Iñaki; Charrier, Guillaume; Lacointe, André; Améglio, Thierry

    2016-10-01

    The onset of the growing season of trees has been earlier by 2.3 days per decade during the last 40 years in temperate Europe because of global warming. The effect of temperature on plant phenology is, however, not linear because temperature has a dual effect on bud development. On one hand, low temperatures are necessary to break bud endodormancy, and, on the other hand, higher temperatures are necessary to promote bud cell growth afterward. Different process-based models have been developed in the last decades to predict the date of budbreak of woody species. They predict that global warming should delay or compromise endodormancy break at the species equatorward range limits leading to a delay or even impossibility to flower or set new leaves. These models are classically parameterized with flowering or budbreak dates only, with no information on the endodormancy break date because this information is very scarce. Here, we evaluated the efficiency of a set of phenological models to accurately predict the endodormancy break dates of three fruit trees. Our results show that models calibrated solely with budbreak dates usually do not accurately predict the endodormancy break date. Providing endodormancy break date for the model parameterization results in much more accurate prediction of this latter, with, however, a higher error than that on budbreak dates. Most importantly, we show that models not calibrated with endodormancy break dates can generate large discrepancies in forecasted budbreak dates when using climate scenarios as compared to models calibrated with endodormancy break dates. This discrepancy increases with mean annual temperature and is therefore the strongest after 2050 in the southernmost regions. Our results claim for the urgent need of massive measurements of endodormancy break dates in forest and fruit trees to yield more robust projections of phenological changes in a near future. PMID:27272707

  17. Can phenological models predict tree phenology accurately in the future? The unrevealed hurdle of endodormancy break.

    PubMed

    Chuine, Isabelle; Bonhomme, Marc; Legave, Jean-Michel; García de Cortázar-Atauri, Iñaki; Charrier, Guillaume; Lacointe, André; Améglio, Thierry

    2016-10-01

    The onset of the growing season of trees has been earlier by 2.3 days per decade during the last 40 years in temperate Europe because of global warming. The effect of temperature on plant phenology is, however, not linear because temperature has a dual effect on bud development. On one hand, low temperatures are necessary to break bud endodormancy, and, on the other hand, higher temperatures are necessary to promote bud cell growth afterward. Different process-based models have been developed in the last decades to predict the date of budbreak of woody species. They predict that global warming should delay or compromise endodormancy break at the species equatorward range limits leading to a delay or even impossibility to flower or set new leaves. These models are classically parameterized with flowering or budbreak dates only, with no information on the endodormancy break date because this information is very scarce. Here, we evaluated the efficiency of a set of phenological models to accurately predict the endodormancy break dates of three fruit trees. Our results show that models calibrated solely with budbreak dates usually do not accurately predict the endodormancy break date. Providing endodormancy break date for the model parameterization results in much more accurate prediction of this latter, with, however, a higher error than that on budbreak dates. Most importantly, we show that models not calibrated with endodormancy break dates can generate large discrepancies in forecasted budbreak dates when using climate scenarios as compared to models calibrated with endodormancy break dates. This discrepancy increases with mean annual temperature and is therefore the strongest after 2050 in the southernmost regions. Our results claim for the urgent need of massive measurements of endodormancy break dates in forest and fruit trees to yield more robust projections of phenological changes in a near future.

  18. Accurate similarity index based on activity and connectivity of node for link prediction

    NASA Astrophysics Data System (ADS)

    Li, Longjie; Qian, Lvjian; Wang, Xiaoping; Luo, Shishun; Chen, Xiaoyun

    2015-05-01

    Recent years have witnessed the increasing of available network data; however, much of those data is incomplete. Link prediction, which can find the missing links of a network, plays an important role in the research and analysis of complex networks. Based on the assumption that two unconnected nodes which are highly similar are very likely to have an interaction, most of the existing algorithms solve the link prediction problem by computing nodes' similarities. The fundamental requirement of those algorithms is accurate and effective similarity indices. In this paper, we propose a new similarity index, namely similarity based on activity and connectivity (SAC), which performs link prediction more accurately. To compute the similarity between two nodes, this index employs the average activity of these two nodes in their common neighborhood and the connectivities between them and their common neighbors. The higher the average activity is and the stronger the connectivities are, the more similar the two nodes are. The proposed index not only commendably distinguishes the contributions of paths but also incorporates the influence of endpoints. Therefore, it can achieve a better predicting result. To verify the performance of SAC, we conduct experiments on 10 real-world networks. Experimental results demonstrate that SAC outperforms the compared baselines.

  19. Accurate prediction of the linear viscoelastic properties of highly entangled mono and bidisperse polymer melts.

    PubMed

    Stephanou, Pavlos S; Mavrantzas, Vlasis G

    2014-06-01

    We present a hierarchical computational methodology which permits the accurate prediction of the linear viscoelastic properties of entangled polymer melts directly from the chemical structure, chemical composition, and molecular architecture of the constituent chains. The method entails three steps: execution of long molecular dynamics simulations with moderately entangled polymer melts, self-consistent mapping of the accumulated trajectories onto a tube model and parameterization or fine-tuning of the model on the basis of detailed simulation data, and use of the modified tube model to predict the linear viscoelastic properties of significantly higher molecular weight (MW) melts of the same polymer. Predictions are reported for the zero-shear-rate viscosity η0 and the spectra of storage G'(ω) and loss G″(ω) moduli for several mono and bidisperse cis- and trans-1,4 polybutadiene melts as well as for their MW dependence, and are found to be in remarkable agreement with experimentally measured rheological data. PMID:24908037

  20. Accurate prediction of the linear viscoelastic properties of highly entangled mono and bidisperse polymer melts

    NASA Astrophysics Data System (ADS)

    Stephanou, Pavlos S.; Mavrantzas, Vlasis G.

    2014-06-01

    We present a hierarchical computational methodology which permits the accurate prediction of the linear viscoelastic properties of entangled polymer melts directly from the chemical structure, chemical composition, and molecular architecture of the constituent chains. The method entails three steps: execution of long molecular dynamics simulations with moderately entangled polymer melts, self-consistent mapping of the accumulated trajectories onto a tube model and parameterization or fine-tuning of the model on the basis of detailed simulation data, and use of the modified tube model to predict the linear viscoelastic properties of significantly higher molecular weight (MW) melts of the same polymer. Predictions are reported for the zero-shear-rate viscosity η0 and the spectra of storage G'(ω) and loss G″(ω) moduli for several mono and bidisperse cis- and trans-1,4 polybutadiene melts as well as for their MW dependence, and are found to be in remarkable agreement with experimentally measured rheological data.

  1. Prediction of Accurate Thermochemistry of Medium and Large Sized Radicals Using Connectivity-Based Hierarchy (CBH).

    PubMed

    Sengupta, Arkajyoti; Raghavachari, Krishnan

    2014-10-14

    Accurate modeling of the chemical reactions in many diverse areas such as combustion, photochemistry, or atmospheric chemistry strongly depends on the availability of thermochemical information of the radicals involved. However, accurate thermochemical investigations of radical systems using state of the art composite methods have mostly been restricted to the study of hydrocarbon radicals of modest size. In an alternative approach, systematic error-canceling thermochemical hierarchy of reaction schemes can be applied to yield accurate results for such systems. In this work, we have extended our connectivity-based hierarchy (CBH) method to the investigation of radical systems. We have calibrated our method using a test set of 30 medium sized radicals to evaluate their heats of formation. The CBH-rad30 test set contains radicals containing diverse functional groups as well as cyclic systems. We demonstrate that the sophisticated error-canceling isoatomic scheme (CBH-2) with modest levels of theory is adequate to provide heats of formation accurate to ∼1.5 kcal/mol. Finally, we predict heats of formation of 19 other large and medium sized radicals for which the accuracy of available heats of formation are less well-known. PMID:26588131

  2. A Novel Method for Accurate Operon Predictions in All SequencedProkaryotes

    SciTech Connect

    Price, Morgan N.; Huang, Katherine H.; Alm, Eric J.; Arkin, Adam P.

    2004-12-01

    We combine comparative genomic measures and the distance separating adjacent genes to predict operons in 124 completely sequenced prokaryotic genomes. Our method automatically tailors itself to each genome using sequence information alone, and thus can be applied to any prokaryote. For Escherichia coli K12 and Bacillus subtilis, our method is 85 and 83% accurate, respectively, which is similar to the accuracy of methods that use the same features but are trained on experimentally characterized transcripts. In Halobacterium NRC-1 and in Helicobacterpylori, our method correctly infers that genes in operons are separated by shorter distances than they are in E.coli, and its predictions using distance alone are more accurate than distance-only predictions trained on a database of E.coli transcripts. We use microarray data from sixphylogenetically diverse prokaryotes to show that combining intergenic distance with comparative genomic measures further improves accuracy and that our method is broadly effective. Finally, we survey operon structure across 124 genomes, and find several surprises: H.pylori has many operons, contrary to previous reports; Bacillus anthracis has an unusual number of pseudogenes within conserved operons; and Synechocystis PCC6803 has many operons even though it has unusually wide spacings between conserved adjacent genes.

  3. Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space.

    PubMed

    Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; Pronobis, Wiktor; von Lilienfeld, O Anatole; Müller, Klaus-Robert; Tkatchenko, Alexandre

    2015-06-18

    Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. In addition, the same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.

  4. Machine learning predictions of molecular properties: Accurate many-body potentials and nonlocality in chemical space

    SciTech Connect

    Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; Pronobis, Wiktor; von Lilienfeld, O. Anatole; Müller, Klaus -Robert; Tkatchenko, Alexandre

    2015-06-04

    Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. The same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.

  5. Machine learning predictions of molecular properties: Accurate many-body potentials and nonlocality in chemical space

    DOE PAGES

    Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; Pronobis, Wiktor; von Lilienfeld, O. Anatole; Müller, Klaus -Robert; Tkatchenko, Alexandre

    2015-06-04

    Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstratemore » prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. The same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.« less

  6. Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space

    PubMed Central

    2015-01-01

    Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. In addition, the same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies. PMID:26113956

  7. Development and Validation of a Multidisciplinary Tool for Accurate and Efficient Rotorcraft Noise Prediction (MUTE)

    NASA Technical Reports Server (NTRS)

    Liu, Yi; Anusonti-Inthra, Phuriwat; Diskin, Boris

    2011-01-01

    A physics-based, systematically coupled, multidisciplinary prediction tool (MUTE) for rotorcraft noise was developed and validated with a wide range of flight configurations and conditions. MUTE is an aggregation of multidisciplinary computational tools that accurately and efficiently model the physics of the source of rotorcraft noise, and predict the noise at far-field observer locations. It uses systematic coupling approaches among multiple disciplines including Computational Fluid Dynamics (CFD), Computational Structural Dynamics (CSD), and high fidelity acoustics. Within MUTE, advanced high-order CFD tools are used around the rotor blade to predict the transonic flow (shock wave) effects, which generate the high-speed impulsive noise. Predictions of the blade-vortex interaction noise in low speed flight are also improved by using the Particle Vortex Transport Method (PVTM), which preserves the wake flow details required for blade/wake and fuselage/wake interactions. The accuracy of the source noise prediction is further improved by utilizing a coupling approach between CFD and CSD, so that the effects of key structural dynamics, elastic blade deformations, and trim solutions are correctly represented in the analysis. The blade loading information and/or the flow field parameters around the rotor blade predicted by the CFD/CSD coupling approach are used to predict the acoustic signatures at far-field observer locations with a high-fidelity noise propagation code (WOPWOP3). The predicted results from the MUTE tool for rotor blade aerodynamic loading and far-field acoustic signatures are compared and validated with a variation of experimental data sets, such as UH60-A data, DNW test data and HART II test data.

  8. SIFTER search: a web server for accurate phylogeny-based protein function prediction

    DOE PAGES

    Sahraeian, Sayed M.; Luo, Kevin R.; Brenner, Steven E.

    2015-05-15

    We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access tomore » precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. Lastly, the SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded.« less

  9. Accurate Prediction of Severe Allergic Reactions by a Small Set of Environmental Parameters (NDVI, Temperature)

    PubMed Central

    Andrianaki, Maria; Azariadis, Kalliopi; Kampouri, Errika; Theodoropoulou, Katerina; Lavrentaki, Katerina; Kastrinakis, Stelios; Kampa, Marilena; Agouridakis, Panagiotis; Pirintsos, Stergios; Castanas, Elias

    2015-01-01

    Severe allergic reactions of unknown etiology,necessitating a hospital visit, have an important impact in the life of affected individuals and impose a major economic burden to societies. The prediction of clinically severe allergic reactions would be of great importance, but current attempts have been limited by the lack of a well-founded applicable methodology and the wide spatiotemporal distribution of allergic reactions. The valid prediction of severe allergies (and especially those needing hospital treatment) in a region, could alert health authorities and implicated individuals to take appropriate preemptive measures. In the present report we have collecterd visits for serious allergic reactions of unknown etiology from two major hospitals in the island of Crete, for two distinct time periods (validation and test sets). We have used the Normalized Difference Vegetation Index (NDVI), a satellite-based, freely available measurement, which is an indicator of live green vegetation at a given geographic area, and a set of meteorological data to develop a model capable of describing and predicting severe allergic reaction frequency. Our analysis has retained NDVI and temperature as accurate identifiers and predictors of increased hospital severe allergic reactions visits. Our approach may contribute towards the development of satellite-based modules, for the prediction of severe allergic reactions in specific, well-defined geographical areas. It could also probably be used for the prediction of other environment related diseases and conditions. PMID:25794106

  10. SIFTER search: a web server for accurate phylogeny-based protein function prediction.

    PubMed

    Sahraeian, Sayed M; Luo, Kevin R; Brenner, Steven E

    2015-07-01

    We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access to precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. The SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded. PMID:25979264

  11. SIFTER search: a web server for accurate phylogeny-based protein function prediction

    SciTech Connect

    Sahraeian, Sayed M.; Luo, Kevin R.; Brenner, Steven E.

    2015-05-15

    We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access to precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. Lastly, the SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded.

  12. Change in heat capacity accurately predicts vibrational coupling in enzyme catalyzed reactions.

    PubMed

    Arcus, Vickery L; Pudney, Christopher R

    2015-08-01

    The temperature dependence of kinetic isotope effects (KIEs) have been used to infer the vibrational coupling of the protein and or substrate to the reaction coordinate, particularly in enzyme-catalyzed hydrogen transfer reactions. We find that a new model for the temperature dependence of experimentally determined observed rate constants (macromolecular rate theory, MMRT) is able to accurately predict the occurrence of vibrational coupling, even where the temperature dependence of the KIE fails. This model, that incorporates the change in heat capacity for enzyme catalysis, demonstrates remarkable consistency with both experiment and theory and in many respects is more robust than models used at present.

  13. Accurate verification of the conserved-vector-current and standard-model predictions

    SciTech Connect

    Sirlin, A.; Zucchini, R.

    1986-10-20

    An approximate analytic calculation of O(Z..cap alpha../sup 2/) corrections to Fermi decays is presented. When the analysis of Koslowsky et al. is modified to take into account the new results, it is found that each of the eight accurately studied scrFt values differs from the average by approx. <1sigma, thus significantly improving the comparison of experiments with conserved-vector-current predictions. The new scrFt values are lower than before, which also brings experiments into very good agreement with the three-generation standard model, at the level of its quantum corrections.

  14. ILT based defect simulation of inspection images accurately predicts mask defect printability on wafer

    NASA Astrophysics Data System (ADS)

    Deep, Prakash; Paninjath, Sankaranarayanan; Pereira, Mark; Buck, Peter

    2016-05-01

    At advanced technology nodes mask complexity has been increased because of large-scale use of resolution enhancement technologies (RET) which includes Optical Proximity Correction (OPC), Inverse Lithography Technology (ILT) and Source Mask Optimization (SMO). The number of defects detected during inspection of such mask increased drastically and differentiation of critical and non-critical defects are more challenging, complex and time consuming. Because of significant defectivity of EUVL masks and non-availability of actinic inspection, it is important and also challenging to predict the criticality of defects for printability on wafer. This is one of the significant barriers for the adoption of EUVL for semiconductor manufacturing. Techniques to decide criticality of defects from images captured using non actinic inspection images is desired till actinic inspection is not available. High resolution inspection of photomask images detects many defects which are used for process and mask qualification. Repairing all defects is not practical and probably not required, however it's imperative to know which defects are severe enough to impact wafer before repair. Additionally, wafer printability check is always desired after repairing a defect. AIMSTM review is the industry standard for this, however doing AIMSTM review for all defects is expensive and very time consuming. Fast, accurate and an economical mechanism is desired which can predict defect printability on wafer accurately and quickly from images captured using high resolution inspection machine. Predicting defect printability from such images is challenging due to the fact that the high resolution images do not correlate with actual mask contours. The challenge is increased due to use of different optical condition during inspection other than actual scanner condition, and defects found in such images do not have correlation with actual impact on wafer. Our automated defect simulation tool predicts

  15. Theoretical Predictions of Freestanding Honeycomb Sheets of Cadmium Chalcogenides

    SciTech Connect

    Zhou, Jia; Huang, Jingsong; Sumpter, Bobby G; Kent, Paul R; Xie, Yu; Terrones Maldonado, Humberto; Smith, Sean C

    2014-01-01

    Two-dimensional (2D) nanocrystals of CdX (X = S, Se, Te) typically grown by colloidal synthesis are coated with organic ligands. Recent experimental work on ZnSe showed that the organic ligands can be removed at elevated temperature, giving a freestanding 2D sheet of ZnSe. In this theoretical work, freestanding single- to few-layer sheets of CdX, each possessing a pseudo honeycomb lattice, are considered by cutting along all possible lattice planes of the bulk zinc blende (ZB) and wurtzite (WZ) phases. Using density functional theory, we have systematically studied their geometric structures, energetics, and electronic properties. A strong surface distortion is found to occur for all of the layered sheets, and yet all of the pseudo honeycomb lattices are preserved, giving unique types of surface corrugations and different electronic properties. The energetics, in combination with phonon mode calculations and molecular dynamics simulations, indicate that the syntheses of these freestanding 2D sheets could be selective, with the single- to few-layer WZ110, WZ100, and ZB110 sheets being favored. Through the GW approximation, it is found that all single-layer sheets have large band gaps falling into the ultraviolet range, while thicker sheets in general have reduced band gaps in the visible and ultraviolet range. On the basis of the present work and the experimental studies on freestanding double-layer sheets of ZnSe, we envision that the freestanding 2D layered sheets of CdX predicted herein are potential synthesis targets, which may offer tunable band gaps depending on their structural features including surface corrugations, stacking motifs, and number of layers.

  16. A simple yet accurate correction for winner's curse can predict signals discovered in much larger genome scans

    PubMed Central

    Bigdeli, T. Bernard; Lee, Donghyung; Webb, Bradley Todd; Riley, Brien P.; Vladimirov, Vladimir I.; Fanous, Ayman H.; Kendler, Kenneth S.; Bacanu, Silviu-Alin

    2016-01-01

    Motivation: For genetic studies, statistically significant variants explain far less trait variance than ‘sub-threshold’ association signals. To dimension follow-up studies, researchers need to accurately estimate ‘true’ effect sizes at each SNP, e.g. the true mean of odds ratios (ORs)/regression coefficients (RRs) or Z-score noncentralities. Naïve estimates of effect sizes incur winner’s curse biases, which are reduced only by laborious winner’s curse adjustments (WCAs). Given that Z-scores estimates can be theoretically translated on other scales, we propose a simple method to compute WCA for Z-scores, i.e. their true means/noncentralities. Results:WCA of Z-scores shrinks these towards zero while, on P-value scale, multiple testing adjustment (MTA) shrinks P-values toward one, which corresponds to the zero Z-score value. Thus, WCA on Z-scores scale is a proxy for MTA on P-value scale. Therefore, to estimate Z-score noncentralities for all SNPs in genome scans, we propose FDR Inverse Quantile Transformation (FIQT). It (i) performs the simpler MTA of P-values using FDR and (ii) obtains noncentralities by back-transforming MTA P-values on Z-score scale. When compared to competitors, realistic simulations suggest that FIQT is more (i) accurate and (ii) computationally efficient by orders of magnitude. Practical application of FIQT to Psychiatric Genetic Consortium schizophrenia cohort predicts a non-trivial fraction of sub-threshold signals which become significant in much larger supersamples. Conclusions: FIQT is a simple, yet accurate, WCA method for Z-scores (and ORs/RRs, via simple transformations). Availability and Implementation: A 10 lines R function implementation is available at https://github.com/bacanusa/FIQT. Contact: sabacanu@vcu.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27187203

  17. Toward an Accurate Prediction of the Arrival Time of Geomagnetic-Effective Coronal Mass Ejections

    NASA Astrophysics Data System (ADS)

    Shi, T.; Wang, Y.; Wan, L.; Cheng, X.; Ding, M.; Zhang, J.

    2015-12-01

    Accurately predicting the arrival of coronal mass ejections (CMEs) to the Earth based on remote images is of critical significance for the study of space weather. Here we make a statistical study of 21 Earth-directed CMEs, specifically exploring the relationship between CME initial speeds and transit times. The initial speed of a CME is obtained by fitting the CME with the Graduated Cylindrical Shell model and is thus free of projection effects. We then use the drag force model to fit results of the transit time versus the initial speed. By adopting different drag regimes, i.e., the viscous, aerodynamics, and hybrid regimes, we get similar results, with a least mean estimation error of the hybrid model of 12.9 hr. CMEs with a propagation angle (the angle between the propagation direction and the Sun-Earth line) larger than their half-angular widths arrive at the Earth with an angular deviation caused by factors other than the radial solar wind drag. The drag force model cannot be reliably applied to such events. If we exclude these events in the sample, the prediction accuracy can be improved, i.e., the estimation error reduces to 6.8 hr. This work suggests that it is viable to predict the arrival time of CMEs to the Earth based on the initial parameters with fairly good accuracy. Thus, it provides a method of forecasting space weather 1-5 days following the occurrence of CMEs.

  18. Intermolecular potentials and the accurate prediction of the thermodynamic properties of water

    SciTech Connect

    Shvab, I.; Sadus, Richard J.

    2013-11-21

    The ability of intermolecular potentials to correctly predict the thermodynamic properties of liquid water at a density of 0.998 g/cm{sup 3} for a wide range of temperatures (298–650 K) and pressures (0.1–700 MPa) is investigated. Molecular dynamics simulations are reported for the pressure, thermal pressure coefficient, thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, and Joule-Thomson coefficient of liquid water using the non-polarizable SPC/E and TIP4P/2005 potentials. The results are compared with both experiment data and results obtained from the ab initio-based Matsuoka-Clementi-Yoshimine non-additive (MCYna) [J. Li, Z. Zhou, and R. J. Sadus, J. Chem. Phys. 127, 154509 (2007)] potential, which includes polarization contributions. The data clearly indicate that both the SPC/E and TIP4P/2005 potentials are only in qualitative agreement with experiment, whereas the polarizable MCYna potential predicts some properties within experimental uncertainty. This highlights the importance of polarizability for the accurate prediction of the thermodynamic properties of water, particularly at temperatures beyond 298 K.

  19. Direct Pressure Monitoring Accurately Predicts Pulmonary Vein Occlusion During Cryoballoon Ablation

    PubMed Central

    Kosmidou, Ioanna; Wooden, Shannnon; Jones, Brian; Deering, Thomas; Wickliffe, Andrew; Dan, Dan

    2013-01-01

    Cryoballoon ablation (CBA) is an established therapy for atrial fibrillation (AF). Pulmonary vein (PV) occlusion is essential for achieving antral contact and PV isolation and is typically assessed by contrast injection. We present a novel method of direct pressure monitoring for assessment of PV occlusion. Transcatheter pressure is monitored during balloon advancement to the PV antrum. Pressure is recorded via a single pressure transducer connected to the inner lumen of the cryoballoon. Pressure curve characteristics are used to assess occlusion in conjunction with fluoroscopic or intracardiac echocardiography (ICE) guidance. PV occlusion is confirmed when loss of typical left atrial (LA) pressure waveform is observed with recordings of PA pressure characteristics (no A wave and rapid V wave upstroke). Complete pulmonary vein occlusion as assessed with this technique has been confirmed with concurrent contrast utilization during the initial testing of the technique and has been shown to be highly accurate and readily reproducible. We evaluated the efficacy of this novel technique in 35 patients. A total of 128 veins were assessed for occlusion with the cryoballoon utilizing the pressure monitoring technique; occlusive pressure was demonstrated in 113 veins with resultant successful pulmonary vein isolation in 111 veins (98.2%). Occlusion was confirmed with subsequent contrast injection during the initial ten procedures, after which contrast utilization was rapidly reduced or eliminated given the highly accurate identification of occlusive pressure waveform with limited initial training. Verification of PV occlusive pressure during CBA is a novel approach to assessing effective PV occlusion and it accurately predicts electrical isolation. Utilization of this method results in significant decrease in fluoroscopy time and volume of contrast. PMID:23485956

  20. A fast and accurate method to predict 2D and 3D aerodynamic boundary layer flows

    NASA Astrophysics Data System (ADS)

    Bijleveld, H. A.; Veldman, A. E. P.

    2014-12-01

    A quasi-simultaneous interaction method is applied to predict 2D and 3D aerodynamic flows. This method is suitable for offshore wind turbine design software as it is a very accurate and computationally reasonably cheap method. This study shows the results for a NACA 0012 airfoil. The two applied solvers converge to the experimental values when the grid is refined. We also show that in separation the eigenvalues remain positive thus avoiding the Goldstein singularity at separation. In 3D we show a flow over a dent in which separation occurs. A rotating flat plat is used to show the applicability of the method for rotating flows. The shown capabilities of the method indicate that the quasi-simultaneous interaction method is suitable for design methods for offshore wind turbine blades.

  1. Distance scaling method for accurate prediction of slowly varying magnetic fields in satellite missions

    NASA Astrophysics Data System (ADS)

    Zacharias, Panagiotis P.; Chatzineofytou, Elpida G.; Spantideas, Sotirios T.; Capsalis, Christos N.

    2016-07-01

    In the present work, the determination of the magnetic behavior of localized magnetic sources from near-field measurements is examined. The distance power law of the magnetic field fall-off is used in various cases to accurately predict the magnetic signature of an equipment under test (EUT) consisting of multiple alternating current (AC) magnetic sources. Therefore, parameters concerning the location of the observation points (magnetometers) are studied towards this scope. The results clearly show that these parameters are independent of the EUT's size and layout. Additionally, the techniques developed in the present study enable the placing of the magnetometers close to the EUT, thus achieving high signal-to-noise ratio (SNR). Finally, the proposed method is verified by real measurements, using a mobile phone as an EUT.

  2. Differential contribution of visual and auditory information to accurately predict the direction and rotational motion of a visual stimulus.

    PubMed

    Park, Seoung Hoon; Kim, Seonjin; Kwon, MinHyuk; Christou, Evangelos A

    2016-03-01

    Vision and auditory information are critical for perception and to enhance the ability of an individual to respond accurately to a stimulus. However, it is unknown whether visual and auditory information contribute differentially to identify the direction and rotational motion of the stimulus. The purpose of this study was to determine the ability of an individual to accurately predict the direction and rotational motion of the stimulus based on visual and auditory information. In this study, we recruited 9 expert table-tennis players and used table-tennis service as our experimental model. Participants watched recorded services with different levels of visual and auditory information. The goal was to anticipate the direction of the service (left or right) and the rotational motion of service (topspin, sidespin, or cut). We recorded their responses and quantified the following outcomes: (i) directional accuracy and (ii) rotational motion accuracy. The response accuracy was the accurate predictions relative to the total number of trials. The ability of the participants to predict the direction of the service accurately increased with additional visual information but not with auditory information. In contrast, the ability of the participants to predict the rotational motion of the service accurately increased with the addition of auditory information to visual information but not with additional visual information alone. In conclusion, this finding demonstrates that visual information enhances the ability of an individual to accurately predict the direction of the stimulus, whereas additional auditory information enhances the ability of an individual to accurately predict the rotational motion of stimulus.

  3. In vitro transcription accurately predicts lac repressor phenotype in vivo in Escherichia coli

    PubMed Central

    2014-01-01

    A multitude of studies have looked at the in vivo and in vitro behavior of the lac repressor binding to DNA and effector molecules in order to study transcriptional repression, however these studies are not always reconcilable. Here we use in vitro transcription to directly mimic the in vivo system in order to build a self consistent set of experiments to directly compare in vivo and in vitro genetic repression. A thermodynamic model of the lac repressor binding to operator DNA and effector is used to link DNA occupancy to either normalized in vitro mRNA product or normalized in vivo fluorescence of a regulated gene, YFP. An accurate measurement of repressor, DNA and effector concentrations were made both in vivo and in vitro allowing for direct modeling of the entire thermodynamic equilibrium. In vivo repression profiles are accurately predicted from the given in vitro parameters when molecular crowding is considered. Interestingly, our measured repressor–operator DNA affinity differs significantly from previous in vitro measurements. The literature values are unable to replicate in vivo binding data. We therefore conclude that the repressor-DNA affinity is much weaker than previously thought. This finding would suggest that in vitro techniques that are specifically designed to mimic the in vivo process may be necessary to replicate the native system. PMID:25097824

  4. Theoretical uncertainties due to AGN subgrid models in predictions of galaxy cluster observable properties

    NASA Astrophysics Data System (ADS)

    Yang, H.-Y. Karen; Sutter, P. M.; Ricker, Paul M.

    2012-12-01

    Cosmological constraints derived from galaxy clusters rely on accurate predictions of cluster observable properties, in which feedback from active galactic nuclei (AGN) is a critical component. In order to model the physical effects due to supermassive black holes (SMBH) on cosmological scales, subgrid modelling is required, and a variety of implementations have been developed in the literature. However, theoretical uncertainties due to model and parameter variations are not yet well understood, limiting the predictive power of simulations including AGN feedback. By performing a detailed parameter-sensitivity study in a single cluster using several commonly adopted AGN accretion and feedback models with FLASH, we quantify the model uncertainties in predictions of cluster integrated properties. We find that quantities that are more sensitive to gas density have larger uncertainties (˜20 per cent for Mgas and a factor of ˜2 for LX at R500), whereas TX, YSZ and YX are more robust (˜10-20 per cent at R500). To make predictions beyond this level of accuracy would require more constraints on the most relevant parameters: the accretion model, mechanical heating efficiency and size of feedback region. By studying the impact of AGN feedback on the scaling relations, we find that an anti-correlation exists between Mgas and TX, which is another reason why YSZ and YX are excellent mass proxies. This anti-correlation also implies that AGN feedback is likely to be an important source of intrinsic scatter in the Mgas-TX and LX-TX relations.

  5. Measuring solar reflectance Part I: Defining a metric that accurately predicts solar heat gain

    SciTech Connect

    Levinson, Ronnen; Akbari, Hashem; Berdahl, Paul

    2010-05-14

    Solar reflectance can vary with the spectral and angular distributions of incident sunlight, which in turn depend on surface orientation, solar position and atmospheric conditions. A widely used solar reflectance metric based on the ASTM Standard E891 beam-normal solar spectral irradiance underestimates the solar heat gain of a spectrally selective 'cool colored' surface because this irradiance contains a greater fraction of near-infrared light than typically found in ordinary (unconcentrated) global sunlight. At mainland U.S. latitudes, this metric RE891BN can underestimate the annual peak solar heat gain of a typical roof or pavement (slope {le} 5:12 [23{sup o}]) by as much as 89 W m{sup -2}, and underestimate its peak surface temperature by up to 5 K. Using R{sub E891BN} to characterize roofs in a building energy simulation can exaggerate the economic value N of annual cool-roof net energy savings by as much as 23%. We define clear-sky air mass one global horizontal ('AM1GH') solar reflectance R{sub g,0}, a simple and easily measured property that more accurately predicts solar heat gain. R{sub g,0} predicts the annual peak solar heat gain of a roof or pavement to within 2 W m{sup -2}, and overestimates N by no more than 3%. R{sub g,0} is well suited to rating the solar reflectances of roofs, pavements and walls. We show in Part II that R{sub g,0} can be easily and accurately measured with a pyranometer, a solar spectrophotometer or version 6 of the Solar Spectrum Reflectometer.

  6. Measuring solar reflectance - Part I: Defining a metric that accurately predicts solar heat gain

    SciTech Connect

    Levinson, Ronnen; Akbari, Hashem; Berdahl, Paul

    2010-09-15

    Solar reflectance can vary with the spectral and angular distributions of incident sunlight, which in turn depend on surface orientation, solar position and atmospheric conditions. A widely used solar reflectance metric based on the ASTM Standard E891 beam-normal solar spectral irradiance underestimates the solar heat gain of a spectrally selective ''cool colored'' surface because this irradiance contains a greater fraction of near-infrared light than typically found in ordinary (unconcentrated) global sunlight. At mainland US latitudes, this metric R{sub E891BN} can underestimate the annual peak solar heat gain of a typical roof or pavement (slope {<=} 5:12 [23 ]) by as much as 89 W m{sup -2}, and underestimate its peak surface temperature by up to 5 K. Using R{sub E891BN} to characterize roofs in a building energy simulation can exaggerate the economic value N of annual cool roof net energy savings by as much as 23%. We define clear sky air mass one global horizontal (''AM1GH'') solar reflectance R{sub g,0}, a simple and easily measured property that more accurately predicts solar heat gain. R{sub g,0} predicts the annual peak solar heat gain of a roof or pavement to within 2 W m{sup -2}, and overestimates N by no more than 3%. R{sub g,0} is well suited to rating the solar reflectances of roofs, pavements and walls. We show in Part II that R{sub g,0} can be easily and accurately measured with a pyranometer, a solar spectrophotometer or version 6 of the Solar Spectrum Reflectometer. (author)

  7. Highly Accurate Prediction of Protein-Protein Interactions via Incorporating Evolutionary Information and Physicochemical Characteristics

    PubMed Central

    Li, Zheng-Wei; You, Zhu-Hong; Chen, Xing; Gui, Jie; Nie, Ru

    2016-01-01

    Protein-protein interactions (PPIs) occur at almost all levels of cell functions and play crucial roles in various cellular processes. Thus, identification of PPIs is critical for deciphering the molecular mechanisms and further providing insight into biological processes. Although a variety of high-throughput experimental techniques have been developed to identify PPIs, existing PPI pairs by experimental approaches only cover a small fraction of the whole PPI networks, and further, those approaches hold inherent disadvantages, such as being time-consuming, expensive, and having high false positive rate. Therefore, it is urgent and imperative to develop automatic in silico approaches to predict PPIs efficiently and accurately. In this article, we propose a novel mixture of physicochemical and evolutionary-based feature extraction method for predicting PPIs using our newly developed discriminative vector machine (DVM) classifier. The improvements of the proposed method mainly consist in introducing an effective feature extraction method that can capture discriminative features from the evolutionary-based information and physicochemical characteristics, and then a powerful and robust DVM classifier is employed. To the best of our knowledge, it is the first time that DVM model is applied to the field of bioinformatics. When applying the proposed method to the Yeast and Helicobacter pylori (H. pylori) datasets, we obtain excellent prediction accuracies of 94.35% and 90.61%, respectively. The computational results indicate that our method is effective and robust for predicting PPIs, and can be taken as a useful supplementary tool to the traditional experimental methods for future proteomics research. PMID:27571061

  8. Highly Accurate Prediction of Protein-Protein Interactions via Incorporating Evolutionary Information and Physicochemical Characteristics.

    PubMed

    Li, Zheng-Wei; You, Zhu-Hong; Chen, Xing; Gui, Jie; Nie, Ru

    2016-01-01

    Protein-protein interactions (PPIs) occur at almost all levels of cell functions and play crucial roles in various cellular processes. Thus, identification of PPIs is critical for deciphering the molecular mechanisms and further providing insight into biological processes. Although a variety of high-throughput experimental techniques have been developed to identify PPIs, existing PPI pairs by experimental approaches only cover a small fraction of the whole PPI networks, and further, those approaches hold inherent disadvantages, such as being time-consuming, expensive, and having high false positive rate. Therefore, it is urgent and imperative to develop automatic in silico approaches to predict PPIs efficiently and accurately. In this article, we propose a novel mixture of physicochemical and evolutionary-based feature extraction method for predicting PPIs using our newly developed discriminative vector machine (DVM) classifier. The improvements of the proposed method mainly consist in introducing an effective feature extraction method that can capture discriminative features from the evolutionary-based information and physicochemical characteristics, and then a powerful and robust DVM classifier is employed. To the best of our knowledge, it is the first time that DVM model is applied to the field of bioinformatics. When applying the proposed method to the Yeast and Helicobacter pylori (H. pylori) datasets, we obtain excellent prediction accuracies of 94.35% and 90.61%, respectively. The computational results indicate that our method is effective and robust for predicting PPIs, and can be taken as a useful supplementary tool to the traditional experimental methods for future proteomics research. PMID:27571061

  9. Highly Accurate Prediction of Protein-Protein Interactions via Incorporating Evolutionary Information and Physicochemical Characteristics.

    PubMed

    Li, Zheng-Wei; You, Zhu-Hong; Chen, Xing; Gui, Jie; Nie, Ru

    2016-01-01

    Protein-protein interactions (PPIs) occur at almost all levels of cell functions and play crucial roles in various cellular processes. Thus, identification of PPIs is critical for deciphering the molecular mechanisms and further providing insight into biological processes. Although a variety of high-throughput experimental techniques have been developed to identify PPIs, existing PPI pairs by experimental approaches only cover a small fraction of the whole PPI networks, and further, those approaches hold inherent disadvantages, such as being time-consuming, expensive, and having high false positive rate. Therefore, it is urgent and imperative to develop automatic in silico approaches to predict PPIs efficiently and accurately. In this article, we propose a novel mixture of physicochemical and evolutionary-based feature extraction method for predicting PPIs using our newly developed discriminative vector machine (DVM) classifier. The improvements of the proposed method mainly consist in introducing an effective feature extraction method that can capture discriminative features from the evolutionary-based information and physicochemical characteristics, and then a powerful and robust DVM classifier is employed. To the best of our knowledge, it is the first time that DVM model is applied to the field of bioinformatics. When applying the proposed method to the Yeast and Helicobacter pylori (H. pylori) datasets, we obtain excellent prediction accuracies of 94.35% and 90.61%, respectively. The computational results indicate that our method is effective and robust for predicting PPIs, and can be taken as a useful supplementary tool to the traditional experimental methods for future proteomics research.

  10. Theoretical model for forming limit diagram predictions without initial inhomogeneity

    NASA Astrophysics Data System (ADS)

    Gologanu, Mihai; Comsa, Dan Sorin; Banabic, Dorel

    2013-05-01

    We report on our attempts to build a theoretical model for determining forming limit diagrams (FLD) based on limit analysis that, contrary to the well-known Marciniak and Kuczynski (M-K) model, does not assume the initial existence of a region with material or geometrical inhomogeneity. We first give a new interpretation based on limit analysis for the onset of necking in the M-K model. Considering the initial thickness defect along a narrow band as postulated by the M-K model, we show that incipient necking is a transition in the plastic mechanism from one of plastic flow in both the sheet and the band to another one where the sheet becomes rigid and all plastic deformation is localized in the band. We then draw on some analogies between the onset of necking in a sheet and the onset of coalescence in a porous bulk body. In fact, the main advance in coalescence modeling has been based on a similar limit analysis with an important new ingredient: the evolution of the spatial distribution of voids, due to the plastic deformation, creating weaker regions with higher porosity surrounded by sound regions with no voids. The onset of coalescence is precisely the transition from a mechanism of plastic deformation in both regions to another one, where the sound regions are rigid. We apply this new ingredient to a necking model based on limit analysis, for the first quadrant of the FLD and a porous sheet. We use Gurson's model with some recent extensions to model the porous material. We follow both the evolution of a homogeneous sheet and the evolution of the distribution of voids. At each moment we test for a potential change of plastic mechanism, by comparing the stresses in the uniform region to those in a virtual band with a larger porosity. The main difference with the coalescence of voids in a bulk solid is that the plastic mechanism for a sheet admits a supplementary degree of freedom, namely the change in the thickness of the virtual band. For strain ratios close to

  11. A graph-theoretic approach for classification and structure prediction of transmembrane β-barrel proteins

    PubMed Central

    2012-01-01

    Background Transmembrane β-barrel proteins are a special class of transmembrane proteins which play several key roles in human body and diseases. Due to experimental difficulties, the number of transmembrane β-barrel proteins with known structures is very small. Over the years, a number of learning-based methods have been introduced for recognition and structure prediction of transmembrane β-barrel proteins. Most of these methods emphasize on homology search rather than any biological or chemical basis. Results We present a novel graph-theoretic model for classification and structure prediction of transmembrane β-barrel proteins. This model folds proteins based on energy minimization rather than a homology search, avoiding any assumption on availability of training dataset. The ab initio model presented in this paper is the first method to allow for permutations in the structure of transmembrane proteins and provides more structural information than any known algorithm. The model is also able to recognize β-barrels by assessing the pseudo free energy. We assess the structure prediction on 41 proteins gathered from existing databases on experimentally validated transmembrane β-barrel proteins. We show that our approach is quite accurate with over 90% F-score on strands and over 74% F-score on residues. The results are comparable to other algorithms suggesting that our pseudo-energy model is close to the actual physical model. We test our classification approach and show that it is able to reject α-helical bundles with 100% accuracy and β-barrel lipocalins with 97% accuracy. Conclusions We show that it is possible to design models for classification and structure prediction for transmembrane β-barrel proteins which do not depend essentially on training sets but on combinatorial properties of the structures to be proved. These models are fairly accurate, robust and can be run very efficiently on PC-like computers. Such models are useful for the genome

  12. Accurate prediction of solvent accessibility using neural networks-based regression.

    PubMed

    Adamczak, Rafał; Porollo, Aleksey; Meller, Jarosław

    2004-09-01

    Accurate prediction of relative solvent accessibilities (RSAs) of amino acid residues in proteins may be used to facilitate protein structure prediction and functional annotation. Toward that goal we developed a novel method for improved prediction of RSAs. Contrary to other machine learning-based methods from the literature, we do not impose a classification problem with arbitrary boundaries between the classes. Instead, we seek a continuous approximation of the real-value RSA using nonlinear regression, with several feed forward and recurrent neural networks, which are then combined into a consensus predictor. A set of 860 protein structures derived from the PFAM database was used for training, whereas validation of the results was carefully performed on several nonredundant control sets comprising a total of 603 structures derived from new Protein Data Bank structures and had no homology to proteins included in the training. Two classes of alternative predictors were developed for comparison with the regression-based approach: one based on the standard classification approach and the other based on a semicontinuous approximation with the so-called thermometer encoding. Furthermore, a weighted approximation, with errors being scaled by the observed levels of variability in RSA for equivalent residues in families of homologous structures, was applied in order to improve the results. The effects of including evolutionary profiles and the growth of sequence databases were assessed. In accord with the observed levels of variability in RSA for different ranges of RSA values, the regression accuracy is higher for buried than for exposed residues, with overall 15.3-15.8% mean absolute errors and correlation coefficients between the predicted and experimental values of 0.64-0.67 on different control sets. The new method outperforms classification-based algorithms when the real value predictions are projected onto two-class classification problems with several commonly

  13. A Simple and Accurate Model to Predict Responses to Multi-electrode Stimulation in the Retina.

    PubMed

    Maturana, Matias I; Apollo, Nicholas V; Hadjinicolaou, Alex E; Garrett, David J; Cloherty, Shaun L; Kameneva, Tatiana; Grayden, David B; Ibbotson, Michael R; Meffin, Hamish

    2016-04-01

    Implantable electrode arrays are widely used in therapeutic stimulation of the nervous system (e.g. cochlear, retinal, and cortical implants). Currently, most neural prostheses use serial stimulation (i.e. one electrode at a time) despite this severely limiting the repertoire of stimuli that can be applied. Methods to reliably predict the outcome of multi-electrode stimulation have not been available. Here, we demonstrate that a linear-nonlinear model accurately predicts neural responses to arbitrary patterns of stimulation using in vitro recordings from single retinal ganglion cells (RGCs) stimulated with a subretinal multi-electrode array. In the model, the stimulus is projected onto a low-dimensional subspace and then undergoes a nonlinear transformation to produce an estimate of spiking probability. The low-dimensional subspace is estimated using principal components analysis, which gives the neuron's electrical receptive field (ERF), i.e. the electrodes to which the neuron is most sensitive. Our model suggests that stimulation proportional to the ERF yields a higher efficacy given a fixed amount of power when compared to equal amplitude stimulation on up to three electrodes. We find that the model captures the responses of all the cells recorded in the study, suggesting that it will generalize to most cell types in the retina. The model is computationally efficient to evaluate and, therefore, appropriate for future real-time applications including stimulation strategies that make use of recorded neural activity to improve the stimulation strategy. PMID:27035143

  14. Accurate load prediction by BEM with airfoil data from 3D RANS simulations

    NASA Astrophysics Data System (ADS)

    Schneider, Marc S.; Nitzsche, Jens; Hennings, Holger

    2016-09-01

    In this paper, two methods for the extraction of airfoil coefficients from 3D CFD simulations of a wind turbine rotor are investigated, and these coefficients are used to improve the load prediction of a BEM code. The coefficients are extracted from a number of steady RANS simulations, using either averaging of velocities in annular sections, or an inverse BEM approach for determination of the induction factors in the rotor plane. It is shown that these 3D rotor polars are able to capture the rotational augmentation at the inner part of the blade as well as the load reduction by 3D effects close to the blade tip. They are used as input to a simple BEM code and the results of this BEM with 3D rotor polars are compared to the predictions of BEM with 2D airfoil coefficients plus common empirical corrections for stall delay and tip loss. While BEM with 2D airfoil coefficients produces a very different radial distribution of loads than the RANS simulation, the BEM with 3D rotor polars manages to reproduce the loads from RANS very accurately for a variety of load cases, as long as the blade pitch angle is not too different from the cases from which the polars were extracted.

  15. A Simple and Accurate Model to Predict Responses to Multi-electrode Stimulation in the Retina

    PubMed Central

    Maturana, Matias I.; Apollo, Nicholas V.; Hadjinicolaou, Alex E.; Garrett, David J.; Cloherty, Shaun L.; Kameneva, Tatiana; Grayden, David B.; Ibbotson, Michael R.; Meffin, Hamish

    2016-01-01

    Implantable electrode arrays are widely used in therapeutic stimulation of the nervous system (e.g. cochlear, retinal, and cortical implants). Currently, most neural prostheses use serial stimulation (i.e. one electrode at a time) despite this severely limiting the repertoire of stimuli that can be applied. Methods to reliably predict the outcome of multi-electrode stimulation have not been available. Here, we demonstrate that a linear-nonlinear model accurately predicts neural responses to arbitrary patterns of stimulation using in vitro recordings from single retinal ganglion cells (RGCs) stimulated with a subretinal multi-electrode array. In the model, the stimulus is projected onto a low-dimensional subspace and then undergoes a nonlinear transformation to produce an estimate of spiking probability. The low-dimensional subspace is estimated using principal components analysis, which gives the neuron’s electrical receptive field (ERF), i.e. the electrodes to which the neuron is most sensitive. Our model suggests that stimulation proportional to the ERF yields a higher efficacy given a fixed amount of power when compared to equal amplitude stimulation on up to three electrodes. We find that the model captures the responses of all the cells recorded in the study, suggesting that it will generalize to most cell types in the retina. The model is computationally efficient to evaluate and, therefore, appropriate for future real-time applications including stimulation strategies that make use of recorded neural activity to improve the stimulation strategy. PMID:27035143

  16. ChIP-seq Accurately Predicts Tissue-Specific Activity of Enhancers

    SciTech Connect

    Visel, Axel; Blow, Matthew J.; Li, Zirong; Zhang, Tao; Akiyama, Jennifer A.; Holt, Amy; Plajzer-Frick, Ingrid; Shoukry, Malak; Wright, Crystal; Chen, Feng; Afzal, Veena; Ren, Bing; Rubin, Edward M.; Pennacchio, Len A.

    2009-02-01

    A major yet unresolved quest in decoding the human genome is the identification of the regulatory sequences that control the spatial and temporal expression of genes. Distant-acting transcriptional enhancers are particularly challenging to uncover since they are scattered amongst the vast non-coding portion of the genome. Evolutionary sequence constraint can facilitate the discovery of enhancers, but fails to predict when and where they are active in vivo. Here, we performed chromatin immunoprecipitation with the enhancer-associated protein p300, followed by massively-parallel sequencing, to map several thousand in vivo binding sites of p300 in mouse embryonic forebrain, midbrain, and limb tissue. We tested 86 of these sequences in a transgenic mouse assay, which in nearly all cases revealed reproducible enhancer activity in those tissues predicted by p300 binding. Our results indicate that in vivo mapping of p300 binding is a highly accurate means for identifying enhancers and their associated activities and suggest that such datasets will be useful to study the role of tissue-specific enhancers in human biology and disease on a genome-wide scale.

  17. Development of a New Model for Accurate Prediction of Cloud Water Deposition on Vegetation

    NASA Astrophysics Data System (ADS)

    Katata, G.; Nagai, H.; Wrzesinsky, T.; Klemm, O.; Eugster, W.; Burkard, R.

    2006-12-01

    Scarcity of water resources in arid and semi-arid areas is of great concern in the light of population growth and food shortages. Several experiments focusing on cloud (fog) water deposition on the land surface suggest that cloud water plays an important role in water resource in such regions. A one-dimensional vegetation model including the process of cloud water deposition on vegetation has been developed to better predict cloud water deposition on the vegetation. New schemes to calculate capture efficiency of leaf, cloud droplet size distribution, and gravitational flux of cloud water were incorporated in the model. Model calculations were compared with the data acquired at the Norway spruce forest at the Waldstein site, Germany. High performance of the model was confirmed by comparisons of calculated net radiation, sensible and latent heat, and cloud water fluxes over the forest with measurements. The present model provided a better prediction of measured turbulent and gravitational fluxes of cloud water over the canopy than the Lovett model, which is a commonly used cloud water deposition model. Detailed calculations of evapotranspiration and of turbulent exchange of heat and water vapor within the canopy and the modifications are necessary for accurate prediction of cloud water deposition. Numerical experiments to examine the dependence of cloud water deposition on the vegetation species (coniferous and broad-leaved trees, flat and cylindrical grasses) and structures (Leaf Area Index (LAI) and canopy height) are performed using the presented model. The results indicate that the differences of leaf shape and size have a large impact on cloud water deposition. Cloud water deposition also varies with the growth of vegetation and seasonal change of LAI. We found that the coniferous trees whose height and LAI are 24 m and 2.0 m2m-2, respectively, produce the largest amount of cloud water deposition in all combinations of vegetation species and structures in the

  18. Aircraft Noise Prediction Program theoretical manual: Propeller aerodynamics and noise

    NASA Technical Reports Server (NTRS)

    Zorumski, W. E. (Editor); Weir, D. S. (Editor)

    1986-01-01

    The prediction sequence used in the aircraft noise prediction program (ANOPP) is described. The elements of the sequence are called program modules. The first group of modules analyzes the propeller geometry, the aerodynamics, including both potential and boundary-layer flow, the propeller performance, and the surface loading distribution. This group of modules is based entirely on aerodynamic strip theory. The next group of modules deals with the first group. Predictions of periodic thickness and loading noise are determined with time-domain methods. Broadband noise is predicted by a semiempirical method. Near-field predictions of fuselage surface pressrues include the effects of boundary layer refraction and scattering. Far-field predictions include atmospheric and ground effects.

  19. Can radiation therapy treatment planning system accurately predict surface doses in postmastectomy radiation therapy patients?

    SciTech Connect

    Wong, Sharon; Back, Michael; Tan, Poh Wee; Lee, Khai Mun; Baggarley, Shaun; Lu, Jaide Jay

    2012-07-01

    Skin doses have been an important factor in the dose prescription for breast radiotherapy. Recent advances in radiotherapy treatment techniques, such as intensity-modulated radiation therapy (IMRT) and new treatment schemes such as hypofractionated breast therapy have made the precise determination of the surface dose necessary. Detailed information of the dose at various depths of the skin is also critical in designing new treatment strategies. The purpose of this work was to assess the accuracy of surface dose calculation by a clinically used treatment planning system and those measured by thermoluminescence dosimeters (TLDs) in a customized chest wall phantom. This study involved the construction of a chest wall phantom for skin dose assessment. Seven TLDs were distributed throughout each right chest wall phantom to give adequate representation of measured radiation doses. Point doses from the CMS Xio Registered-Sign treatment planning system (TPS) were calculated for each relevant TLD positions and results correlated. There were no significant difference between measured absorbed dose by TLD and calculated doses by the TPS (p > 0.05 (1-tailed). Dose accuracy of up to 2.21% was found. The deviations from the calculated absorbed doses were overall larger (3.4%) when wedges and bolus were used. 3D radiotherapy TPS is a useful and accurate tool to assess the accuracy of surface dose. Our studies have shown that radiation treatment accuracy expressed as a comparison between calculated doses (by TPS) and measured doses (by TLD dosimetry) can be accurately predicted for tangential treatment of the chest wall after mastectomy.

  20. Aircraft noise prediction program theoretical manual, part 2

    NASA Astrophysics Data System (ADS)

    Zorumski, W. E.

    1982-02-01

    Detailed prediction methods for specific aircraft noise sources are given. These sources are airframe noise, combustion noise, fan noise, single and dual stream jet noise, and turbine noise. Modifications to the NASA methods which comply with the International Civil Aviation Organization standard method for aircraft noise prediction are given.

  1. How accurately can we predict the melting points of drug-like compounds?

    PubMed

    Tetko, Igor V; Sushko, Yurii; Novotarskyi, Sergii; Patiny, Luc; Kondratov, Ivan; Petrenko, Alexander E; Charochkina, Larisa; Asiri, Abdullah M

    2014-12-22

    This article contributes a highly accurate model for predicting the melting points (MPs) of medicinal chemistry compounds. The model was developed using the largest published data set, comprising more than 47k compounds. The distributions of MPs in drug-like and drug lead sets showed that >90% of molecules melt within [50,250]°C. The final model calculated an RMSE of less than 33 °C for molecules from this temperature interval, which is the most important for medicinal chemistry users. This performance was achieved using a consensus model that performed calculations to a significantly higher accuracy than the individual models. We found that compounds with reactive and unstable groups were overrepresented among outlying compounds. These compounds could decompose during storage or measurement, thus introducing experimental errors. While filtering the data by removing outliers generally increased the accuracy of individual models, it did not significantly affect the results of the consensus models. Three analyzed distance to models did not allow us to flag molecules, which had MP values fell outside the applicability domain of the model. We believe that this negative result and the public availability of data from this article will encourage future studies to develop better approaches to define the applicability domain of models. The final model, MP data, and identified reactive groups are available online at http://ochem.eu/article/55638.

  2. Fast and Accurate Prediction of Numerical Relativity Waveforms from Binary Black Hole Coalescences Using Surrogate Models.

    PubMed

    Blackman, Jonathan; Field, Scott E; Galley, Chad R; Szilágyi, Béla; Scheel, Mark A; Tiglio, Manuel; Hemberger, Daniel A

    2015-09-18

    Simulating a binary black hole coalescence by solving Einstein's equations is computationally expensive, requiring days to months of supercomputing time. Using reduced order modeling techniques, we construct an accurate surrogate model, which is evaluated in a millisecond to a second, for numerical relativity (NR) waveforms from nonspinning binary black hole coalescences with mass ratios in [1, 10] and durations corresponding to about 15 orbits before merger. We assess the model's uncertainty and show that our modeling strategy predicts NR waveforms not used for the surrogate's training with errors nearly as small as the numerical error of the NR code. Our model includes all spherical-harmonic _{-2}Y_{ℓm} waveform modes resolved by the NR code up to ℓ=8. We compare our surrogate model to effective one body waveforms from 50M_{⊙} to 300M_{⊙} for advanced LIGO detectors and find that the surrogate is always more faithful (by at least an order of magnitude in most cases).

  3. Fast and Accurate Prediction of Numerical Relativity Waveforms from Binary Black Hole Coalescences Using Surrogate Models.

    PubMed

    Blackman, Jonathan; Field, Scott E; Galley, Chad R; Szilágyi, Béla; Scheel, Mark A; Tiglio, Manuel; Hemberger, Daniel A

    2015-09-18

    Simulating a binary black hole coalescence by solving Einstein's equations is computationally expensive, requiring days to months of supercomputing time. Using reduced order modeling techniques, we construct an accurate surrogate model, which is evaluated in a millisecond to a second, for numerical relativity (NR) waveforms from nonspinning binary black hole coalescences with mass ratios in [1, 10] and durations corresponding to about 15 orbits before merger. We assess the model's uncertainty and show that our modeling strategy predicts NR waveforms not used for the surrogate's training with errors nearly as small as the numerical error of the NR code. Our model includes all spherical-harmonic _{-2}Y_{ℓm} waveform modes resolved by the NR code up to ℓ=8. We compare our surrogate model to effective one body waveforms from 50M_{⊙} to 300M_{⊙} for advanced LIGO detectors and find that the surrogate is always more faithful (by at least an order of magnitude in most cases). PMID:26430979

  4. How accurately can we predict the melting points of drug-like compounds?

    PubMed

    Tetko, Igor V; Sushko, Yurii; Novotarskyi, Sergii; Patiny, Luc; Kondratov, Ivan; Petrenko, Alexander E; Charochkina, Larisa; Asiri, Abdullah M

    2014-12-22

    This article contributes a highly accurate model for predicting the melting points (MPs) of medicinal chemistry compounds. The model was developed using the largest published data set, comprising more than 47k compounds. The distributions of MPs in drug-like and drug lead sets showed that >90% of molecules melt within [50,250]°C. The final model calculated an RMSE of less than 33 °C for molecules from this temperature interval, which is the most important for medicinal chemistry users. This performance was achieved using a consensus model that performed calculations to a significantly higher accuracy than the individual models. We found that compounds with reactive and unstable groups were overrepresented among outlying compounds. These compounds could decompose during storage or measurement, thus introducing experimental errors. While filtering the data by removing outliers generally increased the accuracy of individual models, it did not significantly affect the results of the consensus models. Three analyzed distance to models did not allow us to flag molecules, which had MP values fell outside the applicability domain of the model. We believe that this negative result and the public availability of data from this article will encourage future studies to develop better approaches to define the applicability domain of models. The final model, MP data, and identified reactive groups are available online at http://ochem.eu/article/55638. PMID:25489863

  5. Accurate prediction of V1 location from cortical folds in a surface coordinate system

    PubMed Central

    Hinds, Oliver P.; Rajendran, Niranjini; Polimeni, Jonathan R.; Augustinack, Jean C.; Wiggins, Graham; Wald, Lawrence L.; Rosas, H. Diana; Potthast, Andreas; Schwartz, Eric L.; Fischl, Bruce

    2008-01-01

    Previous studies demonstrated substantial variability of the location of primary visual cortex (V1) in stereotaxic coordinates when linear volume-based registration is used to match volumetric image intensities (Amunts et al., 2000). However, other qualitative reports of V1 location (Smith, 1904; Stensaas et al., 1974; Rademacher et al., 1993) suggested a consistent relationship between V1 and the surrounding cortical folds. Here, the relationship between folds and the location of V1 is quantified using surface-based analysis to generate a probabilistic atlas of human V1. High-resolution (about 200 μm) magnetic resonance imaging (MRI) at 7 T of ex vivo human cerebral hemispheres allowed identification of the full area via the stria of Gennari: a myeloarchitectonic feature specific to V1. Separate, whole-brain scans were acquired using MRI at 1.5 T to allow segmentation and mesh reconstruction of the cortical gray matter. For each individual, V1 was manually identified in the high-resolution volume and projected onto the cortical surface. Surface-based intersubject registration (Fischl et al., 1999b) was performed to align the primary cortical folds of individual hemispheres to those of a reference template representing the average folding pattern. An atlas of V1 location was constructed by computing the probability of V1 inclusion for each cortical location in the template space. This probabilistic atlas of V1 exhibits low prediction error compared to previous V1 probabilistic atlases built in volumetric coordinates. The increased predictability observed under surface-based registration suggests that the location of V1 is more accurately predicted by the cortical folds than by the shape of the brain embedded in the volume of the skull. In addition, the high quality of this atlas provides direct evidence that surface-based intersubject registration methods are superior to volume-based methods at superimposing functional areas of cortex, and therefore are better

  6. Theoretical prediction and impact of fundamental electric dipole moments

    NASA Astrophysics Data System (ADS)

    Ellis, Sebastian A. R.; Kane, Gordon L.

    2016-01-01

    The predicted Standard Model (SM) electric dipole moments (EDMs) of electrons and quarks are tiny, providing an important window to observe new physics. Theories beyond the SM typically allow relatively large EDMs. The EDMs depend on the relative phases of terms in the effective Lagrangian of the extended theory, which are generally unknown. Underlying theories, such as string/M-theories compactified to four dimensions, could predict the phases and thus EDMs in the resulting supersymmetric (SUSY) theory. Earlier one of us, with collaborators, made such a prediction and found, unexpectedly, that the phases were predicted to be zero at tree level in the theory at the unification or string scale ˜ O(1016 GeV). Electroweak (EW) scale EDMs still arise via running from the high scale, and depend only on the SM Yukawa couplings that also give the CKM phase. Here we extend the earlier work by studying the dependence of the low scale EDMs on the constrained but not fully known fundamental Yukawa couplings. The dominant contribution is from two loop diagrams and is not sensitive to the choice of Yukawa texture. The electron EDM should not be found to be larger than about 5 × 10-30 e cm, and the neutron EDM should not be larger than about 5 × 10-29 e cm. These values are quite a bit smaller than the reported predictions from Split SUSY and typical effective theories, but much larger than the Standard Model prediction. Also, since models with random phases typically give much larger EDMs, it is a significant testable prediction of compactified M-theory that the EDMs should not be above these upper limits. The actual EDMs can be below the limits, so once they are measured they could provide new insight into the fundamental Yukawa couplings of leptons and quarks. We comment also on the role of strong CP violation. EDMs probe fundamental physics near the Planck scale.

  7. Theoretical prediction and impact of fundamental electric dipole moments

    DOE PAGES

    Ellis, Sebastian A. R.; Kane, Gordon L.

    2016-01-13

    The predicted Standard Model (SM) electric dipole moments (EDMs) of electrons and quarks are tiny, providing an important window to observe new physics. Theories beyond the SM typically allow relatively large EDMs. The EDMs depend on the relative phases of terms in the effective Lagrangian of the extended theory, which are generally unknown. Underlying theories, such as string/M-theories compactified to four dimensions, could predict the phases and thus EDMs in the resulting supersymmetric (SUSY) theory. Earlier one of us, with collaborators, made such a prediction and found, unexpectedly, that the phases were predicted to be zero at tree level inmore » the theory at the unification or string scale ~O(1016 GeV). Electroweak (EW) scale EDMs still arise via running from the high scale, and depend only on the SM Yukawa couplings that also give the CKM phase. Here we extend the earlier work by studying the dependence of the low scale EDMs on the constrained but not fully known fundamental Yukawa couplings. The dominant contribution is from two loop diagrams and is not sensitive to the choice of Yukawa texture. The electron EDM should not be found to be larger than about 5 × 10–30e cm, and the neutron EDM should not be larger than about 5 × 10–29e cm. These values are quite a bit smaller than the reported predictions from Split SUSY and typical effective theories, but much larger than the Standard Model prediction. Also, since models with random phases typically give much larger EDMs, it is a significant testable prediction of compactified M-theory that the EDMs should not be above these upper limits. The actual EDMs can be below the limits, so once they are measured they could provide new insight into the fundamental Yukawa couplings of leptons and quarks. As a result, we comment also on the role of strong CP violation. EDMs probe fundamental physics near the Planck scale.« less

  8. Adaptive evolution: evaluating empirical support for theoretical predictions.

    PubMed

    Olson-Manning, Carrie F; Wagner, Maggie R; Mitchell-Olds, Thomas

    2012-12-01

    Adaptive evolution is shaped by the interaction of population genetics, natural selection and underlying network and biochemical constraints. Variation created by mutation, the raw material for evolutionary change, is translated into phenotypes by flux through metabolic pathways and by the topography and dynamics of molecular networks. Finally, the retention of genetic variation and the efficacy of selection depend on population genetics and demographic history. Emergent high-throughput experimental methods and sequencing technologies allow us to gather more evidence and to move beyond the theory in different systems and populations. Here we review the extent to which recent evidence supports long-established theoretical principles of adaptation.

  9. Theoretical prediction of the onset of thermoacoustic instability from the experimental transfer matrix of a thermoacoustic core.

    PubMed

    Guedra, Matthieu; Penelet, Guillaume; Lotton, Pierrick; Dalmont, Jean-Pierre

    2011-07-01

    The aim of this paper is to propose a method to predict the onset conditions of the thermoacoustic instability for various thermoacoustic engines. As an accurate modeling of the heat exchangers and the stack submitted to a temperature gradient is a difficult task, an experimental approach for the characterization of the amplifying properties of the thermoacoustic core is proposed. An experimental apparatus is presented which allows to measure the transfer matrix of a thermoacoustic core under various heating conditions by means of a four-microphone method. An analytical model for the prediction of the onset conditions from this measured transfer matrix is developed. The experimental data are introduced in the model and theoretical predictions of the onset conditions are compared with those actually observed in standing-wave and traveling-wave engines. The results show good agreement between predictions from the model and experiments.

  10. Unilateral Prostate Cancer Cannot be Accurately Predicted in Low-Risk Patients

    SciTech Connect

    Isbarn, Hendrik; Karakiewicz, Pierre I.; Vogel, Susanne

    2010-07-01

    Purpose: Hemiablative therapy (HAT) is increasing in popularity for treatment of patients with low-risk prostate cancer (PCa). The validity of this therapeutic modality, which exclusively treats PCa within a single prostate lobe, rests on accurate staging. We tested the accuracy of unilaterally unremarkable biopsy findings in cases of low-risk PCa patients who are potential candidates for HAT. Methods and Materials: The study population consisted of 243 men with clinical stage {<=}T2a, a prostate-specific antigen (PSA) concentration of <10 ng/ml, a biopsy-proven Gleason sum of {<=}6, and a maximum of 2 ipsilateral positive biopsy results out of 10 or more cores. All men underwent a radical prostatectomy, and pathology stage was used as the gold standard. Univariable and multivariable logistic regression models were tested for significant predictors of unilateral, organ-confined PCa. These predictors consisted of PSA, %fPSA (defined as the quotient of free [uncomplexed] PSA divided by the total PSA), clinical stage (T2a vs. T1c), gland volume, and number of positive biopsy cores (2 vs. 1). Results: Despite unilateral stage at biopsy, bilateral or even non-organ-confined PCa was reported in 64% of all patients. In multivariable analyses, no variable could clearly and independently predict the presence of unilateral PCa. This was reflected in an overall accuracy of 58% (95% confidence interval, 50.6-65.8%). Conclusions: Two-thirds of patients with unilateral low-risk PCa, confirmed by clinical stage and biopsy findings, have bilateral or non-organ-confined PCa at radical prostatectomy. This alarming finding questions the safety and validity of HAT.

  11. Improving DOE-2's RESYS routine: User defined functions to provide more accurate part load energy use and humidity predictions

    SciTech Connect

    Henderson, Hugh I.; Parker, Danny; Huang, Yu J.

    2000-08-04

    In hourly energy simulations, it is important to properly predict the performance of air conditioning systems over a range of full and part load operating conditions. An important component of these calculations is to properly consider the performance of the cycling air conditioner and how it interacts with the building. This paper presents improved approaches to properly account for the part load performance of residential and light commercial air conditioning systems in DOE-2. First, more accurate correlations are given to predict the degradation of system efficiency at part load conditions. In addition, a user-defined function for RESYS is developed that provides improved predictions of air conditioner sensible and latent capacity at part load conditions. The user function also provides more accurate predictions of space humidity by adding ''lumped'' moisture capacitance into the calculations. The improved cooling coil model and the addition of moisture capacitance predicts humidity swings that are more representative of the performance observed in real buildings.

  12. Field theoretical prediction of a property of the tropical cyclone

    NASA Astrophysics Data System (ADS)

    Spineanu, F.; Vlad, M.

    2014-01-01

    The large scale atmospheric vortices (tropical cyclones, tornadoes) are complex physical systems combining thermodynamics and fluid-mechanical processes. The late phase of the evolution towards stationarity consists of the vorticity concentration, a well known tendency to self-organization , an universal property of the two-dimensional fluids. It may then be expected that the stationary state of the tropical cyclone has the same nature as the vortices of many other systems in nature: ideal (Euler) fluids, superconductors, Bose-Einsetin condensate, cosmic strings, etc. Indeed it was found that there is a description of the atmospheric vortex in terms of a classical field theory. It is compatible with the more conventional treatment based on conservation laws, but the field theoretical model reveals properties that are almost inaccessible to the conventional formulation: it identifies the stationary states as being close to self-duality. This is of highest importance: the self-duality is known to be the origin of all coherent structures known in natural systems. Therefore the field theoretical (FT) formulation finds that the cuasi-coherent form of the atmospheric vortex (tropical cyclone) at stationarity is an expression of this particular property. In the present work we examine a strong property of the tropical cyclone, which arises in the FT formulation in a natural way: the equality of the masses of the particles associated to the matter field and respectively to the gauge field in the FT model is translated into the equality between the maximum radial extension of the tropical cyclone and the Rossby radius. For the cases where the FT model is a good approximation we calculate characteristic quantities of the tropical cyclone and find good comparison with observational data.

  13. Theoretical study of gas hydrate decomposition kinetics: model predictions.

    PubMed

    Windmeier, Christoph; Oellrich, Lothar R

    2013-11-27

    In order to provide an estimate of intrinsic gas hydrate dissolution and dissociation kinetics, the Consecutive Desorption and Melting Model (CDM) was developed in a previous publication (Windmeier, C.; Oellrich, L. R. J. Phys. Chem. A 2013, 117, 10151-10161). In this work, an extensive summary of required model data is given. Obtained model predictions are discussed with respect to their temperature dependence as well as their significance for technically relevant areas of gas hydrate decomposition. As a result, an expression for determination of the intrinsic gas hydrate decomposition kinetics for various hydrate formers is given together with an estimate for the maximum possible rates of gas hydrate decomposition. PMID:24199870

  14. Revisiting Theoretical Predictions of the Motion and Direction of FTE's

    NASA Technical Reports Server (NTRS)

    Collado-Vega, Y. M.; Sibeck, D. G.

    2011-01-01

    Flux Transfer Events (FTEs) are magnetopause signatures that result from the passage of flux ropes produced by transient bursts of reconnection. They exhibit bipolar signatures in the component of the magnetic field normal to the magnetopause and transient increases or crater-like structures in the magnetic field strength. We use the bipolar magnetic field signatures and magnetic field strength variations observed by all four Cluster spacecrafts during the years of 2002 and 2003 to determine the velocity and direction fof FTE motion for comparison with predictions for the motion of FTEs generated by the component and anti-parallel reconnection models.

  15. Theoretical predictions of novel potassium chloride phases under pressure.

    PubMed

    Shamp, Andrew; Saitta, Patrick; Zurek, Eva

    2015-05-14

    Evolutionary structure searches predict two hitherto unknown phases of KCl that are the most stable in the pressure regime of 200-600 GPa. I41/amd-KCl, which has the lowest enthalpy between ∼200-350 GPa, can be thought of as being composed of two three-connected nets. This structure can be compared with that of the Cs-IV electride (Cs(+)e(-)): the potassium ions assume the positions of the cesium ions, and the chloride ions are found roughly in the regions of the valence electrons. Above ∼350 GPa a Pnma phase, which is isotypic with phases of CsH and CsI that are stable under pressure, becomes preferred. Just as in Pnma-CsI, the atoms in Pnma-KCl assume an hcp-like lattice; these alkali halides resemble the high-pressure structures of the isoelectronic noble gas solids Xe and Ar, respectively. The equation of state of KCl is extended to 600 GPa, enabling the use of this alkali halide as a pressure guage in ultra-high pressure static compression experiments. KCl is predicted to remain insulating to at least 420 GPa.

  16. Theoretical Predictions of Phase Transitions at Ultra-high Pressures

    NASA Astrophysics Data System (ADS)

    Boates, Brian

    2013-06-01

    We present ab initio calculations of the high-pressure phase diagrams of important planetary materials such as CO2, MgSiO3, and MgO. For CO2, we predict a series of distinct liquid phases over a wide pressure (P) and temperature (T) range, including a first-order transition to a dense polymer liquid. We have computed finite-temperature free energies of liquid and solid CO2 phases to determine the melting curve beyond existing measurements and investigate possible phase separation transitions. The interaction of these phase boundaries with the mantle geotherm will also be discussed. Furthermore, we find evidence for a vast pressure-temperature regime where molten MgSiO3 decomposes into liquid SiO2 and solid MgO, with a volume change of approximately 1.2 percent. The demixing transition is driven by the crystallization of MgO ? the reaction only occurs below the high-pressure MgO melting curve. The predicted transition pressure at 10,000 K is in close proximity to an anomaly reported in recent laser-driven shock experiments of MgSiO3. We also present new results for the high-pressure melting curve of MgO and its B1-B2 solid phase transition, with a triple point near 364 GPa and 12,000 K.

  17. Theoretical Approach to Predict the Performance of Thermoelectric Generator Modules

    NASA Astrophysics Data System (ADS)

    Elarusi, Abdulmunaem H.; Fagehi, Hassan; Lee, Hosung; Attar, Alaa

    2016-10-01

    The aim of this work was to examine the validity of the thermoelectric modules' performance predicted by formulating the effective thermoelectric material properties. The three maximum parameters (output power, current, and efficiency) are defined in terms of the average temperature of the thermoelectric generator (TEG). These three maximum parameters, which are either taken from commercial TEG modules or measurements for particular operating conditions, are used to define the effective material properties (Seebeck coefficient, thermal conductivity, and electrical resistivity). The commercial performance curves provided by the manufacturer were compared with the results obtained here by the effective material properties with the simple standard thermoelectric equations. It has been found that this technique predicts the performance of four commercial thermoelectric modules with fair to good accuracy. The characteristics of the TEGs were represented using the normalized charts constructed by formulating the parameters as a fraction of over the maximum parameters. The normalized charts would be universal for any given TEG module once the thermoelectric material is known.

  18. Theoretical prediction of the vibrational spectra of group IB trimers

    PubMed Central

    Richtsmeier, Steven C.; Gole, James L.; Dixon, David A.

    1980-01-01

    The molecular structures of the group IB trimers, Cu3, Ag3, and Au3, have been determined by using the semi-empirical diatomics-in-molecules theory. The trimers are found to have C2v symmetry with bond angles between 65° and 80°. The trimers are bound with respect to dissociation to the asymptotic limit of an atom plus a diatom. The binding energies per atom for Cu3, Ag3, and Au3 are 1.08, 0.75, and 1.16 eV, respectively. The vibrational frequencies of the trimers have been determined for comparison with experimental results. The vibrational frequencies are characterized by low values for the bending and asymmetric stretch modes. The frequency of the symmetric stretch of the trimer is higher than the stretching frequency of the corresponding diatomic. A detailed comparison of the theoretical results with the previously measured Raman spectra of matrix isolated Ag3 is presented. PMID:16592885

  19. Predicting Innovation Acceptance by Simulation in Virtual Environments (Theoretical Foundations)

    NASA Astrophysics Data System (ADS)

    León, Noel; Duran, Roberto; Aguayo, Humberto; Flores, Myrna

    This paper extends the current development of a methodology for Computer Aided Innovation. It begins with a presentation of concepts related to the perceived capabilities of virtual environments in the Innovation Cycle. The main premise establishes that it is possible to predict the acceptance of a new product in a specific market, by releasing an early prototype in a virtual scenario to quantify its general reception and to receive early feedback from potential customers. The paper continues to focus this research on a synergistic extension of techniques that have their origins in optimization and innovation disciplines. TRIZ (Theory of Inventive Problem Solving), extends the generation of variants with Evolutionary Algorithms (EA) and finally to present the designer and the intended customer, creative and innovative alternatives. All of this developed on a virtual software interface (Virtual World). The work continues with a general description of the project as a step forward to improve the overall strategy.

  20. Relatedness and helping in fish: examining the theoretical predictions

    PubMed Central

    Stiver, Kelly A; Dierkes, Petra; Taborsky, Michael; Lisle Gibbs, H; Balshine, Sigal

    2005-01-01

    Many studies have attempted to explain the evolution of cooperation, yet little attention has been paid to what factors control the amount or kind of cooperation performed. Kin selection theory suggests that more cooperation, or help, should be given by relatives. However, recent theory suggests that under specific ecological and demographic conditions, unrelated individuals must ‘pay to stay’ in the group and therefore may help more. We tested these contrasting predictions using the cooperatively breeding fish, Neolamprologus pulcher, and found that the degree of work effort by helpers depended on which helping behaviours were considered and on their level of relatedness to the breeding male or female. In the field, helpers unrelated to the breeding male performed more territory defence, while helpers unrelated to the breeding female contributed less to territory defence. In the laboratory, unrelated group members helped more. Our work demonstrates that a number of factors in addition to kinship shape cooperative investment patterns. PMID:16048775

  1. Theoretical prediction for several important equilibrium Ge isotope fractionation factors

    NASA Astrophysics Data System (ADS)

    Tang, M.; Li, X.; Liu, Y.

    2008-12-01

    As a newly emerging field, the stable isotope geochemistry of germanium (Ge) needs basic equilibrium fractionation factors to explore its unknown world. In this study, the Ge isotope fractionations between systems including the aqueous Ge(OH)4 and GeO(OH)3- which are the dominant Ge species in seawater, the Ge-bearing organic complexes (e.g. Ge-catechol, Ge-oxalic acid and Ge-citric acid), the quartz- (or opal- ), albite-, K-feldspar- and olivine- like mineral structures are studied. It is the first time that some geologically important equilibrium Ge isotope fractionation factors are reported. Surprisingly, up to 5 per mil large isotopic fractionations between these Ge isotope systems are found at 25 degree. These results suggest a potentially broad application for the Ge isotope geochemistry. Our theoretical calculations are based on the Urey model (or Bigeleisen-Mayer equation) and high level quantum chemistry calculations. The B3LYP/6-311+G(d,p) level quantum chemistry method and the explicit solvent model ("water droplet" method) are used. Many different conformers are also used for the aqueous complexes in order to reduce the possible errors coming from the differences of configurations in solution. The accuracy of our calculation of the Ge isotopic fractionations is estimated about 0.2 per mil. Our results show quartz-like or opal-like structure can enrich most heavy Ge isotopes. Relative to quartz (or opal), some Ge isotopic fractionations are (at 25 C): quartz-organic Ge = 4-5,quartz-Ge(OH)4 =0.9,quartz-GeO(OH)3- =1.5,quartz-albite=0.6,quartz-K-feldspar=0.4 and quartz-olivine=3.9 per mil. The large fractionations between inorganic Ge complexes and organic Ge ones could be used to distinguish the possible bio-involving processes. Our results suggest a good explanation to the experimental observations of Siebert et al. (2006) and Rouxel et al. (2006) and provide important constraints to the study of Ge cycle in ocean.

  2. Synthesis, characterization, theoretical prediction of activities and evaluation of biological activities of some sulfacetamide based hydroxytriazenes.

    PubMed

    Agarwal, Shilpa; Baroliya, Prabhat K; Bhargava, Amit; Tripathi, I P; Goswami, A K

    2016-06-15

    Six new N [(4-aminophenyl)sulfonyl]acetamide based hydroxytriazenes have been synthesized and characterized using elemental analysis, IR, 1H NMR, 13C NMR and MASS spectral analysis. Further, their theoretical predictions for probable activities have been taken using PASS (Prediction of Activity Spectra for Substance). Although a number of activities have been predicted but specifically anti-inflammatory, antiradical, anti-diabetic activities have been experimentally validated which proves that theoretical predictions agree with the experimental results. The object of the Letter is to establish Computer Aided Drug Design (CADD) using our compounds. PMID:27136718

  3. Diverse ruthenium nitrides stabilized under pressure: a theoretical prediction

    PubMed Central

    Zhang, Yunkun; Wu, Lailei; Wan, Biao; Lin, Yangzheng; Hu, Qingyang; Zhao, Yan; Gao, Rui; Li, Zhiping; Zhang, Jingwu; Gou, Huiyang

    2016-01-01

    First-principles calculations were performed to understand the structural stability, synthesis routes, mechanical and electronic properties of diverse ruthenium nitrides. RuN with a new I-4m2 symmetry stabilized by pressure is found to be energetically preferred over the experimental NaCl-type and ZnS-type ones. The Pnnm-RuN2 is found to be stable above 1.1 GPa, in agreement with the experimental results. Specifically, new stoichiometries like RuN3 and RuN4 are proposed firstly to be thermodynamically stable, and the dynamical and mechanical stabilities of the newly predicted structures have been verified by checking their phonon spectra and elastic constants. A phase transition from P4/mmm-RuN4 to C2/c-RuN4 is also uncovered at 23.0 GPa. Drawn from bonding and band structure analysis, P4/mmm-RuN4 exhibits semi-metal-like behavior and becomes a semiconductor for the high-pressure C2/c-RuN4 phase. Meanwhile the P21/c-RuN3 shows metallic feature. Highly directional covalent N-N and Ru-N bonds are formed and dominating in N-enriched Ru nitrides, making them promising hard materials. PMID:27627856

  4. Diverse ruthenium nitrides stabilized under pressure: a theoretical prediction.

    PubMed

    Zhang, Yunkun; Wu, Lailei; Wan, Biao; Lin, Yangzheng; Hu, Qingyang; Zhao, Yan; Gao, Rui; Li, Zhiping; Zhang, Jingwu; Gou, Huiyang

    2016-01-01

    First-principles calculations were performed to understand the structural stability, synthesis routes, mechanical and electronic properties of diverse ruthenium nitrides. RuN with a new I-4m2 symmetry stabilized by pressure is found to be energetically preferred over the experimental NaCl-type and ZnS-type ones. The Pnnm-RuN2 is found to be stable above 1.1 GPa, in agreement with the experimental results. Specifically, new stoichiometries like RuN3 and RuN4 are proposed firstly to be thermodynamically stable, and the dynamical and mechanical stabilities of the newly predicted structures have been verified by checking their phonon spectra and elastic constants. A phase transition from P4/mmm-RuN4 to C2/c-RuN4 is also uncovered at 23.0 GPa. Drawn from bonding and band structure analysis, P4/mmm-RuN4 exhibits semi-metal-like behavior and becomes a semiconductor for the high-pressure C2/c-RuN4 phase. Meanwhile the P21/c-RuN3 shows metallic feature. Highly directional covalent N-N and Ru-N bonds are formed and dominating in N-enriched Ru nitrides, making them promising hard materials. PMID:27627856

  5. Diverse ruthenium nitrides stabilized under pressure: a theoretical prediction

    NASA Astrophysics Data System (ADS)

    Zhang, Yunkun; Wu, Lailei; Wan, Biao; Lin, Yangzheng; Hu, Qingyang; Zhao, Yan; Gao, Rui; Li, Zhiping; Zhang, Jingwu; Gou, Huiyang

    2016-09-01

    First-principles calculations were performed to understand the structural stability, synthesis routes, mechanical and electronic properties of diverse ruthenium nitrides. RuN with a new I-4m2 symmetry stabilized by pressure is found to be energetically preferred over the experimental NaCl-type and ZnS-type ones. The Pnnm-RuN2 is found to be stable above 1.1 GPa, in agreement with the experimental results. Specifically, new stoichiometries like RuN3 and RuN4 are proposed firstly to be thermodynamically stable, and the dynamical and mechanical stabilities of the newly predicted structures have been verified by checking their phonon spectra and elastic constants. A phase transition from P4/mmm-RuN4 to C2/c-RuN4 is also uncovered at 23.0 GPa. Drawn from bonding and band structure analysis, P4/mmm-RuN4 exhibits semi-metal-like behavior and becomes a semiconductor for the high-pressure C2/c-RuN4 phase. Meanwhile the P21/c-RuN3 shows metallic feature. Highly directional covalent N-N and Ru-N bonds are formed and dominating in N-enriched Ru nitrides, making them promising hard materials.

  6. Theoretical prediction of Debye temperature & elastic constants of geophysical mineral

    NASA Astrophysics Data System (ADS)

    Singh, Chandra K.; Pandey, Anjani K.; Pandey, Brijesh K.

    2016-05-01

    Technological applications of the materials can be explored upto the desired limit of accuracy with the better knowledge of its mechanical and thermal properties such as ductility brittleness and Debye temperature. For the resistance to fracture (K) and plastic deformation (G) the ratio K/G is treated as an indication of ductile or brittle character of solids. In the present work we have tested the condition of ductility and brittleness with the calculated values of K/G for the geophysical minerals MgO and CaO, which are in good agreement with the corresponding experimental values. We have also computed the Debye temperature (θD) for the selected samples using average sound velocity obtained by using the values of resistance to fracture (K) and plastic deformation (G). It is observed that both the minerals are Brittle in nature and the calculated values of Debye temperature is in good agreement with the corresponding experimental values. Thus it is concluded that the nature and Debye temperature of geophysical minerals can be predicted upto high temperature simply with the knowledge of its elastic stiffness constant only.

  7. Study of microbial adhesion on some wood species: theoretical prediction.

    PubMed

    Soumya, El abed; Mohamed, Mostakim; Fatimazahra, Berguadi; Hassan, Latrache; Abdellah, Houari; Fatima, Hamadi; Saad, Ibnsouda koraichi

    2011-01-01

    The initial interaction between microorganisms and substrata is mediated by physicochemical forces, which in turn originate from the physicochemical surface properties of both interacting phases. In this context, we have determined the physicochemical proprieties of all microorganisms isolated from cedar wood decay in an old monument at the Medina of Fez-Morocco. The cedar wood was also assayed in terms of hydrophobicity and electron dono-r-electron acceptor (acid-base) properties. Investigations of these two aspects were performed by contact angles measurements via sessile drop technique. Except Bacillus subtilis strain (deltaGiwi < 0), all strains studied showed positive values of the degree ofhydrophobicity (deltaGiwi > 0) and can therefore be considered as hydrophilic while cedar wood revealed a hydrophobic character (deltaGiwi = -58.81 mi m(-2)). All microbial strains were predominantly electron donor. The results show also that all strains were weak electron acceptors. Cedar wood exhibits a weak electron donor/acceptor character. Based on the thermodynamic approach, the Lifshitz-van der Waals interaction free energy, the acid-basic interactions free energy, the total interaction free energy between the microbial cells and six different wood species (cedar, oak, beech, ash, pine and teak) in aqueous media was calculated and used to predict which microbial strains have a higher ability to adhere to wooden surfaces. Except of weak wood, for all the situations studied, generalizations concerning the adhesion of the microbiata on wood species cannot be made and the microbial adhesion on wooden substrata was dependent on wood species and microorganismstested.

  8. Accurate prediction model of bead geometry in crimping butt of the laser brazing using generalized regression neural network

    NASA Astrophysics Data System (ADS)

    Rong, Y. M.; Chang, Y.; Huang, Y.; Zhang, G. J.; Shao, X. Y.

    2015-12-01

    There are few researches that concentrate on the prediction of the bead geometry for laser brazing with crimping butt. This paper addressed the accurate prediction of the bead profile by developing a generalized regression neural network (GRNN) algorithm. Firstly GRNN model was developed and trained to decrease the prediction error that may be influenced by the sample size. Then the prediction accuracy was demonstrated by comparing with other articles and back propagation artificial neural network (BPNN) algorithm. Eventually the reliability and stability of GRNN model were discussed from the points of average relative error (ARE), mean square error (MSE) and root mean square error (RMSE), while the maximum ARE and MSE were 6.94% and 0.0303 that were clearly less than those (14.28% and 0.0832) predicted by BPNN. Obviously, it was proved that the prediction accuracy was improved at least 2 times, and the stability was also increased much more.

  9. Theoretical Prediction of the Structures and Energies of Olympicene and its Isomers

    NASA Astrophysics Data System (ADS)

    Valentine, Andrew J. S.; Mazziotti, David A.

    2013-10-01

    Pentacene, a linear five-ringed polyaromatic hydrocarbon, has recently been used as an organic semiconductor in field-effect transistors. The recently synthesized olympicene molecule, so named because of its resemblance to the olympic rings, is a more compact five-ringed structure. This paper offers the first theoretical study of the kinetic stability of olympicene and its isomers. We use the parametric two-electron reduced density matrix (2-RDM) method, which takes the 2-RDM as the basic variable in lieu of the traditional wave function in calculations [ Mazziotti, D. A. Phys. Rev. Lett. 2008, 101, 253002 ]. Our calculations demonstrate that olympicene-s isomers may be separated into aromatic and diradical isomers, the latter of which require accurate treatment of strong electron correlation to detect multireference character. Albeit formally a single-reference method, the parametric 2-RDM captures the multireference correlation of the diradical isomers; relative to olympicene, the 2-RDM predicts five diradical isomers that are 16-22 kcal/mol lower in energy than those from coupled cluster with single and double excitations-a significant change that causes these isomers to be stable to dissociation by 2-20 kcal/mol. We characterize the transition states between olympicene-s isomers, observe differences in aromaticity among the different isomers, and compare the electronic properties of olympicene to those of pentacene. The olympicene molecule has the potential to complement pentacene as an organic semiconductor.

  10. Theoretical Prediction of Sauter Mean Diameter for Pressure-Swirl Atomizers through Integral Conservation Methods

    NASA Astrophysics Data System (ADS)

    Moradi, Ali

    A new theoretical model was developed utilizing energy conservation methods in order to determine the fully-atomized cross-sectional Sauter mean diameters of pressure-swirl atomizers. A detailed boundary-layer assessment led to the development of a new viscous dissipation model for droplets in the spray. Integral momentum methods were also used to determine the complete velocity history of the droplets and entrained gas in the spray. The model was extensively validated through comparison with experiment and it was found that the model could predict the correct droplet size with high accuracy for a wide range of operating conditions. Based on detailed analysis, it was found that the energy model has a tendency to overestimate the droplet diameters for very low injection velocities, Weber numbers, and cone angles. A full parametric study was also performed in order to unveil some underlying behavior of pressure-swirl atomizers. It was found that at high injection velocities, the kinetic energy in the spray is significantly larger than the surface tension energy, therefore, efforts into improving atomization quality by changing the liquid's surface tension may not be the most productive. From the parametric studies it was also shown how the Sauter mean diameter and entrained velocities vary with increasing ambient gas density. Overall, the present energy model has the potential to provide quick and reasonably accurate solutions for a wide range of operating conditions enabling the user to determine how different injection parameters affect the spray quality.

  11. IMPROVED THEORETICAL PREDICTIONS OF MICROLENSING RATES FOR THE DETECTION OF PRIMORDIAL BLACK HOLE DARK MATTER

    SciTech Connect

    Cieplak, Agnieszka M.; Griest, Kim

    2013-04-20

    Primordial black holes (PBHs) remain a dark matter (DM) candidate of the Standard Model of Particle Physics. Previously, we proposed a new method of constraining the remaining PBH DM mass range using microlensing of stars monitored by NASA's Kepler mission. We improve this analysis using a more accurate treatment of the population of the Kepler source stars, their variability, and limb darkening. We extend the theoretically detectable PBH DM mass range down to 2 Multiplication-Sign 10{sup -10} M{sub Sun }, two orders of magnitude below current limits and one-third order of magnitude below our previous estimate. We address how to extract the DM properties, such as mass and spatial distribution, if PBH microlensing events were detected. We correct an error in a well-known finite-source limb-darkening microlensing formula and also examine the effects of varying the light curve cadence on PBH DM detectability. We also introduce an approximation for estimating the predicted rate of detection per star as a function of the star's properties, thus allowing for selection of source stars in future missions, and extend our analysis to planned surveys, such as the Wide-Field Infrared Survey Telescope.

  12. Towards more accurate wind and solar power prediction by improving NWP model physics

    NASA Astrophysics Data System (ADS)

    Steiner, Andrea; Köhler, Carmen; von Schumann, Jonas; Ritter, Bodo

    2014-05-01

    The growing importance and successive expansion of renewable energies raise new challenges for decision makers, economists, transmission system operators, scientists and many more. In this interdisciplinary field, the role of Numerical Weather Prediction (NWP) is to reduce the errors and provide an a priori estimate of remaining uncertainties associated with the large share of weather-dependent power sources. For this purpose it is essential to optimize NWP model forecasts with respect to those prognostic variables which are relevant for wind and solar power plants. An improved weather forecast serves as the basis for a sophisticated power forecasts. Consequently, a well-timed energy trading on the stock market, and electrical grid stability can be maintained. The German Weather Service (DWD) currently is involved with two projects concerning research in the field of renewable energy, namely ORKA*) and EWeLiNE**). Whereas the latter is in collaboration with the Fraunhofer Institute (IWES), the project ORKA is led by energy & meteo systems (emsys). Both cooperate with German transmission system operators. The goal of the projects is to improve wind and photovoltaic (PV) power forecasts by combining optimized NWP and enhanced power forecast models. In this context, the German Weather Service aims to improve its model system, including the ensemble forecasting system, by working on data assimilation, model physics and statistical post processing. This presentation is focused on the identification of critical weather situations and the associated errors in the German regional NWP model COSMO-DE. First steps leading to improved physical parameterization schemes within the NWP-model are presented. Wind mast measurements reaching up to 200 m height above ground are used for the estimation of the (NWP) wind forecast error at heights relevant for wind energy plants. One particular problem is the daily cycle in wind speed. The transition from stable stratification during

  13. A simple accurate method to predict time of ponding under variable intensity rainfall

    NASA Astrophysics Data System (ADS)

    Assouline, S.; Selker, J. S.; Parlange, J.-Y.

    2007-03-01

    The prediction of the time to ponding following commencement of rainfall is fundamental to hydrologic prediction of flood, erosion, and infiltration. Most of the studies to date have focused on prediction of ponding resulting from simple rainfall patterns. This approach was suitable to rainfall reported as average values over intervals of up to a day but does not take advantage of knowledge of the complex patterns of actual rainfall now commonly recorded electronically. A straightforward approach to include the instantaneous rainfall record in the prediction of ponding time and excess rainfall using only the infiltration capacity curve is presented. This method is tested against a numerical solution of the Richards equation on the basis of an actual rainfall record. The predicted time to ponding showed mean error ≤7% for a broad range of soils, with and without surface sealing. In contrast, the standard predictions had average errors of 87%, and worst-case errors exceeding a factor of 10. In addition to errors intrinsic in the modeling framework itself, errors that arise from averaging actual rainfall records over reporting intervals were evaluated. Averaging actual rainfall records observed in Israel over periods of as little as 5 min significantly reduced predicted runoff (75% for the sealed sandy loam and 46% for the silty clay loam), while hourly averaging gave complete lack of prediction of ponding in some of the cases.

  14. Combining Evolutionary Information and an Iterative Sampling Strategy for Accurate Protein Structure Prediction.

    PubMed

    Braun, Tatjana; Koehler Leman, Julia; Lange, Oliver F

    2015-12-01

    Recent work has shown that the accuracy of ab initio structure prediction can be significantly improved by integrating evolutionary information in form of intra-protein residue-residue contacts. Following this seminal result, much effort is put into the improvement of contact predictions. However, there is also a substantial need to develop structure prediction protocols tailored to the type of restraints gained by contact predictions. Here, we present a structure prediction protocol that combines evolutionary information with the resolution-adapted structural recombination approach of Rosetta, called RASREC. Compared to the classic Rosetta ab initio protocol, RASREC achieves improved sampling, better convergence and higher robustness against incorrect distance restraints, making it the ideal sampling strategy for the stated problem. To demonstrate the accuracy of our protocol, we tested the approach on a diverse set of 28 globular proteins. Our method is able to converge for 26 out of the 28 targets and improves the average TM-score of the entire benchmark set from 0.55 to 0.72 when compared to the top ranked models obtained by the EVFold web server using identical contact predictions. Using a smaller benchmark, we furthermore show that the prediction accuracy of our method is only slightly reduced when the contact prediction accuracy is comparatively low. This observation is of special interest for protein sequences that only have a limited number of homologs.

  15. A machine learning approach to the accurate prediction of multi-leaf collimator positional errors

    NASA Astrophysics Data System (ADS)

    Carlson, Joel N. K.; Park, Jong Min; Park, So-Yeon; In Park, Jong; Choi, Yunseok; Ye, Sung-Joon

    2016-03-01

    Discrepancies between planned and delivered movements of multi-leaf collimators (MLCs) are an important source of errors in dose distributions during radiotherapy. In this work we used machine learning techniques to train models to predict these discrepancies, assessed the accuracy of the model predictions, and examined the impact these errors have on quality assurance (QA) procedures and dosimetry. Predictive leaf motion parameters for the models were calculated from the plan files, such as leaf position and velocity, whether the leaf was moving towards or away from the isocenter of the MLC, and many others. Differences in positions between synchronized DICOM-RT planning files and DynaLog files reported during QA delivery were used as a target response for training of the models. The final model is capable of predicting MLC positions during delivery to a high degree of accuracy. For moving MLC leaves, predicted positions were shown to be significantly closer to delivered positions than were planned positions. By incorporating predicted positions into dose calculations in the TPS, increases were shown in gamma passing rates against measured dose distributions recorded during QA delivery. For instance, head and neck plans with 1%/2 mm gamma criteria had an average increase in passing rate of 4.17% (SD  =  1.54%). This indicates that the inclusion of predictions during dose calculation leads to a more realistic representation of plan delivery. To assess impact on the patient, dose volumetric histograms (DVH) using delivered positions were calculated for comparison with planned and predicted DVHs. In all cases, predicted dose volumetric parameters were in closer agreement to the delivered parameters than were the planned parameters, particularly for organs at risk on the periphery of the treatment area. By incorporating the predicted positions into the TPS, the treatment planner is given a more realistic view of the dose distribution as it will truly be

  16. Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli

    PubMed Central

    Kim, Minseung; Rai, Navneet; Zorraquino, Violeta; Tagkopoulos, Ilias

    2016-01-01

    A significant obstacle in training predictive cell models is the lack of integrated data sources. We develop semi-supervised normalization pipelines and perform experimental characterization (growth, transcriptional, proteome) to create Ecomics, a consistent, quality-controlled multi-omics compendium for Escherichia coli with cohesive meta-data information. We then use this resource to train a multi-scale model that integrates four omics layers to predict genome-wide concentrations and growth dynamics. The genetic and environmental ontology reconstructed from the omics data is substantially different and complementary to the genetic and chemical ontologies. The integration of different layers confers an incremental increase in the prediction performance, as does the information about the known gene regulatory and protein-protein interactions. The predictive performance of the model ranges from 0.54 to 0.87 for the various omics layers, which far exceeds various baselines. This work provides an integrative framework of omics-driven predictive modelling that is broadly applicable to guide biological discovery. PMID:27713404

  17. Empirical approaches to more accurately predict benthic-pelagic coupling in biogeochemical ocean models

    NASA Astrophysics Data System (ADS)

    Dale, Andy; Stolpovsky, Konstantin; Wallmann, Klaus

    2016-04-01

    The recycling and burial of biogenic material in the sea floor plays a key role in the regulation of ocean chemistry. Proper consideration of these processes in ocean biogeochemical models is becoming increasingly recognized as an important step in model validation and prediction. However, the rate of organic matter remineralization in sediments and the benthic flux of redox-sensitive elements are difficult to predict a priori. In this communication, examples of empirical benthic flux models that can be coupled to earth system models to predict sediment-water exchange in the open ocean are presented. Large uncertainties hindering further progress in this field include knowledge of the reactivity of organic carbon reaching the sediment, the importance of episodic variability in bottom water chemistry and particle rain rates (for both the deep-sea and margins) and the role of benthic fauna. How do we meet the challenge?

  18. An endometrial gene expression signature accurately predicts recurrent implantation failure after IVF

    PubMed Central

    Koot, Yvonne E. M.; van Hooff, Sander R.; Boomsma, Carolien M.; van Leenen, Dik; Groot Koerkamp, Marian J. A.; Goddijn, Mariëtte; Eijkemans, Marinus J. C.; Fauser, Bart C. J. M.; Holstege, Frank C. P.; Macklon, Nick S.

    2016-01-01

    The primary limiting factor for effective IVF treatment is successful embryo implantation. Recurrent implantation failure (RIF) is a condition whereby couples fail to achieve pregnancy despite consecutive embryo transfers. Here we describe the collection of gene expression profiles from mid-luteal phase endometrial biopsies (n = 115) from women experiencing RIF and healthy controls. Using a signature discovery set (n = 81) we identify a signature containing 303 genes predictive of RIF. Independent validation in 34 samples shows that the gene signature predicts RIF with 100% positive predictive value (PPV). The strength of the RIF associated expression signature also stratifies RIF patients into distinct groups with different subsequent implantation success rates. Exploration of the expression changes suggests that RIF is primarily associated with reduced cellular proliferation. The gene signature will be of value in counselling and guiding further treatment of women who fail to conceive upon IVF and suggests new avenues for developing intervention. PMID:26797113

  19. Accurate ab initio prediction of NMR chemical shifts of nucleic acids and nucleic acids/protein complexes

    PubMed Central

    Victora, Andrea; Möller, Heiko M.; Exner, Thomas E.

    2014-01-01

    NMR chemical shift predictions based on empirical methods are nowadays indispensable tools during resonance assignment and 3D structure calculation of proteins. However, owing to the very limited statistical data basis, such methods are still in their infancy in the field of nucleic acids, especially when non-canonical structures and nucleic acid complexes are considered. Here, we present an ab initio approach for predicting proton chemical shifts of arbitrary nucleic acid structures based on state-of-the-art fragment-based quantum chemical calculations. We tested our prediction method on a diverse set of nucleic acid structures including double-stranded DNA, hairpins, DNA/protein complexes and chemically-modified DNA. Overall, our quantum chemical calculations yield highly/very accurate predictions with mean absolute deviations of 0.3–0.6 ppm and correlation coefficients (r2) usually above 0.9. This will allow for identifying misassignments and validating 3D structures. Furthermore, our calculations reveal that chemical shifts of protons involved in hydrogen bonding are predicted significantly less accurately. This is in part caused by insufficient inclusion of solvation effects. However, it also points toward shortcomings of current force fields used for structure determination of nucleic acids. Our quantum chemical calculations could therefore provide input for force field optimization. PMID:25404135

  20. Change in body mass accurately and reliably predicts change in body water after endurance exercise.

    PubMed

    Baker, Lindsay B; Lang, James A; Kenney, W Larry

    2009-04-01

    This study tested the hypothesis that the change in body mass (DeltaBM) accurately reflects the change in total body water (DeltaTBW) after prolonged exercise. Subjects (4 men, 4 women; 22-36 year; 66 +/- 10 kg) completed 2 h of interval running (70% VO(2max)) in the heat (30 degrees C), followed by a run to exhaustion (85% VO(2max)), and then sat for a 1 h recovery period. During exercise and recovery, subjects drank fluid or no fluid to maintain their BM, increase BM by 2%, or decrease BM by 2 or 4% in separate trials. Pre- and post-experiment TBW were determined using the deuterium oxide (D(2)O) dilution technique and corrected for D(2)O lost in urine, sweat, breath vapor, and nonaqueous hydrogen exchange. The average difference between DeltaBM and DeltaTBW was 0.07 +/- 1.07 kg (paired t test, P = 0.29). The slope and intercept of the relation between DeltaBM and DeltaTBW were not significantly different from 1 and 0, respectively. The intraclass correlation coefficient between DeltaBM and DeltaTBW was 0.76, which is indicative of excellent reliability between methods. Measuring pre- to post-exercise DeltaBM is an accurate and reliable method to assess the DeltaTBW.

  1. Towards Accurate Residue-Residue Hydrophobic Contact Prediction for Alpha Helical Proteins Via Integer Linear Optimization

    PubMed Central

    Rajgaria, R.; McAllister, S. R.; Floudas, C. A.

    2008-01-01

    A new optimization-based method is presented to predict the hydrophobic residue contacts in α-helical proteins. The proposed approach uses a high resolution distance dependent force field to calculate the interaction energy between different residues of a protein. The formulation predicts the hydrophobic contacts by minimizing the sum of these contact energies. These residue contacts are highly useful in narrowing down the conformational space searched by protein structure prediction algorithms. The proposed algorithm also offers the algorithmic advantage of producing a rank ordered list of the best contact sets. This model was tested on four independent α-helical protein test sets and was found to perform very well. The average accuracy of the predictions (separated by at least six residues) obtained using the presented method was approximately 66% for single domain proteins. The average true positive and false positive distances were also calculated for each protein test set and they are 8.87 Å and 14.67 Å respectively. PMID:18767158

  2. Accurate prediction of kidney allograft outcome based on creatinine course in the first 6 months posttransplant.

    PubMed

    Fritsche, L; Hoerstrup, J; Budde, K; Reinke, P; Neumayer, H-H; Frei, U; Schlaefer, A

    2005-03-01

    Most attempts to predict early kidney allograft loss are based on the patient and donor characteristics at baseline. We investigated how the early posttransplant creatinine course compares to baseline information in the prediction of kidney graft failure within the first 4 years after transplantation. Two approaches to create a prediction rule for early graft failure were evaluated. First, the whole data set was analysed using a decision-tree building software. The software, rpart, builds classification or regression models; the resulting models can be represented as binary trees. In the second approach, a Hill-Climbing algorithm was applied to define cut-off values for the median creatinine level and creatinine slope in the period between day 60 and 180 after transplantation. Of the 497 patients available for analysis, 52 (10.5%) experienced an early graft loss (graft loss within the first 4 years after transplantation). From the rpart algorithm, a single decision criterion emerged: Median creatinine value on days 60 to 180 higher than 3.1 mg/dL predicts early graft failure (accuracy 95.2% but sensitivity = 42.3%). In contrast, the Hill-Climbing algorithm delivered a cut-off of 1.8 mg/dL for the median creatinine level and a cut-off of 0.3 mg/dL per month for the creatinine slope (sensitivity = 69.5% and specificity 79.0%). Prediction rules based on median and slope of creatinine levels in the first half year after transplantation allow early identification of patients who are at risk of loosing their graft early after transplantation. These patients may benefit from therapeutic measures tailored for this high-risk setting. PMID:15848516

  3. Accurate Prediction of Transposon-Derived piRNAs by Integrating Various Sequential and Physicochemical Features

    PubMed Central

    Luo, Longqiang; Li, Dingfang; Zhang, Wen; Tu, Shikui; Zhu, Xiaopeng; Tian, Gang

    2016-01-01

    Background Piwi-interacting RNA (piRNA) is the largest class of small non-coding RNA molecules. The transposon-derived piRNA prediction can enrich the research contents of small ncRNAs as well as help to further understand generation mechanism of gamete. Methods In this paper, we attempt to differentiate transposon-derived piRNAs from non-piRNAs based on their sequential and physicochemical features by using machine learning methods. We explore six sequence-derived features, i.e. spectrum profile, mismatch profile, subsequence profile, position-specific scoring matrix, pseudo dinucleotide composition and local structure-sequence triplet elements, and systematically evaluate their performances for transposon-derived piRNA prediction. Finally, we consider two approaches: direct combination and ensemble learning to integrate useful features and achieve high-accuracy prediction models. Results We construct three datasets, covering three species: Human, Mouse and Drosophila, and evaluate the performances of prediction models by 10-fold cross validation. In the computational experiments, direct combination models achieve AUC of 0.917, 0.922 and 0.992 on Human, Mouse and Drosophila, respectively; ensemble learning models achieve AUC of 0.922, 0.926 and 0.994 on the three datasets. Conclusions Compared with other state-of-the-art methods, our methods can lead to better performances. In conclusion, the proposed methods are promising for the transposon-derived piRNA prediction. The source codes and datasets are available in S1 File. PMID:27074043

  4. Accurate, conformation-dependent predictions of solvent effects on protein ionization constants

    PubMed Central

    Barth, P.; Alber, T.; Harbury, P. B.

    2007-01-01

    Predicting how aqueous solvent modulates the conformational transitions and influences the pKa values that regulate the biological functions of biomolecules remains an unsolved challenge. To address this problem, we developed FDPB_MF, a rotamer repacking method that exhaustively samples side chain conformational space and rigorously calculates multibody protein–solvent interactions. FDPB_MF predicts the effects on pKa values of various solvent exposures, large ionic strength variations, strong energetic couplings, structural reorganizations and sequence mutations. The method achieves high accuracy, with root mean square deviations within 0.3 pH unit of the experimental values measured for turkey ovomucoid third domain, hen lysozyme, Bacillus circulans xylanase, and human and Escherichia coli thioredoxins. FDPB_MF provides a faithful, quantitative assessment of electrostatic interactions in biological macromolecules. PMID:17360348

  5. FastRNABindR: Fast and Accurate Prediction of Protein-RNA Interface Residues

    PubMed Central

    EL-Manzalawy, Yasser; Abbas, Mostafa; Malluhi, Qutaibah; Honavar, Vasant

    2016-01-01

    A wide range of biological processes, including regulation of gene expression, protein synthesis, and replication and assembly of many viruses are mediated by RNA-protein interactions. However, experimental determination of the structures of protein-RNA complexes is expensive and technically challenging. Hence, a number of computational tools have been developed for predicting protein-RNA interfaces. Some of the state-of-the-art protein-RNA interface predictors rely on position-specific scoring matrix (PSSM)-based encoding of the protein sequences. The computational efforts needed for generating PSSMs severely limits the practical utility of protein-RNA interface prediction servers. In this work, we experiment with two approaches, random sampling and sequence similarity reduction, for extracting a representative reference database of protein sequences from more than 50 million protein sequences in UniRef100. Our results suggest that random sampled databases produce better PSSM profiles (in terms of the number of hits used to generate the profile and the distance of the generated profile to the corresponding profile generated using the entire UniRef100 data as well as the accuracy of the machine learning classifier trained using these profiles). Based on our results, we developed FastRNABindR, an improved version of RNABindR for predicting protein-RNA interface residues using PSSM profiles generated using 1% of the UniRef100 sequences sampled uniformly at random. To the best of our knowledge, FastRNABindR is the only protein-RNA interface residue prediction online server that requires generation of PSSM profiles for query sequences and accepts hundreds of protein sequences per submission. Our approach for determining the optimal BLAST database for a protein-RNA interface residue classification task has the potential of substantially speeding up, and hence increasing the practical utility of, other amino acid sequence based predictors of protein-protein and protein

  6. FastRNABindR: Fast and Accurate Prediction of Protein-RNA Interface Residues.

    PubMed

    El-Manzalawy, Yasser; Abbas, Mostafa; Malluhi, Qutaibah; Honavar, Vasant

    2016-01-01

    A wide range of biological processes, including regulation of gene expression, protein synthesis, and replication and assembly of many viruses are mediated by RNA-protein interactions. However, experimental determination of the structures of protein-RNA complexes is expensive and technically challenging. Hence, a number of computational tools have been developed for predicting protein-RNA interfaces. Some of the state-of-the-art protein-RNA interface predictors rely on position-specific scoring matrix (PSSM)-based encoding of the protein sequences. The computational efforts needed for generating PSSMs severely limits the practical utility of protein-RNA interface prediction servers. In this work, we experiment with two approaches, random sampling and sequence similarity reduction, for extracting a representative reference database of protein sequences from more than 50 million protein sequences in UniRef100. Our results suggest that random sampled databases produce better PSSM profiles (in terms of the number of hits used to generate the profile and the distance of the generated profile to the corresponding profile generated using the entire UniRef100 data as well as the accuracy of the machine learning classifier trained using these profiles). Based on our results, we developed FastRNABindR, an improved version of RNABindR for predicting protein-RNA interface residues using PSSM profiles generated using 1% of the UniRef100 sequences sampled uniformly at random. To the best of our knowledge, FastRNABindR is the only protein-RNA interface residue prediction online server that requires generation of PSSM profiles for query sequences and accepts hundreds of protein sequences per submission. Our approach for determining the optimal BLAST database for a protein-RNA interface residue classification task has the potential of substantially speeding up, and hence increasing the practical utility of, other amino acid sequence based predictors of protein-protein and protein

  7. Robust and Accurate Modeling Approaches for Migraine Per-Patient Prediction from Ambulatory Data

    PubMed Central

    Pagán, Josué; Irene De Orbe, M.; Gago, Ana; Sobrado, Mónica; Risco-Martín, José L.; Vivancos Mora, J.; Moya, José M.; Ayala, José L.

    2015-01-01

    Migraine is one of the most wide-spread neurological disorders, and its medical treatment represents a high percentage of the costs of health systems. In some patients, characteristic symptoms that precede the headache appear. However, they are nonspecific, and their prediction horizon is unknown and pretty variable; hence, these symptoms are almost useless for prediction, and they are not useful to advance the intake of drugs to be effective and neutralize the pain. To solve this problem, this paper sets up a realistic monitoring scenario where hemodynamic variables from real patients are monitored in ambulatory conditions with a wireless body sensor network (WBSN). The acquired data are used to evaluate the predictive capabilities and robustness against noise and failures in sensors of several modeling approaches. The obtained results encourage the development of per-patient models based on state-space models (N4SID) that are capable of providing average forecast windows of 47 min and a low rate of false positives. PMID:26134103

  8. Revisiting the blind tests in crystal structure prediction: accurate energy ranking of molecular crystals.

    PubMed

    Asmadi, Aldi; Neumann, Marcus A; Kendrick, John; Girard, Pascale; Perrin, Marc-Antoine; Leusen, Frank J J

    2009-12-24

    In the 2007 blind test of crystal structure prediction hosted by the Cambridge Crystallographic Data Centre (CCDC), a hybrid DFT/MM method correctly ranked each of the four experimental structures as having the lowest lattice energy of all the crystal structures predicted for each molecule. The work presented here further validates this hybrid method by optimizing the crystal structures (experimental and submitted) of the first three CCDC blind tests held in 1999, 2001, and 2004. Except for the crystal structures of compound IX, all structures were reminimized and ranked according to their lattice energies. The hybrid method computes the lattice energy of a crystal structure as the sum of the DFT total energy and a van der Waals (dispersion) energy correction. Considering all four blind tests, the crystal structure with the lowest lattice energy corresponds to the experimentally observed structure for 12 out of 14 molecules. Moreover, good geometrical agreement is observed between the structures determined by the hybrid method and those measured experimentally. In comparison with the correct submissions made by the blind test participants, all hybrid optimized crystal structures (apart from compound II) have the smallest calculated root mean squared deviations from the experimentally observed structures. It is predicted that a new polymorph of compound V exists under pressure.

  9. Fast and accurate numerical method for predicting gas chromatography retention time.

    PubMed

    Claumann, Carlos Alberto; Wüst Zibetti, André; Bolzan, Ariovaldo; Machado, Ricardo A F; Pinto, Leonel Teixeira

    2015-08-01

    Predictive modeling for gas chromatography compound retention depends on the retention factor (ki) and on the flow of the mobile phase. Thus, different approaches for determining an analyte ki in column chromatography have been developed. The main one is based on the thermodynamic properties of the component and on the characteristics of the stationary phase. These models can be used to estimate the parameters and to optimize the programming of temperatures, in gas chromatography, for the separation of compounds. Different authors have proposed the use of numerical methods for solving these models, but these methods demand greater computational time. Hence, a new method for solving the predictive modeling of analyte retention time is presented. This algorithm is an alternative to traditional methods because it transforms its attainments into root determination problems within defined intervals. The proposed approach allows for tr calculation, with accuracy determined by the user of the methods, and significant reductions in computational time; it can also be used to evaluate the performance of other prediction methods.

  10. Accurate structure prediction of peptide–MHC complexes for identifying highly immunogenic antigens

    SciTech Connect

    Park, Min-Sun; Park, Sung Yong; Miller, Keith R.; Collins, Edward J.; Lee, Ha Youn

    2013-11-01

    Designing an optimal HIV-1 vaccine faces the challenge of identifying antigens that induce a broad immune capacity. One factor to control the breadth of T cell responses is the surface morphology of a peptide–MHC complex. Here, we present an in silico protocol for predicting peptide–MHC structure. A robust signature of a conformational transition was identified during all-atom molecular dynamics, which results in a model with high accuracy. A large test set was used in constructing our protocol and we went another step further using a blind test with a wild-type peptide and two highly immunogenic mutants, which predicted substantial conformational changes in both mutants. The center residues at position five of the analogs were configured to be accessible to solvent, forming a prominent surface, while the residue of the wild-type peptide was to point laterally toward the side of the binding cleft. We then experimentally determined the structures of the blind test set, using high resolution of X-ray crystallography, which verified predicted conformational changes. Our observation strongly supports a positive association of the surface morphology of a peptide–MHC complex to its immunogenicity. Our study offers the prospect of enhancing immunogenicity of vaccines by identifying MHC binding immunogens.

  11. Revisiting the blind tests in crystal structure prediction: accurate energy ranking of molecular crystals.

    PubMed

    Asmadi, Aldi; Neumann, Marcus A; Kendrick, John; Girard, Pascale; Perrin, Marc-Antoine; Leusen, Frank J J

    2009-12-24

    In the 2007 blind test of crystal structure prediction hosted by the Cambridge Crystallographic Data Centre (CCDC), a hybrid DFT/MM method correctly ranked each of the four experimental structures as having the lowest lattice energy of all the crystal structures predicted for each molecule. The work presented here further validates this hybrid method by optimizing the crystal structures (experimental and submitted) of the first three CCDC blind tests held in 1999, 2001, and 2004. Except for the crystal structures of compound IX, all structures were reminimized and ranked according to their lattice energies. The hybrid method computes the lattice energy of a crystal structure as the sum of the DFT total energy and a van der Waals (dispersion) energy correction. Considering all four blind tests, the crystal structure with the lowest lattice energy corresponds to the experimentally observed structure for 12 out of 14 molecules. Moreover, good geometrical agreement is observed between the structures determined by the hybrid method and those measured experimentally. In comparison with the correct submissions made by the blind test participants, all hybrid optimized crystal structures (apart from compound II) have the smallest calculated root mean squared deviations from the experimentally observed structures. It is predicted that a new polymorph of compound V exists under pressure. PMID:19950907

  12. HAAD: A quick algorithm for accurate prediction of hydrogen atoms in protein structures.

    PubMed

    Li, Yunqi; Roy, Ambrish; Zhang, Yang

    2009-08-20

    Hydrogen constitutes nearly half of all atoms in proteins and their positions are essential for analyzing hydrogen-bonding interactions and refining atomic-level structures. However, most protein structures determined by experiments or computer prediction lack hydrogen coordinates. We present a new algorithm, HAAD, to predict the positions of hydrogen atoms based on the positions of heavy atoms. The algorithm is built on the basic rules of orbital hybridization followed by the optimization of steric repulsion and electrostatic interactions. We tested the algorithm using three independent data sets: ultra-high-resolution X-ray structures, structures determined by neutron diffraction, and NOE proton-proton distances. Compared with the widely used programs CHARMM and REDUCE, HAAD has a significantly higher accuracy, with the average RMSD of the predicted hydrogen atoms to the X-ray and neutron diffraction structures decreased by 26% and 11%, respectively. Furthermore, hydrogen atoms placed by HAAD have more matches with the NOE restraints and fewer clashes with heavy atoms. The average CPU cost by HAAD is 18 and 8 times lower than that of CHARMM and REDUCE, respectively. The significant advantage of HAAD in both the accuracy and the speed of the hydrogen additions should make HAAD a useful tool for the detailed study of protein structure and function. Both an executable and the source code of HAAD are freely available at http://zhang.bioinformatics.ku.edu/HAAD.

  13. Accurate single-sequence prediction of solvent accessible surface area using local and global features.

    PubMed

    Faraggi, Eshel; Zhou, Yaoqi; Kloczkowski, Andrzej

    2014-11-01

    We present a new approach for predicting the Accessible Surface Area (ASA) using a General Neural Network (GENN). The novelty of the new approach lies in not using residue mutation profiles generated by multiple sequence alignments as descriptive inputs. Instead we use solely sequential window information and global features such as single-residue and two-residue compositions of the chain. The resulting predictor is both highly more efficient than sequence alignment-based predictors and of comparable accuracy to them. Introduction of the global inputs significantly helps achieve this comparable accuracy. The predictor, termed ASAquick, is tested on predicting the ASA of globular proteins and found to perform similarly well for so-called easy and hard cases indicating generalizability and possible usability for de-novo protein structure prediction. The source code and a Linux executables for GENN and ASAquick are available from Research and Information Systems at http://mamiris.com, from the SPARKS Lab at http://sparks-lab.org, and from the Battelle Center for Mathematical Medicine at http://mathmed.org. PMID:25204636

  14. Rational Design of Lanthanoid Single-Ion Magnets: Predictive Power of the Theoretical Models.

    PubMed

    Baldoví, José J; Duan, Yan; Morales, Roser; Gaita-Ariño, Alejandro; Ruiz, Eliseo; Coronado, Eugenio

    2016-09-12

    We report two new single-ion magnets (SIMs) of a family of oxydiacetate lanthanide complexes with D3 symmetry to test the predictive capabilities of complete active space ab initio methods (CASSCF and CASPT2) and the semiempirical radial effective charge (REC) model. Comparison of the theoretical predictions of the energy levels, wave functions and magnetic properties with detailed spectroscopic and magnetic characterisation is used to critically discuss the limitations of these theoretical approaches. The need for spectroscopic information for a reliable description of the properties of lanthanide SIMs is emphasised. PMID:27465352

  15. Rational Design of Lanthanoid Single-Ion Magnets: Predictive Power of the Theoretical Models.

    PubMed

    Baldoví, José J; Duan, Yan; Morales, Roser; Gaita-Ariño, Alejandro; Ruiz, Eliseo; Coronado, Eugenio

    2016-09-12

    We report two new single-ion magnets (SIMs) of a family of oxydiacetate lanthanide complexes with D3 symmetry to test the predictive capabilities of complete active space ab initio methods (CASSCF and CASPT2) and the semiempirical radial effective charge (REC) model. Comparison of the theoretical predictions of the energy levels, wave functions and magnetic properties with detailed spectroscopic and magnetic characterisation is used to critically discuss the limitations of these theoretical approaches. The need for spectroscopic information for a reliable description of the properties of lanthanide SIMs is emphasised.

  16. Accurate prediction of interfacial residues in two-domain proteins using evolutionary information: implications for three-dimensional modeling.

    PubMed

    Bhaskara, Ramachandra M; Padhi, Amrita; Srinivasan, Narayanaswamy

    2014-07-01

    With the preponderance of multidomain proteins in eukaryotic genomes, it is essential to recognize the constituent domains and their functions. Often function involves communications across the domain interfaces, and the knowledge of the interacting sites is essential to our understanding of the structure-function relationship. Using evolutionary information extracted from homologous domains in at least two diverse domain architectures (single and multidomain), we predict the interface residues corresponding to domains from the two-domain proteins. We also use information from the three-dimensional structures of individual domains of two-domain proteins to train naïve Bayes classifier model to predict the interfacial residues. Our predictions are highly accurate (∼85%) and specific (∼95%) to the domain-domain interfaces. This method is specific to multidomain proteins which contain domains in at least more than one protein architectural context. Using predicted residues to constrain domain-domain interaction, rigid-body docking was able to provide us with accurate full-length protein structures with correct orientation of domains. We believe that these results can be of considerable interest toward rational protein and interaction design, apart from providing us with valuable information on the nature of interactions.

  17. Comparative motif discovery combined with comparative transcriptomics yields accurate targetome and enhancer predictions.

    PubMed

    Naval-Sánchez, Marina; Potier, Delphine; Haagen, Lotte; Sánchez, Máximo; Munck, Sebastian; Van de Sande, Bram; Casares, Fernando; Christiaens, Valerie; Aerts, Stein

    2013-01-01

    The identification of transcription factor binding sites, enhancers, and transcriptional target genes often relies on the integration of gene expression profiling and computational cis-regulatory sequence analysis. Methods for the prediction of cis-regulatory elements can take advantage of comparative genomics to increase signal-to-noise levels. However, gene expression data are usually derived from only one species. Here we investigate tissue-specific cross-species gene expression profiling by high-throughput sequencing, combined with cross-species motif discovery. First, we compared different methods for expression level quantification and cross-species integration using Tag-seq data. Using the optimal pipeline, we derived a set of genes with conserved expression during retinal determination across Drosophila melanogaster, Drosophila yakuba, and Drosophila virilis. These genes are enriched for binding sites of eye-related transcription factors including the zinc-finger Glass, a master regulator of photoreceptor differentiation. Validation of predicted Glass targets using RNA-seq in homozygous glass mutants confirms that the majority of our predictions are expressed downstream from Glass. Finally, we tested nine candidate enhancers by in vivo reporter assays and found eight of them to drive GFP in the eye disc, of which seven colocalize with the Glass protein, namely, scrt, chp, dpr10, CG6329, retn, Lim3, and dmrt99B. In conclusion, we show for the first time the combined use of cross-species expression profiling with cross-species motif discovery as a method to define a core developmental program, and we augment the candidate Glass targetome from a single known target gene, lozenge, to at least 62 conserved transcriptional targets. PMID:23070853

  18. Accurate and Rigorous Prediction of the Changes in Protein Free Energies in a Large-Scale Mutation Scan.

    PubMed

    Gapsys, Vytautas; Michielssens, Servaas; Seeliger, Daniel; de Groot, Bert L

    2016-06-20

    The prediction of mutation-induced free-energy changes in protein thermostability or protein-protein binding is of particular interest in the fields of protein design, biotechnology, and bioengineering. Herein, we achieve remarkable accuracy in a scan of 762 mutations estimating changes in protein thermostability based on the first principles of statistical mechanics. The remaining error in the free-energy estimates appears to be due to three sources in approximately equal parts, namely sampling, force-field inaccuracies, and experimental uncertainty. We propose a consensus force-field approach, which, together with an increased sampling time, leads to a free-energy prediction accuracy that matches those reached in experiments. This versatile approach enables accurate free-energy estimates for diverse proteins, including the prediction of changes in the melting temperature of the membrane protein neurotensin receptor 1. PMID:27122231

  19. Accurate prediction of cellular co-translational folding indicates proteins can switch from post- to co-translational folding

    NASA Astrophysics Data System (ADS)

    Nissley, Daniel A.; Sharma, Ajeet K.; Ahmed, Nabeel; Friedrich, Ulrike A.; Kramer, Günter; Bukau, Bernd; O'Brien, Edward P.

    2016-02-01

    The rates at which domains fold and codons are translated are important factors in determining whether a nascent protein will co-translationally fold and function or misfold and malfunction. Here we develop a chemical kinetic model that calculates a protein domain's co-translational folding curve during synthesis using only the domain's bulk folding and unfolding rates and codon translation rates. We show that this model accurately predicts the course of co-translational folding measured in vivo for four different protein molecules. We then make predictions for a number of different proteins in yeast and find that synonymous codon substitutions, which change translation-elongation rates, can switch some protein domains from folding post-translationally to folding co-translationally--a result consistent with previous experimental studies. Our approach explains essential features of co-translational folding curves and predicts how varying the translation rate at different codon positions along a transcript's coding sequence affects this self-assembly process.

  20. An information-theoretic model for link prediction in complex networks

    PubMed Central

    Zhu, Boyao; Xia, Yongxiang

    2015-01-01

    Various structural features of networks have been applied to develop link prediction methods. However, because different features highlight different aspects of network structural properties, it is very difficult to benefit from all of the features that might be available. In this paper, we investigate the role of network topology in predicting missing links from the perspective of information theory. In this way, the contributions of different structural features to link prediction are measured in terms of their values of information. Then, an information-theoretic model is proposed that is applicable to multiple structural features. Furthermore, we design a novel link prediction index, called Neighbor Set Information (NSI), based on the information-theoretic model. According to our experimental results, the NSI index performs well in real-world networks, compared with other typical proximity indices. PMID:26335758

  1. PSI: A Comprehensive and Integrative Approach for Accurate Plant Subcellular Localization Prediction

    PubMed Central

    Chen, Ming

    2013-01-01

    Predicting the subcellular localization of proteins conquers the major drawbacks of high-throughput localization experiments that are costly and time-consuming. However, current subcellular localization predictors are limited in scope and accuracy. In particular, most predictors perform well on certain locations or with certain data sets while poorly on others. Here, we present PSI, a novel high accuracy web server for plant subcellular localization prediction. PSI derives the wisdom of multiple specialized predictors via a joint-approach of group decision making strategy and machine learning methods to give an integrated best result. The overall accuracy obtained (up to 93.4%) was higher than best individual (CELLO) by ∼10.7%. The precision of each predicable subcellular location (more than 80%) far exceeds that of the individual predictors. It can also deal with multi-localization proteins. PSI is expected to be a powerful tool in protein location engineering as well as in plant sciences, while the strategy employed could be applied to other integrative problems. A user-friendly web server, PSI, has been developed for free access at http://bis.zju.edu.cn/psi/. PMID:24194827

  2. CRYSpred: accurate sequence-based protein crystallization propensity prediction using sequence-derived structural characteristics.

    PubMed

    Mizianty, Marcin J; Kurgan, Lukasz A

    2012-01-01

    Relatively low success rates of X-ray crystallography, which is the most popular method for solving proteins structures, motivate development of novel methods that support selection of tractable protein targets. This aspect is particularly important in the context of the current structural genomics efforts that allow for a certain degree of flexibility in the target selection. We propose CRYSpred, a novel in-silico crystallization propensity predictor that uses a set of 15 novel features which utilize a broad range of inputs including charge, hydrophobicity, and amino acid composition derived from the protein chain, and the solvent accessibility and disorder predicted from the protein sequence. Our method outperforms seven modern crystallization propensity predictors on three, independent from training dataset, benchmark test datasets. The strong predictive performance offered by the CRYSpred is attributed to the careful design of the features, utilization of the comprehensive set of inputs, and the usage of the Support Vector Machine classifier. The inputs utilized by CRYSpred are well-aligned with the existing rules-of-thumb that are used in the structural genomics studies. PMID:21919861

  3. CRYSpred: accurate sequence-based protein crystallization propensity prediction using sequence-derived structural characteristics.

    PubMed

    Mizianty, Marcin J; Kurgan, Lukasz A

    2012-01-01

    Relatively low success rates of X-ray crystallography, which is the most popular method for solving proteins structures, motivate development of novel methods that support selection of tractable protein targets. This aspect is particularly important in the context of the current structural genomics efforts that allow for a certain degree of flexibility in the target selection. We propose CRYSpred, a novel in-silico crystallization propensity predictor that uses a set of 15 novel features which utilize a broad range of inputs including charge, hydrophobicity, and amino acid composition derived from the protein chain, and the solvent accessibility and disorder predicted from the protein sequence. Our method outperforms seven modern crystallization propensity predictors on three, independent from training dataset, benchmark test datasets. The strong predictive performance offered by the CRYSpred is attributed to the careful design of the features, utilization of the comprehensive set of inputs, and the usage of the Support Vector Machine classifier. The inputs utilized by CRYSpred are well-aligned with the existing rules-of-thumb that are used in the structural genomics studies.

  4. Size-extensivity-corrected multireference configuration interaction schemes to accurately predict bond dissociation energies of oxygenated hydrocarbons

    SciTech Connect

    Oyeyemi, Victor B.; Krisiloff, David B.; Keith, John A.; Libisch, Florian; Pavone, Michele; Carter, Emily A.

    2014-01-28

    Oxygenated hydrocarbons play important roles in combustion science as renewable fuels and additives, but many details about their combustion chemistry remain poorly understood. Although many methods exist for computing accurate electronic energies of molecules at equilibrium geometries, a consistent description of entire combustion reaction potential energy surfaces (PESs) requires multireference correlated wavefunction theories. Here we use bond dissociation energies (BDEs) as a foundational metric to benchmark methods based on multireference configuration interaction (MRCI) for several classes of oxygenated compounds (alcohols, aldehydes, carboxylic acids, and methyl esters). We compare results from multireference singles and doubles configuration interaction to those utilizing a posteriori and a priori size-extensivity corrections, benchmarked against experiment and coupled cluster theory. We demonstrate that size-extensivity corrections are necessary for chemically accurate BDE predictions even in relatively small molecules and furnish examples of unphysical BDE predictions resulting from using too-small orbital active spaces. We also outline the specific challenges in using MRCI methods for carbonyl-containing compounds. The resulting complete basis set extrapolated, size-extensivity-corrected MRCI scheme produces BDEs generally accurate to within 1 kcal/mol, laying the foundation for this scheme's use on larger molecules and for more complex regions of combustion PESs.

  5. Accurate predictions of dielectrophoretic force and torque on particles with strong mutual field, particle, and wall interactions

    NASA Astrophysics Data System (ADS)

    Liu, Qianlong; Reifsnider, Kenneth

    2012-11-01

    The basis of dielectrophoresis (DEP) is the prediction of the force and torque on particles. The classical approach to the prediction is based on the effective moment method, which, however, is an approximate approach, assumes infinitesimal particles. Therefore, it is well-known that for finite-sized particles, the DEP approximation is inaccurate as the mutual field, particle, wall interactions become strong, a situation presently attracting extensive research for practical significant applications. In the present talk, we provide accurate calculations of the force and torque on the particles from first principles, by directly resolving the local geometry and properties and accurately accounting for the mutual interactions for finite-sized particles with both dielectric polarization and conduction in a sinusoidally steady-state electric field. Since the approach has a significant advantage, compared to other numerical methods, to efficiently simulate many closely packed particles, it provides an important, unique, and accurate technique to investigate complex DEP phenomena, for example heterogeneous mixtures containing particle chains, nanoparticle assembly, biological cells, non-spherical effects, etc. This study was supported by the Department of Energy under funding for an EFRC (the HeteroFoaM Center), grant no. DE-SC0001061.

  6. Size-extensivity-corrected multireference configuration interaction schemes to accurately predict bond dissociation energies of oxygenated hydrocarbons

    NASA Astrophysics Data System (ADS)

    Oyeyemi, Victor B.; Krisiloff, David B.; Keith, John A.; Libisch, Florian; Pavone, Michele; Carter, Emily A.

    2014-01-01

    Oxygenated hydrocarbons play important roles in combustion science as renewable fuels and additives, but many details about their combustion chemistry remain poorly understood. Although many methods exist for computing accurate electronic energies of molecules at equilibrium geometries, a consistent description of entire combustion reaction potential energy surfaces (PESs) requires multireference correlated wavefunction theories. Here we use bond dissociation energies (BDEs) as a foundational metric to benchmark methods based on multireference configuration interaction (MRCI) for several classes of oxygenated compounds (alcohols, aldehydes, carboxylic acids, and methyl esters). We compare results from multireference singles and doubles configuration interaction to those utilizing a posteriori and a priori size-extensivity corrections, benchmarked against experiment and coupled cluster theory. We demonstrate that size-extensivity corrections are necessary for chemically accurate BDE predictions even in relatively small molecules and furnish examples of unphysical BDE predictions resulting from using too-small orbital active spaces. We also outline the specific challenges in using MRCI methods for carbonyl-containing compounds. The resulting complete basis set extrapolated, size-extensivity-corrected MRCI scheme produces BDEs generally accurate to within 1 kcal/mol, laying the foundation for this scheme's use on larger molecules and for more complex regions of combustion PESs.

  7. Accurate Predictions of Mean Geomagnetic Dipole Excursion and Reversal Frequencies, Mean Paleomagnetic Field Intensity, and the Radius of Earth's Core Using McLeod's Rule

    NASA Technical Reports Server (NTRS)

    Voorhies, Coerte V.; Conrad, Joy

    1996-01-01

    The geomagnetic spatial power spectrum R(sub n)(r) is the mean square magnetic induction represented by degree n spherical harmonic coefficients of the internal scalar potential averaged over the geocentric sphere of radius r. McLeod's Rule for the magnetic field generated by Earth's core geodynamo says that the expected core surface power spectrum (R(sub nc)(c)) is inversely proportional to (2n + 1) for 1 less than n less than or equal to N(sub E). McLeod's Rule is verified by locating Earth's core with main field models of Magsat data; the estimated core radius of 3485 kn is close to the seismologic value for c of 3480 km. McLeod's Rule and similar forms are then calibrated with the model values of R(sub n) for 3 less than or = n less than or = 12. Extrapolation to the degree 1 dipole predicts the expectation value of Earth's dipole moment to be about 5.89 x 10(exp 22) Am(exp 2)rms (74.5% of the 1980 value) and the expected geomagnetic intensity to be about 35.6 (mu)T rms at Earth's surface. Archeo- and paleomagnetic field intensity data show these and related predictions to be reasonably accurate. The probability distribution chi(exp 2) with 2n+1 degrees of freedom is assigned to (2n + 1)R(sub nc)/(R(sub nc). Extending this to the dipole implies that an exceptionally weak absolute dipole moment (less than or = 20% of the 1980 value) will exist during 2.5% of geologic time. The mean duration for such major geomagnetic dipole power excursions, one quarter of which feature durable axial dipole reversal, is estimated from the modern dipole power time-scale and the statistical model of excursions. The resulting mean excursion duration of 2767 years forces us to predict an average of 9.04 excursions per million years, 2.26 axial dipole reversals per million years, and a mean reversal duration of 5533 years. Paleomagnetic data show these predictions to be quite accurate. McLeod's Rule led to accurate predictions of Earth's core radius, mean paleomagnetic field

  8. The Compensatory Reserve For Early and Accurate Prediction Of Hemodynamic Compromise: A Review of the Underlying Physiology.

    PubMed

    Convertino, Victor A; Wirt, Michael D; Glenn, John F; Lein, Brian C

    2016-06-01

    Shock is deadly and unpredictable if it is not recognized and treated in early stages of hemorrhage. Unfortunately, measurements of standard vital signs that are displayed on current medical monitors fail to provide accurate or early indicators of shock because of physiological mechanisms that effectively compensate for blood loss. As a result of new insights provided by the latest research on the physiology of shock using human experimental models of controlled hemorrhage, it is now recognized that measurement of the body's reserve to compensate for reduced circulating blood volume is the single most important indicator for early and accurate assessment of shock. We have called this function the "compensatory reserve," which can be accurately assessed by real-time measurements of changes in the features of the arterial waveform. In this paper, the physiology underlying the development and evaluation of a new noninvasive technology that allows for real-time measurement of the compensatory reserve will be reviewed, with its clinical implications for earlier and more accurate prediction of shock. PMID:26950588

  9. A novel method to predict visual field progression more accurately, using intraocular pressure measurements in glaucoma patients

    PubMed Central

    Asaoka, Ryo; Fujino, Yuri; Murata, Hiroshi; Miki, Atsuya; Tanito, Masaki; Mizoue, Shiro; Mori, Kazuhiko; Suzuki, Katsuyoshi; Yamashita, Takehiro; Kashiwagi, Kenji; Shoji, Nobuyuki

    2016-01-01

    Visual field (VF) data were retrospectively obtained from 491 eyes in 317 patients with open angle glaucoma who had undergone ten VF tests (Humphrey Field Analyzer, 24-2, SITA standard). First, mean of total deviation values (mTD) in the tenth VF was predicted using standard linear regression of the first five VFs (VF1-5) through to using all nine preceding VFs (VF1-9). Then an ‘intraocular pressure (IOP)-integrated VF trend analysis’ was carried out by simply using time multiplied by IOP as the independent term in the linear regression model. Prediction errors (absolute prediction error or root mean squared error: RMSE) for predicting mTD and also point wise TD values of the tenth VF were obtained from both approaches. The mTD absolute prediction errors associated with the IOP-integrated VF trend analysis were significantly smaller than those from the standard trend analysis when VF1-6 through to VF1-8 were used (p < 0.05). The point wise RMSEs from the IOP-integrated trend analysis were significantly smaller than those from the standard trend analysis when VF1-5 through to VF1-9 were used (p < 0.05). This was especially the case when IOP was measured more frequently. Thus a significantly more accurate prediction of VF progression is possible using a simple trend analysis that incorporates IOP measurements. PMID:27562553

  10. A novel method to predict visual field progression more accurately, using intraocular pressure measurements in glaucoma patients.

    PubMed

    2016-01-01

    Visual field (VF) data were retrospectively obtained from 491 eyes in 317 patients with open angle glaucoma who had undergone ten VF tests (Humphrey Field Analyzer, 24-2, SITA standard). First, mean of total deviation values (mTD) in the tenth VF was predicted using standard linear regression of the first five VFs (VF1-5) through to using all nine preceding VFs (VF1-9). Then an 'intraocular pressure (IOP)-integrated VF trend analysis' was carried out by simply using time multiplied by IOP as the independent term in the linear regression model. Prediction errors (absolute prediction error or root mean squared error: RMSE) for predicting mTD and also point wise TD values of the tenth VF were obtained from both approaches. The mTD absolute prediction errors associated with the IOP-integrated VF trend analysis were significantly smaller than those from the standard trend analysis when VF1-6 through to VF1-8 were used (p < 0.05). The point wise RMSEs from the IOP-integrated trend analysis were significantly smaller than those from the standard trend analysis when VF1-5 through to VF1-9 were used (p < 0.05). This was especially the case when IOP was measured more frequently. Thus a significantly more accurate prediction of VF progression is possible using a simple trend analysis that incorporates IOP measurements. PMID:27562553

  11. Combining multiple regression and principal component analysis for accurate predictions for column ozone in Peninsular Malaysia

    NASA Astrophysics Data System (ADS)

    Rajab, Jasim M.; MatJafri, M. Z.; Lim, H. S.

    2013-06-01

    This study encompasses columnar ozone modelling in the peninsular Malaysia. Data of eight atmospheric parameters [air surface temperature (AST), carbon monoxide (CO), methane (CH4), water vapour (H2Ovapour), skin surface temperature (SSKT), atmosphere temperature (AT), relative humidity (RH), and mean surface pressure (MSP)] data set, retrieved from NASA's Atmospheric Infrared Sounder (AIRS), for the entire period (2003-2008) was employed to develop models to predict the value of columnar ozone (O3) in study area. The combined method, which is based on using both multiple regressions combined with principal component analysis (PCA) modelling, was used to predict columnar ozone. This combined approach was utilized to improve the prediction accuracy of columnar ozone. Separate analysis was carried out for north east monsoon (NEM) and south west monsoon (SWM) seasons. The O3 was negatively correlated with CH4, H2Ovapour, RH, and MSP, whereas it was positively correlated with CO, AST, SSKT, and AT during both the NEM and SWM season periods. Multiple regression analysis was used to fit the columnar ozone data using the atmospheric parameter's variables as predictors. A variable selection method based on high loading of varimax rotated principal components was used to acquire subsets of the predictor variables to be comprised in the linear regression model of the atmospheric parameter's variables. It was found that the increase in columnar O3 value is associated with an increase in the values of AST, SSKT, AT, and CO and with a drop in the levels of CH4, H2Ovapour, RH, and MSP. The result of fitting the best models for the columnar O3 value using eight of the independent variables gave about the same values of the R (≈0.93) and R2 (≈0.86) for both the NEM and SWM seasons. The common variables that appeared in both regression equations were SSKT, CH4 and RH, and the principal precursor of the columnar O3 value in both the NEM and SWM seasons was SSKT.

  12. An empiricist's guide to theoretical predictions on the evolution of dispersal

    PubMed Central

    Duputié, Anne; Massol, François

    2013-01-01

    Dispersal, the tendency for organisms to reproduce away from their parents, influences many evolutionary and ecological processes, from speciation and extinction events, to the coexistence of genotypes within species or biological invasions. Understanding how dispersal evolves is crucial to predict how global changes might affect species persistence and geographical distribution. The factors driving the evolution of dispersal have been well characterized from a theoretical standpoint, and predictions have been made about their respective influence on, for example, dispersal polymorphism or the emergence of dispersal syndromes. However, the experimental tests of some theories remain scarce partly because a synthetic view of theoretical advances is still lacking. Here, we review the different ingredients of models of dispersal evolution, from selective pressures and types of predictions, through mathematical and ecological assumptions, to the methods used to obtain predictions. We provide perspectives as to which predictions are easiest to test, how theories could be better exploited to provide testable predictions, what theoretical developments are needed to tackle this topic, and we place the question of the evolution of dispersal within the larger interdisciplinary framework of eco-evolutionary dynamics. PMID:24516715

  13. Prognostic breast cancer signature identified from 3D culture model accurately predicts clinical outcome across independent datasets

    SciTech Connect

    Martin, Katherine J.; Patrick, Denis R.; Bissell, Mina J.; Fournier, Marcia V.

    2008-10-20

    One of the major tenets in breast cancer research is that early detection is vital for patient survival by increasing treatment options. To that end, we have previously used a novel unsupervised approach to identify a set of genes whose expression predicts prognosis of breast cancer patients. The predictive genes were selected in a well-defined three dimensional (3D) cell culture model of non-malignant human mammary epithelial cell morphogenesis as down-regulated during breast epithelial cell acinar formation and cell cycle arrest. Here we examine the ability of this gene signature (3D-signature) to predict prognosis in three independent breast cancer microarray datasets having 295, 286, and 118 samples, respectively. Our results show that the 3D-signature accurately predicts prognosis in three unrelated patient datasets. At 10 years, the probability of positive outcome was 52, 51, and 47 percent in the group with a poor-prognosis signature and 91, 75, and 71 percent in the group with a good-prognosis signature for the three datasets, respectively (Kaplan-Meier survival analysis, p<0.05). Hazard ratios for poor outcome were 5.5 (95% CI 3.0 to 12.2, p<0.0001), 2.4 (95% CI 1.6 to 3.6, p<0.0001) and 1.9 (95% CI 1.1 to 3.2, p = 0.016) and remained significant for the two larger datasets when corrected for estrogen receptor (ER) status. Hence the 3D-signature accurately predicts breast cancer outcome in both ER-positive and ER-negative tumors, though individual genes differed in their prognostic ability in the two subtypes. Genes that were prognostic in ER+ patients are AURKA, CEP55, RRM2, EPHA2, FGFBP1, and VRK1, while genes prognostic in ER patients include ACTB, FOXM1 and SERPINE2 (Kaplan-Meier p<0.05). Multivariable Cox regression analysis in the largest dataset showed that the 3D-signature was a strong independent factor in predicting breast cancer outcome. The 3D-signature accurately predicts breast cancer outcome across multiple datasets and holds prognostic

  14. nuMap: a web platform for accurate prediction of nucleosome positioning.

    PubMed

    Alharbi, Bader A; Alshammari, Thamir H; Felton, Nathan L; Zhurkin, Victor B; Cui, Feng

    2014-10-01

    Nucleosome positioning is critical for gene expression and of major biological interest. The high cost of experimentally mapping nucleosomal arrangement signifies the need for computational approaches to predict nucleosome positions at high resolution. Here, we present a web-based application to fulfill this need by implementing two models, YR and W/S schemes, for the translational and rotational positioning of nucleosomes, respectively. Our methods are based on sequence-dependent anisotropic bending that dictates how DNA is wrapped around a histone octamer. This application allows users to specify a number of options such as schemes and parameters for threading calculation and provides multiple layout formats. The nuMap is implemented in Java/Perl/MySQL and is freely available for public use at http://numap.rit.edu. The user manual, implementation notes, description of the methodology and examples are available at the site. PMID:25220945

  15. A Foundation for the Accurate Prediction of the Soft Error Vulnerability of Scientific Applications

    SciTech Connect

    Bronevetsky, G; de Supinski, B; Schulz, M

    2009-02-13

    Understanding the soft error vulnerability of supercomputer applications is critical as these systems are using ever larger numbers of devices that have decreasing feature sizes and, thus, increasing frequency of soft errors. As many large scale parallel scientific applications use BLAS and LAPACK linear algebra routines, the soft error vulnerability of these methods constitutes a large fraction of the applications overall vulnerability. This paper analyzes the vulnerability of these routines to soft errors by characterizing how their outputs are affected by injected errors and by evaluating several techniques for predicting how errors propagate from the input to the output of each routine. The resulting error profiles can be used to understand the fault vulnerability of full applications that use these routines.

  16. Simplified versus geometrically accurate models of forefoot anatomy to predict plantar pressures: A finite element study.

    PubMed

    Telfer, Scott; Erdemir, Ahmet; Woodburn, James; Cavanagh, Peter R

    2016-01-25

    Integration of patient-specific biomechanical measurements into the design of therapeutic footwear has been shown to improve clinical outcomes in patients with diabetic foot disease. The addition of numerical simulations intended to optimise intervention design may help to build on these advances, however at present the time and labour required to generate and run personalised models of foot anatomy restrict their routine clinical utility. In this study we developed second-generation personalised simple finite element (FE) models of the forefoot with varying geometric fidelities. Plantar pressure predictions from barefoot, shod, and shod with insole simulations using simplified models were compared to those obtained from CT-based FE models incorporating more detailed representations of bone and tissue geometry. A simplified model including representations of metatarsals based on simple geometric shapes, embedded within a contoured soft tissue block with outer geometry acquired from a 3D surface scan was found to provide pressure predictions closest to the more complex model, with mean differences of 13.3kPa (SD 13.4), 12.52kPa (SD 11.9) and 9.6kPa (SD 9.3) for barefoot, shod, and insole conditions respectively. The simplified model design could be produced in <1h compared to >3h in the case of the more detailed model, and solved on average 24% faster. FE models of the forefoot based on simplified geometric representations of the metatarsal bones and soft tissue surface geometry from 3D surface scans may potentially provide a simulation approach with improved clinical utility, however further validity testing around a range of therapeutic footwear types is required.

  17. Four-protein signature accurately predicts lymph node metastasis and survival in oral squamous cell carcinoma.

    PubMed

    Zanaruddin, Sharifah Nurain Syed; Saleh, Amyza; Yang, Yi-Hsin; Hamid, Sharifah; Mustafa, Wan Mahadzir Wan; Khairul Bariah, A A N; Zain, Rosnah Binti; Lau, Shin Hin; Cheong, Sok Ching

    2013-03-01

    The presence of lymph node (LN) metastasis significantly affects the survival of patients with oral squamous cell carcinoma (OSCC). Successful detection and removal of positive LNs are crucial in the treatment of this disease. Current evaluation methods still have their limitations in detecting the presence of tumor cells in the LNs, where up to a third of clinically diagnosed metastasis-negative (N0) patients actually have metastasis-positive LNs in the neck. We developed a molecular signature in the primary tumor that could predict LN metastasis in OSCC. A total of 211 cores from 55 individuals were included in the study. Eleven proteins were evaluated using immunohistochemical analysis in a tissue microarray. Of the 11 biomarkers evaluated using receiver operating curve analysis, epidermal growth factor receptor (EGFR), v-erb-b2 erythroblastic leukemia viral oncogene homolog 2 (HER-2/neu), laminin, gamma 2 (LAMC2), and ras homolog family member C (RHOC) were found to be significantly associated with the presence of LN metastasis. Unsupervised hierarchical clustering-demonstrated expression patterns of these 4 proteins could be used to differentiate specimens that have positive LN metastasis from those that are negative for LN metastasis. Collectively, EGFR, HER-2/neu, LAMC2, and RHOC have a specificity of 87.5% and a sensitivity of 70%, with a prognostic accuracy of 83.4% for LN metastasis. We also demonstrated that the LN signature could independently predict disease-specific survival (P = .036). The 4-protein LN signature validated in an independent set of samples strongly suggests that it could reliably distinguish patients with LN metastasis from those who were metastasis-free and therefore could be a prognostic tool for the management of patients with OSCC.

  18. Four-protein signature accurately predicts lymph node metastasis and survival in oral squamous cell carcinoma.

    PubMed

    Zanaruddin, Sharifah Nurain Syed; Saleh, Amyza; Yang, Yi-Hsin; Hamid, Sharifah; Mustafa, Wan Mahadzir Wan; Khairul Bariah, A A N; Zain, Rosnah Binti; Lau, Shin Hin; Cheong, Sok Ching

    2013-03-01

    The presence of lymph node (LN) metastasis significantly affects the survival of patients with oral squamous cell carcinoma (OSCC). Successful detection and removal of positive LNs are crucial in the treatment of this disease. Current evaluation methods still have their limitations in detecting the presence of tumor cells in the LNs, where up to a third of clinically diagnosed metastasis-negative (N0) patients actually have metastasis-positive LNs in the neck. We developed a molecular signature in the primary tumor that could predict LN metastasis in OSCC. A total of 211 cores from 55 individuals were included in the study. Eleven proteins were evaluated using immunohistochemical analysis in a tissue microarray. Of the 11 biomarkers evaluated using receiver operating curve analysis, epidermal growth factor receptor (EGFR), v-erb-b2 erythroblastic leukemia viral oncogene homolog 2 (HER-2/neu), laminin, gamma 2 (LAMC2), and ras homolog family member C (RHOC) were found to be significantly associated with the presence of LN metastasis. Unsupervised hierarchical clustering-demonstrated expression patterns of these 4 proteins could be used to differentiate specimens that have positive LN metastasis from those that are negative for LN metastasis. Collectively, EGFR, HER-2/neu, LAMC2, and RHOC have a specificity of 87.5% and a sensitivity of 70%, with a prognostic accuracy of 83.4% for LN metastasis. We also demonstrated that the LN signature could independently predict disease-specific survival (P = .036). The 4-protein LN signature validated in an independent set of samples strongly suggests that it could reliably distinguish patients with LN metastasis from those who were metastasis-free and therefore could be a prognostic tool for the management of patients with OSCC. PMID:23026198

  19. Nonempirically Tuned Range-Separated DFT Accurately Predicts Both Fundamental and Excitation Gaps in DNA and RNA Nucleobases

    PubMed Central

    2012-01-01

    Using a nonempirically tuned range-separated DFT approach, we study both the quasiparticle properties (HOMO–LUMO fundamental gaps) and excitation energies of DNA and RNA nucleobases (adenine, thymine, cytosine, guanine, and uracil). Our calculations demonstrate that a physically motivated, first-principles tuned DFT approach accurately reproduces results from both experimental benchmarks and more computationally intensive techniques such as many-body GW theory. Furthermore, in the same set of nucleobases, we show that the nonempirical range-separated procedure also leads to significantly improved results for excitation energies compared to conventional DFT methods. The present results emphasize the importance of a nonempirically tuned range-separation approach for accurately predicting both fundamental and excitation gaps in DNA and RNA nucleobases. PMID:22904693

  20. Theoretical predictions of volatile bearing phases and volatile resources in some carbonaceous chondrites

    NASA Technical Reports Server (NTRS)

    Ganguly, Jibamitra; Saxena, Surendra K.

    1989-01-01

    Results are presented from theoretical calculations to predict the modal abundances and compositions of the major mineral phases and the vapor phase that could develop in the bulk compositions of carbonaceous chondrites. The abundances and compositions are obtained as functions of temperature and pressure. The calculations are used to evaluate the volatile and mineralogical resource potential of C1 and C2 carbonaceous chondrites.

  1. Cooperative dynamics in polymer melts: a comparison of theoretical predictions with Neutron Spin Echo experiments

    NASA Astrophysics Data System (ADS)

    Guenza, Marina

    2009-03-01

    We present a comparison between theoretical predictions of the Generalized Langevin Equation for Cooperative Dynamics (CDGLE) and Neutron Spin Echo data of dynamics structure factors for polyethylene melts. Experiments, peformed by Zamponi end coowrkers, cover an extended range of length- and time-scales providing a compelling test for the theoretical approach. Samples investigated include chains with increasing molecular weights, undergoing dynamics across the unentangled to entangled transition. Measured center-of- mass mean-square displacements display a crossover from subdiffusive to diffusive dynamics. The Generalized Langevin Equation for Cooperative Dynamics relates this anomalous diffusion to the presence of the interpolymer potential, which correlates the dynamics of a group of slowly diffusing molecules in a dynamically heterogeneous liquid. Theoretical predictions of the subdiffusive behavior, its crossover to free diffusion, and of the number of macromolecules undergoing cooperative motion are in quantitative agreement with experiments.

  2. Lateral impact validation of a geometrically accurate full body finite element model for blunt injury prediction.

    PubMed

    Vavalle, Nicholas A; Moreno, Daniel P; Rhyne, Ashley C; Stitzel, Joel D; Gayzik, F Scott

    2013-03-01

    This study presents four validation cases of a mid-sized male (M50) full human body finite element model-two lateral sled tests at 6.7 m/s, one sled test at 8.9 m/s, and a lateral drop test. Model results were compared to transient force curves, peak force, chest compression, and number of fractures from the studies. For one of the 6.7 m/s impacts (flat wall impact), the peak thoracic, abdominal and pelvic loads were 8.7, 3.1 and 14.9 kN for the model and 5.2 ± 1.1 kN, 3.1 ± 1.1 kN, and 6.3 ± 2.3 kN for the tests. For the same test setup in the 8.9 m/s case, they were 12.6, 6, and 21.9 kN for the model and 9.1 ± 1.5 kN, 4.9 ± 1.1 kN, and 17.4 ± 6.8 kN for the experiments. The combined torso load and the pelvis load simulated in a second rigid wall impact at 6.7 m/s were 11.4 and 15.6 kN, respectively, compared to 8.5 ± 0.2 kN and 8.3 ± 1.8 kN experimentally. The peak thorax load in the drop test was 6.7 kN for the model, within the range in the cadavers, 5.8-7.4 kN. When analyzing rib fractures, the model predicted Abbreviated Injury Scale scores within the reported range in three of four cases. Objective comparison methods were used to quantitatively compare the model results to the literature studies. The results show a good match in the thorax and abdomen regions while the pelvis results over predicted the reaction loads from the literature studies. These results are an important milestone in the development and validation of this globally developed average male FEA model in lateral impact.

  3. NIBBS-Search for Fast and Accurate Prediction of Phenotype-Biased Metabolic Systems

    PubMed Central

    Padmanabhan, Kanchana; Shpanskaya, Yekaterina; Banfield, Jill; Scott, Kathleen; Mihelcic, James R.; Samatova, Nagiza F.

    2012-01-01

    Understanding of genotype-phenotype associations is important not only for furthering our knowledge on internal cellular processes, but also essential for providing the foundation necessary for genetic engineering of microorganisms for industrial use (e.g., production of bioenergy or biofuels). However, genotype-phenotype associations alone do not provide enough information to alter an organism's genome to either suppress or exhibit a phenotype. It is important to look at the phenotype-related genes in the context of the genome-scale network to understand how the genes interact with other genes in the organism. Identification of metabolic subsystems involved in the expression of the phenotype is one way of placing the phenotype-related genes in the context of the entire network. A metabolic system refers to a metabolic network subgraph; nodes are compounds and edges labels are the enzymes that catalyze the reaction. The metabolic subsystem could be part of a single metabolic pathway or span parts of multiple pathways. Arguably, comparative genome-scale metabolic network analysis is a promising strategy to identify these phenotype-related metabolic subsystems. Network Instance-Based Biased Subgraph Search (NIBBS) is a graph-theoretic method for genome-scale metabolic network comparative analysis that can identify metabolic systems that are statistically biased toward phenotype-expressing organismal networks. We set up experiments with target phenotypes like hydrogen production, TCA expression, and acid-tolerance. We show via extensive literature search that some of the resulting metabolic subsystems are indeed phenotype-related and formulate hypotheses for other systems in terms of their role in phenotype expression. NIBBS is also orders of magnitude faster than MULE, one of the most efficient maximal frequent subgraph mining algorithms that could be adjusted for this problem. Also, the set of phenotype-biased metabolic systems output by NIBBS comes very close to

  4. Accurate prediction of the refractive index of polymers using first principles and data modeling

    NASA Astrophysics Data System (ADS)

    Afzal, Mohammad Atif Faiz; Cheng, Chong; Hachmann, Johannes

    Organic polymers with a high refractive index (RI) have recently attracted considerable interest due to their potential application in optical and optoelectronic devices. The ability to tailor the molecular structure of polymers is the key to increasing the accessible RI values. Our work concerns the creation of predictive in silico models for the optical properties of organic polymers, the screening of large-scale candidate libraries, and the mining of the resulting data to extract the underlying design principles that govern their performance. This work was set up to guide our experimentalist partners and allow them to target the most promising candidates. Our model is based on the Lorentz-Lorenz equation and thus includes the polarizability and number density values for each candidate. For the former, we performed a detailed benchmark study of different density functionals, basis sets, and the extrapolation scheme towards the polymer limit. For the number density we devised an exceedingly efficient machine learning approach to correlate the polymer structure and the packing fraction in the bulk material. We validated the proposed RI model against the experimentally known RI values of 112 polymers. We could show that the proposed combination of physical and data modeling is both successful and highly economical to characterize a wide range of organic polymers, which is a prerequisite for virtual high-throughput screening.

  5. Accurate predictions of C-SO2R bond dissociation enthalpies using density functional theory methods.

    PubMed

    Yu, Hai-Zhu; Fu, Fang; Zhang, Liang; Fu, Yao; Dang, Zhi-Min; Shi, Jing

    2014-10-14

    The dissociation of the C-SO2R bond is frequently involved in organic and bio-organic reactions, and the C-SO2R bond dissociation enthalpies (BDEs) are potentially important for understanding the related mechanisms. The primary goal of the present study is to provide a reliable calculation method to predict the different C-SO2R bond dissociation enthalpies (BDEs). Comparing the accuracies of 13 different density functional theory (DFT) methods (such as B3LYP, TPSS, and M05 etc.), and different basis sets (such as 6-31G(d) and 6-311++G(2df,2p)), we found that M06-2X/6-31G(d) gives the best performance in reproducing the various C-S BDEs (and especially the C-SO2R BDEs). As an example for understanding the mechanisms with the aid of C-SO2R BDEs, some primary mechanistic studies were carried out on the chemoselective coupling (in the presence of a Cu-catalyst) or desulfinative coupling reactions (in the presence of a Pd-catalyst) between sulfinic acid salts and boryl/sulfinic acid salts.

  6. Towards Accurate Prediction of Turbulent, Three-Dimensional, Recirculating Flows with the NCC

    NASA Technical Reports Server (NTRS)

    Iannetti, A.; Tacina, R.; Jeng, S.-M.; Cai, J.

    2001-01-01

    The National Combustion Code (NCC) was used to calculate the steady state, nonreacting flow field of a prototype Lean Direct Injection (LDI) swirler. This configuration used nine groups of eight holes drilled at a thirty-five degree angle to induce swirl. These nine groups created swirl in the same direction, or a corotating pattern. The static pressure drop across the holes was fixed at approximately four percent. Computations were performed on one quarter of the geometry, because the geometry is considered rotationally periodic every ninety degrees. The final computational grid used was approximately 2.26 million tetrahedral cells, and a cubic nonlinear k - epsilon model was used to model turbulence. The NCC results were then compared to time averaged Laser Doppler Velocimetry (LDV) data. The LDV measurements were performed on the full geometry, but four ninths of the geometry was measured. One-, two-, and three-dimensional representations of both flow fields are presented. The NCC computations compare both qualitatively and quantitatively well to the LDV data, but differences exist downstream. The comparison is encouraging, and shows that NCC can be used for future injector design studies. To improve the flow prediction accuracy of turbulent, three-dimensional, recirculating flow fields with the NCC, recommendations are given.

  7. An improved method for accurate prediction of mass flows through combustor liner holes

    SciTech Connect

    Adkins, R.C.; Gueroui, D.

    1986-01-01

    The objective of this paper is to present a simple approach to the solution of flow through combustor liner holes which can be used by practicing combustor engineers as well as providing the specialist modeler with a convenient boundary condition. For modeling, suppose that all relevant details of the incoming jets can be readily predicted, then the computational boundary can be limited to the inner wall of the liner and to the jets themselves. The scope of this paper is limited to the derivation of a simple analysis, the development of a reliable test technique, and to the correlation of data for plane holes having a diameter which is large when compared to the liner wall thickness. The effect of internal liner flow on the performance of the holes is neglected; this is considered to be justifiable because the analysis terminates at a short distance downstream of the hole and the significantly lower velocities inside the combustor have had little opportunity to have taken any effect. It is intended to extend the procedure to more complex hole forms and flow configurations in later papers.

  8. Neural network approach to quantum-chemistry data: Accurate prediction of density functional theory energies

    NASA Astrophysics Data System (ADS)

    Balabin, Roman M.; Lomakina, Ekaterina I.

    2009-08-01

    Artificial neural network (ANN) approach has been applied to estimate the density functional theory (DFT) energy with large basis set using lower-level energy values and molecular descriptors. A total of 208 different molecules were used for the ANN training, cross validation, and testing by applying BLYP, B3LYP, and BMK density functionals. Hartree-Fock results were reported for comparison. Furthermore, constitutional molecular descriptor (CD) and quantum-chemical molecular descriptor (QD) were used for building the calibration model. The neural network structure optimization, leading to four to five hidden neurons, was also carried out. The usage of several low-level energy values was found to greatly reduce the prediction error. An expected error, mean absolute deviation, for ANN approximation to DFT energies was 0.6±0.2 kcal mol-1. In addition, the comparison of the different density functionals with the basis sets and the comparison of multiple linear regression results were also provided. The CDs were found to overcome limitation of the QD. Furthermore, the effective ANN model for DFT/6-311G(3df,3pd) and DFT/6-311G(2df,2pd) energy estimation was developed, and the benchmark results were provided.

  9. Line Shape Parameters for CO_2 Transitions: Accurate Predictions from Complex Robert-Bonamy Calculations

    NASA Astrophysics Data System (ADS)

    Lamouroux, Julien; Gamache, Robert R.

    2013-06-01

    A model for the prediction of the vibrational dependence of CO_2 half-widths and line shifts for several broadeners, based on a modification of the model proposed by Gamache and Hartmann, is presented. This model allows the half-widths and line shifts for a ro-vibrational transition to be expressed in terms of the number of vibrational quanta exchanged in the transition raised to a power p and a reference ro-vibrational transition. Complex Robert-Bonamy calculations were made for 24 bands for lower rotational quantum numbers J'' from 0 to 160 for N_2-, O_2-, air-, and self-collisions with CO_2. In the model a Quantum Coordinate is defined by (c_1 Δν_1 + c_2 Δν_2 + c_3 Δν_3)^p where a linear least-squares fit to the data by the model expression is made. The model allows the determination of the slope and intercept as a function of rotational transition, broadening gas, and temperature. From these fit data, the half-width, line shift, and the temperature dependence of the half-width can be estimated for any ro-vibrational transition, allowing spectroscopic CO_2 databases to have complete information for the line shape parameters. R. R. Gamache, J.-M. Hartmann, J. Quant. Spectrosc. Radiat. Transfer. {{83}} (2004), 119. R. R. Gamache, J. Lamouroux, J. Quant. Spectrosc. Radiat. Transfer. {{117}} (2013), 93.

  10. The development and verification of a highly accurate collision prediction model for automated noncoplanar plan delivery

    PubMed Central

    Yu, Victoria Y.; Tran, Angelia; Nguyen, Dan; Cao, Minsong; Ruan, Dan; Low, Daniel A.; Sheng, Ke

    2015-01-01

    attributed to phantom setup errors due to the slightly deformable and flexible phantom extremities. The estimated site-specific safety buffer distance with 0.001% probability of collision for (gantry-to-couch, gantry-to-phantom) was (1.23 cm, 3.35 cm), (1.01 cm, 3.99 cm), and (2.19 cm, 5.73 cm) for treatment to the head, lung, and prostate, respectively. Automated delivery to all three treatment sites was completed in 15 min and collision free using a digital Linac. Conclusions: An individualized collision prediction model for the purpose of noncoplanar beam delivery was developed and verified. With the model, the study has demonstrated the feasibility of predicting deliverable beams for an individual patient and then guiding fully automated noncoplanar treatment delivery. This work motivates development of clinical workflows and quality assurance procedures to allow more extensive use and automation of noncoplanar beam geometries. PMID:26520735

  11. The development and verification of a highly accurate collision prediction model for automated noncoplanar plan delivery

    SciTech Connect

    Yu, Victoria Y.; Tran, Angelia; Nguyen, Dan; Cao, Minsong; Ruan, Dan; Low, Daniel A.; Sheng, Ke

    2015-11-15

    attributed to phantom setup errors due to the slightly deformable and flexible phantom extremities. The estimated site-specific safety buffer distance with 0.001% probability of collision for (gantry-to-couch, gantry-to-phantom) was (1.23 cm, 3.35 cm), (1.01 cm, 3.99 cm), and (2.19 cm, 5.73 cm) for treatment to the head, lung, and prostate, respectively. Automated delivery to all three treatment sites was completed in 15 min and collision free using a digital Linac. Conclusions: An individualized collision prediction model for the purpose of noncoplanar beam delivery was developed and verified. With the model, the study has demonstrated the feasibility of predicting deliverable beams for an individual patient and then guiding fully automated noncoplanar treatment delivery. This work motivates development of clinical workflows and quality assurance procedures to allow more extensive use and automation of noncoplanar beam geometries.

  12. How Accurate Are the Anthropometry Equations in in Iranian Military Men in Predicting Body Composition?

    PubMed Central

    Shakibaee, Abolfazl; Faghihzadeh, Soghrat; Alishiri, Gholam Hossein; Ebrahimpour, Zeynab; Faradjzadeh, Shahram; Sobhani, Vahid; Asgari, Alireza

    2015-01-01

    Background: The body composition varies according to different life styles (i.e. intake calories and caloric expenditure). Therefore, it is wise to record military personnel’s body composition periodically and encourage those who abide to the regulations. Different methods have been introduced for body composition assessment: invasive and non-invasive. Amongst them, the Jackson and Pollock equation is most popular. Objectives: The recommended anthropometric prediction equations for assessing men’s body composition were compared with dual-energy X-ray absorptiometry (DEXA) gold standard to develop a modified equation to assess body composition and obesity quantitatively among Iranian military men. Patients and Methods: A total of 101 military men aged 23 - 52 years old with a mean age of 35.5 years were recruited and evaluated in the present study (average height, 173.9 cm and weight, 81.5 kg). The body-fat percentages of subjects were assessed both with anthropometric assessment and DEXA scan. The data obtained from these two methods were then compared using multiple regression analysis. Results: The mean and standard deviation of body fat percentage of the DEXA assessment was 21.2 ± 4.3 and body fat percentage obtained from three Jackson and Pollock 3-, 4- and 7-site equations were 21.1 ± 5.8, 22.2 ± 6.0 and 20.9 ± 5.7, respectively. There was a strong correlation between these three equations and DEXA (R² = 0.98). Conclusions: The mean percentage of body fat obtained from the three equations of Jackson and Pollock was very close to that of body fat obtained from DEXA; however, we suggest using a modified Jackson-Pollock 3-site equation for volunteer military men because the 3-site equation analysis method is simpler and faster than other methods. PMID:26715964

  13. Industrial Compositional Streamline Simulation for Efficient and Accurate Prediction of Gas Injection and WAG Processes

    SciTech Connect

    Margot Gerritsen

    2008-10-31

    Gas-injection processes are widely and increasingly used for enhanced oil recovery (EOR). In the United States, for example, EOR production by gas injection accounts for approximately 45% of total EOR production and has tripled since 1986. The understanding of the multiphase, multicomponent flow taking place in any displacement process is essential for successful design of gas-injection projects. Due to complex reservoir geometry, reservoir fluid properties and phase behavior, the design of accurate and efficient numerical simulations for the multiphase, multicomponent flow governing these processes is nontrivial. In this work, we developed, implemented and tested a streamline based solver for gas injection processes that is computationally very attractive: as compared to traditional Eulerian solvers in use by industry it computes solutions with a computational speed orders of magnitude higher and a comparable accuracy provided that cross-flow effects do not dominate. We contributed to the development of compositional streamline solvers in three significant ways: improvement of the overall framework allowing improved streamline coverage and partial streamline tracing, amongst others; parallelization of the streamline code, which significantly improves wall clock time; and development of new compositional solvers that can be implemented along streamlines as well as in existing Eulerian codes used by industry. We designed several novel ideas in the streamline framework. First, we developed an adaptive streamline coverage algorithm. Adding streamlines locally can reduce computational costs by concentrating computational efforts where needed, and reduce mapping errors. Adapting streamline coverage effectively controls mass balance errors that mostly result from the mapping from streamlines to pressure grid. We also introduced the concept of partial streamlines: streamlines that do not necessarily start and/or end at wells. This allows more efficient coverage and avoids

  14. An Accurate Method for Prediction of Protein-Ligand Binding Site on Protein Surface Using SVM and Statistical Depth Function

    PubMed Central

    Wang, Kui; Gao, Jianzhao; Shen, Shiyi; Tuszynski, Jack A.; Ruan, Jishou

    2013-01-01

    Since proteins carry out their functions through interactions with other molecules, accurately identifying the protein-ligand binding site plays an important role in protein functional annotation and rational drug discovery. In the past two decades, a lot of algorithms were present to predict the protein-ligand binding site. In this paper, we introduce statistical depth function to define negative samples and propose an SVM-based method which integrates sequence and structural information to predict binding site. The results show that the present method performs better than the existent ones. The accuracy, sensitivity, and specificity on training set are 77.55%, 56.15%, and 87.96%, respectively; on the independent test set, the accuracy, sensitivity, and specificity are 80.36%, 53.53%, and 92.38%, respectively. PMID:24195070

  15. Deformation, Failure, and Fatigue Life of SiC/Ti-15-3 Laminates Accurately Predicted by MAC/GMC

    NASA Technical Reports Server (NTRS)

    Bednarcyk, Brett A.; Arnold, Steven M.

    2002-01-01

    NASA Glenn Research Center's Micromechanics Analysis Code with Generalized Method of Cells (MAC/GMC) (ref.1) has been extended to enable fully coupled macro-micro deformation, failure, and fatigue life predictions for advanced metal matrix, ceramic matrix, and polymer matrix composites. Because of the multiaxial nature of the code's underlying micromechanics model, GMC--which allows the incorporation of complex local inelastic constitutive models--MAC/GMC finds its most important application in metal matrix composites, like the SiC/Ti-15-3 composite examined here. Furthermore, since GMC predicts the microscale fields within each constituent of the composite material, submodels for local effects such as fiber breakage, interfacial debonding, and matrix fatigue damage can and have been built into MAC/GMC. The present application of MAC/GMC highlights the combination of these features, which has enabled the accurate modeling of the deformation, failure, and life of titanium matrix composites.

  16. A theoretical model to predict both horizontal displacement and vertical displacement for electromagnetic induction-based deep displacement sensors.

    PubMed

    Shentu, Nanying; Zhang, Hongjian; Li, Qing; Zhou, Hongliang; Tong, Renyuan; Li, Xiong

    2012-01-01

    Deep displacement observation is one basic means of landslide dynamic study and early warning monitoring and a key part of engineering geological investigation. In our previous work, we proposed a novel electromagnetic induction-based deep displacement sensor (I-type) to predict deep horizontal displacement and a theoretical model called equation-based equivalent loop approach (EELA) to describe its sensing characters. However in many landslide and related geological engineering cases, both horizontal displacement and vertical displacement vary apparently and dynamically so both may require monitoring. In this study, a II-type deep displacement sensor is designed by revising our I-type sensor to simultaneously monitor the deep horizontal displacement and vertical displacement variations at different depths within a sliding mass. Meanwhile, a new theoretical modeling called the numerical integration-based equivalent loop approach (NIELA) has been proposed to quantitatively depict II-type sensors' mutual inductance properties with respect to predicted horizontal displacements and vertical displacements. After detailed examinations and comparative studies between measured mutual inductance voltage, NIELA-based mutual inductance and EELA-based mutual inductance, NIELA has verified to be an effective and quite accurate analytic model for characterization of II-type sensors. The NIELA model is widely applicable for II-type sensors' monitoring on all kinds of landslides and other related geohazards with satisfactory estimation accuracy and calculation efficiency.

  17. A Theoretical Model to Predict Both Horizontal Displacement and Vertical Displacement for Electromagnetic Induction-Based Deep Displacement Sensors

    PubMed Central

    Shentu, Nanying; Zhang, Hongjian; Li, Qing; Zhou, Hongliang; Tong, Renyuan; Li, Xiong

    2012-01-01

    Deep displacement observation is one basic means of landslide dynamic study and early warning monitoring and a key part of engineering geological investigation. In our previous work, we proposed a novel electromagnetic induction-based deep displacement sensor (I-type) to predict deep horizontal displacement and a theoretical model called equation-based equivalent loop approach (EELA) to describe its sensing characters. However in many landslide and related geological engineering cases, both horizontal displacement and vertical displacement vary apparently and dynamically so both may require monitoring. In this study, a II-type deep displacement sensor is designed by revising our I-type sensor to simultaneously monitor the deep horizontal displacement and vertical displacement variations at different depths within a sliding mass. Meanwhile, a new theoretical modeling called the numerical integration-based equivalent loop approach (NIELA) has been proposed to quantitatively depict II-type sensors’ mutual inductance properties with respect to predicted horizontal displacements and vertical displacements. After detailed examinations and comparative studies between measured mutual inductance voltage, NIELA-based mutual inductance and EELA-based mutual inductance, NIELA has verified to be an effective and quite accurate analytic model for characterization of II-type sensors. The NIELA model is widely applicable for II-type sensors’ monitoring on all kinds of landslides and other related geohazards with satisfactory estimation accuracy and calculation efficiency. PMID:22368467

  18. A cross-race effect in metamemory: Predictions of face recognition are more accurate for members of our own race.

    PubMed

    Hourihan, Kathleen L; Benjamin, Aaron S; Liu, Xiping

    2012-09-01

    The Cross-Race Effect (CRE) in face recognition is the well-replicated finding that people are better at recognizing faces from their own race, relative to other races. The CRE reveals systematic limitations on eyewitness identification accuracy and suggests that some caution is warranted in evaluating cross-race identification. The CRE is a problem because jurors value eyewitness identification highly in verdict decisions. In the present paper, we explore how accurate people are in predicting their ability to recognize own-race and other-race faces. Caucasian and Asian participants viewed photographs of Caucasian and Asian faces, and made immediate judgments of learning during study. An old/new recognition test replicated the CRE: both groups displayed superior discriminability of own-race faces, relative to other-race faces. Importantly, relative metamnemonic accuracy was also greater for own-race faces, indicating that the accuracy of predictions about face recognition is influenced by race. This result indicates another source of concern when eliciting or evaluating eyewitness identification: people are less accurate in judging whether they will or will not recognize a face when that face is of a different race than they are. This new result suggests that a witness's claim of being likely to recognize a suspect from a lineup should be interpreted with caution when the suspect is of a different race than the witness.

  19. A Weibull statistics-based lignocellulose saccharification model and a built-in parameter accurately predict lignocellulose hydrolysis performance.

    PubMed

    Wang, Mingyu; Han, Lijuan; Liu, Shasha; Zhao, Xuebing; Yang, Jinghua; Loh, Soh Kheang; Sun, Xiaomin; Zhang, Chenxi; Fang, Xu

    2015-09-01

    Renewable energy from lignocellulosic biomass has been deemed an alternative to depleting fossil fuels. In order to improve this technology, we aim to develop robust mathematical models for the enzymatic lignocellulose degradation process. By analyzing 96 groups of previously published and newly obtained lignocellulose saccharification results and fitting them to Weibull distribution, we discovered Weibull statistics can accurately predict lignocellulose saccharification data, regardless of the type of substrates, enzymes and saccharification conditions. A mathematical model for enzymatic lignocellulose degradation was subsequently constructed based on Weibull statistics. Further analysis of the mathematical structure of the model and experimental saccharification data showed the significance of the two parameters in this model. In particular, the λ value, defined the characteristic time, represents the overall performance of the saccharification system. This suggestion was further supported by statistical analysis of experimental saccharification data and analysis of the glucose production levels when λ and n values change. In conclusion, the constructed Weibull statistics-based model can accurately predict lignocellulose hydrolysis behavior and we can use the λ parameter to assess the overall performance of enzymatic lignocellulose degradation. Advantages and potential applications of the model and the λ value in saccharification performance assessment were discussed.

  20. A Weibull statistics-based lignocellulose saccharification model and a built-in parameter accurately predict lignocellulose hydrolysis performance.

    PubMed

    Wang, Mingyu; Han, Lijuan; Liu, Shasha; Zhao, Xuebing; Yang, Jinghua; Loh, Soh Kheang; Sun, Xiaomin; Zhang, Chenxi; Fang, Xu

    2015-09-01

    Renewable energy from lignocellulosic biomass has been deemed an alternative to depleting fossil fuels. In order to improve this technology, we aim to develop robust mathematical models for the enzymatic lignocellulose degradation process. By analyzing 96 groups of previously published and newly obtained lignocellulose saccharification results and fitting them to Weibull distribution, we discovered Weibull statistics can accurately predict lignocellulose saccharification data, regardless of the type of substrates, enzymes and saccharification conditions. A mathematical model for enzymatic lignocellulose degradation was subsequently constructed based on Weibull statistics. Further analysis of the mathematical structure of the model and experimental saccharification data showed the significance of the two parameters in this model. In particular, the λ value, defined the characteristic time, represents the overall performance of the saccharification system. This suggestion was further supported by statistical analysis of experimental saccharification data and analysis of the glucose production levels when λ and n values change. In conclusion, the constructed Weibull statistics-based model can accurately predict lignocellulose hydrolysis behavior and we can use the λ parameter to assess the overall performance of enzymatic lignocellulose degradation. Advantages and potential applications of the model and the λ value in saccharification performance assessment were discussed. PMID:26121186

  1. Why don't we learn to accurately forecast feelings? How misremembering our predictions blinds us to past forecasting errors.

    PubMed

    Meyvis, Tom; Ratner, Rebecca K; Levav, Jonathan

    2010-11-01

    Why do affective forecasting errors persist in the face of repeated disconfirming evidence? Five studies demonstrate that people misremember their forecasts as consistent with their experience and thus fail to perceive the extent of their forecasting error. As a result, people do not learn from past forecasting errors and fail to adjust subsequent forecasts. In the context of a Super Bowl loss (Study 1), a presidential election (Studies 2 and 3), an important purchase (Study 4), and the consumption of candies (Study 5), individuals mispredicted their affective reactions to these experiences and subsequently misremembered their predictions as more accurate than they actually had been. The findings indicate that this recall error results from people's tendency to anchor on their current affective state when trying to recall their affective forecasts. Further, those who showed larger recall errors were less likely to learn to adjust their subsequent forecasts and reminding people of their actual forecasts enhanced learning. These results suggest that a failure to accurately recall one's past predictions contributes to the perpetuation of forecasting errors.

  2. A Physically Based Theoretical Model of Spore Deposition for Predicting Spread of Plant Diseases.

    PubMed

    Isard, Scott A; Chamecki, Marcelo

    2016-03-01

    A physically based theory for predicting spore deposition downwind from an area source of inoculum is presented. The modeling framework is based on theories of turbulence dispersion in the atmospheric boundary layer and applies only to spores that escape from plant canopies. A "disease resistance" coefficient is introduced to convert the theoretical spore deposition model into a simple tool for predicting disease spread at the field scale. Results from the model agree well with published measurements of Uromyces phaseoli spore deposition and measurements of wheat leaf rust disease severity. The theoretical model has the advantage over empirical models in that it can be used to assess the influence of source distribution and geometry, spore characteristics, and meteorological conditions on spore deposition and disease spread. The modeling framework is refined to predict the detailed two-dimensional spatial pattern of disease spread from an infection focus. Accounting for the time variations of wind speed and direction in the refined modeling procedure improves predictions, especially near the inoculum source, and enables application of the theoretical modeling framework to field experiment design. PMID:26595112

  3. A Physically Based Theoretical Model of Spore Deposition for Predicting Spread of Plant Diseases.

    PubMed

    Isard, Scott A; Chamecki, Marcelo

    2016-03-01

    A physically based theory for predicting spore deposition downwind from an area source of inoculum is presented. The modeling framework is based on theories of turbulence dispersion in the atmospheric boundary layer and applies only to spores that escape from plant canopies. A "disease resistance" coefficient is introduced to convert the theoretical spore deposition model into a simple tool for predicting disease spread at the field scale. Results from the model agree well with published measurements of Uromyces phaseoli spore deposition and measurements of wheat leaf rust disease severity. The theoretical model has the advantage over empirical models in that it can be used to assess the influence of source distribution and geometry, spore characteristics, and meteorological conditions on spore deposition and disease spread. The modeling framework is refined to predict the detailed two-dimensional spatial pattern of disease spread from an infection focus. Accounting for the time variations of wind speed and direction in the refined modeling procedure improves predictions, especially near the inoculum source, and enables application of the theoretical modeling framework to field experiment design.

  4. Predicting excitonic gaps of semiconducting single-walled carbon nanotubes from a field theoretic analysis

    NASA Astrophysics Data System (ADS)

    Konik, Robert M.; Sfeir, Matthew Y.; Misewich, James A.

    2015-02-01

    We demonstrate that a nonperturbative framework for the treatment of the excitations of single-walled carbon nanotubes based upon a field theoretic reduction is able to accurately describe experiment observations of the absolute values of excitonic energies. This theoretical framework yields a simple scaling function from which the excitonic energies can be read off. This scaling function is primarily determined by a single parameter, the charge Luttinger parameter of the tube, which is in turn a function of the tube chirality, dielectric environment, and the tube's dimensions, thus expressing disparate influences on the excitonic energies in a unified fashion. We test this theory explicitly on the data reported by Dukovic et al. [Nano Lett. 5, 2314 (2005), 10.1021/nl0518122] and Sfeir et al. [Phys. Rev. B 82, 195424 (2010), 10.1103/PhysRevB.82.195424] and so demonstrate the method works over a wide range of reported excitonic spectra.

  5. Predicting excitonic gaps of semiconducting single-walled carbon nanotubes from a field theoretic analysis

    SciTech Connect

    Konik, Robert M.; Sfeir, Matthew Y.; Misewich, James A.

    2015-02-17

    We demonstrate that a non-perturbative framework for the treatment of the excitations of single walled carbon nanotubes based upon a field theoretic reduction is able to accurately describe experiment observations of the absolute values of excitonic energies. This theoretical framework yields a simple scaling function from which the excitonic energies can be read off. This scaling function is primarily determined by a single parameter, the charge Luttinger parameter of the tube, which is in turn a function of the tube chirality, dielectric environment, and the tube's dimensions, thus expressing disparate influences on the excitonic energies in a unified fashion. As a result, we test this theory explicitly on the data reported in [NanoLetters 5, 2314 (2005)] and [Phys. Rev. B 82, 195424 (2010)] and so demonstrate the method works over a wide range of reported excitonic spectra.

  6. Predicting excitonic gaps of semiconducting single-walled carbon nanotubes from a field theoretic analysis

    DOE PAGES

    Konik, Robert M.; Sfeir, Matthew Y.; Misewich, James A.

    2015-02-17

    We demonstrate that a non-perturbative framework for the treatment of the excitations of single walled carbon nanotubes based upon a field theoretic reduction is able to accurately describe experiment observations of the absolute values of excitonic energies. This theoretical framework yields a simple scaling function from which the excitonic energies can be read off. This scaling function is primarily determined by a single parameter, the charge Luttinger parameter of the tube, which is in turn a function of the tube chirality, dielectric environment, and the tube's dimensions, thus expressing disparate influences on the excitonic energies in a unified fashion. Asmore » a result, we test this theory explicitly on the data reported in [NanoLetters 5, 2314 (2005)] and [Phys. Rev. B 82, 195424 (2010)] and so demonstrate the method works over a wide range of reported excitonic spectra.« less

  7. Theoretical predictions and experimental observations of genomic mapping by anchoring random clones

    SciTech Connect

    Grigoriev, A.V. )

    1993-02-01

    Genome mapping by anchoring random clones has recently been the subject of intensive theoretical study. In this paper, differences between published predictions of properties of anchored groups of clones ( contigs') are analyzed and simplifications of the mathematical formulae describing these properties are presented. The theoretical predictions are compared with the experimental results from the physical mapping of the genome of Schizosaccharomyces pombe. Information about the number of genome sections with no anchored clone on them ( oceans') and the number of undetected overlaps between the contigs at a given stage of the experiment is required for the decision to change from the random strategy to that of a directed closure of gaps. We demonstrate that the expected number of oceans can be approximated by the number of groups of clones anchored by a single probe ( singletons'), as can the expected number of undetected overlaps between contigs by the number of contigs containing more than one anchor. 14 refs., 4 figs.

  8. Theoretical prediction of stationary positions in the rectangular chamber during asymmetric electroosmotic flow

    NASA Technical Reports Server (NTRS)

    1985-01-01

    Most microscopic cell electrophoretic work depends on the theortical prediction of stationary positions by Smoluchowski and Komagata. Their theoretical solutions are based on the assumption that the electroosmotic flow in a chamber is symmetric. Because experiences with the rectangular chamber indicate that symmetric flow occurs during less than 8% of the experiments, the existing theory for stationary position determination is expanded to include the more general case of asymmetric flow. Smoluchowski's equation for symmetric electroosmotic flow in a rectangular chamber having a width much smaller than its height or length is examined. Smoluchowski's approach is used to approximate stationary positions in rectangular chambers with height/width ratios greater than 40. Support for the theoretical prediction of stationary positions using is given by three types of experimental evidence.

  9. Theoretical prediction of regression rates in swirl-injection hybrid rocket engines

    NASA Astrophysics Data System (ADS)

    Ozawa, K.; Shimada, T.

    2016-07-01

    The authors theoretically and analytically predict what times regression rates of swirl injection hybrid rocket engines increase higher than the axial injection ones by estimating heat flux from boundary layer combustion to the fuel port. The schematic of engines is assumed as ones whose oxidizer is injected from the opposite side of the nozzle such as ones of Yuasa et al. propose. To simplify the estimation, we assume some hypotheses such as three-dimensional (3D) axisymmetric flows have been assumed. The results of this prediction method are largely consistent with Yuasa's experiments data in the range of high swirl numbers.

  10. Accurate prediction of cellular co-translational folding indicates proteins can switch from post- to co-translational folding

    PubMed Central

    Nissley, Daniel A.; Sharma, Ajeet K.; Ahmed, Nabeel; Friedrich, Ulrike A.; Kramer, Günter; Bukau, Bernd; O'Brien, Edward P.

    2016-01-01

    The rates at which domains fold and codons are translated are important factors in determining whether a nascent protein will co-translationally fold and function or misfold and malfunction. Here we develop a chemical kinetic model that calculates a protein domain's co-translational folding curve during synthesis using only the domain's bulk folding and unfolding rates and codon translation rates. We show that this model accurately predicts the course of co-translational folding measured in vivo for four different protein molecules. We then make predictions for a number of different proteins in yeast and find that synonymous codon substitutions, which change translation-elongation rates, can switch some protein domains from folding post-translationally to folding co-translationally—a result consistent with previous experimental studies. Our approach explains essential features of co-translational folding curves and predicts how varying the translation rate at different codon positions along a transcript's coding sequence affects this self-assembly process. PMID:26887592

  11. Accurate prediction of cellular co-translational folding indicates proteins can switch from post- to co-translational folding.

    PubMed

    Nissley, Daniel A; Sharma, Ajeet K; Ahmed, Nabeel; Friedrich, Ulrike A; Kramer, Günter; Bukau, Bernd; O'Brien, Edward P

    2016-01-01

    The rates at which domains fold and codons are translated are important factors in determining whether a nascent protein will co-translationally fold and function or misfold and malfunction. Here we develop a chemical kinetic model that calculates a protein domain's co-translational folding curve during synthesis using only the domain's bulk folding and unfolding rates and codon translation rates. We show that this model accurately predicts the course of co-translational folding measured in vivo for four different protein molecules. We then make predictions for a number of different proteins in yeast and find that synonymous codon substitutions, which change translation-elongation rates, can switch some protein domains from folding post-translationally to folding co-translationally--a result consistent with previous experimental studies. Our approach explains essential features of co-translational folding curves and predicts how varying the translation rate at different codon positions along a transcript's coding sequence affects this self-assembly process. PMID:26887592

  12. Small-scale field experiments accurately scale up to predict density dependence in reef fish populations at large scales.

    PubMed

    Steele, Mark A; Forrester, Graham E

    2005-09-20

    Field experiments provide rigorous tests of ecological hypotheses but are usually limited to small spatial scales. It is thus unclear whether these findings extrapolate to larger scales relevant to conservation and management. We show that the results of experiments detecting density-dependent mortality of reef fish on small habitat patches scale up to have similar effects on much larger entire reefs that are the size of small marine reserves and approach the scale at which some reef fisheries operate. We suggest that accurate scaling is due to the type of species interaction causing local density dependence and the fact that localized events can be aggregated to describe larger-scale interactions with minimal distortion. Careful extrapolation from small-scale experiments identifying species interactions and their effects should improve our ability to predict the outcomes of alternative management strategies for coral reef fishes and their habitats.

  13. Effects of the inlet conditions and blood models on accurate prediction of hemodynamics in the stented coronary arteries

    NASA Astrophysics Data System (ADS)

    Jiang, Yongfei; Zhang, Jun; Zhao, Wanhua

    2015-05-01

    Hemodynamics altered by stent implantation is well-known to be closely related to in-stent restenosis. Computational fluid dynamics (CFD) method has been used to investigate the hemodynamics in stented arteries in detail and help to analyze the performances of stents. In this study, blood models with Newtonian or non-Newtonian properties were numerically investigated for the hemodynamics at steady or pulsatile inlet conditions respectively employing CFD based on the finite volume method. The results showed that the blood model with non-Newtonian property decreased the area of low wall shear stress (WSS) compared with the blood model with Newtonian property and the magnitude of WSS varied with the magnitude and waveform of the inlet velocity. The study indicates that the inlet conditions and blood models are all important for accurately predicting the hemodynamics. This will be beneficial to estimate the performances of stents and also help clinicians to select the proper stents for the patients.

  14. TIMP2•IGFBP7 biomarker panel accurately predicts acute kidney injury in high-risk surgical patients

    PubMed Central

    Gunnerson, Kyle J.; Shaw, Andrew D.; Chawla, Lakhmir S.; Bihorac, Azra; Al-Khafaji, Ali; Kashani, Kianoush; Lissauer, Matthew; Shi, Jing; Walker, Michael G.; Kellum, John A.

    2016-01-01

    BACKGROUND Acute kidney injury (AKI) is an important complication in surgical patients. Existing biomarkers and clinical prediction models underestimate the risk for developing AKI. We recently reported data from two trials of 728 and 408 critically ill adult patients in whom urinary TIMP2•IGFBP7 (NephroCheck, Astute Medical) was used to identify patients at risk of developing AKI. Here we report a preplanned analysis of surgical patients from both trials to assess whether urinary tissue inhibitor of metalloproteinase 2 (TIMP-2) and insulin-like growth factor–binding protein 7 (IGFBP7) accurately identify surgical patients at risk of developing AKI. STUDY DESIGN We enrolled adult surgical patients at risk for AKI who were admitted to one of 39 intensive care units across Europe and North America. The primary end point was moderate-severe AKI (equivalent to KDIGO [Kidney Disease Improving Global Outcomes] stages 2–3) within 12 hours of enrollment. Biomarker performance was assessed using the area under the receiver operating characteristic curve, integrated discrimination improvement, and category-free net reclassification improvement. RESULTS A total of 375 patients were included in the final analysis of whom 35 (9%) developed moderate-severe AKI within 12 hours. The area under the receiver operating characteristic curve for [TIMP-2]•[IGFBP7] alone was 0.84 (95% confidence interval, 0.76–0.90; p < 0.0001). Biomarker performance was robust in sensitivity analysis across predefined subgroups (urgency and type of surgery). CONCLUSION For postoperative surgical intensive care unit patients, a single urinary TIMP2•IGFBP7 test accurately identified patients at risk for developing AKI within the ensuing 12 hours and its inclusion in clinical risk prediction models significantly enhances their performance. LEVEL OF EVIDENCE Prognostic study, level I. PMID:26816218

  15. A novel fibrosis index comprising a non-cholesterol sterol accurately predicts HCV-related liver cirrhosis.

    PubMed

    Ydreborg, Magdalena; Lisovskaja, Vera; Lagging, Martin; Brehm Christensen, Peer; Langeland, Nina; Buhl, Mads Rauning; Pedersen, Court; Mørch, Kristine; Wejstål, Rune; Norkrans, Gunnar; Lindh, Magnus; Färkkilä, Martti; Westin, Johan

    2014-01-01

    Diagnosis of liver cirrhosis is essential in the management of chronic hepatitis C virus (HCV) infection. Liver biopsy is invasive and thus entails a risk of complications as well as a potential risk of sampling error. Therefore, non-invasive diagnostic tools are preferential. The aim of the present study was to create a model for accurate prediction of liver cirrhosis based on patient characteristics and biomarkers of liver fibrosis, including a panel of non-cholesterol sterols reflecting cholesterol synthesis and absorption and secretion. We evaluated variables with potential predictive significance for liver fibrosis in 278 patients originally included in a multicenter phase III treatment trial for chronic HCV infection. A stepwise multivariate logistic model selection was performed with liver cirrhosis, defined as Ishak fibrosis stage 5-6, as the outcome variable. A new index, referred to as Nordic Liver Index (NoLI) in the paper, was based on the model: Log-odds (predicting cirrhosis) = -12.17+ (age × 0.11) + (BMI (kg/m(2)) × 0.23) + (D7-lathosterol (μg/100 mg cholesterol)×(-0.013)) + (Platelet count (x10(9)/L) × (-0.018)) + (Prothrombin-INR × 3.69). The area under the ROC curve (AUROC) for prediction of cirrhosis was 0.91 (95% CI 0.86-0.96). The index was validated in a separate cohort of 83 patients and the AUROC for this cohort was similar (0.90; 95% CI: 0.82-0.98). In conclusion, the new index may complement other methods in diagnosing cirrhosis in patients with chronic HCV infection.

  16. A comparison of naïve and sophisticated subject behavior with game theoretic predictions.

    PubMed

    McCabe, K A; Smith, V L

    2000-03-28

    We use an extensive form two-person game as the basis for two experiments designed to compare the behavior of two groups of subjects with each other and with the subgame perfect theoretical prediction in an anonymous interaction protocol. The two subject groups are undergraduates and advanced graduate students, the latter having studied economics and game theory. There is no difference in their choice behavior, and both groups depart substantially from game theoretic predictions. We also compare a subsample of the same graduate students with a typical undergraduate sample in an asset trading environment in which inexperienced undergraduates invariably produce substantial departures from the rational expectations prediction. In this way, we examine how robust are the results across two distinct anonymous interactive environments. In the constant sum trading game, the graduate students closely track the predictions of rational theory. Our interpretation is that the graduate student subjects' departure from subgame perfection to achieve cooperative outcomes in the two-person bargaining game is a consequence of a deliberate strategy and is not the result of error or inadequate learning.

  17. Accurate electrical prediction of memory array through SEM-based edge-contour extraction using SPICE simulation

    NASA Astrophysics Data System (ADS)

    Shauly, Eitan; Rotstein, Israel; Peltinov, Ram; Latinski, Sergei; Adan, Ofer; Levi, Shimon; Menadeva, Ovadya

    2009-03-01

    The continues transistors scaling efforts, for smaller devices, similar (or larger) drive current/um and faster devices, increase the challenge to predict and to control the transistor off-state current. Typically, electrical simulators like SPICE, are using the design intent (as-drawn GDS data). At more sophisticated cases, the simulators are fed with the pattern after lithography and etch process simulations. As the importance of electrical simulation accuracy is increasing and leakage is becoming more dominant, there is a need to feed these simulators, with more accurate information extracted from physical on-silicon transistors. Our methodology to predict changes in device performances due to systematic lithography and etch effects was used in this paper. In general, the methodology consists on using the OPCCmaxTM for systematic Edge-Contour-Extraction (ECE) from transistors, taking along the manufacturing and includes any image distortions like line-end shortening, corner rounding and line-edge roughness. These measurements are used for SPICE modeling. Possible application of this new metrology is to provide a-head of time, physical and electrical statistical data improving time to market. In this work, we applied our methodology to analyze a small and large array's of 2.14um2 6T-SRAM, manufactured using Tower Standard Logic for General Purposes Platform. 4 out of the 6 transistors used "U-Shape AA", known to have higher variability. The predicted electrical performances of the transistors drive current and leakage current, in terms of nominal values and variability are presented. We also used the methodology to analyze an entire SRAM Block array. Study of an isolation leakage and variability are presented.

  18. A theoretical prediction of hydrogen molecule dissociation-recombination rates including an accurate treatment of internal state nonequilibrium effects

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.

    1990-01-01

    The dissociation and recombination of H2 over the temperature range 1000-5000 K are calculated in a nonempirical manner. The computation procedure involves the calculation of the state-to-state energy transfer rate coefficients, the solution of the 349 coupled equations which form the master equation, and the determination of the phenomenological rate coefficients. The nonempirical results presented here are in good agreement with experimental data at 1000 and 3000 K.

  19. The flow of a thin liquid film on a stationary and rotating disk. II - Theoretical prediction

    NASA Technical Reports Server (NTRS)

    Rahman, M. M.; Faghri, A.; Hankey, W. L.

    1990-01-01

    The existing theoretical models are improved and a systematic procedure to compute the free surface flow of a thin liquid film is suggested. The solutions for axisymmetric radial flow on a stationary horizontal disk and for the disk rotating around its axis are presented. The theoretical predictions are compared with the experimental data presented in Part I of this report. The analysis shows results for both supercritical and subcritical flows and the flow structure in the vicinity of a hydraulic jump which isolates these two flow types. The detailed flow structure in a hydraulic jump was computed and shown to contain regions of separation including a 'surface roller'. The effects of surface tension are found to be important near the outer edge of the disk where the fluid experiences a free fall. At other locations, the surface tension is negligible. For a rotating disk, the frictional resistance in the angular direction is found to be as important as that in the radial direction.

  20. Comparisons of theoretically predicted transport from ion temperature gradient instabilities to L-mode tokamak experiments

    SciTech Connect

    Kotschenreuther, M.; Wong, H.V.; Lyster, P.L.; Berk, H.L.; Denton, R.; Miner, W.H.; Valanju, P.

    1991-12-01

    The theoretical transport from kinetic micro-instabilities driven by ion temperature gradients is a sheared slab is compared to experimentally inferred transport in L-mode tokamaks. Low noise gyrokinetic simulation techniques are used to obtain the ion thermal transport coefficient X. This X is much smaller than in experiments, and so cannot explain L-mode confinement. Previous predictions based on fluid models gave much greater X than experiments. Linear and nonlinear comparisons with the fluid model show that it greatly overestimates transport for experimental parameters. In addition, disagreements among previous analytic and simulation calculations of X in the fluid model are reconciled.

  1. Fission barriers of hot rotating nuclei: Theoretical predictions and experimental tests

    SciTech Connect

    Mustafa, M.G.

    1987-07-07

    Recent theoretical developments in calculating fission barriers of hot rotating nuclei and their experimental tests are reviewed. The discussions are limited to macroscopic fission models (no shell effects), since experimental tests come primarily from heavy-ion induced reactions involving large angular momenta and internal excitation energies. The physics of the rotating finite range models with temperature is emphasized and the predictions of our model are compared with those of other macroscopic models and with statistically deduced experimental results. The difficulties associated with the statistical model analysis at high temperatures are discussed. 43 refs., 8 figs., 1 tab.

  2. Simple Learned Weighted Sums of Inferior Temporal Neuronal Firing Rates Accurately Predict Human Core Object Recognition Performance.

    PubMed

    Majaj, Najib J; Hong, Ha; Solomon, Ethan A; DiCarlo, James J

    2015-09-30

    database of images for evaluating object recognition performance. We used multielectrode arrays to characterize hundreds of neurons in the visual ventral stream of nonhuman primates and measured the object recognition performance of >100 human observers. Remarkably, we found that simple learned weighted sums of firing rates of neurons in monkey inferior temporal (IT) cortex accurately predicted human performance. Although previous work led us to expect that IT would outperform V4, we were surprised by the quantitative precision with which simple IT-based linking hypotheses accounted for human behavior. PMID:26424887

  3. Simple Learned Weighted Sums of Inferior Temporal Neuronal Firing Rates Accurately Predict Human Core Object Recognition Performance

    PubMed Central

    Hong, Ha; Solomon, Ethan A.; DiCarlo, James J.

    2015-01-01

    database of images for evaluating object recognition performance. We used multielectrode arrays to characterize hundreds of neurons in the visual ventral stream of nonhuman primates and measured the object recognition performance of >100 human observers. Remarkably, we found that simple learned weighted sums of firing rates of neurons in monkey inferior temporal (IT) cortex accurately predicted human performance. Although previous work led us to expect that IT would outperform V4, we were surprised by the quantitative precision with which simple IT-based linking hypotheses accounted for human behavior. PMID:26424887

  4. Simple Learned Weighted Sums of Inferior Temporal Neuronal Firing Rates Accurately Predict Human Core Object Recognition Performance.

    PubMed

    Majaj, Najib J; Hong, Ha; Solomon, Ethan A; DiCarlo, James J

    2015-09-30

    database of images for evaluating object recognition performance. We used multielectrode arrays to characterize hundreds of neurons in the visual ventral stream of nonhuman primates and measured the object recognition performance of >100 human observers. Remarkably, we found that simple learned weighted sums of firing rates of neurons in monkey inferior temporal (IT) cortex accurately predicted human performance. Although previous work led us to expect that IT would outperform V4, we were surprised by the quantitative precision with which simple IT-based linking hypotheses accounted for human behavior.

  5. Theoretical prediction of gold vein location in deposits originated by a wall magma intrusion

    NASA Astrophysics Data System (ADS)

    Martin, Pablo; Maass-Artigas, Fernando; Cortés-Vega, Luis

    2016-05-01

    The isotherm time-evolution resulting from the intrusion of a hot dike in a cold rock is analized considering the general case of nonvertical walls. This is applied to the theoretical prediction of the gold veins location due to isothermal evolution. As in previous treatments earth surface effects are considered and the gold veins are determined by the envelope of the isotherms. The locations of the gold veins in the Callao mines of Venezuela are now well predicted. The new treatment is now more elaborated and complex that in the case of vertical walls, performed in previous papers, but it is more adequated to the real cases as the one in El Callao, where the wall is not vertical.

  6. Propagation predictions and studies using a ray tracing program combined with a theoretical ionospheric model

    NASA Technical Reports Server (NTRS)

    Lee, M. K.; Nisbet, J. S.

    1975-01-01

    Radio wave propagation predictions are described in which modern comprehensive theoretical ionospheric models are coupled with ray-tracing programs. In the computer code described, a network of electron density and collision frequency parameters along a band about the great circle path is calculated by specifying the transmitter and receiver geographic coordinates, time, the day number, and the 2800-MHz solar flux. The ray paths are calculated on specifying the frequency, mode, range of elevation angles, and range of azimuth angles from the great circle direction. The current program uses a combination of the Penn State MKI E and F region models and the Mitra-Rowe D and E region model. Application of the technique to the prediction of satellite to ground propagation and calculation of oblique incidence propagation paths and absorption are described. The implications of the study to the development of the next generation of ionospheric models are discussed.

  7. The adaptive evolution of virulence: a review of theoretical predictions and empirical tests.

    PubMed

    Cressler, Clayton E; McLEOD, David V; Rozins, Carly; VAN DEN Hoogen, Josée; Day, Troy

    2016-06-01

    Why is it that some parasites cause high levels of host damage (i.e. virulence) whereas others are relatively benign? There are now numerous reviews of virulence evolution in the literature but it is nevertheless still difficult to find a comprehensive treatment of the theory and data on the subject that is easily accessible to non-specialists. Here we attempt to do so by distilling the vast theoretical literature on the topic into a set of relatively few robust predictions. We then provide a comprehensive assessment of the available empirical literature that tests these predictions. Our results show that there have been some notable successes in integrating theory and data but also that theory and empiricism in this field do not 'speak' to each other very well. We offer a few suggestions for how the connection between the two might be improved. PMID:26302775

  8. Computational finite element bone mechanics accurately predicts mechanical competence in the human radius of an elderly population.

    PubMed

    Mueller, Thomas L; Christen, David; Sandercott, Steve; Boyd, Steven K; van Rietbergen, Bert; Eckstein, Felix; Lochmüller, Eva-Maria; Müller, Ralph; van Lenthe, G Harry

    2011-06-01

    High-resolution peripheral quantitative computed tomography (HR-pQCT) is clinically available today and provides a non-invasive measure of 3D bone geometry and micro-architecture with unprecedented detail. In combination with microarchitectural finite element (μFE) models it can be used to determine bone strength using a strain-based failure criterion. Yet, images from only a relatively small part of the radius are acquired and it is not known whether the region recommended for clinical measurements does predict forearm fracture load best. Furthermore, it is questionable whether the currently used failure criterion is optimal because of improvements in image resolution, changes in the clinically measured volume of interest, and because the failure criterion depends on the amount of bone present. Hence, we hypothesized that bone strength estimates would improve by measuring a region closer to the subchondral plate, and by defining a failure criterion that would be independent of the measured volume of interest. To answer our hypotheses, 20% of the distal forearm length from 100 cadaveric but intact human forearms was measured using HR-pQCT. μFE bone strength was analyzed for different subvolumes, as well as for the entire 20% of the distal radius length. Specifically, failure criteria were developed that provided accurate estimates of bone strength as assessed experimentally. It was shown that distal volumes were better in predicting bone strength than more proximal ones. Clinically speaking, this would argue to move the volume of interest for the HR-pQCT measurements even more distally than currently recommended by the manufacturer. Furthermore, new parameter settings using the strain-based failure criterion are presented providing better accuracy for bone strength estimates.

  9. Accurate ab initio prediction of propagation rate coefficients in free-radical polymerization: Acrylonitrile and vinyl chloride

    NASA Astrophysics Data System (ADS)

    Izgorodina, Ekaterina I.; Coote, Michelle L.

    2006-05-01

    A systematic methodology for calculating accurate propagation rate coefficients in free-radical polymerization was designed and tested for vinyl chloride and acrylonitrile polymerization. For small to medium-sized polymer systems, theoretical reaction barriers are calculated using G3(MP2)-RAD. For larger systems, G3(MP2)-RAD barriers can be approximated (to within 1 kJ mol -1) via an ONIOM-based approach in which the core is studied at G3(MP2)-RAD and the substituent effects are modeled with ROMP2/6-311+G(3df,2p). DFT methods (including BLYP, B3LYP, MPWB195, BB1K and MPWB1K) failed to reproduce the correct trends in the reaction barriers and enthalpies with molecular size, though KMLYP showed some promise as a low cost option for very large systems. Reaction rates are calculated via standard transition state theory in conjunction with the one-dimensional hindered rotor model. The harmonic oscillator approximation was shown to introduce an error of a factor of 2-3, and would be suitable for "order-of-magnitude" estimates. A systematic study of chain length effects indicated that rate coefficients had largely converged to their long chain limit at the dimer radical stage, and the inclusion of the primary substituent of the penultimate unit was sufficient for practical purposes. Solvent effects, as calculated using the COSMO model, were found to be relatively minor. The overall methodology reproduced the available experimental data for both of these monomers within a factor of 2.

  10. A Support Vector Machine model for the prediction of proteotypic peptides for accurate mass and time proteomics

    SciTech Connect

    Webb-Robertson, Bobbie-Jo M.; Cannon, William R.; Oehmen, Christopher S.; Shah, Anuj R.; Gurumoorthi, Vidhya; Lipton, Mary S.; Waters, Katrina M.

    2008-07-01

    Motivation: The standard approach to identifying peptides based on accurate mass and elution time (AMT) compares these profiles obtained from a high resolution mass spectrometer to a database of peptides previously identified from tandem mass spectrometry (MS/MS) studies. It would be advantageous, with respect to both accuracy and cost, to only search for those peptides that are detectable by MS (proteotypic). Results: We present a Support Vector Machine (SVM) model that uses a simple descriptor space based on 35 properties of amino acid content, charge, hydrophilicity, and polarity for the quantitative prediction of proteotypic peptides. Using three independently derived AMT databases (Shewanella oneidensis, Salmonella typhimurium, Yersinia pestis) for training and validation within and across species, the SVM resulted in an average accuracy measure of ~0.8 with a standard deviation of less than 0.025. Furthermore, we demonstrate that these results are achievable with a small set of 12 variables and can achieve high proteome coverage. Availability: http://omics.pnl.gov/software/STEPP.php

  11. High IFIT1 expression predicts improved clinical outcome, and IFIT1 along with MGMT more accurately predicts prognosis in newly diagnosed glioblastoma.

    PubMed

    Zhang, Jin-Feng; Chen, Yao; Lin, Guo-Shi; Zhang, Jian-Dong; Tang, Wen-Long; Huang, Jian-Huang; Chen, Jin-Shou; Wang, Xing-Fu; Lin, Zhi-Xiong

    2016-06-01

    Interferon-induced protein with tetratricopeptide repeat 1 (IFIT1) plays a key role in growth suppression and apoptosis promotion in cancer cells. Interferon was reported to induce the expression of IFIT1 and inhibit the expression of O-6-methylguanine-DNA methyltransferase (MGMT).This study aimed to investigate the expression of IFIT1, the correlation between IFIT1 and MGMT, and their impact on the clinical outcome in newly diagnosed glioblastoma. The expression of IFIT1 and MGMT and their correlation were investigated in the tumor tissues from 70 patients with newly diagnosed glioblastoma. The effects on progression-free survival and overall survival were evaluated. Of 70 cases, 57 (81.4%) tissue samples showed high expression of IFIT1 by immunostaining. The χ(2) test indicated that the expression of IFIT1 and MGMT was negatively correlated (r = -0.288, P = .016). Univariate and multivariate analyses confirmed high IFIT1 expression as a favorable prognostic indicator for progression-free survival (P = .005 and .017) and overall survival (P = .001 and .001), respectively. Patients with 2 favorable factors (high IFIT1 and low MGMT) had an improved prognosis as compared with others. The results demonstrated significantly increased expression of IFIT1 in newly diagnosed glioblastoma tissue. The negative correlation between IFIT1 and MGMT expression may be triggered by interferon. High IFIT1 can be a predictive biomarker of favorable clinical outcome, and IFIT1 along with MGMT more accurately predicts prognosis in newly diagnosed glioblastoma. PMID:26980050

  12. A time accurate prediction of the viscous flow in a turbine stage including a rotor in motion

    NASA Astrophysics Data System (ADS)

    Shavalikul, Akamol

    accurate flow characteristics in the NGV domain and the rotor domain with less computational time and computer memory requirements. In contrast, the time accurate flow simulation can predict all unsteady flow characteristics occurring in the turbine stage, but with high computational resource requirements. (Abstract shortened by UMI.)

  13. A Systematic Review of Predictions of Survival in Palliative Care: How Accurate Are Clinicians and Who Are the Experts?

    PubMed Central

    Harris, Adam; Harries, Priscilla

    2016-01-01

    overall accuracy being reported. Data were extracted using a standardised tool, by one reviewer, which could have introduced bias. Devising search terms for prognostic studies is challenging. Every attempt was made to devise search terms that were sufficiently sensitive to detect all prognostic studies; however, it remains possible that some studies were not identified. Conclusion Studies of prognostic accuracy in palliative care are heterogeneous, but the evidence suggests that clinicians’ predictions are frequently inaccurate. No sub-group of clinicians was consistently shown to be more accurate than any other. Implications of Key Findings Further research is needed to understand how clinical predictions are formulated and how their accuracy can be improved. PMID:27560380

  14. Human Emotion Experiences Can Be Predicted on Theoretical Grounds: Evidence from Verbal Labeling

    PubMed Central

    Scherer, Klaus R.; Meuleman, Ben

    2013-01-01

    In an effort to demonstrate that the verbal labeling of emotional experiences obeys lawful principles, we tested the feasibility of using an expert system called the Geneva Emotion Analyst (GEA), which generates predictions based on an appraisal theory of emotion. Several thousand respondents participated in an Internet survey that applied GEA to self-reported emotion experiences. Users recalled appraisals of emotion-eliciting events and labeled the experienced emotion with one or two words, generating a massive data set on realistic, intense emotions in everyday life. For a final sample of 5969 respondents we show that GEA achieves a high degree of predictive accuracy by matching a user’s appraisal input to one of 13 theoretically predefined emotion prototypes. The first prediction was correct in 51% of the cases and the overall diagnosis was considered as at least partially correct or appropriate in more than 90% of all cases. These results support a component process model that encourages focused, hypothesis-guided research on elicitation and differentiation, memory storage and retrieval, and categorization and labeling of emotion episodes. We discuss the implications of these results for the study of emotion terms in natural language semantics. PMID:23483988

  15. Theoretical prediction of high pressure phase transition in ScC and YC: Ab initio calculations

    NASA Astrophysics Data System (ADS)

    Sahoo, B. D.; Joshi, K. D.; Gupta, Satish C.

    2013-08-01

    The structural stability of ScC and YC has been analyzed under hydrostatic compression employing the first-principles calculations using the plane-wave pseudopotential method. The comparison of theoretically calculated enthalpies of rocksalt type (B1), primitive orthorhombic (Pmmn), and CsCl type (B2) structures as a function of pressure suggests that the B1 structure transforms to Pmmn phase instead of transforming to B2 phase that predicted by Soni et al. [J. Phys. Chem. Solids 72, 810 (2011)]. The pressure for B1 to Pmmn transition predicted for ScC and YC are ˜80 GPa and ˜30 GPa, respectively. To further substantiate the outcomes of our static lattice calculations, we have performed lattice dynamic calculations also. Our lattice dynamic calculations correctly demonstrate that the B1 phase is dynamically stable structure at ambient condition. Further, for both the carbides, we find that the Pmmn structure becomes dynamically stable around the transition pressure whereas the B2 structure remains unstable, supporting the B1 to Pmmn phase transition predicted by our static lattice calculations.

  16. Isotopic Soret effect in ternary mixtures: Theoretical predictions and molecular simulations

    SciTech Connect

    Artola, Pierre-Arnaud; Rousseau, Bernard

    2015-11-07

    In this paper, we study the Soret effect in ternary fluid mixtures of isotopic argon like atoms. Soret coefficients have been computed using non-equilibrium molecular dynamics and a theoretical approach based on our extended Prigogine model (with mass effect) and generalized to mixtures with any number of components. As is well known for binary mixture studies, the heaviest component always accumulates on the cold side whereas the lightest species accumulate on the hot side. An interesting behavior is observed for the species with the intermediate mass: it can accumulate on both sides, depending on composition and mass ratios. A simple picture can be given to understand this change of sign: the intermediate mass species can be seen as evolving in an equivalent fluid whose species mass varies with composition. An excellent prediction of all simulated data has been obtained using our model including the change of sign of the Soret coefficient for species with intermediate mass.

  17. The costs and benefits of occasional sex: theoretical predictions and a case study.

    PubMed

    D'Souza, Thomas G; Michiels, Nico K

    2010-01-01

    Theory predicts that occasional sexual reproduction in predominantly parthenogenetic organisms offers all the advantages of obligate sexuality without paying its full costs. However, empirical examples identifying and evaluating the costs and benefits of rare sex are scarce. After reviewing the theoretical perspective on rare sex, we present our findings of potential costs and benefits of occasional sex in polyploid, sperm-dependent parthenogens of the planarian flatworm Schmidtea polychroa. Despite costs associated with the production of less fertile tetraploids as sexual intermediates, the benefits of rare sex prevail in S. polychroa and may be sufficiently strong to prevent extinction of parthenogenetic populations. This offers an explanation for the dominance of parthenogenesis in S. polychroa. We discuss the enigmatic question why not all organisms show a mixed reproduction mode.

  18. Theoretical predictions for hot-carrier generation from surface plasmon decay

    NASA Astrophysics Data System (ADS)

    Sundararaman, Ravishankar; Narang, Prineha; Jermyn, Adam S.; Goddard, William A., III; Atwater, Harry A.

    2014-12-01

    Decay of surface plasmons to hot carriers finds a wide variety of applications in energy conversion, photocatalysis and photodetection. However, a detailed theoretical description of plasmonic hot-carrier generation in real materials has remained incomplete. Here we report predictions for the prompt distributions of excited ‘hot’ electrons and holes generated by plasmon decay, before inelastic relaxation, using a quantized plasmon model with detailed electronic structure. We find that carrier energy distributions are sensitive to the electronic band structure of the metal: gold and copper produce holes hotter than electrons by 1-2 eV, while silver and aluminium distribute energies more equitably between electrons and holes. Momentum-direction distributions for hot carriers are anisotropic, dominated by the plasmon polarization for aluminium and by the crystal orientation for noble metals. We show that in thin metallic films intraband transitions can alter the carrier distributions, producing hotter electrons in gold, but interband transitions remain dominant.

  19. Theoretical predictions for hot-carrier generation from surface plasmon decay

    PubMed Central

    Sundararaman, Ravishankar; Narang, Prineha; Jermyn, Adam S.; Goddard III, William A.; Atwater, Harry A.

    2014-01-01

    Decay of surface plasmons to hot carriers finds a wide variety of applications in energy conversion, photocatalysis and photodetection. However, a detailed theoretical description of plasmonic hot-carrier generation in real materials has remained incomplete. Here we report predictions for the prompt distributions of excited ‘hot’ electrons and holes generated by plasmon decay, before inelastic relaxation, using a quantized plasmon model with detailed electronic structure. We find that carrier energy distributions are sensitive to the electronic band structure of the metal: gold and copper produce holes hotter than electrons by 1–2 eV, while silver and aluminium distribute energies more equitably between electrons and holes. Momentum-direction distributions for hot carriers are anisotropic, dominated by the plasmon polarization for aluminium and by the crystal orientation for noble metals. We show that in thin metallic films intraband transitions can alter the carrier distributions, producing hotter electrons in gold, but interband transitions remain dominant. PMID:25511713

  20. Rheological investigations on the theoretical predicted “Poisoning” effect in bidisperse ferrofluids

    NASA Astrophysics Data System (ADS)

    Siebert, E.; Dupuis, V.; Neveu, S.; Odenbach, S.

    2015-01-01

    Interparticle interactions in ferrofluids especially the influence of small particles on the agglomeration behaviour of large particles were the topic of numerous theoretical predictions and simulations as well as of experimental investigations. In this context the "Poisoning" effect describes the decrease of the magnetoviscous effect in the presence of small particles in a bidisperse model fluid. In order to examine this effect rheological experiments have been carried out by means of a specially designed rheometer, which allows measurements under the influence of an applied magnetic field. We were able to synthesize ferrofluids with a narrow particle size distribution containing only small or large cobalt ferrite nanoparticles, which were mixed to receive various bidisperse fluid samples. With these fluids changes of the viscous behaviour in a magnetic field have been measured and compared according to their individual compositions.

  1. Theoretical Prediction of Hydrogen Separation Performance of Two-Dimensional Carbon Network of Fused Pentagon.

    PubMed

    Zhu, Lei; Xue, Qingzhong; Li, Xiaofang; Jin, Yakang; Zheng, Haixia; Wu, Tiantian; Guo, Qikai

    2015-12-30

    Using the van-der-Waals-corrected density functional theory (DFT) and molecular dynamic (MD) simulations, we theoretically predict the H2 separation performance of a new two-dimensional sp(2) carbon allotropes-fused pentagon network. The DFT calculations demonstrate that the fused pentagon network with proper pore sizes presents a surmountable energy barrier (0.18 eV) for H2 molecule passing through. Furthermore, the fused pentagon network shows an exceptionally high selectivity for H2/gas (CO, CH4, CO2, N2, et al.) at 300 and 450 K. Besides, using MD simulations we demonstrate that the fused pentagon network exhibits a H2 permeance of 4 × 10(7) GPU at 450 K, which is much higher than the value (20 GPU) in the current industrial applications. With high selectivity and excellent permeability, the fused pentagon network should be an excellent candidate for H2 separation. PMID:26632974

  2. Drug release from extruded solid lipid matrices: theoretical predictions and independent experiments.

    PubMed

    Güres, Sinan; Siepmann, Florence; Siepmann, Juergen; Kleinebudde, Peter

    2012-01-01

    The aim of this study was to use a mechanistically realistic mathematical model based on Fick's second law to quantitatively predict the release profiles from solid lipid extrudates consisting of a ternary matrix. Diprophylline was studied as a freely water-soluble model drug, glycerol tristearate as a matrix former and polyethylene glycol or crospovidone as a pore former (blend ratio: 50:45:5%w/w/w). The choice of these ratios is based on former studies. Strains with a diameter of 0.6, 1, 1.5, 2.7 and 3.5mm were prepared using a twin-screw extruder at 65 °C and cut into cylinders of varying lengths. Drug release in demineralised water was measured using the USP 32 basket apparatus. Based on SEM pictures of extrudates before and after exposure to the release medium as well as on DSC measurements and visual observations, an analytical solution of Fick's second law of diffusion was identified in order to quantify the resulting diprophylline release kinetics from the systems. Fitting the model to one set of experimentally determined diprophylline release kinetics from PEG containing extrudates allowed determining the apparent diffusion coefficient of this drug (or water) in this lipid matrix. Knowing this value, the impact of the dimensions of the cylinders on drug release could be quantitatively predicted. Importantly, these theoretical predictions could be confirmed by independent experimental results. Thus, diffusion is the dominant mass transport mechanism controlling drug release in this type of advanced drug delivery systems. In contrast, theoretical predictions of the impact of the device dimensions in the case of crospovidone containing extrudates significantly underestimated the real diprophylline release rates. This could be attributed to the disintegration of this type of dosage forms when exceeding a specific minimal device diameter. Thus, mathematical modelling can potentially significantly speed up the development of solid lipid extrudates, but care has

  3. Chaotic advection at large Péclet number: Electromagnetically driven experiments, numerical simulations, and theoretical predictions

    SciTech Connect

    Figueroa, Aldo; Meunier, Patrice; Villermaux, Emmanuel; Cuevas, Sergio; Ramos, Eduardo

    2014-01-15

    We present a combination of experiment, theory, and modelling on laminar mixing at large Péclet number. The flow is produced by oscillating electromagnetic forces in a thin electrolytic fluid layer, leading to oscillating dipoles, quadrupoles, octopoles, and disordered flows. The numerical simulations are based on the Diffusive Strip Method (DSM) which was recently introduced (P. Meunier and E. Villermaux, “The diffusive strip method for scalar mixing in two-dimensions,” J. Fluid Mech. 662, 134–172 (2010)) to solve the advection-diffusion problem by combining Lagrangian techniques and theoretical modelling of the diffusion. Numerical simulations obtained with the DSM are in reasonable agreement with quantitative dye visualization experiments of the scalar fields. A theoretical model based on log-normal Probability Density Functions (PDFs) of stretching factors, characteristic of homogeneous turbulence in the Batchelor regime, allows to predict the PDFs of scalar in agreement with numerical and experimental results. This model also indicates that the PDFs of scalar are asymptotically close to log-normal at late stages, except for the large concentration levels which correspond to low stretching factors.

  4. Suitability of frequency modulated thermal wave imaging for skin cancer detection-A theoretical prediction.

    PubMed

    Bhowmik, Arka; Repaka, Ramjee; Mulaveesala, Ravibabu; Mishra, Subhash C

    2015-07-01

    A theoretical study on the quantification of surface thermal response of cancerous human skin using the frequency modulated thermal wave imaging (FMTWI) technique has been presented in this article. For the first time, the use of the FMTWI technique for the detection and the differentiation of skin cancer has been demonstrated in this article. A three dimensional multilayered skin has been considered with the counter-current blood vessels in individual skin layers along with different stages of cancerous lesions based on geometrical, thermal and physical parameters available in the literature. Transient surface thermal responses of melanoma during FMTWI of skin cancer have been obtained by integrating the heat transfer model for biological tissue along with the flow model for blood vessels. It has been observed from the numerical results that, flow of blood in the subsurface region leads to a substantial alteration on the surface thermal response of the human skin. The alteration due to blood flow further causes a reduction in the performance of the thermal imaging technique during the thermal evaluation of earliest melanoma stages (small volume) compared to relatively large volume. Based on theoretical study, it has been predicted that the method is suitable for detection and differentiation of melanoma with comparatively large volume than the earliest development stages (small volume). The study has also performed phase based image analysis of the raw thermograms to resolve the different stages of melanoma volume. The phase images have been found to be clearly individuate the different development stages of melanoma compared to raw thermograms.

  5. Automatic Earthquake Shear Stress Measurement Method Developed for Accurate Time- Prediction Analysis of Forthcoming Major Earthquakes Along Shallow Active Faults

    NASA Astrophysics Data System (ADS)

    Serata, S.

    2006-12-01

    The Serata Stressmeter has been developed to measure and monitor earthquake shear stress build-up along shallow active faults. The development work made in the past 25 years has established the Stressmeter as an automatic stress measurement system to study timing of forthcoming major earthquakes in support of the current earthquake prediction studies based on statistical analysis of seismological observations. In early 1982, a series of major Man-made earthquakes (magnitude 4.5-5.0) suddenly occurred in an area over deep underground potash mine in Saskatchewan, Canada. By measuring underground stress condition of the mine, the direct cause of the earthquake was disclosed. The cause was successfully eliminated by controlling the stress condition of the mine. The Japanese government was interested in this development and the Stressmeter was introduced to the Japanese government research program for earthquake stress studies. In Japan the Stressmeter was first utilized for direct measurement of the intrinsic lateral tectonic stress gradient G. The measurement, conducted at the Mt. Fuji Underground Research Center of the Japanese government, disclosed the constant natural gradients of maximum and minimum lateral stresses in an excellent agreement with the theoretical value, i.e., G = 0.25. All the conventional methods of overcoring, hydrofracturing and deformation, which were introduced to compete with the Serata method, failed demonstrating the fundamental difficulties of the conventional methods. The intrinsic lateral stress gradient determined by the Stressmeter for the Japanese government was found to be the same with all the other measurements made by the Stressmeter in Japan. The stress measurement results obtained by the major international stress measurement work in the Hot Dry Rock Projects conducted in USA, England and Germany are found to be in good agreement with the Stressmeter results obtained in Japan. Based on this broad agreement, a solid geomechanical

  6. Theoretical prediction of nuclear magnetic shieldings and indirect spin-spin coupling constants in 1,1-, cis-, and trans-1,2-difluoroethylenes

    SciTech Connect

    Nozirov, Farhod E-mail: farhod.nozirov@gmail.com; Stachów, Michał; Kupka, Teobald E-mail: farhod.nozirov@gmail.com

    2014-04-14

    A theoretical prediction of nuclear magnetic shieldings and indirect spin-spin coupling constants in 1,1-, cis- and trans-1,2-difluoroethylenes is reported. The results obtained using density functional theory (DFT) combined with large basis sets and gauge-independent atomic orbital calculations were critically compared with experiment and conventional, higher level correlated electronic structure methods. Accurate structural, vibrational, and NMR parameters of difluoroethylenes were obtained using several density functionals combined with dedicated basis sets. B3LYP/6-311++G(3df,2pd) optimized structures of difluoroethylenes closely reproduced experimental geometries and earlier reported benchmark coupled cluster results, while BLYP/6-311++G(3df,2pd) produced accurate harmonic vibrational frequencies. The most accurate vibrations were obtained using B3LYP/6-311++G(3df,2pd) with correction for anharmonicity. Becke half and half (BHandH) density functional predicted more accurate {sup 19}F isotropic shieldings and van Voorhis and Scuseria's τ-dependent gradient-corrected correlation functional yielded better carbon shieldings than B3LYP. A surprisingly good performance of Hartree-Fock (HF) method in predicting nuclear shieldings in these molecules was observed. Inclusion of zero-point vibrational correction markedly improved agreement with experiment for nuclear shieldings calculated by HF, MP2, CCSD, and CCSD(T) methods but worsened the DFT results. The threefold improvement in accuracy when predicting {sup 2}J(FF) in 1,1-difluoroethylene for BHandH density functional compared to B3LYP was observed (the deviations from experiment were −46 vs. −115 Hz)

  7. Experimental data and theoretical predictions for the rate of electrophoretic clarification of colloidal suspensions

    SciTech Connect

    Johnson, T.J.; Davis, E.J.

    2000-05-01

    An experimental and theoretical investigation of the electrophoretic clarification rate of colloidal suspensions was conducted. The suspensions included a coal-washing effluent and a model system of TiO{sub 2} particles. A parametric study of TiO{sub 2} suspensions was performed to validate and analysis of the electrophoretic motion of the clarification front formed between a clear zone and the suspension. To measure the electric field strength needed in the prediction of the location of the front, a moveable probe and salt bridge were connected to a reference electrode. Using the measured electric field strengths, it was found that the numerical solution to the unit cell electrophoresis model agrees with the measured clarification rates. For suspensions with moderately thick electric double layers and high particle volume fractions the deviations from classical Smoluchowski theory are substantial, and the numerical analysis is in somewhat better agreement with the data than a prior solution of the problem. The numerical model reduces to the predictions of previous theories as the thickness of the electric double layer decreases, and it is in good agreement with the clarification rate measured for a coal-washing effluent suspension with thin electric double layers.

  8. Computational tools for experimental determination and theoretical prediction of protein structure

    SciTech Connect

    O`Donoghue, S.; Rost, B.

    1995-12-31

    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. The authors intend to review the state of the art in the experimental determination of protein 3D structure (focus on nuclear magnetic resonance), and in the theoretical prediction of protein function and of protein structure in 1D, 2D and 3D from sequence. All the atomic resolution structures determined so far have been derived from either X-ray crystallography (the majority so far) or Nuclear Magnetic Resonance (NMR) Spectroscopy (becoming increasingly more important). The authors briefly describe the physical methods behind both of these techniques; the major computational methods involved will be covered in some detail. They highlight parallels and differences between the methods, and also the current limitations. Special emphasis will be given to techniques which have application to ab initio structure prediction. Large scale sequencing techniques increase the gap between the number of known proteins sequences and that of known protein structures. They describe the scope and principles of methods that contribute successfully to closing that gap. Emphasis will be given on the specification of adequate testing procedures to validate such methods.

  9. FINs: lattice theoretic tools for improving prediction of sugar production from populations of measurements.

    PubMed

    Kaburlasos, Vassilis George

    2004-04-01

    This paper presents novel mathematical tools developed during a study of an industrial-yield prediction problem. The set F of fuzzy interval numbers, or FINs for short, is studied in the framework of lattice theory. A FIN is defined as a mapping to a metric lattice of generalized intervals, moreover it is shown analytically that the set F of FINs is a metric lattice. A FIN can be interpreted as a convex fuzzy set, moreover a statistical interpretation is proposed here. Algorithm CALFIN is presented for constructing a FIN from a population of samples. An underlying positive valuation function implies both a metric distance and an inclusion measure function in the set F of FINs. Substantial advantages, both theoretical and practical, are shown. Several examples illustrate geometrically on the plane both the utility and the effectiveness of novel tools. It is outlined comparatively how some of the proposed tools have been employed for improving prediction of sugar production from populations of measurements for Hellenic Sugar Industry, Greece.

  10. Theoretical Predictions and Experimental Assessments of the Performance of Alumina RF Windows

    SciTech Connect

    Karen Ann Cummings

    1998-07-01

    Radio frequency (RF) windows are the most likely place for catastrophic failure to occur in input power couplers for particle accelerators. Reliable RF windows are essential for the success of the Accelerator Production of Tritium (APT) program because there are over 1000 windows on the accelerator, and it takes more than one day to recover from a window failure. The goals of this research are to analytically predict the lifetime of the windows, to develop a conditioning procedure, and to evaluate the performance of the RF windows. The analytical goal is to predict the lifetime of the windows. The probability of failure is predicted by the combination of a finite element model of the window, Weibull probabilistic analysis, and fracture mechanics. The window assembly is modeled in a finite element electromagnetic code in order to calculate the electric fields in the window. The geometry (i.e. mesh) and electric fields are input into a translator program to generate the mesh and boundary conditions for a finite element thermal structural code. The temperatures and stresses are determined in the thermal/structural code. The geometry and thermal structural results are input into another translator program to generate an input file for the reliability code. Material, geometry and service data are also input into the reliability code. To obtain accurate Weibull and fatigue data for the analytical model, four point bend tests were done. The analytical model is validated by comparing the measurements to the calculations. The lifetime of the windows is then determined using the reliability code. The analytical model shows the window has a good thermal mechanical design and that fast fracture is unlikely to occur below a power level of 9 Mw. The experimental goal is to develop a conditioning procedure and evaluate the performance of RF windows. During the experimental evaluation, much was learned about processing of the windows to improve the RF performance. Methods of

  11. Quantitative comparison between theoretical predictions and experimental results for Bragg spectroscopy of a strongly interacting Fermi superfluid

    SciTech Connect

    Zou Peng; Kuhnle, Eva D.; Vale, Chris J.; Hu Hui

    2010-12-15

    Theoretical predictions for the dynamic structure factor of a harmonically trapped Fermi superfluid near the Bose-Einstein condensate-Bardeen-Cooper-Schrieffer (BEC-BCS) crossover are compared with recent Bragg spectroscopy measurements at large transferred momenta. The calculations are based on a random-phase (or time-dependent Hartree-Fock-Gorkov) approximation generalized to the strongly interacting regime. Excellent agreement with experimental spectra at low temperatures is obtained, with no free parameters. Theoretical predictions for zero-temperature static structure factor are also found to agree well with the experimental results and independent theoretical calculations based on the exact Tan relations. The temperature dependence of the structure factors at unitarity is predicted.

  12. Theoretical predictions of a bucky-diamond SiC cluster.

    PubMed

    Yu, Ming; Jayanthi, C S; Wu, S Y

    2012-06-15

    A study of structural relaxations of Si(n)C(m) clusters corresponding to different compositions, different relative arrangements of Si/C atoms, and different types of initial structure, reveals that the Si(n)C(m) bucky-diamond structure can be obtained for an initial network structure constructed from a truncated bulk 3C-SiC for a magic composition corresponding to n = 68 and m = 79. This study was performed using a semi-empirical Hamiltonian (SCED-LCAO) since it allowed an extensive search of different types of initial structures. However, the bucky-diamond structure predicted by this method was also confirmed by a more accurate density functional theory (DFT) based method. The bucky-diamond structure exhibited by a SiC-based system represents an interesting paradigm where a Si atom can form three-coordinated as well as four-coordinated networks with carbon atoms and vice versa and with both types of network co-existing in the same structure. Specifically, the bucky-diamond structure of the Si(68)C(79) cluster consists of a 35-atom diamond-like inner core (four-atom coordinations) suspended inside a 112-atom fullerene-like shell (three-atom coordinations).

  13. Theoretical prediction of ion conductivity in solid state HfO2

    NASA Astrophysics Data System (ADS)

    Zhang, Wei; Chen, Wen-Zhou; Sun, Jiu-Yu; Jiang, Zhen-Yi

    2013-01-01

    A theoretical prediction of ion conductivity for solid state HfO2 is carried out in analogy to ZrO2 based on the density functional calculation. Geometric and electronic structures of pure bulks exhibit similarity for the two materials. Negative formation enthalpy and negative vacancy formation energy are found for YSH (yttria-stabilized hafnia) and YSZ (yttria-stabilized zirconia), suggesting the stability of both materials. Low activation energies (below 0.7 eV) of diffusion are found in both materials, and YSH's is a little higher than that of YSZ. In addition, for both HfO2 and ZrO2, the supercells with native oxygen vacancies are also studied. The so-called defect states are observed in the supercells with neutral and +1 charge native vacancy but not in the +2 charge one. It can give an explanation to the relatively lower activation energies of yttria-doped oxides and +2 charge vacancy supercells. A brief discussion is presented to explain the different YSH ion conductivities in the experiment and obtained by us, and we attribute this to the different ion vibrations at different temperatures.

  14. Possible Function of the ribT Gene of Bacillus subtilis: Theoretical Prediction, Cloning, and Expression.

    PubMed

    Yakimov, A P; Seregina, T A; Kholodnyak, A A; Kreneva, R A; Mironov, A S; Perumov, D A; Timkovskii, A L

    2014-07-01

    The complete decipherment of the functions and interactions of the elements of the riboflavin biosynthesis operon (rib operon) of Bacillus subtilis are necessary for the development of superproducers of this important vitamin. The function of its terminal ribT gene has not been established to date. In this work, a search for homologs of the hypothetical amino acid sequence of the gene product through databases, as well as an analysis of the homolgs, was performed; the distribution of secondary structure elements was theoretically predicted; and the tertiary structure of the RibT protein was proposed. The ribT gene nucleotide sequence was amplified and cloned into the standard high-copy expression vector pET15b and then expressed after induction with IPTG in E. coli BL21 (DE3) strain cells containing the inducible phage T7 RNA polymerase gene. The ribT gene expression was confirmed by SDS-PAGE. The protein product of the expression was purified by affinity chromatography. Therefore, the real possibility of RibT protein production in quantities sufficient for further investigation of its structure and functional activity was demonstrated. PMID:25349719

  15. Theoretical Prediction of Experimental Jump and Pull-In Dynamics in a MEMS Sensor

    PubMed Central

    Ruzziconi, Laura; Ramini, Abdallah H.; Younis, Mohammad I.; Lenci, Stefano

    2014-01-01

    The present research study deals with an electrically actuated MEMS device. An experimental investigation is performed, via frequency sweeps in a neighbourhood of the first natural frequency. Resonant behavior is explored, with special attention devoted to jump and pull-in dynamics. A theoretical single degree-of-freedom spring-mass model is derived. Classical numerical simulations are observed to properly predict the main nonlinear features. Nevertheless, some discrepancies arise, which are particularly visible in the resonant branch. They mainly concern the practical range of existence of each attractor and the final outcome after its disappearance. These differences are likely due to disturbances, which are unavoidable in practice, but have not been included in the model. To take disturbances into account, in addition to the classical local investigations, we consider the global dynamics and explore the robustness of the obtained results by performing a dynamical integrity analysis. Our aim is that of developing an applicable confident estimate of the system response. Integrity profiles and integrity charts are built to detect the parameter range where reliability is practically strong and where it becomes weak. Integrity curves exactly follow the experimental data. They inform about the practical range of actuality. We discuss the combined use of integrity charts in the engineering design. Although we refer to a particular case-study, the approach is very general. PMID:25225873

  16. Flow-injection chemiluminescence determination of chrysin and baicalein assisted by theoretical prediction of chemiluminescence behavior of chrysin and baicalein

    NASA Astrophysics Data System (ADS)

    Li, Baoxin; Guo, Lili; Xu, Chunli; Ma, Limei

    2008-12-01

    In this paper, the molecular connectivity indices were applied to theoretically predict the direct chemiluminescence (CL) behavior of chrysin and baicalein with our recently proposed discriminant function. Then, combined with flow-injection analysis, a new CL system for determination of chrysin and baicalein was proposed. The method was based on the oxidation of chrysin and baicalein by acidic KMnO 4 in the presence of formaldehyde to produce strong CL emission. The present paper suggested a new model to discover new CL analytical system: first, to theoretical predict the CL behavior, and the second, to suggest analytical system.

  17. Comparison of experimental surface pressures with theoretical predictions on twin two-dimensional convergent-divergent nozzles

    NASA Technical Reports Server (NTRS)

    Carlson, J. R.; Pendergraft, O. C., Jr.; Burley, J. R., II

    1986-01-01

    A three-dimensional subsonic aerodynamic panel code (VSAERO) was used to predict the effects of upper and lower external nozzle flap geometry on the external afterbody/nozzle pressure coefficient distributions and external nozzle drag of nonaxisymmetric convergent-divergent exhaust nozzles having parallel external sidewalls installed on a generic twin-engine high performance aircraft model. Nozzle static pressure coefficient distributions along the upper and lower surfaces near the model centerline and near the outer edges (corner) of the two surfaces were calculated, and nozzle drag was predicted using these surface pressure distributions. A comparison between the theoretical predictions and experimental wind tunnel data is made to evaluate the utility of the code in calculating the flow about these types of non-axisymmetric afterbody configurations. For free-stream Mach numbers of 0.60 and 0.90, the conditions where the flows were attached on the boattails yielded the best comparison between the theoretical predictions and the experimental data. For the Boattail terminal angles of greater than 15 deg., the experimental data for M = 0.60 and 0.90 indicated areas of separated flow, so the theoretical predictions failed to match the experimental data. Even though calculations of regions of separated flows are within the capabilities of the theoretical method, acceptable solutions were not obtained.

  18. PSSP-RFE: Accurate Prediction of Protein Structural Class by Recursive Feature Extraction from PSI-BLAST Profile, Physical-Chemical Property and Functional Annotations

    PubMed Central

    Yu, Sanjiu; Zhang, Yuan; Luo, Zhong; Yang, Hua; Zhou, Yue; Zheng, Xiaoqi

    2014-01-01

    Protein structure prediction is critical to functional annotation of the massively accumulated biological sequences, which prompts an imperative need for the development of high-throughput technologies. As a first and key step in protein structure prediction, protein structural class prediction becomes an increasingly challenging task. Amongst most homological-based approaches, the accuracies of protein structural class prediction are sufficiently high for high similarity datasets, but still far from being satisfactory for low similarity datasets, i.e., below 40% in pairwise sequence similarity. Therefore, we present a novel method for accurate and reliable protein structural class prediction for both high and low similarity datasets. This method is based on Support Vector Machine (SVM) in conjunction with integrated features from position-specific score matrix (PSSM), PROFEAT and Gene Ontology (GO). A feature selection approach, SVM-RFE, is also used to rank the integrated feature vectors through recursively removing the feature with the lowest ranking score. The definitive top features selected by SVM-RFE are input into the SVM engines to predict the structural class of a query protein. To validate our method, jackknife tests were applied to seven widely used benchmark datasets, reaching overall accuracies between 84.61% and 99.79%, which are significantly higher than those achieved by state-of-the-art tools. These results suggest that our method could serve as an accurate and cost-effective alternative to existing methods in protein structural classification, especially for low similarity datasets. PMID:24675610

  19. A Mathematical Solution to the Theoretical Band Gap Underestimation: Predictive Calculations of Properties of Semiconductors

    NASA Astrophysics Data System (ADS)

    Bagayoko, Diola

    2008-03-01

    Most density functional theory (DFT) calculations find band gaps that are 30-50 percent smaller than the experimental ones, as illustrated in this presentation that recalls some popular explanations of this band gap problem, i.e., self-interaction effects and derivative discontinuities of the exchange correlation energy. A survey of the increasingly numerous approaches aimed at resolving the theoretical underestimation follows these explanations. These approaches include the Green function and screened Coulomb approximation (GWA), time dependent density functional theory (TDDFT), the exact exchange and screened exchange methods, and the use of local density approximation (LDA) potentials plus additional potentials located at atomic sites. Using the Rayleigh theorem, we describe a basis set and variational effect inherently associated with calculations that employ a linear combination of atomic orbitals (LCAO) in a variational approach of the Rayleigh-Ritz type. This description concomitantly shows a source of large underestimation errors in calculated band gaps, i.e., an often dramatic lowering of some unoccupied energies on account of the Rayleigh theorem as opposed to the Hamiltonian. We present the Bagayoko, Zhao, and Williams (BZW) method [Phys. Rev. B 60, 1563 (1999); PRB 74, 245214 (2006); and PRB 76, 037101 (2007)] that follows from the description of the aforementioned effect and that leads (a) to DFT and LDA calculated band gaps of semiconductors in agreement with experiment and (b) theoretical predictions of band gaps that are confirmed by experiment. Unlike most calculations, BZW computations solve, self-consistently, a system of two coupled equations. DFT-BZW calculated effective masses and optical properties (dielectric functions) also agree with measurements. We illustrate ten years of success of the BZW method with its results for GaN, C, Si, 3C-SIC, 4H-SiC, ZnO, AlAs, Ge, ZnSe, w-InN, InAs, and AlN. We conclude with a request to revisit beliefs

  20. Theoretical prediction of new mineral phases in Earth's mantle and core (Invited)

    NASA Astrophysics Data System (ADS)

    Oganov, A. R.

    2010-12-01

    After theoretical-experimental discovery of MgSiO3 post-perovskite [1,2], many other important mineral phases have been proposed in the deep Earth’s interior. We have developed [3] and further enhanced [4] an evolutionary method for predicting the most stable crystal structure at given thermodynamic conditions. Here, I will illustrate several examples from our recent works. For example, we have predicted new phases of CaCO3, MgCO3 and CO2 at Earth’s mantle pressures, and many of these phases have already found experimental support [5-7]. These results shed new light on the behavior of carbon in the Earth’s mantle [7]. More recently, we have studied the behavior of methane at high pressures and temperatures [8], and we confirm that indeed CH4 should break down under pressure - first, into hydrocarbons (ethane, butane) and hydrogen, and then into diamond and hydrogen. Crucial role here is played by lattice vibrations (zero-point vibrations and entropic factor). These vibrational effects are frequently neglected, but we have demonstrated that without them the decomposition into diamond and hydrogen would not be possible. Considering variable-composition systems, we have demonstrated [9] that FeSi with the CsCl-type structure is the only iron silicide stable at pressures of the Earth’s inner core. Similar studies can be performed also for Fe-O, Fe-S, Fe-O and Fe-H systems, addressing the common assumptions on their behavior at ultrahigh pressures of the inner core. REFERENCES: [1] Murakami M., et al., Science 304, 855-858 (2004). [2] Oganov A.R., Ono S., Nature 430, 445-448 (2004). [3] Oganov A.R., Glass C.W., J. Chem. Phys. 124, 244704 (2006). [4] Lyakhov A.O., Oganov A.R., Valle M. Comp. Phys. Comm. 181, 1623-1632 (2010). [5] Oganov A.R., Glass C.W., Ono S., Earth Planet. Sci. Lett. 241, 95-103 (2006). [6] Ono S., Kikegawa T., Ohishi Y. Am. Mineral. 92, 1246-1249 (2007). [7] Oganov A.R., et al., Earth Planet. Sci. Lett. 273, 38-47 (2008). [8] Gao G., Oganov A

  1. An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1.

    PubMed

    Kosakovsky Pond, Sergei L; Posada, David; Stawiski, Eric; Chappey, Colombe; Poon, Art F Y; Hughes, Gareth; Fearnhill, Esther; Gravenor, Mike B; Leigh Brown, Andrew J; Frost, Simon D W

    2009-11-01

    Genetically diverse pathogens (such as Human Immunodeficiency virus type 1, HIV-1) are frequently stratified into phylogenetically or immunologically defined subtypes for classification purposes. Computational identification of such subtypes is helpful in surveillance, epidemiological analysis and detection of novel variants, e.g., circulating recombinant forms in HIV-1. A number of conceptually and technically different techniques have been proposed for determining the subtype of a query sequence, but there is not a universally optimal approach. We present a model-based phylogenetic method for automatically subtyping an HIV-1 (or other viral or bacterial) sequence, mapping the location of breakpoints and assigning parental sequences in recombinant strains as well as computing confidence levels for the inferred quantities. Our Subtype Classification Using Evolutionary ALgorithms (SCUEAL) procedure is shown to perform very well in a variety of simulation scenarios, runs in parallel when multiple sequences are being screened, and matches or exceeds the performance of existing approaches on typical empirical cases. We applied SCUEAL to all available polymerase (pol) sequences from two large databases, the Stanford Drug Resistance database and the UK HIV Drug Resistance Database. Comparing with subtypes which had previously been assigned revealed that a minor but substantial (approximately 5%) fraction of pure subtype sequences may in fact be within- or inter-subtype recombinants. A free implementation of SCUEAL is provided as a module for the HyPhy package and the Datamonkey web server. Our method is especially useful when an accurate automatic classification of an unknown strain is desired, and is positioned to complement and extend faster but less accurate methods. Given the increasingly frequent use of HIV subtype information in studies focusing on the effect of subtype on treatment, clinical outcome, pathogenicity and vaccine design, the importance of accurate

  2. Conformations of 1,2-dimethoxypropane and 5-methoxy-1,3-dioxane: are ab initio quantum chemistry predictions accurate?

    NASA Astrophysics Data System (ADS)

    Smith, Grant D.; Jaffe, Richard L.; Yoon, Do. Y.

    1998-06-01

    High-level ab initio quantum chemistry calculations are shown to predict conformer populations of 1,2-dimethoxypropane and 5-methoxy-1,3-dioxane that are consistent with gas-phase NMR vicinal coupling constant measurements. The conformational energies of the cyclic ether 5-methoxy-1,3-dioxane are found to be consistent with those predicted by a rotational isomeric state (RIS) model based upon the acyclic analog 1,2-dimethoxypropane. The quantum chemistry and RIS calculations indicate the presence of strong attractive 1,5 C(H 3)⋯O electrostatic interactions in these molecules, similar to those found in 1,2-dimethoxyethane.

  3. A Maximal Graded Exercise Test to Accurately Predict VO2max in 18-65-Year-Old Adults

    ERIC Educational Resources Information Center

    George, James D.; Bradshaw, Danielle I.; Hyde, Annette; Vehrs, Pat R.; Hager, Ronald L.; Yanowitz, Frank G.

    2007-01-01

    The purpose of this study was to develop an age-generalized regression model to predict maximal oxygen uptake (VO sub 2 max) based on a maximal treadmill graded exercise test (GXT; George, 1996). Participants (N = 100), ages 18-65 years, reached a maximal level of exertion (mean plus or minus standard deviation [SD]; maximal heart rate [HR sub…

  4. Survival outcomes scores (SOFT, BAR, and Pedi-SOFT) are accurate in predicting post-liver transplant survival in adolescents.

    PubMed

    Conjeevaram Selvakumar, Praveen Kumar; Maksimak, Brian; Hanouneh, Ibrahim; Youssef, Dalia H; Lopez, Rocio; Alkhouri, Naim

    2016-09-01

    SOFT and BAR scores utilize recipient, donor, and graft factors to predict the 3-month survival after LT in adults (≥18 years). Recently, Pedi-SOFT score was developed to predict 3-month survival after LT in young children (≤12 years). These scoring systems have not been studied in adolescent patients (13-17 years). We evaluated the accuracy of these scoring systems in predicting the 3-month post-LT survival in adolescents through a retrospective analysis of data from UNOS of patients aged 13-17 years who received LT between 03/01/2002 and 12/31/2012. Recipients of combined organ transplants, donation after cardiac death, or living donor graft were excluded. A total of 711 adolescent LT recipients were included with a mean age of 15.2±1.4 years. A total of 100 patients died post-LT including 33 within 3 months. SOFT, BAR, and Pedi-SOFT scores were all found to be good predictors of 3-month post-transplant survival outcome with areas under the ROC curve of 0.81, 0.80, and 0.81, respectively. All three scores provided good accuracy for predicting 3-month survival post-LT in adolescents and may help clinical decision making to optimize survival rate and organ utilization. PMID:27478012

  5. Is demography destiny? Application of machine learning techniques to accurately predict population health outcomes from a minimal demographic dataset.

    PubMed

    Luo, Wei; Nguyen, Thin; Nichols, Melanie; Tran, Truyen; Rana, Santu; Gupta, Sunil; Phung, Dinh; Venkatesh, Svetha; Allender, Steve

    2015-01-01

    For years, we have relied on population surveys to keep track of regional public health statistics, including the prevalence of non-communicable diseases. Because of the cost and limitations of such surveys, we often do not have the up-to-date data on health outcomes of a region. In this paper, we examined the feasibility of inferring regional health outcomes from socio-demographic data that are widely available and timely updated through national censuses and community surveys. Using data for 50 American states (excluding Washington DC) from 2007 to 2012, we constructed a machine-learning model to predict the prevalence of six non-communicable disease (NCD) outcomes (four NCDs and two major clinical risk factors), based on population socio-demographic characteristics from the American Community Survey. We found that regional prevalence estimates for non-communicable diseases can be reasonably predicted. The predictions were highly correlated with the observed data, in both the states included in the derivation model (median correlation 0.88) and those excluded from the development for use as a completely separated validation sample (median correlation 0.85), demonstrating that the model had sufficient external validity to make good predictions, based on demographics alone, for areas not included in the model development. This highlights both the utility of this sophisticated approach to model development, and the vital importance of simple socio-demographic characteristics as both indicators and determinants of chronic disease.

  6. Genomic Models of Short-Term Exposure Accurately Predict Long-Term Chemical Carcinogenicity and Identify Putative Mechanisms of Action

    PubMed Central

    Gusenleitner, Daniel; Auerbach, Scott S.; Melia, Tisha; Gómez, Harold F.; Sherr, David H.; Monti, Stefano

    2014-01-01

    Background Despite an overall decrease in incidence of and mortality from cancer, about 40% of Americans will be diagnosed with the disease in their lifetime, and around 20% will die of it. Current approaches to test carcinogenic chemicals adopt the 2-year rodent bioassay, which is costly and time-consuming. As a result, fewer than 2% of the chemicals on the market have actually been tested. However, evidence accumulated to date suggests that gene expression profiles from model organisms exposed to chemical compounds reflect underlying mechanisms of action, and that these toxicogenomic models could be used in the prediction of chemical carcinogenicity. Results In this study, we used a rat-based microarray dataset from the NTP DrugMatrix Database to test the ability of toxicogenomics to model carcinogenicity. We analyzed 1,221 gene-expression profiles obtained from rats treated with 127 well-characterized compounds, including genotoxic and non-genotoxic carcinogens. We built a classifier that predicts a chemical's carcinogenic potential with an AUC of 0.78, and validated it on an independent dataset from the Japanese Toxicogenomics Project consisting of 2,065 profiles from 72 compounds. Finally, we identified differentially expressed genes associated with chemical carcinogenesis, and developed novel data-driven approaches for the molecular characterization of the response to chemical stressors. Conclusion Here, we validate a toxicogenomic approach to predict carcinogenicity and provide strong evidence that, with a larger set of compounds, we should be able to improve the sensitivity and specificity of the predictions. We found that the prediction of carcinogenicity is tissue-dependent and that the results also confirm and expand upon previous studies implicating DNA damage, the peroxisome proliferator-activated receptor, the aryl hydrocarbon receptor, and regenerative pathology in the response to carcinogen exposure. PMID:25058030

  7. Length of sick leave – Why not ask the sick-listed? Sick-listed individuals predict their length of sick leave more accurately than professionals

    PubMed Central

    Fleten, Nils; Johnsen, Roar; Førde, Olav Helge

    2004-01-01

    Background The knowledge of factors accurately predicting the long lasting sick leaves is sparse, but information on medical condition is believed to be necessary to identify persons at risk. Based on the current practice, with identifying sick-listed individuals at risk of long-lasting sick leaves, the objectives of this study were to inquire the diagnostic accuracy of length of sick leaves predicted in the Norwegian National Insurance Offices, and to compare their predictions with the self-predictions of the sick-listed. Methods Based on medical certificates, two National Insurance medical consultants and two National Insurance officers predicted, at day 14, the length of sick leave in 993 consecutive cases of sick leave, resulting from musculoskeletal or mental disorders, in this 1-year follow-up study. Two months later they reassessed 322 cases based on extended medical certificates. Self-predictions were obtained in 152 sick-listed subjects when their sick leave passed 14 days. Diagnostic accuracy of the predictions was analysed by ROC area, sensitivity, specificity, likelihood ratio, and positive predictive value was included in the analyses of predictive validity. Results The sick-listed identified sick leave lasting 12 weeks or longer with an ROC area of 80.9% (95% CI 73.7–86.8), while the corresponding estimates for medical consultants and officers had ROC areas of 55.6% (95% CI 45.6–65.6%) and 56.0% (95% CI 46.6–65.4%), respectively. The predictions of sick-listed males were significantly better than those of female subjects, and older subjects predicted somewhat better than younger subjects. Neither formal medical competence, nor additional medical information, noticeably improved the diagnostic accuracy based on medical certificates. Conclusion This study demonstrates that the accuracy of a prognosis based on medical documentation in sickness absence forms, is lower than that of one based on direct communication with the sick-listed themselves

  8. Accurate and efficient prediction of fine-resolution hydrologic and carbon dynamic simulations from coarse-resolution models

    NASA Astrophysics Data System (ADS)

    Pau, George Shu Heng; Shen, Chaopeng; Riley, William J.; Liu, Yaning

    2016-02-01

    The topography, and the biotic and abiotic parameters are typically upscaled to make watershed-scale hydrologic-biogeochemical models computationally tractable. However, upscaling procedure can produce biases when nonlinear interactions between different processes are not fully captured at coarse resolutions. Here we applied the Proper Orthogonal Decomposition Mapping Method (PODMM) to downscale the field solutions from a coarse (7 km) resolution grid to a fine (220 m) resolution grid. PODMM trains a reduced-order model (ROM) with coarse-resolution and fine-resolution solutions, here obtained using PAWS+CLM, a quasi-3-D watershed processes model that has been validated for many temperate watersheds. Subsequent fine-resolution solutions were approximated based only on coarse-resolution solutions and the ROM. The approximation errors were efficiently quantified using an error estimator. By jointly estimating correlated variables and temporally varying the ROM parameters, we further reduced the approximation errors by up to 20%. We also improved the method's robustness by constructing multiple ROMs using different set of variables, and selecting the best approximation based on the error estimator. The ROMs produced accurate downscaling of soil moisture, latent heat flux, and net primary production with O(1000) reduction in computational cost. The subgrid distributions were also nearly indistinguishable from the ones obtained using the fine-resolution model. Compared to coarse-resolution solutions, biases in upscaled ROM solutions were reduced by up to 80%. This method has the potential to help address the long-standing spatial scaling problem in hydrology and enable long-time integration, parameter estimation, and stochastic uncertainty analysis while accurately representing the heterogeneities.

  9. Prognostic models and risk scores: can we accurately predict postoperative nausea and vomiting in children after craniotomy?

    PubMed

    Neufeld, Susan M; Newburn-Cook, Christine V; Drummond, Jane E

    2008-10-01

    Postoperative nausea and vomiting (PONV) is a problem for many children after craniotomy. Prognostic models and risk scores help identify who is at risk for an adverse event such as PONV to help guide clinical care. The purpose of this article is to assess whether an existing prognostic model or risk score can predict PONV in children after craniotomy. The concepts of transportability, calibration, and discrimination are presented to identify what is required to have a valid tool for clinical use. Although previous work may inform clinical practice and guide future research, existing prognostic models and risk scores do not appear to be options for predicting PONV in children undergoing craniotomy. However, until risk factors are further delineated, followed by the development and validation of prognostic models and risk scores that include children after craniotomy, clinical judgment in the context of current research may serve as a guide for clinical care in this population. PMID:18939320

  10. How accurately can subject-specific finite element models predict strains and strength of human femora? Investigation using full-field measurements.

    PubMed

    Grassi, Lorenzo; Väänänen, Sami P; Ristinmaa, Matti; Jurvelin, Jukka S; Isaksson, Hanna

    2016-03-21

    Subject-specific finite element models have been proposed as a tool to improve fracture risk assessment in individuals. A thorough laboratory validation against experimental data is required before introducing such models in clinical practice. Results from digital image correlation can provide full-field strain distribution over the specimen surface during in vitro test, instead of at a few pre-defined locations as with strain gauges. The aim of this study was to validate finite element models of human femora against experimental data from three cadaver femora, both in terms of femoral strength and of the full-field strain distribution collected with digital image correlation. The results showed a high accuracy between predicted and measured principal strains (R(2)=0.93, RMSE=10%, 1600 validated data points per specimen). Femoral strength was predicted using a rate dependent material model with specific strain limit values for yield and failure. This provided an accurate prediction (<2% error) for two out of three specimens. In the third specimen, an accidental change in the boundary conditions occurred during the experiment, which compromised the femoral strength validation. The achieved strain accuracy was comparable to that obtained in state-of-the-art studies which validated their prediction accuracy against 10-16 strain gauge measurements. Fracture force was accurately predicted, with the predicted failure location being very close to the experimental fracture rim. Despite the low sample size and the single loading condition tested, the present combined numerical-experimental method showed that finite element models can predict femoral strength by providing a thorough description of the local bone mechanical response. PMID:26944687

  11. An Optimized Method for Accurate Fetal Sex Prediction and Sex Chromosome Aneuploidy Detection in Non-Invasive Prenatal Testing.

    PubMed

    Wang, Ting; He, Quanze; Li, Haibo; Ding, Jie; Wen, Ping; Zhang, Qin; Xiang, Jingjing; Li, Qiong; Xuan, Liming; Kong, Lingyin; Mao, Yan; Zhu, Yijun; Shen, Jingjing; Liang, Bo; Li, Hong

    2016-01-01

    Massively parallel sequencing (MPS) combined with bioinformatic analysis has been widely applied to detect fetal chromosomal aneuploidies such as trisomy 21, 18, 13 and sex chromosome aneuploidies (SCAs) by sequencing cell-free fetal DNA (cffDNA) from maternal plasma, so-called non-invasive prenatal testing (NIPT). However, many technical challenges, such as dependency on correct fetal sex prediction, large variations of chromosome Y measurement and high sensitivity to random reads mapping, may result in higher false negative rate (FNR) and false positive rate (FPR) in fetal sex prediction as well as in SCAs detection. Here, we developed an optimized method to improve the accuracy of the current method by filtering out randomly mapped reads in six specific regions of the Y chromosome. The method reduces the FNR and FPR of fetal sex prediction from nearly 1% to 0.01% and 0.06%, respectively and works robustly under conditions of low fetal DNA concentration (1%) in testing and simulation of 92 samples. The optimized method was further confirmed by large scale testing (1590 samples), suggesting that it is reliable and robust enough for clinical testing.

  12. Coronary Computed Tomographic Angiography Does Not Accurately Predict the Need of Coronary Revascularization in Patients with Stable Angina

    PubMed Central

    Hong, Sung-Jin; Her, Ae-Young; Suh, Yongsung; Won, Hoyoun; Cho, Deok-Kyu; Cho, Yun-Hyeong; Yoon, Young-Won; Lee, Kyounghoon; Kang, Woong Chol; Kim, Yong Hoon; Kim, Sang-Wook; Shin, Dong-Ho; Kim, Jung-Sun; Kim, Byeong-Keuk; Ko, Young-Guk; Choi, Byoung-Wook; Choi, Donghoon; Jang, Yangsoo

    2016-01-01

    Purpose To evaluate the ability of coronary computed tomographic angiography (CCTA) to predict the need of coronary revascularization in symptomatic patients with stable angina who were referred to a cardiac catheterization laboratory for coronary revascularization. Materials and Methods Pre-angiography CCTA findings were analyzed in 1846 consecutive symptomatic patients with stable angina, who were referred to a cardiac catheterization laboratory at six hospitals and were potential candidates for coronary revascularization between July 2011 and December 2013. The number of patients requiring revascularization was determined based on the severity of coronary stenosis as assessed by CCTA. This was compared to the actual number of revascularization procedures performed in the cardiac catheterization laboratory. Results Based on CCTA findings, coronary revascularization was indicated in 877 (48%) and not indicated in 969 (52%) patients. Of the 877 patients indicated for revascularization by CCTA, only 600 (68%) underwent the procedure, whereas 285 (29%) of the 969 patients not indicated for revascularization, as assessed by CCTA, underwent the procedure. When the coronary arteries were divided into 15 segments using the American Heart Association coronary tree model, the sensitivity, specificity, positive predictive value, and negative predictive value of CCTA for therapeutic decision making on a per-segment analysis were 42%, 96%, 40%, and 96%, respectively. Conclusion CCTA-based assessment of coronary stenosis severity does not sufficiently differentiate between coronary segments requiring revascularization versus those not requiring revascularization. Conventional coronary angiography should be considered to determine the need of revascularization in symptomatic patients with stable angina. PMID:27401637

  13. An Optimized Method for Accurate Fetal Sex Prediction and Sex Chromosome Aneuploidy Detection in Non-Invasive Prenatal Testing.

    PubMed

    Wang, Ting; He, Quanze; Li, Haibo; Ding, Jie; Wen, Ping; Zhang, Qin; Xiang, Jingjing; Li, Qiong; Xuan, Liming; Kong, Lingyin; Mao, Yan; Zhu, Yijun; Shen, Jingjing; Liang, Bo; Li, Hong

    2016-01-01

    Massively parallel sequencing (MPS) combined with bioinformatic analysis has been widely applied to detect fetal chromosomal aneuploidies such as trisomy 21, 18, 13 and sex chromosome aneuploidies (SCAs) by sequencing cell-free fetal DNA (cffDNA) from maternal plasma, so-called non-invasive prenatal testing (NIPT). However, many technical challenges, such as dependency on correct fetal sex prediction, large variations of chromosome Y measurement and high sensitivity to random reads mapping, may result in higher false negative rate (FNR) and false positive rate (FPR) in fetal sex prediction as well as in SCAs detection. Here, we developed an optimized method to improve the accuracy of the current method by filtering out randomly mapped reads in six specific regions of the Y chromosome. The method reduces the FNR and FPR of fetal sex prediction from nearly 1% to 0.01% and 0.06%, respectively and works robustly under conditions of low fetal DNA concentration (1%) in testing and simulation of 92 samples. The optimized method was further confirmed by large scale testing (1590 samples), suggesting that it is reliable and robust enough for clinical testing. PMID:27441628

  14. An Optimized Method for Accurate Fetal Sex Prediction and Sex Chromosome Aneuploidy Detection in Non-Invasive Prenatal Testing

    PubMed Central

    Li, Haibo; Ding, Jie; Wen, Ping; Zhang, Qin; Xiang, Jingjing; Li, Qiong; Xuan, Liming; Kong, Lingyin; Mao, Yan; Zhu, Yijun; Shen, Jingjing; Liang, Bo; Li, Hong

    2016-01-01

    Massively parallel sequencing (MPS) combined with bioinformatic analysis has been widely applied to detect fetal chromosomal aneuploidies such as trisomy 21, 18, 13 and sex chromosome aneuploidies (SCAs) by sequencing cell-free fetal DNA (cffDNA) from maternal plasma, so-called non-invasive prenatal testing (NIPT). However, many technical challenges, such as dependency on correct fetal sex prediction, large variations of chromosome Y measurement and high sensitivity to random reads mapping, may result in higher false negative rate (FNR) and false positive rate (FPR) in fetal sex prediction as well as in SCAs detection. Here, we developed an optimized method to improve the accuracy of the current method by filtering out randomly mapped reads in six specific regions of the Y chromosome. The method reduces the FNR and FPR of fetal sex prediction from nearly 1% to 0.01% and 0.06%, respectively and works robustly under conditions of low fetal DNA concentration (1%) in testing and simulation of 92 samples. The optimized method was further confirmed by large scale testing (1590 samples), suggesting that it is reliable and robust enough for clinical testing. PMID:27441628

  15. A highly accurate protein structural class prediction approach using auto cross covariance transformation and recursive feature elimination.

    PubMed

    Li, Xiaowei; Liu, Taigang; Tao, Peiying; Wang, Chunhua; Chen, Lanming

    2015-12-01

    Structural class characterizes the overall folding type of a protein or its domain. Many methods have been proposed to improve the prediction accuracy of protein structural class in recent years, but it is still a challenge for the low-similarity sequences. In this study, we introduce a feature extraction technique based on auto cross covariance (ACC) transformation of position-specific score matrix (PSSM) to represent a protein sequence. Then support vector machine-recursive feature elimination (SVM-RFE) is adopted to select top K features according to their importance and these features are input to a support vector machine (SVM) to conduct the prediction. Performance evaluation of the proposed method is performed using the jackknife test on three low-similarity datasets, i.e., D640, 1189 and 25PDB. By means of this method, the overall accuracies of 97.2%, 96.2%, and 93.3% are achieved on these three datasets, which are higher than those of most existing methods. This suggests that the proposed method could serve as a very cost-effective tool for predicting protein structural class especially for low-similarity datasets.

  16. Comparison of statistical and theoretical habitat models for conservation planning: the benefit of ensemble prediction

    USGS Publications Warehouse

    Jones-Farrand, D. Todd; Fearer, Todd M.; Thogmartin, Wayne E.; Thompson, Frank R.; Nelson, Mark D.; Tirpak, John M.

    2011-01-01

    Selection of a modeling approach is an important step in the conservation planning process, but little guidance is available. We compared two statistical and three theoretical habitat modeling approaches representing those currently being used for avian conservation planning at landscape and regional scales: hierarchical spatial count (HSC), classification and regression tree (CRT), habitat suitability index (HSI), forest structure database (FS), and habitat association database (HA). We focused our comparison on models for five priority forest-breeding species in the Central Hardwoods Bird Conservation Region: Acadian Flycatcher, Cerulean Warbler, Prairie Warbler, Red-headed Woodpecker, and Worm-eating Warbler. Lacking complete knowledge on the distribution and abundance of each species with which we could illuminate differences between approaches and provide strong grounds for recommending one approach over another, we used two approaches to compare models: rank correlations among model outputs and comparison of spatial correspondence. In general, rank correlations were significantly positive among models for each species, indicating general agreement among the models. Worm-eating Warblers had the highest pairwise correlations, all of which were significant (P , 0.05). Red-headed Woodpeckers had the lowest agreement among models, suggesting greater uncertainty in the relative conservation value of areas within the region. We assessed model uncertainty by mapping the spatial congruence in priorities (i.e., top ranks) resulting from each model for each species and calculating the coefficient of variation across model ranks for each location. This allowed identification of areas more likely to be good targets of conservation effort for a species, those areas that were least likely, and those in between where uncertainty is higher and thus conservation action incorporates more risk. Based on our results, models developed independently for the same purpose

  17. Transmembrane topography of nicotinic acetylcholine receptor: immunochemical tests contradict theoretical predictions based on hydrophobicity profiles.

    PubMed

    Ratnam, M; Nguyen, D L; Rivier, J; Sargent, P B; Lindstrom, J

    1986-05-01

    In our preceding paper [Ratnam, M., Sargent, P. B., Sarin, V., Fox, J. L., Le Nguyen, D., Rivier, J., Criado, M., & Lindstrom, J. (1986) Biochemistry (preceding paper in this issue)], we presented results from peptide mapping studies of purified subunits of the Torpedo acetylcholine receptor which suggested that the sequence beta 429-441 is on the cytoplasmic surface of the receptor. Since this finding contradicts earlier theoretical models of the transmembrane structure of the receptor, which placed this sequence of the beta subunit on the extracellular surface, we investigated the location of the corresponding sequence (389-408) and adjacent sequences of the alpha subunit by a more direct approach. We synthesized peptides including the sequences alpha 330-346, alpha 349-364, alpha 360-378, alpha 379-385, and alpha 389-408 and shorter parts of these peptides. These peptides corresponded to a highly immunogenic region, and by using 125I-labeled peptides as antigens, we were able to detect in our library of monoclonal antibodies to alpha subunits between two and six which bound specifically to each of these peptides, except alpha 389-408. We obtained antibodies specific for alpha 389-408 both from antisera against the denatured alpha subunit and from antisera made against the peptide. These antibodies were specific to alpha 389-396. In binding assays, antibodies specific for all of these five peptides bound to receptor-rich membrane vesicles only after permeabilization of the vesicles to permit access of the antibodies to the cytoplasmic surface of the receptors, suggesting that the receptor sequences which bound these antibodies were located on the intracellular side of the membrane. Electron microscopy using colloidal gold to visualize the bound antibodies was used to conclusively demonstrate that all of these sequences are exposed on the cytoplasmic surface of the receptor. These results, along with our previous demonstration that the C-terminal 10 amino acids of

  18. Theoretical Predictions of Ice Crystal Shape in CO2 Clouds on Mars

    NASA Astrophysics Data System (ADS)

    Wood, S. E.

    2001-11-01

    Carbon dioxide ice crystals that form in the Martian atmosphere play very important roles in the climate of Mars, primarily through their radiative effects. Unlike water ice, small CO2 ice particles are very efficient scatterers of thermal infrared radiation [1]. On present-day Mars, CO2 clouds over the polar regions during winter have been observed to reduce the net cooling rate to space [2]. Theoretical studies have shown that the presence of CO2 clouds in a dense (>=1 bar) CO2 atmosphere on early Mars (≈3.8 Ga) could have had a net warming effect and maintained surface temperatures above the melting point of water [3,4], for certain assumptions regarding the optical depth and areal coverage of the clouds, and the size and shape of the cloud particles. Modeling studies to date have assumed spherical particles in their radiative transfer calculations. While this may be true for evaporating crystals, for growing crystals it is certainly not. In order to predict the actual shapes of crystals in CO2 ice clouds, I have derived values for the surface energy, edge energy, and surface diffusion distance for molecules on each of the singular crystallographic faces [5]. Using these values in a model of crystal growth, I find that CO2 ice crystals in the Martian atmosphere will be cubes, octahedrons, or a combination thereof (truncated octahedrons), depending largely on which crystal growth mechanism is active. The values of these physical parameters are also important for calculating the nucleation and growth rates of cloud particles in a microphysical model. I will present calculations of the scattering phase function for these shapes, at visible and infrared wavelengths, for comparison with the Mie phase functions for spheres. [1] Hansen, G. B., JGR v.102, p.21569, 1997 [2] Kieffer, H. H. and T. Z. Martin, JGR v. 82, p.4249, 1977 [3] Forget, F. and R. T. Pierrehumbert, Science v.278, p.1273, 1997 [4] Mischna, M. A. et al., Icarus v.145, p.546, 2000 [5] Wood, S. E., Ph

  19. TheoReTS - An information system for theoretical spectra based on variational predictions from molecular potential energy and dipole moment surfaces

    NASA Astrophysics Data System (ADS)

    Rey, Michaël; Nikitin, Andrei V.; Babikov, Yurii L.; Tyuterev, Vladimir G.

    2016-09-01

    Knowledge of intensities of rovibrational transitions of various molecules and theirs isotopic species in wide spectral and temperature ranges is essential for the modeling of optical properties of planetary atmospheres, brown dwarfs and for other astrophysical applications. TheoReTS ("Theoretical Reims-Tomsk Spectral data") is an Internet accessible information system devoted to ab initio based rotationally resolved spectra predictions for some relevant molecular species. All data were generated from potential energy and dipole moment surfaces computed via high-level electronic structure calculations using variational methods for vibration-rotation energy levels and transitions. When available, empirical corrections to band centers were applied, all line intensities remaining purely ab initio. The current TheoReTS implementation contains information on four-to-six atomic molecules, including phosphine, methane, ethylene, silane, methyl-fluoride, and their isotopic species 13CH4 , 12CH3D , 12CH2D2 , 12CD4 , 13C2H4, … . Predicted hot methane line lists up to T = 2000 K are included. The information system provides the associated software for spectra simulation including absorption coefficient, absorption and emission cross-sections, transmittance and radiance. The simulations allow Lorentz, Gauss and Voight line shapes. Rectangular, triangular, Lorentzian, Gaussian, sinc and sinc squared apparatus function can be used with user-defined specifications for broadening parameters and spectral resolution. All information is organized as a relational database with the user-friendly graphical interface according to Model-View-Controller architectural tools. The full-featured web application is written on PHP using Yii framework and C++ software modules. In case of very large high-temperature line lists, a data compression is implemented for fast interactive spectra simulations of a quasi-continual absorption due to big line density. Applications for the TheoReTS may

  20. aPPRove: An HMM-Based Method for Accurate Prediction of RNA-Pentatricopeptide Repeat Protein Binding Events.

    PubMed

    Harrison, Thomas; Ruiz, Jaime; Sloan, Daniel B; Ben-Hur, Asa; Boucher, Christina

    2016-01-01

    Pentatricopeptide repeat containing proteins (PPRs) bind to RNA transcripts originating from mitochondria and plastids. There are two classes of PPR proteins. The [Formula: see text] class contains tandem [Formula: see text]-type motif sequences, and the [Formula: see text] class contains alternating [Formula: see text], [Formula: see text] and [Formula: see text] type sequences. In this paper, we describe a novel tool that predicts PPR-RNA interaction; specifically, our method, which we call aPPRove, determines where and how a [Formula: see text]-class PPR protein will bind to RNA when given a PPR and one or more RNA transcripts by using a combinatorial binding code for site specificity proposed by Barkan et al. Our results demonstrate that aPPRove successfully locates how and where a PPR protein belonging to the [Formula: see text] class can bind to RNA. For each binding event it outputs the binding site, the amino-acid-nucleotide interaction, and its statistical significance. Furthermore, we show that our method can be used to predict binding events for [Formula: see text]-class proteins using a known edit site and the statistical significance of aligning the PPR protein to that site. In particular, we use our method to make a conjecture regarding an interaction between CLB19 and the second intronic region of ycf3. The aPPRove web server can be found at www.cs.colostate.edu/~approve. PMID:27560805

  1. A 3D-CFD code for accurate prediction of fluid flows and fluid forces in seals

    NASA Technical Reports Server (NTRS)

    Athavale, M. M.; Przekwas, A. J.; Hendricks, R. C.

    1994-01-01

    Current and future turbomachinery requires advanced seal configurations to control leakage, inhibit mixing of incompatible fluids and to control the rotodynamic response. In recognition of a deficiency in the existing predictive methodology for seals, a seven year effort was established in 1990 by NASA's Office of Aeronautics Exploration and Technology, under the Earth-to-Orbit Propulsion program, to develop validated Computational Fluid Dynamics (CFD) concepts, codes and analyses for seals. The effort will provide NASA and the U.S. Aerospace Industry with advanced CFD scientific codes and industrial codes for analyzing and designing turbomachinery seals. An advanced 3D CFD cylindrical seal code has been developed, incorporating state-of-the-art computational methodology for flow analysis in straight, tapered and stepped seals. Relevant computational features of the code include: stationary/rotating coordinates, cylindrical and general Body Fitted Coordinates (BFC) systems, high order differencing schemes, colocated variable arrangement, advanced turbulence models, incompressible/compressible flows, and moving grids. This paper presents the current status of code development, code demonstration for predicting rotordynamic coefficients, numerical parametric study of entrance loss coefficients for generic annular seals, and plans for code extensions to labyrinth, damping, and other seal configurations.

  2. aPPRove: An HMM-Based Method for Accurate Prediction of RNA-Pentatricopeptide Repeat Protein Binding Events

    PubMed Central

    Harrison, Thomas; Ruiz, Jaime; Sloan, Daniel B.; Ben-Hur, Asa; Boucher, Christina

    2016-01-01

    Pentatricopeptide repeat containing proteins (PPRs) bind to RNA transcripts originating from mitochondria and plastids. There are two classes of PPR proteins. The P class contains tandem P-type motif sequences, and the PLS class contains alternating P, L and S type sequences. In this paper, we describe a novel tool that predicts PPR-RNA interaction; specifically, our method, which we call aPPRove, determines where and how a PLS-class PPR protein will bind to RNA when given a PPR and one or more RNA transcripts by using a combinatorial binding code for site specificity proposed by Barkan et al. Our results demonstrate that aPPRove successfully locates how and where a PPR protein belonging to the PLS class can bind to RNA. For each binding event it outputs the binding site, the amino-acid-nucleotide interaction, and its statistical significance. Furthermore, we show that our method can be used to predict binding events for PLS-class proteins using a known edit site and the statistical significance of aligning the PPR protein to that site. In particular, we use our method to make a conjecture regarding an interaction between CLB19 and the second intronic region of ycf3. The aPPRove web server can be found at www.cs.colostate.edu/~approve. PMID:27560805

  3. High Speed Research Noise Prediction Code (HSRNOISE) User's and Theoretical Manual

    NASA Technical Reports Server (NTRS)

    Golub, Robert (Technical Monitor); Rawls, John W., Jr.; Yeager, Jessie C.

    2004-01-01

    This report describes a computer program, HSRNOISE, that predicts noise levels for a supersonic aircraft powered by mixed flow turbofan engines with rectangular mixer-ejector nozzles. It fully documents the noise prediction algorithms, provides instructions for executing the HSRNOISE code, and provides predicted noise levels for the High Speed Research (HSR) program Technology Concept (TC) aircraft. The component source noise prediction algorithms were developed jointly by Boeing, General Electric Aircraft Engines (GEAE), NASA and Pratt & Whitney during the course of the NASA HSR program. Modern Technologies Corporation developed an alternative mixer ejector jet noise prediction method under contract to GEAE that has also been incorporated into the HSRNOISE prediction code. Algorithms for determining propagation effects and calculating noise metrics were taken from the NASA Aircraft Noise Prediction Program.

  4. IrisPlex: a sensitive DNA tool for accurate prediction of blue and brown eye colour in the absence of ancestry information.

    PubMed

    Walsh, Susan; Liu, Fan; Ballantyne, Kaye N; van Oven, Mannis; Lao, Oscar; Kayser, Manfred

    2011-06-01

    A new era of 'DNA intelligence' is arriving in forensic biology, due to the impending ability to predict externally visible characteristics (EVCs) from biological material such as those found at crime scenes. EVC prediction from forensic samples, or from body parts, is expected to help concentrate police investigations towards finding unknown individuals, at times when conventional DNA profiling fails to provide informative leads. Here we present a robust and sensitive tool, termed IrisPlex, for the accurate prediction of blue and brown eye colour from DNA in future forensic applications. We used the six currently most eye colour-informative single nucleotide polymorphisms (SNPs) that previously revealed prevalence-adjusted prediction accuracies of over 90% for blue and brown eye colour in 6168 Dutch Europeans. The single multiplex assay, based on SNaPshot chemistry and capillary electrophoresis, both widely used in forensic laboratories, displays high levels of genotyping sensitivity with complete profiles generated from as little as 31pg of DNA, approximately six human diploid cell equivalents. We also present a prediction model to correctly classify an individual's eye colour, via probability estimation solely based on DNA data, and illustrate the accuracy of the developed prediction test on 40 individuals from various geographic origins. Moreover, we obtained insights into the worldwide allele distribution of these six SNPs using the HGDP-CEPH samples of 51 populations. Eye colour prediction analyses from HGDP-CEPH samples provide evidence that the test and model presented here perform reliably without prior ancestry information, although future worldwide genotype and phenotype data shall confirm this notion. As our IrisPlex eye colour prediction test is capable of immediate implementation in forensic casework, it represents one of the first steps forward in the creation of a fully individualised EVC prediction system for future use in forensic DNA intelligence.

  5. Accurate prediction of secreted substrates and identification of a conserved putative secretion signal for type III secretion systems

    SciTech Connect

    Samudrala, Ram; Heffron, Fred; McDermott, Jason E.

    2009-04-24

    The type III secretion system is an essential component for virulence in many Gram-negative bacteria. Though components of the secretion system apparatus are conserved, its substrates, effector proteins, are not. We have used a machine learning approach to identify new secreted effectors. The method integrates evolutionary measures, such as the pattern of homologs in a range of other organisms, and sequence-based features, such as G+C content, amino acid composition and the N-terminal 30 residues of the protein sequence. The method was trained on known effectors from Salmonella typhimurium and validated on a corresponding set of effectors from Pseudomonas syringae, after eliminating effectors with detectable sequence similarity. The method was able to identify all of the known effectors in P. syringae with a specificity of 84% and sensitivity of 82%. The reciprocal validation, training on P. syringae and validating on S. typhimurium, gave similar results with a specificity of 86% when the sensitivity level was 87%. These results show that type III effectors in disparate organisms share common features. We found that maximal performance is attained by including an N-terminal sequence of only 30 residues, which agrees with previous studies indicating that this region contains the secretion signal. We then used the method to define the most important residues in this putative secretion signal. Finally, we present novel predictions of secreted effectors in S. typhimurium, some of which have been experimentally validated, and apply the method to predict secreted effectors in the genetically intractable human pathogen Chlamydia trachomatis. This approach is a novel and effective way to identify secreted effectors in a broad range of pathogenic bacteria for further experimental characterization and provides insight into the nature of the type III secretion signal.

  6. Breaking the Theoretical Scaling Limit for Predicting Quasiparticle Energies: The Stochastic GW Approach

    NASA Astrophysics Data System (ADS)

    Neuhauser, Daniel; Gao, Yi; Arntsen, Christopher; Karshenas, Cyrus; Rabani, Eran; Baer, Roi

    2014-08-01

    We develop a formalism to calculate the quasiparticle energy within the GW many-body perturbation correction to the density functional theory. The occupied and virtual orbitals of the Kohn-Sham Hamiltonian are replaced by stochastic orbitals used to evaluate the Green function G, the polarization potential W, and, thereby, the GW self-energy. The stochastic GW (sGW) formalism relies on novel theoretical concepts such as stochastic time-dependent Hartree propagation, stochastic matrix compression, and spatial or temporal stochastic decoupling techniques. Beyond the theoretical interest, the formalism enables linear scaling GW calculations breaking the theoretical scaling limit for GW as well as circumventing the need for energy cutoff approximations. We illustrate the method for silicon nanocrystals of varying sizes with Ne>3000 electrons.

  7. Predicting College Students' First Year Success: Should Soft Skills Be Taken into Consideration to More Accurately Predict the Academic Achievement of College Freshmen?

    ERIC Educational Resources Information Center

    Powell, Erica Dion

    2013-01-01

    This study presents a survey developed to measure the skills of entering college freshmen in the areas of responsibility, motivation, study habits, literacy, and stress management, and explores the predictive power of this survey as a measure of academic performance during the first semester of college. The survey was completed by 334 incoming…

  8. Predicting Antimicrobial Resistance Prevalence and Incidence from Indicators of Antimicrobial Use: What Is the Most Accurate Indicator for Surveillance in Intensive Care Units?

    PubMed Central

    Fortin, Élise; Platt, Robert W.; Fontela, Patricia S.; Buckeridge, David L.; Quach, Caroline

    2015-01-01

    Objective The optimal way to measure antimicrobial use in hospital populations, as a complement to surveillance of resistance is still unclear. Using respiratory isolates and antimicrobial prescriptions of nine intensive care units (ICUs), this study aimed to identify the indicator of antimicrobial use that predicted prevalence and incidence rates of resistance with the best accuracy. Methods Retrospective cohort study including all patients admitted to three neonatal (NICU), two pediatric (PICU) and four adult ICUs between April 2006 and March 2010. Ten different resistance / antimicrobial use combinations were studied. After adjustment for ICU type, indicators of antimicrobial use were successively tested in regression models, to predict resistance prevalence and incidence rates, per 4-week time period, per ICU. Binomial regression and Poisson regression were used to model prevalence and incidence rates, respectively. Multiplicative and additive models were tested, as well as no time lag and a one 4-week-period time lag. For each model, the mean absolute error (MAE) in prediction of resistance was computed. The most accurate indicator was compared to other indicators using t-tests. Results Results for all indicators were equivalent, except for 1/20 scenarios studied. In this scenario, where prevalence of carbapenem-resistant Pseudomonas sp. was predicted with carbapenem use, recommended daily doses per 100 admissions were less accurate than courses per 100 patient-days (p = 0.0006). Conclusions A single best indicator to predict antimicrobial resistance might not exist. Feasibility considerations such as ease of computation or potential external comparisons could be decisive in the choice of an indicator for surveillance of healthcare antimicrobial use. PMID:26710322

  9. The calculation of theoretical chromospheric models and predicted OSO 1 spectra

    NASA Technical Reports Server (NTRS)

    Avrett, E. H.

    1975-01-01

    Theoretical solar chromospheric and photospheric models are computed for use in analyzing OSO 8 spectra. The Vernazza, Avrett, and Loeser (1976) solar model is updated and self-consistent non-LTE number densities for H I, He I, He II, C I, Mg I, Al I, Si I, and H(-) are produced. These number densities are used in the calculation of a theoretical solar spectrum from 90 to 250 nm, including approximately 7000 lines in non-LTE. More than 60,000 lines of other elements are treated with approximate source functions.

  10. Microdosing of a Carbon-14 Labeled Protein in Healthy Volunteers Accurately Predicts Its Pharmacokinetics at Therapeutic Dosages.

    PubMed

    Vlaming, M L H; van Duijn, E; Dillingh, M R; Brands, R; Windhorst, A D; Hendrikse, N H; Bosgra, S; Burggraaf, J; de Koning, M C; Fidder, A; Mocking, J A J; Sandman, H; de Ligt, R A F; Fabriek, B O; Pasman, W J; Seinen, W; Alves, T; Carrondo, M; Peixoto, C; Peeters, P A M; Vaes, W H J

    2015-08-01

    Preclinical development of new biological entities (NBEs), such as human protein therapeutics, requires considerable expenditure of time and costs. Poor prediction of pharmacokinetics in humans further reduces net efficiency. In this study, we show for the first time that pharmacokinetic data of NBEs in humans can be successfully obtained early in the drug development process by the use of microdosing in a small group of healthy subjects combined with ultrasensitive accelerator mass spectrometry (AMS). After only minimal preclinical testing, we performed a first-in-human phase 0/phase 1 trial with a human recombinant therapeutic protein (RESCuing Alkaline Phosphatase, human recombinant placental alkaline phosphatase [hRESCAP]) to assess its safety and kinetics. Pharmacokinetic analysis showed dose linearity from microdose (53 μg) [(14) C]-hRESCAP to therapeutic doses (up to 5.3 mg) of the protein in healthy volunteers. This study demonstrates the value of a microdosing approach in a very small cohort for accelerating the clinical development of NBEs. PMID:25869840

  11. A new accurate ground-state potential energy surface of ethylene and predictions for rotational and vibrational energy levels

    NASA Astrophysics Data System (ADS)

    Delahaye, Thibault; Nikitin, Andrei; Rey, Michaël; Szalay, Péter G.; Tyuterev, Vladimir G.

    2014-09-01

    In this paper we report a new ground state potential energy surface for ethylene (ethene) C2H4 obtained from extended ab initio calculations. The coupled-cluster approach with the perturbative inclusion of the connected triple excitations CCSD(T) and correlation consistent polarized valence basis set cc-pVQZ was employed for computations of electronic ground state energies. The fit of the surface included 82 542 nuclear configurations using sixth order expansion in curvilinear symmetry-adapted coordinates involving 2236 parameters. A good convergence for variationally computed vibrational levels of the C2H4 molecule was obtained with a RMS(Obs.-Calc.) deviation of 2.7 cm-1 for fundamental bands centers and 5.9 cm-1 for vibrational bands up to 7800 cm-1. Large scale vibrational and rotational calculations for 12C2H4, 13C2H4, and 12C2D4 isotopologues were performed using this new surface. Energy levels for J = 20 up to 6000 cm-1 are in a good agreement with observations. This represents a considerable improvement with respect to available global predictions of vibrational levels of 13C2H4 and 12C2D4 and rovibrational levels of 12C2H4.

  12. Integrating metabolic performance, thermal tolerance, and plasticity enables for more accurate predictions on species vulnerability to acute and chronic effects of global warming.

    PubMed

    Magozzi, Sarah; Calosi, Piero

    2015-01-01

    Predicting species vulnerability to global warming requires a comprehensive, mechanistic understanding of sublethal and lethal thermal tolerances. To date, however, most studies investigating species physiological responses to increasing temperature have focused on the underlying physiological traits of either acute or chronic tolerance in isolation. Here we propose an integrative, synthetic approach including the investigation of multiple physiological traits (metabolic performance and thermal tolerance), and their plasticity, to provide more accurate and balanced predictions on species and assemblage vulnerability to both acute and chronic effects of global warming. We applied this approach to more accurately elucidate relative species vulnerability to warming within an assemblage of six caridean prawns occurring in the same geographic, hence macroclimatic, region, but living in different thermal habitats. Prawns were exposed to four incubation temperatures (10, 15, 20 and 25 °C) for 7 days, their metabolic rates and upper thermal limits were measured, and plasticity was calculated according to the concept of Reaction Norms, as well as Q10 for metabolism. Compared to species occupying narrower/more stable thermal niches, species inhabiting broader/more variable thermal environments (including the invasive Palaemon macrodactylus) are likely to be less vulnerable to extreme acute thermal events as a result of their higher upper thermal limits. Nevertheless, they may be at greater risk from chronic exposure to warming due to the greater metabolic costs they incur. Indeed, a trade-off between acute and chronic tolerance was apparent in the assemblage investigated. However, the invasive species P. macrodactylus represents an exception to this pattern, showing elevated thermal limits and plasticity of these limits, as well as a high metabolic control. In general, integrating multiple proxies for species physiological acute and chronic responses to increasing

  13. Infectious titres of sheep scrapie and bovine spongiform encephalopathy agents cannot be accurately predicted from quantitative laboratory test results.

    PubMed

    González, Lorenzo; Thorne, Leigh; Jeffrey, Martin; Martin, Stuart; Spiropoulos, John; Beck, Katy E; Lockey, Richard W; Vickery, Christopher M; Holder, Thomas; Terry, Linda

    2012-11-01

    It is widely accepted that abnormal forms of the prion protein (PrP) are the best surrogate marker for the infectious agent of prion diseases and, in practice, the detection of such disease-associated (PrP(d)) and/or protease-resistant (PrP(res)) forms of PrP is the cornerstone of diagnosis and surveillance of the transmissible spongiform encephalopathies (TSEs). Nevertheless, some studies question the consistent association between infectivity and abnormal PrP detection. To address this discrepancy, 11 brain samples of sheep affected with natural scrapie or experimental bovine spongiform encephalopathy were selected on the basis of the magnitude and predominant types of PrP(d) accumulation, as shown by immunohistochemical (IHC) examination; contra-lateral hemi-brain samples were inoculated at three different dilutions into transgenic mice overexpressing ovine PrP and were also subjected to quantitative analysis by three biochemical tests (BCTs). Six samples gave 'low' infectious titres (10⁶·⁵ to 10⁶·⁷ LD₅₀ g⁻¹) and five gave 'high titres' (10⁸·¹ to ≥ 10⁸·⁷ LD₅₀ g⁻¹) and, with the exception of the Western blot analysis, those two groups tended to correspond with samples with lower PrP(d)/PrP(res) results by IHC/BCTs. However, no statistical association could be confirmed due to high individual sample variability. It is concluded that although detection of abnormal forms of PrP by laboratory methods remains useful to confirm TSE infection, infectivity titres cannot be predicted from quantitative test results, at least for the TSE sources and host PRNP genotypes used in this study. Furthermore, the near inverse correlation between infectious titres and Western blot results (high protease pre-treatment) argues for a dissociation between infectivity and PrP(res).

  14. A new accurate ground-state potential energy surface of ethylene and predictions for rotational and vibrational energy levels

    SciTech Connect

    Delahaye, Thibault Rey, Michaël Tyuterev, Vladimir G.; Nikitin, Andrei; Szalay, Péter G.

    2014-09-14

    In this paper we report a new ground state potential energy surface for ethylene (ethene) C{sub 2}H{sub 4} obtained from extended ab initio calculations. The coupled-cluster approach with the perturbative inclusion of the connected triple excitations CCSD(T) and correlation consistent polarized valence basis set cc-pVQZ was employed for computations of electronic ground state energies. The fit of the surface included 82 542 nuclear configurations using sixth order expansion in curvilinear symmetry-adapted coordinates involving 2236 parameters. A good convergence for variationally computed vibrational levels of the C{sub 2}H{sub 4} molecule was obtained with a RMS(Obs.–Calc.) deviation of 2.7 cm{sup −1} for fundamental bands centers and 5.9 cm{sup −1} for vibrational bands up to 7800 cm{sup −1}. Large scale vibrational and rotational calculations for {sup 12}C{sub 2}H{sub 4}, {sup 13}C{sub 2}H{sub 4}, and {sup 12}C{sub 2}D{sub 4} isotopologues were performed using this new surface. Energy levels for J = 20 up to 6000 cm{sup −1} are in a good agreement with observations. This represents a considerable improvement with respect to available global predictions of vibrational levels of {sup 13}C{sub 2}H{sub 4} and {sup 12}C{sub 2}D{sub 4} and rovibrational levels of {sup 12}C{sub 2}H{sub 4}.

  15. Theoretical predictions of jet interaction effects for USB and OWB configurations

    NASA Technical Reports Server (NTRS)

    Lan, C. E.; Campbell, J. F.

    1976-01-01

    A wing jet interaction theory is presented for predicting the aerodynamic characteristics of upper surface blowing and over wing blowing configurations. For the latter configurations, a new jet entrainment theory is developed. Comparison of predicted results with some available data showed good agreement. Some applications of the theory are also presented.

  16. Noncontrast computed tomography can predict the outcome of shockwave lithotripsy via accurate stone measurement and abdominal fat distribution determination.

    PubMed

    Geng, Jiun-Hung; Tu, Hung-Pin; Shih, Paul Ming-Chen; Shen, Jung-Tsung; Jang, Mei-Yu; Wu, Wen-Jen; Li, Ching-Chia; Chou, Yii-Her; Juan, Yung-Shun

    2015-01-01

    Urolithiasis is a common disease of the urinary system. Extracorporeal shockwave lithotripsy (SWL) has become one of the standard treatments for renal and ureteral stones; however, the success rates range widely and failure of stone disintegration may cause additional outlay, alternative procedures, and even complications. We used the data available from noncontrast abdominal computed tomography (NCCT) to evaluate the impact of stone parameters and abdominal fat distribution on calculus-free rates following SWL. We retrospectively reviewed 328 patients who had urinary stones and had undergone SWL from August 2012 to August 2013. All of them received pre-SWL NCCT; 1 month after SWL, radiography was arranged to evaluate the condition of the fragments. These patients were classified into stone-free group and residual stone group. Unenhanced computed tomography variables, including stone attenuation, abdominal fat area, and skin-to-stone distance (SSD) were analyzed. In all, 197 (60%) were classified as stone-free and 132 (40%) as having residual stone. The mean ages were 49.35 ± 13.22 years and 55.32 ± 13.52 years, respectively. On univariate analysis, age, stone size, stone surface area, stone attenuation, SSD, total fat area (TFA), abdominal circumference, serum creatinine, and the severity of hydronephrosis revealed statistical significance between these two groups. From multivariate logistic regression analysis, the independent parameters impacting SWL outcomes were stone size, stone attenuation, TFA, and serum creatinine. [Adjusted odds ratios and (95% confidence intervals): 9.49 (3.72-24.20), 2.25 (1.22-4.14), 2.20 (1.10-4.40), and 2.89 (1.35-6.21) respectively, all p < 0.05]. In the present study, stone size, stone attenuation, TFA and serum creatinine were four independent predictors for stone-free rates after SWL. These findings suggest that pretreatment NCCT may predict the outcomes after SWL. Consequently, we can use these predictors for selecting

  17. Theoretical Predictions of the thermodynamic Properties of Solid Sorbents Capture CO2 Applications

    SciTech Connect

    Duan, Yuhua; Sorescu, Dan; Luebke David; Pennline, Henry

    2012-05-02

    We are establishing a theoretical procedure to identify most potential candidates of CO{sub 2} solid sorbents from a large solid material databank to meet the DOE programmatic goal for energy conversion; and to explore the optimal working conditions for the promising CO{sub 2} solid sorbents, especially from room to warm T ranges with optimal energy usage, used for both pre- and post-combustion capture technologies.

  18. Ultrasonic Imaging and Theoretical Prediction of Orthotropic Plate Stiffness in all Planar Directions

    SciTech Connect

    Telschow, Kenneth Louis; Deason, Vance Albert; Mukdadi, O.; Datta, S. K.

    2000-07-01

    Exact and approximate theoretical analysis of the wavelengths of plate wave mode propagation in all planar directions for the dispersive antisymmetric Lamb wave mode are compared with measurements from a laser ultrasonic imaging approach that records the out of plane ultrasonic motion over a large area in a single frame without scanning. Good agreement is demonstrated, based on independent determination of the elastic constants, for two different types of paper.

  19. An Accurate GPS-IMU/DR Data Fusion Method for Driverless Car Based on a Set of Predictive Models and Grid Constraints.

    PubMed

    Wang, Shiyao; Deng, Zhidong; Yin, Gang

    2016-02-24

    A high-performance differential global positioning system (GPS)  receiver with real time kinematics provides absolute localization for driverless cars. However, it is not only susceptible to multipath effect but also unable to effectively fulfill precise error correction in a wide range of driving areas. This paper proposes an accurate GPS-inertial measurement unit (IMU)/dead reckoning (DR) data fusion method based on a set of predictive models and occupancy grid constraints. First, we employ a set of autoregressive and moving average (ARMA) equations that have different structural parameters to build maximum likelihood models of raw navigation. Second, both grid constraints and spatial consensus checks on all predictive results and current measurements are required to have removal of outliers. Navigation data that satisfy stationary stochastic process are further fused to achieve accurate localization results. Third, the standard deviation of multimodal data fusion can be pre-specified by grid size. Finally, we perform a lot of field tests on a diversity of real urban scenarios. The experimental results demonstrate that the method can significantly smooth small jumps in bias and considerably reduce accumulated position errors due to DR. With low computational complexity, the position accuracy of our method surpasses existing state-of-the-arts on the same dataset and the new data fusion method is practically applied in our driverless car.

  20. An Accurate GPS-IMU/DR Data Fusion Method for Driverless Car Based on a Set of Predictive Models and Grid Constraints

    PubMed Central

    Wang, Shiyao; Deng, Zhidong; Yin, Gang

    2016-01-01

    A high-performance differential global positioning system (GPS)  receiver with real time kinematics provides absolute localization for driverless cars. However, it is not only susceptible to multipath effect but also unable to effectively fulfill precise error correction in a wide range of driving areas. This paper proposes an accurate GPS–inertial measurement unit (IMU)/dead reckoning (DR) data fusion method based on a set of predictive models and occupancy grid constraints. First, we employ a set of autoregressive and moving average (ARMA) equations that have different structural parameters to build maximum likelihood models of raw navigation. Second, both grid constraints and spatial consensus checks on all predictive results and current measurements are required to have removal of outliers. Navigation data that satisfy stationary stochastic process are further fused to achieve accurate localization results. Third, the standard deviation of multimodal data fusion can be pre-specified by grid size. Finally, we perform a lot of field tests on a diversity of real urban scenarios. The experimental results demonstrate that the method can significantly smooth small jumps in bias and considerably reduce accumulated position errors due to DR. With low computational complexity, the position accuracy of our method surpasses existing state-of-the-arts on the same dataset and the new data fusion method is practically applied in our driverless car. PMID:26927108

  1. An Accurate GPS-IMU/DR Data Fusion Method for Driverless Car Based on a Set of Predictive Models and Grid Constraints.

    PubMed

    Wang, Shiyao; Deng, Zhidong; Yin, Gang

    2016-01-01

    A high-performance differential global positioning system (GPS)  receiver with real time kinematics provides absolute localization for driverless cars. However, it is not only susceptible to multipath effect but also unable to effectively fulfill precise error correction in a wide range of driving areas. This paper proposes an accurate GPS-inertial measurement unit (IMU)/dead reckoning (DR) data fusion method based on a set of predictive models and occupancy grid constraints. First, we employ a set of autoregressive and moving average (ARMA) equations that have different structural parameters to build maximum likelihood models of raw navigation. Second, both grid constraints and spatial consensus checks on all predictive results and current measurements are required to have removal of outliers. Navigation data that satisfy stationary stochastic process are further fused to achieve accurate localization results. Third, the standard deviation of multimodal data fusion can be pre-specified by grid size. Finally, we perform a lot of field tests on a diversity of real urban scenarios. The experimental results demonstrate that the method can significantly smooth small jumps in bias and considerably reduce accumulated position errors due to DR. With low computational complexity, the position accuracy of our method surpasses existing state-of-the-arts on the same dataset and the new data fusion method is practically applied in our driverless car. PMID:26927108

  2. Profile-QSAR: a novel meta-QSAR method that combines activities across the kinase family to accurately predict affinity, selectivity, and cellular activity.

    PubMed

    Martin, Eric; Mukherjee, Prasenjit; Sullivan, David; Jansen, Johanna

    2011-08-22

    Profile-QSAR is a novel 2D predictive model building method for kinases. This "meta-QSAR" method models the activity of each compound against a new kinase target as a linear combination of its predicted activities against a large panel of 92 previously studied kinases comprised from 115 assays. Profile-QSAR starts with a sparse incomplete kinase by compound (KxC) activity matrix, used to generate Bayesian QSAR models for the 92 "basis-set" kinases. These Bayesian QSARs generate a complete "synthetic" KxC activity matrix of predictions. These synthetic activities are used as "chemical descriptors" to train partial-least squares (PLS) models, from modest amounts of medium-throughput screening data, for predicting activity against new kinases. The Profile-QSAR predictions for the 92 kinases (115 assays) gave a median external R²(ext) = 0.59 on 25% held-out test sets. The method has proven accurate enough to predict pairwise kinase selectivities with a median correlation of R²(ext) = 0.61 for 958 kinase pairs with at least 600 common compounds. It has been further expanded by adding a "C(k)XC" cellular activity matrix to the KxC matrix to predict cellular activity for 42 kinase driven cellular assays with median R²(ext) = 0.58 for 24 target modulation assays and R²(ext) = 0.41 for 18 cell proliferation assays. The 2D Profile-QSAR, along with the 3D Surrogate AutoShim, are the foundations of an internally developed iterative medium-throughput screening (IMTS) methodology for virtual screening (VS) of compound archives as an alternative to experimental high-throughput screening (HTS). The method has been applied to 20 actual prospective kinase projects. Biological results have so far been obtained in eight of them. Q² values ranged from 0.3 to 0.7. Hit-rates at 10 uM for experimentally tested compounds varied from 25% to 80%, except in K5, which was a special case aimed specifically at finding "type II" binders, where none of the compounds were predicted to be

  3. Predicting the viscosity and electrical conductivity of ionic liquids on the basis of theoretically calculated ionic volumes

    NASA Astrophysics Data System (ADS)

    Wileńska, Dorota; Anusiewicz, Iwona; Freza, Sylwia; Bobrowski, Maciej; Laux, Edith; Uhl, Stefanie; Keppner, Herbert; Skurski, Piotr

    2015-03-01

    Selected physical properties of the ionic liquids might be quantitatively predicted based on the volumes of the ions these systems are composed of. It is demonstrated that the ionic volumes calculated using relatively simple theoretical quantum chemistry methods can be utilised to estimate the viscosities and electrical conductivities of various commonly used ionic liquids. The fitting formulas of the exponential form are offered and their predictive usefulness is verified. The quality of such predictions is discussed on the basis of several ionic liquids involving [Tf2N]‑ and [BF4]‑ anions and 16 various cations. The dependence of the viscosity and electrical conductivity of the ionic liquids on the temperature is also investigated and the temperature-dependent equations are derived and compared to the experimentally measured values.

  4. A comparison between theoretical prediction and experimental measurement of the dynamic behavior of spur gears

    NASA Technical Reports Server (NTRS)

    Rebbechi, Brian; Forrester, B. David; Oswald, Fred B.; Townsend, Dennis P.

    1992-01-01

    A comparison was made between computer model predictions of gear dynamics behavior and experimental results. The experimental data were derived from the NASA gear noise rig, which was used to record dynamic tooth loads and vibration. The experimental results were compared with predictions from the DSTO Aeronautical Research Laboratory's gear dynamics code for a matrix of 28 load speed points. At high torque the peak dynamic load predictions agree with the experimental results with an average error of 5 percent in the speed range 800 to 6000 rpm. Tooth separation (or bounce), which was observed in the experimental data for light torque, high speed conditions, was simulated by the computer model. The model was also successful in simulating the degree of load sharing between gear teeth in the multiple tooth contact region.

  5. Advanced turboprop noise prediction: Development of a code at NASA Langley based on recent theoretical results

    NASA Technical Reports Server (NTRS)

    Farassat, F.; Dunn, M. H.; Padula, S. L.

    1986-01-01

    The development of a high speed propeller noise prediction code at Langley Research Center is described. The code utilizes two recent acoustic formulations in the time domain for subsonic and supersonic sources. The structure and capabilities of the code are discussed. Grid size study for accuracy and speed of execution on a computer is also presented. The code is tested against an earlier Langley code. Considerable increase in accuracy and speed of execution are observed. Some examples of noise prediction of a high speed propeller for which acoustic test data are available are given. A brisk derivation of formulations used is given in an appendix.

  6. A theoretical model for the prediction of vertical axis wind turbine performance

    NASA Astrophysics Data System (ADS)

    Fortunato, B.; Dadone, A.; Trifoni, V.

    1993-01-01

    The present paper provides a two-dimensional model for the computation of the flow field around vertical axis wind turbines. The model considers the effect of the blades in a time averaged sense by means of an actuator porous cylinder, having the turbine radius. The numerical method here employed is the 'fast solver', which is a natural extension of the classical lambda formulation and is based on the integration of the compatibility conditions along bicharacteristic lines. The vertical axis wind turbine performance obtained with the present method are compared with other theoretical and experimental results.

  7. A theoretical model to predict tensile deformation behavior of balloon catheter.

    PubMed

    Todo, Mitsugu; Yoshiya, Keiji; Matsumoto, Takuya

    2016-09-01

    In this technical note, a simple theoretical model was proposed to express the tensile deformation and fracture of balloon catheter tested by the ISO standard using piece-wise linear force-displacement relations. The model was then validated by comparing with the tensile force-displacement behaviors of two types of typical balloon catheters clinically used worldwide. It was shown that the proposed model can effectively be used to express the tensile deformation behavior and easily be handled by physicians who are not familiar with mechanics of materials. PMID:27214691

  8. Recombination rate variation and speciation: theoretical predictions and empirical results from rabbits and mice.

    PubMed

    Nachman, Michael W; Payseur, Bret A

    2012-02-01

    Recently diverged taxa may continue to exchange genes. A number of models of speciation with gene flow propose that the frequency of gene exchange will be lower in genomic regions of low recombination and that these regions will therefore be more differentiated. However, several population-genetic models that focus on selection at linked sites also predict greater differentiation in regions of low recombination simply as a result of faster sorting of ancestral alleles even in the absence of gene flow. Moreover, identifying the actual amount of gene flow from patterns of genetic variation is tricky, because both ancestral polymorphism and migration lead to shared variation between recently diverged taxa. New analytic methods have been developed to help distinguish ancestral polymorphism from migration. Along with a growing number of datasets of multi-locus DNA sequence variation, these methods have spawned a renewed interest in speciation models with gene flow. Here, we review both speciation and population-genetic models that make explicit predictions about how the rate of recombination influences patterns of genetic variation within and between species. We then compare those predictions with empirical data of DNA sequence variation in rabbits and mice. We find strong support for the prediction that genomic regions experiencing low levels of recombination are more differentiated. In most cases, reduced gene flow appears to contribute to the pattern, although disentangling the relative contribution of reduced gene flow and selection at linked sites remains a challenge. We suggest fruitful areas of research that might help distinguish between different models.

  9. Information-theoretic indices usage for the prediction and calculation of octanol-water partition coefficient.

    PubMed

    Persona, Marek; Kutarov, Vladimir V; Kats, Boris M; Persona, Andrzej; Marczewska, Barbara

    2007-01-01

    The paper describes the new prediction method of octanol-water partition coefficient, which is based on molecular graph theory. The results obtained using the new method are well correlated with experimental values. These results were compared with the ones obtained by use of ten other structure correlated methods. The comparison shows that graph theory can be very useful in structure correlation research.

  10. Theoretical prediction of the vibrational spectrum of naphthalene in the first excited singlet state

    NASA Astrophysics Data System (ADS)

    Swiderek, Petra; Hohlneicher, Georg; Maluendes, Sergio A.; Dupuis, Michel

    1993-01-01

    Complete harmonic force fields have been calculated for the ground state (S0) and the first excited singlet state (S1) of naphthalene using the multiconfiguration self-consistent field (MCSCF) approach. Identical calculations were performed for benzene to test the methodology with already available theoretical and empirical force fields. Two different basis sets were applied (STO-3G and near double-zeta) and all π-orbitals included in the active space. The geometries of ground and excited states were separately optimized. Following the ideas of Pulay, the force constants were scaled before calculating frequencies and normal modes. For the ground states the influence of correlation is discussed by comparison with Pulay's results. Except for special vibrations where correlation effects turn out to be important, the use of Pulay's scaling factors leads to a satisfactory description of the in-plane-vibrations. In the case of benzene the calculated frequency shifts between S0 and S1 are in complete qualitative agreement with experimental observations. In the case of naphthalene the new theoretical results suggest several revisions of earlier empirical assignments.

  11. Prediction of redox potentials of adrenaline and its supramolecular complex with glycine: theoretical and experimental studies.

    PubMed

    Liu, Tao; Du, Chunmei; Yu, Zhangyu; Han, Lingli; Zhang, Dongju

    2013-02-21

    Protonated adrenaline (PAd) can be oxidized to protonated adrenaline quinone (PAdquinone) through a one-step, two-electron redox reaction. The electron-transfer property of PAd and its supramolecular complex with glycine has been investigated by cyclic voltammetry (CV) experiment and theoretical calculations. From CV curves, the conditional formal redox potential E°' of PAd/PAdquinone couple at the pH value of 0.29 is determined to be 0.540 V. The calculated E°' using the G3MP2//B3LYP method and the B3LYP method with 6-31G(d,p), 6-31+G(d,p), 6-311G(d,p), and B3LYP/6-311+G(d,p) basis sets are in reasonable agreement with the experimental value. PAd can form supramolecular complex (PAd-Gly) with glycine (Gly) through hydrogen bond (H-bond), and the calculated E°' values of PAd-Gly/PAdquinone-Gly redox couple are larger than those of PAd/PAdquinone couple. The theoretical results are in good agreement with the experimental finding that the formation of H-bonds weaken the electron-donating ability of PAd.

  12. An empirical/theoretical model with dimensionless numbers to predict the performance of electrodialysis systems on the basis of operating conditions.

    PubMed

    Karimi, Leila; Ghassemi, Abbas

    2016-07-01

    Among the different technologies developed for desalination, the electrodialysis/electrodialysis reversal (ED/EDR) process is one of the most promising for treating brackish water with low salinity when there is high risk of scaling. Multiple researchers have investigated ED/EDR to optimize the process, determine the effects of operating parameters, and develop theoretical/empirical models. Previously published empirical/theoretical models have evaluated the effect of the hydraulic conditions of the ED/EDR on the limiting current density using dimensionless numbers. The reason for previous studies' emphasis on limiting current density is twofold: 1) to maximize ion removal, most ED/EDR systems are operated close to limiting current conditions if there is not a scaling potential in the concentrate chamber due to a high concentration of less-soluble salts; and 2) for modeling the ED/EDR system with dimensionless numbers, it is more accurate and convenient to use limiting current density, where the boundary layer's characteristics are known at constant electrical conditions. To improve knowledge of ED/EDR systems, ED/EDR models should be also developed for the Ohmic region, where operation reduces energy consumption, facilitates targeted ion removal, and prolongs membrane life compared to limiting current conditions. In this paper, theoretical/empirical models were developed for ED/EDR performance in a wide range of operating conditions. The presented ion removal and selectivity models were developed for the removal of monovalent ions and divalent ions utilizing the dominant dimensionless numbers obtained from laboratory scale electrodialysis experiments. At any system scale, these models can predict ED/EDR performance in terms of monovalent and divalent ion removal.

  13. An empirical/theoretical model with dimensionless numbers to predict the performance of electrodialysis systems on the basis of operating conditions.

    PubMed

    Karimi, Leila; Ghassemi, Abbas

    2016-07-01

    Among the different technologies developed for desalination, the electrodialysis/electrodialysis reversal (ED/EDR) process is one of the most promising for treating brackish water with low salinity when there is high risk of scaling. Multiple researchers have investigated ED/EDR to optimize the process, determine the effects of operating parameters, and develop theoretical/empirical models. Previously published empirical/theoretical models have evaluated the effect of the hydraulic conditions of the ED/EDR on the limiting current density using dimensionless numbers. The reason for previous studies' emphasis on limiting current density is twofold: 1) to maximize ion removal, most ED/EDR systems are operated close to limiting current conditions if there is not a scaling potential in the concentrate chamber due to a high concentration of less-soluble salts; and 2) for modeling the ED/EDR system with dimensionless numbers, it is more accurate and convenient to use limiting current density, where the boundary layer's characteristics are known at constant electrical conditions. To improve knowledge of ED/EDR systems, ED/EDR models should be also developed for the Ohmic region, where operation reduces energy consumption, facilitates targeted ion removal, and prolongs membrane life compared to limiting current conditions. In this paper, theoretical/empirical models were developed for ED/EDR performance in a wide range of operating conditions. The presented ion removal and selectivity models were developed for the removal of monovalent ions and divalent ions utilizing the dominant dimensionless numbers obtained from laboratory scale electrodialysis experiments. At any system scale, these models can predict ED/EDR performance in terms of monovalent and divalent ion removal. PMID:27108213

  14. Unprecedently Large-Scale Kinase Inhibitor Set Enabling the Accurate Prediction of Compound-Kinase Activities: A Way toward Selective Promiscuity by Design?

    PubMed

    Christmann-Franck, Serge; van Westen, Gerard J P; Papadatos, George; Beltran Escudie, Fanny; Roberts, Alexander; Overington, John P; Domine, Daniel

    2016-09-26

    Drug discovery programs frequently target members of the human kinome and try to identify small molecule protein kinase inhibitors, primarily for cancer treatment, additional indications being increasingly investigated. One of the challenges is controlling the inhibitors degree of selectivity, assessed by in vitro profiling against panels of protein kinases. We manually extracted, compiled, and standardized such profiles published in the literature: we collected 356 908 data points corresponding to 482 protein kinases, 2106 inhibitors, and 661 patents. We then analyzed this data set in terms of kinome coverage, results reproducibility, popularity, and degree of selectivity of both kinases and inhibitors. We used the data set to create robust proteochemometric models capable of predicting kinase activity (the ligand-target space was modeled with an externally validated RMSE of 0.41 ± 0.02 log units and R02 0.74 ± 0.03), in order to account for missing or unreliable measurements. The influence on the prediction quality of parameters such as number of measurements, Murcko scaffold frequency or inhibitor type was assessed. Interpretation of the models enabled to highlight inhibitors and kinases properties correlated with higher affinities, and an analysis in the context of kinases crystal structures was performed. Overall, the models quality allows the accurate prediction of kinase-inhibitor activities and their structural interpretation, thus paving the way for the rational design of compounds with a targeted selectivity profile.

  15. Unprecedently Large-Scale Kinase Inhibitor Set Enabling the Accurate Prediction of Compound–Kinase Activities: A Way toward Selective Promiscuity by Design?

    PubMed Central

    2016-01-01

    Drug discovery programs frequently target members of the human kinome and try to identify small molecule protein kinase inhibitors, primarily for cancer treatment, additional indications being increasingly investigated. One of the challenges is controlling the inhibitors degree of selectivity, assessed by in vitro profiling against panels of protein kinases. We manually extracted, compiled, and standardized such profiles published in the literature: we collected 356 908 data points corresponding to 482 protein kinases, 2106 inhibitors, and 661 patents. We then analyzed this data set in terms of kinome coverage, results reproducibility, popularity, and degree of selectivity of both kinases and inhibitors. We used the data set to create robust proteochemometric models capable of predicting kinase activity (the ligand–target space was modeled with an externally validated RMSE of 0.41 ± 0.02 log units and R02 0.74 ± 0.03), in order to account for missing or unreliable measurements. The influence on the prediction quality of parameters such as number of measurements, Murcko scaffold frequency or inhibitor type was assessed. Interpretation of the models enabled to highlight inhibitors and kinases properties correlated with higher affinities, and an analysis in the context of kinases crystal structures was performed. Overall, the models quality allows the accurate prediction of kinase-inhibitor activities and their structural interpretation, thus paving the way for the rational design of compounds with a targeted selectivity profile. PMID:27482722

  16. Unprecedently Large-Scale Kinase Inhibitor Set Enabling the Accurate Prediction of Compound-Kinase Activities: A Way toward Selective Promiscuity by Design?

    PubMed

    Christmann-Franck, Serge; van Westen, Gerard J P; Papadatos, George; Beltran Escudie, Fanny; Roberts, Alexander; Overington, John P; Domine, Daniel

    2016-09-26

    Drug discovery programs frequently target members of the human kinome and try to identify small molecule protein kinase inhibitors, primarily for cancer treatment, additional indications being increasingly investigated. One of the challenges is controlling the inhibitors degree of selectivity, assessed by in vitro profiling against panels of protein kinases. We manually extracted, compiled, and standardized such profiles published in the literature: we collected 356 908 data points corresponding to 482 protein kinases, 2106 inhibitors, and 661 patents. We then analyzed this data set in terms of kinome coverage, results reproducibility, popularity, and degree of selectivity of both kinases and inhibitors. We used the data set to create robust proteochemometric models capable of predicting kinase activity (the ligand-target space was modeled with an externally validated RMSE of 0.41 ± 0.02 log units and R02 0.74 ± 0.03), in order to account for missing or unreliable measurements. The influence on the prediction quality of parameters such as number of measurements, Murcko scaffold frequency or inhibitor type was assessed. Interpretation of the models enabled to highlight inhibitors and kinases properties correlated with higher affinities, and an analysis in the context of kinases crystal structures was performed. Overall, the models quality allows the accurate prediction of kinase-inhibitor activities and their structural interpretation, thus paving the way for the rational design of compounds with a targeted selectivity profile. PMID:27482722

  17. Theoretical prediction of familial amyotrophic lateral sclerosis missense mutation effects on Cu/Zn superoxide dismutase structural stability

    SciTech Connect

    Potier, M.; Tu, Y.

    1994-09-01

    Cu/Zn superoxide dismutase (SOD) deficiency is associated with the progressive paralytic disorder familial amyotrophic lateral sclerosis (FALS). Fifteen missense mutations in the SOD gene were identified in several patients. These mutations may prevent correct promoter folding or hamper homodimer formation necessary for SOD activity. To understand the effect of the missense mutations on SOD structure and function, we used a theoretical analysis of structural effects based on two predictive methods using the modeled tertiary structure of human SOD. The first method uses the TORSO program which optimizes amino acid side-chains repacking in both wild-type and mutant SODs and calculates protein internal packing energy. The second method uses a hydrophobicity scale of the amino acid residues and considers both solvent accessibility and hydrophobic nature of residue substitutions to compute a stabilization energy change ({delta}E). These predictive methods have been tested in 187 single and multiple missense mutants of 8 proteins (T4 lysozyme, human carbonic anhydrase II, chymotrypsin inhibitor 2, f1 gene V protein, barnase, {lambda}-repressor, chicken and human lysozymes) with experimentally determined thermostability. The overall prediction accuracy with these proteins was 88%. Analysis of FALS missense mutations {delta}E predicts that 14 of 15 mutations destabilize the SOD structure. The other missense mutation is located at the homodimer interface and may hinder dimer formation. This approach is applicable to any protein with known tertiary structure to predict missense mutation effects on protein stability.

  18. An attempt to theoretically predict third-phase formation in the dimethyldibutyltetradecylmalonamide (DMDBTDMA)/dodecane/water/nitric acid extraction system

    SciTech Connect

    LeFrancois, L.; Tondre, C.; Belnet, F.; Noel, D.

    1999-03-01

    The formation of a third phase in solvent extraction (due to splitting of the organic phase into two layers) often occurs when the aqueous phase is highly concentrated in acids. This has been reported with the extraction system dimethyldibutyltetradecylmalonamide (DMDBTDMA)/n-dodecane/water/nitric acid, both in the presence and absence of metal ions. Whereas many experimental efforts have been made to investigate the effects of different parameters on third-phase formation, very few attempts have been made to predict this phenomenon on theoretical grounds. Because the part played by aggregation of the extractant molecules is recognized, the authors propose a new predictive approach based on the use of the Flory-Huggins theory of polymer solutions, which had been successfully applied for the prediction of phase separation phenomena in nonionic surfactant solutions. The authors show that this model can provide an excellent prediction of the demixing curve (in the absence of metal ions) when establishing the relation between the interaction parameter {chi}{sub 12} calculated from this theory and the nitric acid content of the aqueous phase. Apparent values of the solubility parameter {delta}{sub 2} of the diamide extractant at different acid loadings have been calculated, from which the effect of the nature of the diluent can also be very nicely predicted.

  19. Predicting the growth of fractal particle agglomeration networks with graph theoretical methods.

    NASA Astrophysics Data System (ADS)

    Hubler, Alfred

    2007-03-01

    We study an electromechanical system [J. Jun, A. Hubler, PNAS 102, 536 (2005); J. Jun, Ph.D. thesis, UIUC (2004)], where conducting particles self-organize into dendritic patterns under the influence of an electric field for the purpose of collecting and transporting charge. The system forms stable open-loop networks with many reproducible statistical quantities, such as the number of termini and the number of branch points, but the final topology of the network is sensitive to the initial conditions of the particles. Small differences in the initial configuration may lead to very different stationary states. We present robust and reliable ensemble prediction algorithms for the growth of such fractal charge transportation networks. These predictors may lead to the discovery of common properties and serve a prototype to predict fractal growth in other areas, including neural systems; blood vessel systems, river networks, and dielectric break through.

  20. Theoretical prediction of coordination environments and stability constants of lanthanum lactate complexes in solution

    DOE PAGES

    Roy, Lindsay E.; Martin, Leigh R.

    2016-09-12

    Using Density Functional Theory calculations in combination with explicit solvent and a continuum solvent model, this work sets out to understand the coordination environment and relevant thermodynamics of La(III)-lactate complexes. Calculations focus on the coordination modes for the complexes and changes in Gibbs free energy for complexation in solution. These results confirm that the α-hydroxyl group should be protonated, or at least hydrogen bonded to a water molecule, upon successive addition of the lactate ligand to the La(III) center using Bader's Atoms-in Molecules (AIM) approach. In addition, we present a straightforward method for predicting stability constants at the semi-quantitative levelmore » for La(III)-lactate complexes in solution. Furthermore, the proposed method could be particularly useful for prediction of lanthanide complex formation in various biochemical, environmental, and nuclear separations processes.« less

  1. Communication: Theoretical prediction of free-energy landscapes for complex self-assembly

    SciTech Connect

    Jacobs, William M.; Reinhardt, Aleks; Frenkel, Daan

    2015-01-14

    We present a technique for calculating free-energy profiles for the nucleation of multicomponent structures that contain as many species as building blocks. We find that a key factor is the topology of the graph describing the connectivity of the target assembly. By considering the designed interactions separately from weaker, incidental interactions, our approach yields predictions for the equilibrium yield and nucleation barriers. These predictions are in good agreement with corresponding Monte Carlo simulations. We show that a few fundamental properties of the connectivity graph determine the most prominent features of the assembly thermodynamics. Surprisingly, we find that polydispersity in the strengths of the designed interactions stabilizes intermediate structures and can be used to sculpt the free-energy landscape for self-assembly. Finally, we demonstrate that weak incidental interactions can preclude assembly at equilibrium due to the combinatorial possibilities for incorrect association.

  2. Theoretical prediction of low-density hexagonal ZnO hollow structures

    NASA Astrophysics Data System (ADS)

    Tuoc, Vu Ngoc; Huan, Tran Doan; Thao, Nguyen Thi; Tuan, Le Manh

    2016-10-01

    Along with wurtzite and zinc blende, zinc oxide (ZnO) has been found in a large number of polymorphs with substantially different properties and, hence, applications. Therefore, predicting and synthesizing new classes of ZnO polymorphs are of great significance and have been gaining considerable interest. Herein, we perform a density functional theory based tight-binding study, predicting several new series of ZnO hollow structures using the bottom-up approach. The geometry of the building blocks allows for obtaining a variety of hexagonal, low-density nanoporous, and flexible ZnO hollow structures. Their stability is discussed by means of the free energy computed within the lattice-dynamics approach. Our calculations also indicate that all the reported hollow structures are wide band gap semiconductors in the same fashion with bulk ZnO. The electronic band structures of the ZnO hollow structures are finally examined in detail.

  3. Reference dosimetry at the Australian Synchrotron's imaging and medical beamline using free-air ionization chamber measurements and theoretical predictions of air kerma rate and half value layer

    SciTech Connect

    Crosbie, Jeffrey C.; Rogers, Peter A. W.; Stevenson, Andrew W.; Hall, Christopher J.; Lye, Jessica E.; Nordstroem, Terese; Midgley, Stewart M.; Lewis, Robert A.

    2013-06-15

    Purpose: Novel, preclinical radiotherapy modalities are being developed at synchrotrons around the world, most notably stereotactic synchrotron radiation therapy and microbeam radiotherapy at the European Synchrotron Radiation Facility in Grenoble, France. The imaging and medical beamline (IMBL) at the Australian Synchrotron has recently become available for preclinical radiotherapy and imaging research with clinical trials, a distinct possibility in the coming years. The aim of this present study was to accurately characterize the synchrotron-generated x-ray beam for the purposes of air kerma-based absolute dosimetry. Methods: The authors used a theoretical model of the energy spectrum from the wiggler source and validated this model by comparing the transmission through copper absorbers (0.1-3.0 mm) against real measurements conducted at the beamline. The authors used a low energy free air ionization chamber (LEFAC) from the Australian Radiation Protection and Nuclear Safety Agency and a commercially available free air chamber (ADC-105) for the measurements. The dimensions of these two chambers are different from one another requiring careful consideration of correction factors. Results: Measured and calculated half value layer (HVL) and air kerma rates differed by less than 3% for the LEFAC when the ion chamber readings were corrected for electron energy loss and ion recombination. The agreement between measured and predicted air kerma rates was less satisfactory for the ADC-105 chamber, however. The LEFAC and ADC measurements produced a first half value layer of 0.405 {+-} 0.015 and 0.412 {+-} 0.016 mm Cu, respectively, compared to the theoretical prediction of 0.427 {+-} 0.012 mm Cu. The theoretical model based upon a spectrum calculator derived a mean beam energy of 61.4 keV with a first half value layer of approximately 30 mm in water. Conclusions: The authors showed in this study their ability to verify the predicted air kerma rate and x-ray attenuation

  4. Theoretical research program to predict the properties of molecules and clusters containing transition metal atoms

    NASA Technical Reports Server (NTRS)

    Walch, S.

    1984-01-01

    The primary focus of this research has been the theoretical study of transition metal (TM) chemistry. A major goal of this work is to provide reliable information about the interaction of H atoms with iron metal. This information is needed to understand the effect of H atoms on the processes of embrittlement and crack propagation in iron. The method in the iron hydrogen studies is the cluster method in which the bulk metal is modelled by a finite number of iron atoms. There are several difficulties in the application of this approach to the hydrogen iron system. First the nature of TM-TM and TM-H bonding for even diatomic molecules was not well understood when these studies were started. Secondly relatively large iron clusters are needed to provide reasonable results.

  5. Theoretical Prediction of Pressure Distributions on Nonlifting Airfoils at High Subsonic Speeds

    NASA Technical Reports Server (NTRS)

    Spreiter, John R; Alksne, Alberta

    1955-01-01

    Theoretical pressure distributions on nonlifting circular-arc airfoils in two-dimensional flows with high subsonic free-stream velocity are found by determining approximate solutions, through an iteration process, of an integral equation for transonic flow proposed by Oswatitsch. The integral equation stems directly from the small-disturbance theory for transonic flow. This method of analysis possesses the advantage of remaining in the physical, rather than the hodograph, variable and can be applied in airfoils having curved surfaces. After discussion of the derivation of the integral equation and qualitative aspects of the solution, results of calculations carried out for circular-arc airfoils in flows with free-stream Mach numbers up to unity are described. These results indicate most of the principal phenomena observed in experimental studies.

  6. Theoretical study of phase transition, surface tension, and nucleation rate predictions for argon.

    PubMed

    Zhou, Di; Zeng, Ming; Mi, Jianguo; Zhong, Chongli

    2011-01-13

    In this work, a weighted density functional theory has been used to study the equilibrium and metastable processes for argon. In the theoretical approach, the two- and three-body interactions of the fluid molecules are considered simultaneously, and the renormalization group transformation is applied to address the long-range fluctuations inside the critical region. The global phase equilibria, planar and curvature-dependent surface tensions, critical radius, and nucleation rates of argon are investigated systematically. The results are in good agreement with the experimental data. Meanwhile, this work applies a methodology for calculating the curved surface tension in local supersaturated environments, showing that the Tolman length is negligible far from the critical region. Near the critical point, however, the Tolman length becomes positive and appears to diverge.

  7. Theoretical prediction of the impact of Auger recombination on charge collection from an ion track

    NASA Technical Reports Server (NTRS)

    Edmonds, Larry D.

    1991-01-01

    A recombination mechanism that significantly reduces charge collection from very dense ion tracks in silicon devices was postulated by Zoutendyk et al. The theoretical analysis presented here concludes that Auger recombination is such a mechanism and is of marginal importance for higher density tracks produced by 270-MeV krypton, but of major importance for higher density tracks. The analysis shows that recombination loss is profoundly affected by track diffusion. As the track diffuses, the density and recombination rate decrease so fast that the linear density (number of electron-hole pairs per unit length) approaches a non-zero limiting value as t yields infinity. Furthermore, the linear density is very nearly equal to this limiting value in a few picoseconds or less. When Auger recombination accompanies charge transport processes that have much longer time scales, it can be simulated by assigning a reduced linear energy transfer to the ion.

  8. Theoretical prediction of the impact of Auger recombination on charge collection from an ion track

    NASA Technical Reports Server (NTRS)

    Edmonds, Larry D.

    1991-01-01

    The theoretical analysis presented indicates that Auger recombination can reduce charge collection from very dense ion tracks in silicon devices. It is of marginal importance for tracks produced by 270-MeV krypton, and therefore it is of major importance for ions exhibiting a significantly larger loss. The analysis shows that recombination loss is profoundly affected by track diffusion. As the track diffuses, the density and recombination rate decrease so fast that the linear density (number of electron-hole pairs per unit length) approaches a nonzero limiting value as t approaches infinity. Furthermore, the linear density is very nearly equal to this limiting value in a few picoseconds or less. When Auger recombination accompanies charge transport processes that have much longer time scales, it can be simulated by assigning a reduced linear energy transfer to the ion.

  9. Effects of solution composition on the theoretical prediction of ice nucleation kinetics and thermodynamics.

    PubMed

    Karlsson, Jens O M

    2010-02-01

    Predictions by various mathematical models of intracellular ice formation (proposed by Mazur, Pitt, Toner, and Karlsson, respectively) were compared to the known thermodynamic and kinetic behavior of ice formation in supercooled aqueous systems. The older models (Mazur, Pitt, and Toner) significantly underestimated the magnitude of colligative nonequilibrium freezing point depression in response to increased concentration of solutes, such as salts or cryoprotectants. Furthermore, kinetics predicted using phenomenological models (by Mazur and Pitt) exhibited implausible temperature-dependence, with the probability of intracellular ice formation being allowed to increase even at temperatures below the glass transition point. The Toner model, on the other hand, produced invalid results at temperatures below -48 degrees C. The Karlsson model was the only model that consistently yielded realistic predictions over a wide range of temperatures and solute concentrations, especially in the presence of cryoprotectant additives. To facilitate adoption of the Karlsson model of intracellular ice nucleation, the complete set of model equations has been collected and described in detail.

  10. Predicting Flaw-Induced Resonance Spectrum Shift with Theoretical Perturbation Analysis

    SciTech Connect

    Lai, Canhai; Sun, Xin

    2013-10-28

    Resonance inspection is an emerging non-destructive evaluation (NDE) technique which uses the resonance spectra differences between the good part population and the flawed parts to identify anomalous parts. It was previously established that finite-element (FE)-based modal analysis can be used to predict the resonance spectrum for an engineering scale part with relatively good accuracy. However, FE-based simulations can be time consuming in examining the spectrum shifts induced by all possible structural flaws. This paper aims at developing a computationally efficient perturbation technique to quantify the frequency shifts induced by small structural flaws, based on the FE simulated resonance spectrum for the perfect part. A generic automotive connecting rod is used as the example part for our study. The results demonstrate that the linear perturbation theory provides a very promising way in predicting frequency changes induced by small structural flaws. As the flaw size increases, the discrepancy between the perturbation analysis and the actual FE simulation results increases due to nonlinearity, yet the perturbation analysis is still able to predict the right trend in frequency shift.

  11. Predicting flaw-induced resonance spectrum shift with theoretical perturbation analysis

    NASA Astrophysics Data System (ADS)

    Lai, C.; Sun, X.

    2013-10-01

    Resonance inspection is an emerging non-destructive evaluation (NDE) technique used by the automotive casting industry which uses the resonance spectra differences between the good part population and the flawed parts to identify anomalous parts. It was previously established that finite-element (FE)-based modal analysis can be used to predict the resonance spectrum for an engineering scale part with relatively good accuracy. However, FE-based simulations can be time consuming in examining the spectrum shifts induced by all possible structural flaws. This paper aims at developing a computationally efficient perturbation technique to quantify the frequency shifts induced by small structural flaws, based on the FE simulated resonance spectrum for the perfect part. A generic automotive connecting rod is used as the example part for our study. The results demonstrate that the linear perturbation theory provides a very promising way in predicting frequency changes induced by small structural flaws. As the flaw size increases, the discrepancy between the perturbation analysis and the actual FE simulation results increases due to nonlinearity, yet the perturbation analysis is still able to predict the right trend in frequency shift.

  12. Theoretical predictions of the impact of nuclear dynamics and environment on core-level spectra of organic molecules

    NASA Astrophysics Data System (ADS)

    Prendergast, David; Schwartz, Craig; Uejio, Janel; Saykally, Richard

    2009-03-01

    Core-level spectroscopy provides an element-specific probe of local electronic structure and bonding, but linking details of atomic structure to measured spectra relies heavily on accurate theoretical interpretation. We present first principles simulations of the x-ray absorption of a range of organic molecules both in isolation and aqueous solvation, highlighting the spectral impact of internal nuclear motion as well as solvent interactions. Our approach uses density functional theory with explicit inclusion of the core-level excited state within a plane-wave supercell framework. Nuclear degrees of freedom are sampled using various molecular dynamics techniques. We indicate specific cases for molecules in their vibrational ground state at experimental conditions, where nuclear quantum effects must be included. Prepared by LBNL under Contract DE-AC02-05CH11231.

  13. The turbulent recirculating flow field in a coreless induction furnace. A comparison of theoretical predictions with measurements

    NASA Technical Reports Server (NTRS)

    El-Kaddah, N.; Szekely, J.

    1982-01-01

    A mathematical representation for the electromagnetic force field and the fluid flow field in a coreless induction furnace is presented. The fluid flow field was represented by writing the axisymmetric turbulent Navier-Stokes equation, containing the electromagnetic body force term. The electromagnetic body force field was calculated by using a technique of mutual inductances. The kappa-epsilon model was employed for evaluating the turbulent viscosity and the resultant differential equations were solved numerically. Theoretically predicted velocity fields are in reasonably good agreement with the experimental measurements reported by Hunt and Moore; furthermore, the agreement regarding the turbulent intensities are essentially quantitative. These results indicate that the kappa-epsilon model provides a good engineering representation of the turbulent recirculating flows occurring in induction furnaces. At this stage it is not clear whether the discrepancies between measurements and the predictions, which were not very great in any case, are attributable either to the model or to the measurement techniques employed.

  14. PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions.

    PubMed

    Bendl, Jaroslav; Musil, Miloš; Štourač, Jan; Zendulka, Jaroslav; Damborský, Jiří; Brezovský, Jan

    2016-05-01

    An important message taken from human genome sequencing projects is that the human population exhibits approximately 99.9% genetic similarity. Variations in the remaining parts of the genome determine our identity, trace our history and reveal our heritage. The precise delineation of phenotypically causal variants plays a key role in providing accurate personalized diagnosis, prognosis, and treatment of inherited diseases. Several computational methods for achieving such delineation have been reported recently. However, their ability to pinpoint potentially deleterious variants is limited by the fact that their mechanisms of prediction do not account for the existence of different categories of variants. Consequently, their output is biased towards the variant categories that are most strongly represented in the variant databases. Moreover, most such methods provide numeric scores but not binary predictions of the deleteriousness of variants or confidence scores that would be more easily understood by users. We have constructed three datasets covering different types of disease-related variants, which were divided across five categories: (i) regulatory, (ii) splicing, (iii) missense, (iv) synonymous, and (v) nonsense variants. These datasets were used to develop category-optimal decision thresholds and to evaluate six tools for variant prioritization: CADD, DANN, FATHMM, FitCons, FunSeq2 and GWAVA. This evaluation revealed some important advantages of the category-based approach. The results obtained with the five best-performing tools were then combined into a consensus score. Additional comparative analyses showed that in the case of missense variations, protein-based predictors perform better than DNA sequence-based predictors. A user-friendly web interface was developed that provides easy access to the five tools' predictions, and their consensus scores, in a user-understandable format tailored to the specific features of different categories of variations. To

  15. PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions

    PubMed Central

    Brezovský, Jan

    2016-01-01

    An important message taken from human genome sequencing projects is that the human population exhibits approximately 99.9% genetic similarity. Variations in the remaining parts of the genome determine our identity, trace our history and reveal our heritage. The precise delineation of phenotypically causal variants plays a key role in providing accurate personalized diagnosis, prognosis, and treatment of inherited diseases. Several computational methods for achieving such delineation have been reported recently. However, their ability to pinpoint potentially deleterious variants is limited by the fact that their mechanisms of prediction do not account for the existence of different categories of variants. Consequently, their output is biased towards the variant categories that are most strongly represented in the variant databases. Moreover, most such methods provide numeric scores but not binary predictions of the deleteriousness of variants or confidence scores that would be more easily understood by users. We have constructed three datasets covering different types of disease-related variants, which were divided across five categories: (i) regulatory, (ii) splicing, (iii) missense, (iv) synonymous, and (v) nonsense variants. These datasets were used to develop category-optimal decision thresholds and to evaluate six tools for variant prioritization: CADD, DANN, FATHMM, FitCons, FunSeq2 and GWAVA. This evaluation revealed some important advantages of the category-based approach. The results obtained with the five best-performing tools were then combined into a consensus score. Additional comparative analyses showed that in the case of missense variations, protein-based predictors perform better than DNA sequence-based predictors. A user-friendly web interface was developed that provides easy access to the five tools’ predictions, and their consensus scores, in a user-understandable format tailored to the specific features of different categories of variations

  16. Absolute Measurements of Macrophage Migration Inhibitory Factor and Interleukin-1-β mRNA Levels Accurately Predict Treatment Response in Depressed Patients

    PubMed Central

    Ferrari, Clarissa; Uher, Rudolf; Bocchio-Chiavetto, Luisella; Riva, Marco Andrea; Pariante, Carmine M.

    2016-01-01

    Background: Increased levels of inflammation have been associated with a poorer response to antidepressants in several clinical samples, but these findings have had been limited by low reproducibility of biomarker assays across laboratories, difficulty in predicting response probability on an individual basis, and unclear molecular mechanisms. Methods: Here we measured absolute mRNA values (a reliable quantitation of number of molecules) of Macrophage Migration Inhibitory Factor and interleukin-1β in a previously published sample from a randomized controlled trial comparing escitalopram vs nortriptyline (GENDEP) as well as in an independent, naturalistic replication sample. We then used linear discriminant analysis to calculate mRNA values cutoffs that best discriminated between responders and nonresponders after 12 weeks of antidepressants. As Macrophage Migration Inhibitory Factor and interleukin-1β might be involved in different pathways, we constructed a protein-protein interaction network by the Search Tool for the Retrieval of Interacting Genes/Proteins. Results: We identified cutoff values for the absolute mRNA measures that accurately predicted response probability on an individual basis, with positive predictive values and specificity for nonresponders of 100% in both samples (negative predictive value=82% to 85%, sensitivity=52% to 61%). Using network analysis, we identified different clusters of targets for these 2 cytokines, with Macrophage Migration Inhibitory Factor interacting predominantly with pathways involved in neurogenesis, neuroplasticity, and cell proliferation, and interleukin-1β interacting predominantly with pathways involved in the inflammasome complex, oxidative stress, and neurodegeneration. Conclusion: We believe that these data provide a clinically suitable approach to the personalization of antidepressant therapy: patients who have absolute mRNA values above the suggested cutoffs could be directed toward earlier access to more

  17. Dose Addition Models Based on Biologically Relevant Reductions in Fetal Testosterone Accurately Predict Postnatal Reproductive Tract Alterations by a Phthalate Mixture in Rats.

    PubMed

    Howdeshell, Kembra L; Rider, Cynthia V; Wilson, Vickie S; Furr, Johnathan R; Lambright, Christy R; Gray, L Earl

    2015-12-01

    Challenges in cumulative risk assessment of anti-androgenic phthalate mixtures include a lack of data on all the individual phthalates and difficulty determining the biological relevance of reduction in fetal testosterone (T) on postnatal development. The objectives of the current study were 2-fold: (1) to test whether a mixture model of dose addition based on the fetal T production data of individual phthalates would predict the effects of a 5 phthalate mixture on androgen-sensitive postnatal male reproductive tract development, and (2) to determine the biological relevance of the reductions in fetal T to induce abnormal postnatal reproductive tract development using data from the mixture study. We administered a dose range of the mixture (60, 40, 20, 10, and 5% of the top dose used in the previous fetal T production study consisting of 300 mg/kg per chemical of benzyl butyl (BBP), di(n)butyl (DBP), diethyl hexyl phthalate (DEHP), di-isobutyl phthalate (DiBP), and 100 mg dipentyl (DPP) phthalate/kg; the individual phthalates were present in equipotent doses based on their ability to reduce fetal T production) via gavage to Sprague Dawley rat dams on GD8-postnatal day 3. We compared observed mixture responses to predictions of dose addition based on the previously published potencies of the individual phthalates to reduce fetal T production relative to a reference chemical and published postnatal data for the reference chemical (called DAref). In addition, we predicted DA (called DAall) and response addition (RA) based on logistic regression analysis of all 5 individual phthalates when complete data were available. DA ref and DA all accurately predicted the observed mixture effect for 11 of 14 endpoints. Furthermore, reproductive tract malformations were seen in 17-100% of F1 males when fetal T production was reduced by about 25-72%, respectively. PMID:26350170

  18. Prediction of nonlinear optical properties of organic materials. General theoretical considerations

    NASA Technical Reports Server (NTRS)

    Cardelino, B.; Moore, C.; Zutaut, S.

    1993-01-01

    The prediction of nonlinear optical properties of organic materials is geared to assist materials scientists in the selection of good candidate molecules. A brief summary of the quantum mechanical methods used for estimating hyperpolarizabilities will be presented. The advantages and limitations of each technique will be discussed. Particular attention will be given to the finite-field method for calculating first and second order hyperpolarizabilities, since this method is better suited for large molecules. Corrections for dynamic fields and bulk effects will be discussed in detail, focusing on solvent effects, conformational isomerization, core effects, dispersion, and hydrogen bonding. Several results will be compared with data obtained from third-harmonic-generation (THG) and dc-induced second harmonic generation (EFISH) measurements. These comparisons will demonstrate the qualitative ability of the method to predict the relative strengths of hyperpolarizabilities of a class of compounds. The future application of molecular mechanics, as well as other techniques, in the study of bulk properties and solid state defects will be addressed. The relationship between large values for nonlinear optical properties and large conjugation lengths is well known, and is particularly important for third-order processes. For this reason, the materials with the largest observed nonresonant third-order properties are conjugated polymers. An example of this type of polymer is polydiacetylene. One of the problems in dealing with polydiacetylene is that substituents which may enhance its nonlinear properties may ultimately prevent it from polymerizing. A model which attempts to predict the likelihood of solid-state polymerization is considered, along with the implications of the assumptions that are used. Calculations of the third-order optical properties and their relationship to first-order properties and energy gaps will be discussed. The relationship between monomeric and

  19. Theoretical Prediction of Am(III)/Eu(III) Selectivity to Aid the Design of Actinide-Lanthanide Separation Agents

    DOE PAGES

    Bryantsev, Vyacheslav S.; Hay, Benjamin P.

    2015-03-20

    Selective extraction of minor actinides from lanthanides is a critical step in the reduction of radiotoxicity of spent nuclear fuels. However, the design of suitable ligands for separating chemically similar 4f- and 5f-block trivalent metal ions poses a significant challenge. Furthermore, first-principles calculations should play an important role in the design of new separation agents, but their ability to predict metal ion selectivity has not been systematically evaluated. We examine the ability of several density functional theory methods to predict selectivity of Am(III) and Eu(III) with oxygen, mixed oxygen–nitrogen, and sulfur donor ligands. The results establish a computational method capablemore » of predicting the correct order of selectivities obtained from liquid–liquid extraction and aqueous phase complexation studies. To allow reasonably accurate predictions, it was critical to employ sufficiently flexible basis sets and provide proper account of solvation effects. The approach is utilized to estimate the selectivity of novel amide-functionalized diazine and 1,2,3-triazole ligands.« less

  20. Theoretical Prediction of Am(III)/Eu(III) Selectivity to Aid the Design of Actinide-Lanthanide Separation Agents

    SciTech Connect

    Bryantsev, Vyacheslav S.; Hay, Benjamin P.

    2015-03-20

    Selective extraction of minor actinides from lanthanides is a critical step in the reduction of radiotoxicity of spent nuclear fuels. However, the design of suitable ligands for separating chemically similar 4f- and 5f-block trivalent metal ions poses a significant challenge. Furthermore, first-principles calculations should play an important role in the design of new separation agents, but their ability to predict metal ion selectivity has not been systematically evaluated. We examine the ability of several density functional theory methods to predict selectivity of Am(III) and Eu(III) with oxygen, mixed oxygen–nitrogen, and sulfur donor ligands. The results establish a computational method capable of predicting the correct order of selectivities obtained from liquid–liquid extraction and aqueous phase complexation studies. To allow reasonably accurate predictions, it was critical to employ sufficiently flexible basis sets and provide proper account of solvation effects. The approach is utilized to estimate the selectivity of novel amide-functionalized diazine and 1,2,3-triazole ligands.

  1. Low power underwater acoustic DPSK detection: Theoretical prediction and experimental results

    NASA Astrophysics Data System (ADS)

    Dunne, Andrew

    This thesis presents two methods of analyzing the effectiveness of a prototype differential phase-shift keying (DPSK) detection circuit. The first method is to make modifications to the existing hardware to reliably output and record the cross-correlation values of the DPSK detection process. The second method is to write a MATLAB detection algorithm which accurately simulates the detection results of the hardware system without the need of any electronics. These two systems were tested and verified with a bench test using computer generated DPSK signals. The hardware system was tested using real acoustic data from shallow and deep water at-sea tests to determine the effectiveness of the DPSK detection circuit in different ocean environments. The hydrophone signals from the tests were recorded so that the cross-correlation values could be verified using the MATLAB detector. As a result of this study, these two systems provided more insight into how well the DPSK detection prototype works and helped to identify ways of improving the detection reliability and overall performance of the prototype DPSK detection circuit.

  2. Experimental and theoretical analysis of a method to predict thermal runaway in Li-ion cells

    NASA Astrophysics Data System (ADS)

    Shah, Krishna; Chalise, Divya; Jain, Ankur

    2016-10-01

    Thermal runaway is a well-known safety concern in Li-ion cells. Methods to predict and prevent thermal runaway are critically needed for enhanced safety and performance. While much work has been done on understanding the kinetics of various heat generation processes during thermal runaway, relatively lesser work exists on understanding how heat removal from the cell influences thermal runaway. Through a unified analysis of heat generation and heat removal, this paper derives and experimentally validates a non-dimensional parameter whose value governs whether or not thermal runaway will occur in a Li-ion cell. This parameter is named the Thermal Runaway Number (TRN), and comprises contributions from thermal transport within and outside the cell, as well as the temperature dependence of heat generation rate. Experimental data using a 26650 thermal test cell are in good agreement with the model, and demonstrate the dependence of thermal runaway on various thermal transport and heat generation parameters. This parameter is used to predict the thermal design space in which the cell will or will not experience thermal runaway. By combining all thermal processes contributing to thermal runaway in a single parameter, this work contributes towards a unified understanding of thermal runaway, and provides the fundamental basis for design tools for safe, high-performance Li-ion batteries.

  3. Applications and limits of theoretical adsorption models for predicting the adsorption properties of adsorbents.

    PubMed

    Park, Hyun Ju; Nguyen, Duc Canh; Na, Choon-Ki; Kim, Chung-il

    2015-01-01

    The objective of this study is to evaluate the applicability of adsorption models for predicting the properties of adsorbents. The kinetics of the adsorption of NO3- ions on a PP-g-AA-Am non-woven fabric have been investigated under equilibrium conditions in both batch and fixed bed column processes. The adsorption equilibrium experiments in the batch process were carried out under different adsorbate concentration and adsorbent dosage conditions and the results were analyzed using adsorption isotherm models, energy models, and kinetic models. The results of the analysis indicate that the adsorption occurring at a fixed adsorbate concentration with a varying adsorbent dosage occur more easily compared to those under a fixed adsorbent dosage with a varying adsorbate concentration. In the second part of the study, the experimental data obtained using fixed bed columns were fit to Bed Depth Service Time, Bohart-Adams, Clark, and Wolborska models, to predict the breakthrough curves and determine the column kinetic parameters. The adsorption properties of the NO3- ions on the PP-g-AA-Am non-woven fabric were differently described by different models for both the batch and fixed bed column process. Therefore, it appears reasonable to assume that the adsorption properties were dominated by multiple mechanisms, depending on the experimental conditions.

  4. Misalignment Effect Function Measurement for Oblique Rotation Axes: Counterintuitive Predictions and Theoretical Extensions

    NASA Technical Reports Server (NTRS)

    Ellis, Stephen R.; Adelstein, Bernard D.; Yeom, Kiwon

    2013-01-01

    The Misalignment Effect Function (MEF) describes the decrement in manual performance associated with a rotation between operators' visual display frame of reference and that of their manual control. It now has been empirically determined for rotation axes oblique to canonical body axes and is compared with the MEF previously measured for rotations about canonical axes. A targeting rule, called the Secant Rule, based on these earlier measurements is derived from a hypothetical process and shown to describe some of the data from three previous experiments. It explains the motion trajectories determined for rotations less than 65deg in purely kinematic terms without the need to appeal to a mental rotation process. Further analysis of this rule in three dimensions applied to oblique rotation axes leads to a somewhat surprising expectation that the difficulty posed by rotational misalignment should get harder as the required movement is shorter. This prediction is confirmed. Geometry underlying this rule also suggests analytic extensions for predicting more generally the difficulty of making movements in arbitrary directions subject to arbitrary misalignments.

  5. Theoretical basis for predicting climate-induced abrupt shifts in the oceans

    PubMed Central

    Beaugrand, Gregory

    2015-01-01

    Among the responses of marine species and their ecosystems to climate change, abrupt community shifts (ACSs), also called regime shifts, have often been observed. However, despite their effects for ecosystem functioning and both provisioning and regulating services, our understanding of the underlying mechanisms involved remains elusive. This paper proposes a theory showing that some ACSs originate from the interaction between climate-induced environmental changes and the species ecological niche. The theory predicts that a substantial stepwise shift in the thermal regime of a marine ecosystem leads indubitably to an ACS and explains why some species do not change during the phenomenon. It also explicates why the timing of ACSs may differ or why some studies may detect or not detect a shift in the same ecosystem, independently of the statistical method of detection and simply because they focus on different species or taxonomic groups. The present theory offers a way to predict future climate-induced community shifts and their potential associated trophic cascades and amplifications.

  6. Morphoelastic control of gastro-intestinal organogenesis: Theoretical predictions and numerical insights

    NASA Astrophysics Data System (ADS)

    Balbi, V.; Kuhl, E.; Ciarletta, P.

    2015-05-01

    With nine meters in length, the gastrointestinal tract is not only our longest, but also our structurally most diverse organ. During embryonic development, it evolves as a bilayered tube with an inner endodermal lining and an outer mesodermal layer. Its inner surface displays a wide variety of morphological patterns, which are closely correlated to digestive function. However, the evolution of these intestinal patterns remains poorly understood. Here we show that geometric and mechanical factors can explain intestinal pattern formation. Using the nonlinear field theories of mechanics, we model surface morphogenesis as the instability problem of constrained differential growth. To allow for internal and external expansion, we model the gastrointestinal tract with homogeneous Neumann boundary conditions. To establish estimates for the folding pattern at the onset of folding, we perform a linear stability analysis supplemented by the perturbation theory. To predict pattern evolution in the post-buckling regime, we perform a series of nonlinear finite element simulations. Our model explains why longitudinal folds emerge in the esophagus with a thick and stiff outer layer, whereas circumferential folds emerge in the jejunum with a thinner and softer outer layer. In intermediate regions like the feline esophagus, longitudinal and circumferential folds emerge simultaneously. Our model could serve as a valuable tool to explain and predict alterations in esophageal morphology as a result of developmental disorders or certain digestive pathologies including food allergies.

  7. A combined theoretical and in vitro modeling approach for predicting the magnetic capture and retention of magnetic nanoparticles in vivo

    PubMed Central

    David, Allan E.; Cole, Adam J.; Chertok, Beata; Park, Yoon Shin; Yang, Victor C.

    2011-01-01

    Magnetic nanoparticles (MNP) continue to draw considerable attention as potential diagnostic and therapeutic tools in the fight against cancer. Although many interacting forces present themselves during magnetic targeting of MNP to tumors, most theoretical considerations of this process ignore all except for the magnetic and drag forces. Our validation of a simple in vitro model against in vivo data, and subsequent reproduction of the in vitro results with a theoretical model indicated that these two forces do indeed dominate the magnetic capture of MNP. However, because nanoparticles can be subject to aggregation, and large MNP experience an increased magnetic force, the effects of surface forces on MNP stability cannot be ignored. We accounted for the aggregating surface forces simply by measuring the size of MNP retained from flow by magnetic fields, and utilized this size in the mathematical model. This presumably accounted for all particle-particle interactions, including those between magnetic dipoles. Thus, our “corrected” mathematical model provided a reasonable estimate of not only fractional MNP retention, but also predicted the regions of accumulation in a simulated capillary. Furthermore, the model was also utilized to calculate the effects of MNP size and spatial location, relative to the magnet, on targeting of MNPs to tumors. This combination of an in vitro model with a theoretical model could potentially assist with parametric evaluations of magnetic targeting, and enable rapid enhancement and optimization of magnetic targeting methodologies. PMID:21295085

  8. Ground/satellite signatures of field line resonance: A test of theoretical predictions

    NASA Astrophysics Data System (ADS)

    Vellante, M.; Lühr, H.; Zhang, T. L.; Wesztergom, V.; Villante, U.; de Lauretis, M.; Piancatelli, A.; Rother, M.; Schwingenschuh, K.; Koren, W.; Magnes, W.

    2004-06-01

    During June-July 2002 the low-altitude (h ˜ 400 km) Challenging Minisatellite Payload (CHAMP) satellite passed approximately every 2nd day close to the South European Geomagnetic Array (SEGMA, 1.56 < L < 1.88) during daytime hours. We present here the analysis of a Pc3 geomagnetic pulsation event observed simultaneously in space and at the ground array during the conjunction of 6 July 2002. Both compressional and transverse oscillations were identified in CHAMP magnetic measurements. A close correspondence between the compressional component and the ground signals is observed. The behavior of the CHAMP azimuthal component shows evidence for the occurrence of a field line resonance at L ≅ 1.6. The frequency of these azimuthal oscillations is ˜20% higher than the frequency of both the compressional oscillation and the ground pulsations. Such a difference is explained in terms of a sort of Doppler shift caused by the fast movement of the satellite across the resonance region where the phase signal changes rapidly. A further analysis verifies for the first time by space measurements the theoretical pattern of the wave polarization sense in the resonance region. The comparison with corresponding SEGMA measurements also provides an unprecedented direct confirmation of the well-known 90° rotation of the ULF wave polarization ellipse through the ionosphere.

  9. Theoretical predictions for hexagonal BN based nanomaterials as electrocatalysts for the oxygen reduction reaction.

    PubMed

    Lyalin, Andrey; Nakayama, Akira; Uosaki, Kohei; Taketsugu, Tetsuya

    2013-02-28

    The catalytic activity for the oxygen reduction reaction (ORR) of both the pristine and defect-possessing hexagonal boron nitride (h-BN) monolayer and H-terminated nanoribbon have been studied theoretically using density functional theory. It is demonstrated that an inert h-BN monolayer can be functionalized and become catalytically active by nitrogen doping. It is shown that the energetics of adsorption of O(2), O, OH, OOH, and H(2)O on N atom impurities in the h-BN monolayer (N(B)@h-BN) is quite similar to that known for a Pt(111) surface. The specific mechanism of destructive and cooperative adsorption of ORR intermediates on the surface point defects is discussed. It is demonstrated that accounting for entropy and zero-point energy (ZPE) corrections results in destabilization of the ORR intermediates adsorbed on N(B)@h-BN, while solvent effects lead to their stabilization. Therefore, entropy, ZPE and solvent effects partly cancel each other and have to be taken into account simultaneously. Analysis of the free energy changes along the ORR pathway allows us to suggest that a N-doped h-BN monolayer can demonstrate catalytic properties for the ORR under the condition that electron transport to the catalytically active center is provided. PMID:23338859

  10. The theoretical tensile strength of fcc crystals predicted from shear strength calculations

    NASA Astrophysics Data System (ADS)

    Černý, M.; Pokluda, J.

    2009-04-01

    This work presents a simple way of estimating uniaxial tensile strength on the basis of theoretical shear strength calculations, taking into account its dependence on a superimposed normal stress. The presented procedure enables us to avoid complicated and time-consuming analyses of elastic stability of crystals under tensile loading. The atomistic simulations of coupled shear and tensile deformations in cubic crystals are performed using first principles computational code based on pseudo-potentials and the plane wave basis set. Six fcc crystals are subjected to shear deformations in convenient slip systems and a special relaxation procedure controls the stress tensor. The obtained dependence of the ideal shear strength on the normal tensile stress seems to be almost linearly decreasing for all investigated crystals. Taking these results into account, the uniaxial tensile strength values in three crystallographic directions were evaluated by assuming a collapse of the weakest shear system. Calculated strengths for \\langle 001\\rangle and \\langle 111\\rangle loading were found to be mostly lower than previously calculated stresses related to tensile instability but rather close to those obtained by means of the shear instability analysis. On the other hand, the strengths for \\langle 110\\rangle loading almost match the stresses related to tensile instability.

  11. Discovery of a general method of solving the Schrödinger and dirac equations that opens a way to accurately predictive quantum chemistry.

    PubMed

    Nakatsuji, Hiroshi

    2012-09-18

    Just as Newtonian law governs classical physics, the Schrödinger equation (SE) and the relativistic Dirac equation (DE) rule the world of chemistry. So, if we can solve these equations accurately, we can use computation to predict chemistry precisely. However, for approximately 80 years after the discovery of these equations, chemists believed that they could not solve SE and DE for atoms and molecules that included many electrons. This Account reviews ideas developed over the past decade to further the goal of predictive quantum chemistry. Between 2000 and 2005, I discovered a general method of solving the SE and DE accurately. As a first inspiration, I formulated the structure of the exact wave function of the SE in a compact mathematical form. The explicit inclusion of the exact wave function's structure within the variational space allows for the calculation of the exact wave function as a solution of the variational method. Although this process sounds almost impossible, it is indeed possible, and I have published several formulations and applied them to solve the full configuration interaction (CI) with a very small number of variables. However, when I examined analytical solutions for atoms and molecules, the Hamiltonian integrals in their secular equations diverged. This singularity problem occurred in all atoms and molecules because it originates from the singularity of the Coulomb potential in their Hamiltonians. To overcome this problem, I first introduced the inverse SE and then the scaled SE. The latter simpler idea led to immediate and surprisingly accurate solution for the SEs of the hydrogen atom, helium atom, and hydrogen molecule. The free complement (FC) method, also called the free iterative CI (free ICI) method, was efficient for solving the SEs. In the FC method, the basis functions that span the exact wave function are produced by the Hamiltonian of the system and the zeroth-order wave function. These basis functions are called complement

  12. Theoretical prediction of hydrogen bond strength for use in molecular modeling.

    PubMed

    Nocker, Monika; Handschuh, Sandra; Tautermann, Christofer; Liedl, Klaus R

    2009-09-01

    Hybrid density functional theory calculations are used to investigate the strength of hydrogen bonds of structurally different molecules in complex with a standard donor and acceptor in vacuo. B3LYP/aug-cc-pVDZ calculations with one angle constraint lead to excellent correlations with experimental data (R(2) = 0.94, s(y) = 0.45 for acceptors and R(2) = 0.77, s(y) = 0.88 for donors). Substitutions of aromatic systems by electron donating and -withdrawing groups show a reinforcement of the interaction when substituting an acceptor with electron donating groups and weakening by substitution with electron withdrawing groups. For donor systems the opposite effect can be observed. Drug design of novel ligands will be able to profit from the predictive power of the method established, as hydrogen bonds between receptor and drug molecules are an important criterion for binding affinities.

  13. Theoretical Predictions for the Chemical Identification of Superheavy Elements. Role of Relativistic Effects

    NASA Astrophysics Data System (ADS)

    Pershina, Valeria; Bastug, Turgut

    2005-09-01

    Adsorption behaviour of element 112 and its homolog Hg on inert and transition-metal surfaces was predicted on the basis of fully relativistic density functional theory calculations. Influence of relativistic effects on the adsorption enthalpy and temperature was established by comparing results of the relativistic and nonrelativistic calculations. Relativistic effects were found to increase the adsorption enthalpy, or increase the adsorption temperature of element 112 on both types of the surfaces. They, however, influence the trend in group 12 in a different way depending on the surface. Thus, for adsorption on inert surfaces, Tadsrel(112) > Tads(Hg) > Tadsnr(112), while for adsorption on transition-metal surfaces, Tads(Hg) > Tadsrel(112) > Tadsnr(112).

  14. Main magnetic focus ion source: Basic principles, theoretical predictions and experimental confirmations

    NASA Astrophysics Data System (ADS)

    Ovsyannikov, V. P.; Nefiodov, A. V.

    2016-03-01

    It is proposed to produce highly charged ions in the local potential traps formed by the rippled electron beam in a focusing magnetic field. In this method, extremely high electron current densities can be attained on short length of the ion trap. The design of very compact ion sources of the new generation is presented. The computer simulations predict that for such ions as, for example, Ne8+ and Xe44+, the intensities of about 109 and 106 ions per second, respectively, can be obtained. The experiments with pilot example of the ion source confirm efficiency of the suggested method. The X-ray emission from Ir59+, Xe44+ and Ar16+ ions was detected. The control over depth of the local ion trap is shown to be feasible.

  15. AB Initio Protein Tertiary Structure Prediction: Comparative-Genetic Algorithm with Graph Theoretical Methods

    SciTech Connect

    Gregurick, S. K.

    2001-04-20

    During the period from September 1, 1998 until September 1, 2000 I was awarded a Sloan/DOE postdoctoral fellowship to work in collaboration with Professor John Moult at the Center for Advanced Research in Biotechnology (CARB). Our research project, ''Ab Initio Protein Tertiary Structure Prediction and a Comparative Genetic algorithm'', yielded promising initial results. In short, the project is designed to predict the native fold, or native tertiary structure, of a given protein by inputting only the primary sequence of the protein (one or three letter code). The algorithm is based on a general learning, or evolutionary algorithm and is called Genetic Algorithm (GAS). In our particular application of GAS, we search for native folds, or lowest energy structures, using two different descriptions for the interactions of the atoms and residues in a given protein sequence. One potential energy function is based on a free energy description, while the other function is a threading potential derived by Moult and Samudrala. This modified genetic algorithm was loosely termed a Comparative Genetic Algorithm and was designed to search for native folded structures on both potential energy surfaces, simultaneously. We tested the algorithm on a series of peptides ranging from 11 to 15 residues in length, which are thought to be independent folding units and thereby will fold to native structures independent of the larger protein environment. Our initial results indicated a modest increase in accuracy, as compared to a standard Genetic Algorithm. We are now in the process of improving the algorithm to increase the sensitivity to other inputs, such as secondary structure requirements. The project did not involve additional students and as of yet, the work has not been published.

  16. Theoretical prediction of hydrogen-bond basicity pKBHX using quantum chemical topology descriptors.

    PubMed

    Green, Anthony J; Popelier, Paul L A

    2014-02-24

    Hydrogen bonding plays an important role in the interaction of biological molecules and their local environment. Hydrogen-bond strengths have been described in terms of basicities by several different scales. The pKBHX scale has been developed with the interests of medicinal chemists in mind. The scale uses equilibrium constants of acid···base complexes to describe basicity and is therefore linked to Gibbs free energy. Site specific data for polyfunctional bases are also available. The pKBHX scale applies to all hydrogen-bond donors (HBDs) where the HBD functional group is either OH, NH, or NH+. It has been found that pKBHX can be described in terms of a descriptor defined by quantum chemical topology, ΔE(H), which is the change in atomic energy of the hydrogen atom upon complexation. Essentially the computed energy of the HBD hydrogen atom correlates with a set of 41 HBAs for five common HBDs, water (r2=0.96), methanol (r2=0.95), 4-fluorophenol (r2=0.91), serine (r2=0.93), and methylamine (r2=0.97). The connection between experiment and computation was strengthened with the finding that there is no relationship between ΔE(H) and pKBHX when hydrogen fluoride was used as the HBD. Using the methanol model, pKBHX predictions were made for an external set of bases yielding r2=0.90. Furthermore, the basicities of polyfunctional bases correlate with ΔE(H), giving r2=0.93. This model is promising for the future of computation in fragment-based drug design. Not only has a model been established that links computation to experiment, but the model may also be extrapolated to predict external experimental pKBHX values.

  17. Comparison of methods for predicting dissolution and the theoretical implications of particle-size-dependent solubility.

    PubMed

    Johnson, Kevin C

    2012-02-01

    Experimental dissolution data of cilostazol suspensions and hydrocortisone powders were simulated using either the Wang-Flanagan equation (1999. J Pharm Sci 88:731-738; 2002. J Pharm Sci 91:534-542) or the method of Johnson and coworkers (1989. Int J Pharm 51:9-17; 1993. Pharm Res 10:1308-1314; 1996. Pharm Res 13:1795-1798; 2003. Drug Dev Ind Pharm 29:833-842). Both methods were able to simulate experimental data with similar accuracy. For the method of Johnson and coworkers (1989. Int J Pharm 51:9-17; 1993. Pharm Res 10:1308-1314; 1996. Pharm Res 13:1795-1798; 2003. Drug Dev Ind Pharm 29:833-842), a single set of hydrodynamic assumptions was able to simulate both cilostazol and hydrocortisone with similar accuracy. For the Wang-Flanagan equation (1999. J Pharm Sci 88:731-738; 2002. J Pharm Sci 91:534-542), significantly different diffusion layer thicknesses gave the best simulations for cilostazol and hydrocortisone, but a single value of 38 µm provided good overall simulation of dissolution. The general computational method was enhanced to make solubility dependent on particle size, according to the Ostwald-Freundlich equation; it was also able to simulate Ostwald ripening. The enhanced computational method provided no way to explain the large increase in bioavailability of cilostazol in dogs when the drug was dosed as a nanoparticle versus micronized preparation. The method provides a computational tool for exploring theoretical implications and explaining the behavior of nanoparticles.

  18. Predicting peptide vaccine candidates against H1N1 influenza virus through theoretical approaches.

    PubMed

    Bello, Martiniano; Campos-Rodriguez, Rafael; Rojas-Hernandez, Saul; Contis-Montes de Oca, Arturo; Correa-Basurto, José

    2015-05-01

    Identification of potential epitopes that might activate the immune system has been facilitated by the employment of algorithms that use experimental data as templates. However, in order to prove the affinity and the map of interactions between the receptor (major histocompatibility complex, MHC, or T-cell receptor) and the potential epitope, further computational studies are required. Docking and molecular dynamics (MDs) simulations have been an effective source of generating structural information at molecular level in immunology. Herein, in order to provide a detailed understanding of the origins of epitope recognition and to select the best peptide candidate to develop an epitope-based vaccine, docking and MDs simulations in combination with MMGBSA free energy calculations and per-residue free energy decomposition were performed, taking as starting complexes those formed between four designed epitopes (P1-P4) from hemagglutinin (HA) of the H1N1 influenza virus and MHC-II anchored in POPC membrane. Our results revealed that the energetic contributions of individual amino acids within the pMHC-II complexes are mainly dictated by van der Waals interactions and the nonpolar part of solvation energy, whereas the electrostatic interactions corresponding to hydrogen bonds and salt bridges determine the binding specificity, being the most favorable interactions formed between p4 and MHC-II. Then, P1-P4 epitopes were synthesized and tested experimentally to compare theoretical and experimental results. Experimental results show that P4 elicited the highest strong humoral immune response to HA of the H1N1 and may induce antibodies that are cross-reactive to other influenza subtypes, suggesting that it could be a good candidate for the development of a peptide-based vaccine.

  19. Tuning of Strouhal number for high propulsive efficiency accurately predicts how wingbeat frequency and stroke amplitude relate and scale with size and flight speed in birds.

    PubMed Central

    Nudds, Robert L.; Taylor, Graham K.; Thomas, Adrian L. R.

    2004-01-01

    The wing kinematics of birds vary systematically with body size, but we still, after several decades of research, lack a clear mechanistic understanding of the aerodynamic selection pressures that shape them. Swimming and flying animals have recently been shown to cruise at Strouhal numbers (St) corresponding to a regime of vortex growth and shedding in which the propulsive efficiency of flapping foils peaks (St approximately fA/U, where f is wingbeat frequency, U is cruising speed and A approximately bsin(theta/2) is stroke amplitude, in which b is wingspan and theta is stroke angle). We show that St is a simple and accurate predictor of wingbeat frequency in birds. The Strouhal numbers of cruising birds have converged on the lower end of the range 0.2 < St < 0.4 associated with high propulsive efficiency. Stroke angle scales as theta approximately 67b-0.24, so wingbeat frequency can be predicted as f approximately St.U/bsin(33.5b-0.24), with St0.21 and St0.25 for direct and intermittent fliers, respectively. This simple aerodynamic model predicts wingbeat frequency better than any other relationship proposed to date, explaining 90% of the observed variance in a sample of 60 bird species. Avian wing kinematics therefore appear to have been tuned by natural selection for high aerodynamic efficiency: physical and physiological constraints upon wing kinematics must be reconsidered in this light. PMID:15451698

  20. Genome-Scale Metabolic Model for the Green Alga Chlorella vulgaris UTEX 395 Accurately Predicts Phenotypes under Autotrophic, Heterotrophic, and Mixotrophic Growth Conditions.

    PubMed

    Zuñiga, Cristal; Li, Chien-Ting; Huelsman, Tyler; Levering, Jennifer; Zielinski, Daniel C; McConnell, Brian O; Long, Christopher P; Knoshaug, Eric P; Guarnieri, Michael T; Antoniewicz, Maciek R; Betenbaugh, Michael J; Zengler, Karsten

    2016-09-01

    The green microalga Chlorella vulgaris has been widely recognized as a promising candidate for biofuel production due to its ability to store high lipid content and its natural metabolic versatility. Compartmentalized genome-scale metabolic models constructed from genome sequences enable quantitative insight into the transport and metabolism of compounds within a target organism. These metabolic models have long been utilized to generate optimized design strategies for an improved production process. Here, we describe the reconstruction, validation, and application of a genome-scale metabolic model for C. vulgaris UTEX 395, iCZ843. The reconstruction represents the most comprehensive model for any eukaryotic photosynthetic organism to date, based on the genome size and number of genes in the reconstruction. The highly curated model accurately predicts phenotypes under photoautotrophic, heterotrophic, and mixotrophic conditions. The model was validated against experimental data and lays the foundation for model-driven strain design and medium alteration to improve yield. Calculated flux distributions under different trophic conditions show that a number of key pathways are affected by nitrogen starvation conditions, including central carbon metabolism and amino acid, nucleotide, and pigment biosynthetic pathways. Furthermore, model prediction of growth rates under various medium compositions and subsequent experimental validation showed an increased growth rate with the addition of tryptophan and methionine. PMID:27372244

  1. The Model for End-stage Liver Disease accurately predicts 90-day liver transplant wait-list mortality in Atlantic Canada

    PubMed Central

    Renfrew, Paul Douglas; Quan, Hude; Doig, Christopher James; Dixon, Elijah; Molinari, Michele

    2011-01-01

    OBJECTIVE: To determine the generalizability of the predictions for 90-day mortality generated by Model for End-stage Liver Disease (MELD) and the serum sodium augmented MELD (MELDNa) to Atlantic Canadian adults with end-stage liver disease awaiting liver transplantation (LT). METHODS: The predictive accuracy of the MELD and the MELDNa was evaluated by measurement of the discrimination and calibration of the respective models’ estimates for the occurrence of 90-day mortality in a consecutive cohort of LT candidates accrued over a five-year period. Accuracy of discrimination was measured by the area under the ROC curves. Calibration accuracy was evaluated by comparing the observed and model-estimated incidences of 90-day wait-list failure for the total cohort and within quantiles of risk. RESULTS: The area under the ROC curve for the MELD was 0.887 (95% CI 0.705 to 0.978) – consistent with very good accuracy of discrimination. The area under the ROC curve for the MELDNa was 0.848 (95% CI 0.681 to 0.965). The observed incidence of 90-day wait-list mortality in the validation cohort was 7.9%, which was not significantly different from the MELD estimate of 6.6% (95% CI 4.9% to 8.4%; P=0.177) or the MELDNa estimate of 5.8% (95% CI 3.5% to 8.0%; P=0.065). Global goodness-of-fit testing found no evidence of significant lack of fit for either model (Hosmer-Lemeshow χ2 [df=3] for MELD 2.941, P=0.401; for MELDNa 2.895, P=0.414). CONCLUSION: Both the MELD and the MELDNa accurately predicted the occurrence of 90-day wait-list mortality in the study cohort and, therefore, are generalizable to Atlantic Canadians with end-stage liver disease awaiting LT. PMID:21876856

  2. The VACS Index Accurately Predicts Mortality and Treatment Response among Multi-Drug Resistant HIV Infected Patients Participating in the Options in Management with Antiretrovirals (OPTIMA) Study

    PubMed Central

    Brown, Sheldon T.; Tate, Janet P.; Kyriakides, Tassos C.; Kirkwood, Katherine A.; Holodniy, Mark; Goulet, Joseph L.; Angus, Brian J.; Cameron, D. William; Justice, Amy C.

    2014-01-01

    Objectives The VACS Index is highly predictive of all-cause mortality among HIV infected individuals within the first few years of combination antiretroviral therapy (cART). However, its accuracy among highly treatment experienced individuals and its responsiveness to treatment interventions have yet to be evaluated. We compared the accuracy and responsiveness of the VACS Index with a Restricted Index of age and traditional HIV biomarkers among patients enrolled in the OPTIMA study. Methods Using data from 324/339 (96%) patients in OPTIMA, we evaluated associations between indices and mortality using Kaplan-Meier estimates, proportional hazards models, Harrel’s C-statistic and net reclassification improvement (NRI). We also determined the association between study interventions and risk scores over time, and change in score and mortality. Results Both the Restricted Index (c = 0.70) and VACS Index (c = 0.74) predicted mortality from baseline, but discrimination was improved with the VACS Index (NRI = 23%). Change in score from baseline to 48 weeks was more strongly associated with survival for the VACS Index than the Restricted Index with respective hazard ratios of 0.26 (95% CI 0.14–0.49) and 0.39(95% CI 0.22–0.70) among the 25% most improved scores, and 2.08 (95% CI 1.27–3.38) and 1.51 (95%CI 0.90–2.53) for the 25% least improved scores. Conclusions The VACS Index predicts all-cause mortality more accurately among multi-drug resistant, treatment experienced individuals and is more responsive to changes in risk associated with treatment intervention than an index restricted to age and HIV biomarkers. The VACS Index holds promise as an intermediate outcome for intervention research. PMID:24667813

  3. Radiometric Calibration of EUNIS-06 With Theoretical Predicted `Insensitive' Line Ratios

    NASA Astrophysics Data System (ADS)

    Wang, T.; Brosius, J. W.; Thomas, R. J.; Rabin, D. M.

    2007-12-01

    The Extreme-Ultraviolet Normal-Incidence Spectrograph (EUNIS) is a sounding-rocket payload that obtains imaged high-resolution spectra of solar active and quiet-Sun regions, providing information about the corona and upper transition region. EUNIS incorporates two independent, co-pointing imaging spectrographs, one covering EUV lines between 300 and 370 Å\\ seen in first order (the longwave [LW] channel), and a second covering lines between 170 and 205 Å\\ seen in second order (the shortwave [SW] channel). Shortly after the payload's initial successful flight on 2006 April 12, a complete end-to-end radiometric calibration of its LW bandpass was carried out at the Rutherford Appleton Laboratory in England. Here we develop and apply a technique for deriving the absolute radiometric calibration of its SW bandpass from these direct LW results by means of density- and temperature-insensitive line intensity ratios. The first step is to use the EUNIS LW calibration to get absolute intensities for EUV lines recorded from solar positions along its LW slit during the 2006 flight. Then co-registered SOHO/CDS images taken within minutes of the flight are used to transfer these absolute values to solar locations observed by the EUNIS SW slit, spatially offset by about 1 arcmin. Finally, theoretical `insensitive' line ratios obtained from CHIANTI allow us to determine absolute intensities of emission lines within the EUNIS SW bandpass from those observed in its LW channel. A total of 29 ratios composed of 11 LW and 15 SW emission lines from Fe~X - Fe~XIII yield an instrumental response curve that matches very well to a relative calibration which relied on combining measurements of individual optical components. The second EUNIS flight, now scheduled for 2007 October 30, will make coordinated observations and provide similar calibration updates for Hinode/EIS. We will also present some preliminary results from the new observations. EUNIS is supported by the NASA Heliophysics

  4. Colloid filtration in surface dense vegetation: experimental results and theoretical predictions.

    PubMed

    Wu, Lei; Muñoz-Carpena, Rafael; Gao, Bin; Yang, Wen; Pachepsky, Yakov A

    2014-04-01

    Understanding colloid and colloid-facilitated contaminant transport in overland flow through dense vegetation is important to protect water quality in the environment, especially for water bodies receiving agricultural and urban runoff. In previous studies, a single-stem efficiency theory for rigid and clean stem systems was developed to predict colloid filtration by plant stems of vegetation in laminar overland flow. Hence, in order to improve the accuracy of the single-stem efficiency theory to real dense vegetation system, we incorporated the effect of natural organic matter (NOM) on the filtration of colloids by stems. Laboratory dense vegetation flow chamber experiments and model simulations were used to determine the kinetic deposition (filtration) rate of colloids under various conditions. The results show that, in addition to flow hydrodynamics and solution chemistry, steric repulsion afforded by NOM layer on the plants stem surface also plays a significant role in controlling colloid deposition on vegetation in overland flow. For the first time, a refined single-stem efficiency theory with considerations of the NOM effect is developed that describes the experimental data with good accuracy. This theory can be used to not only help construct and refine mathematical models of colloid transport in real vegetation systems in overland flow, but also inform the development of theories of colloid deposition on NOM-coated surfaces in natural, engineered, and biomedical systems.

  5. Colloid filtration in surface dense vegetation: experimental results and theoretical predictions.

    PubMed

    Wu, Lei; Muñoz-Carpena, Rafael; Gao, Bin; Yang, Wen; Pachepsky, Yakov A

    2014-04-01

    Understanding colloid and colloid-facilitated contaminant transport in overland flow through dense vegetation is important to protect water quality in the environment, especially for water bodies receiving agricultural and urban runoff. In previous studies, a single-stem efficiency theory for rigid and clean stem systems was developed to predict colloid filtration by plant stems of vegetation in laminar overland flow. Hence, in order to improve the accuracy of the single-stem efficiency theory to real dense vegetation system, we incorporated the effect of natural organic matter (NOM) on the filtration of colloids by stems. Laboratory dense vegetation flow chamber experiments and model simulations were used to determine the kinetic deposition (filtration) rate of colloids under various conditions. The results show that, in addition to flow hydrodynamics and solution chemistry, steric repulsion afforded by NOM layer on the plants stem surface also plays a significant role in controlling colloid deposition on vegetation in overland flow. For the first time, a refined single-stem efficiency theory with considerations of the NOM effect is developed that describes the experimental data with good accuracy. This theory can be used to not only help construct and refine mathematical models of colloid transport in real vegetation systems in overland flow, but also inform the development of theories of colloid deposition on NOM-coated surfaces in natural, engineered, and biomedical systems. PMID:24597773

  6. Temperature dependences of growth rates and carrying capacities of marine bacteria depart from metabolic theoretical predictions.

    PubMed

    Huete-Stauffer, Tamara Megan; Arandia-Gorostidi, Nestor; Díaz-Pérez, Laura; Morán, Xosé Anxelu G

    2015-10-01

    Using the metabolic theory of ecology (MTE) framework, we evaluated over a whole annual cycle the monthly responses to temperature of the growth rates (μ) and carrying capacities (K) of heterotrophic bacterioplankton at a temperate coastal site. We used experimental incubations spanning 6ºC with bacterial physiological groups identified by flow cytometry according to membrane integrity (live), nucleic acid content (HNA and LNA) and respiratory activity (CTC+). The temperature dependence of μ at the exponential phase of growth was summarized by the activation energy (E), which was variable (-0.52 to 0.72 eV) but followed a seasonal pattern, only reaching the hypothesized value for aerobic heterotrophs of 0.65 eV during the spring bloom for the most active bacterial groups (live, HNA, CTC+). K (i.e. maximum experimental abundance) peaked at 4 × 10(6) cells mL(-1) and generally covaried with μ but, contrary to MTE predictions, it did not decrease consistently with temperature. In the case of live cells, the responses of μ and K to temperature were positively correlated and related to seasonal changes in substrate availability, indicating that the responses of bacteria to warming are far from homogeneous and poorly explained by MTE at our site. PMID:26362925

  7. Using Game Theoretic Models to Predict Pilot Behavior in NextGen Merging and Landing Scenario

    NASA Technical Reports Server (NTRS)

    Yildiz, Yildiray; Lee, Ritchie; Brat, Guillaume

    2012-01-01

    In this paper, we present an implementation of the Semi Network-Form Game framework to predict pilot behavior in a merging and landing scenario. In this scenario, two aircraft are approaching to a freeze horizon with approximately equal distance when they become aware of each other via an ADS-B communication link that will be available in NextGen airspace. Both pilots want to gain advantage over the other by entering the freeze horizon earlier and obtain the first place in landing. They re-adjust their speed accordingly. However, they cannot simply increase their speed to the maximum allowable values since they are concerned with safety, separation distance, effort, possibility of being vectored-off from landing and possibility of violating speed constraints. We present how to model these concerns and the rest of the system using semi network-from game framework. Using this framework, based on certain assumptions on pilot utility functions and on system configuration, we provide estimates of pilot behavior and overall system evolution in time. We also discuss the possible employment of this modeling tool for airspace design optimization. To support this discussion, we provide a case where we investigate the effect of increasing the merging point speed limit on the commanded speed distribution and on the percentage of vectored aircraft.

  8. Theoretical Prediction of Isotope Effects on Charge Transport in Organic Semiconductors.

    PubMed

    Jiang, Yuqian; Geng, Hua; Shi, Wen; Peng, Qian; Zheng, Xiaoyan; Shuai, Zhigang

    2014-07-01

    We suggest that the nuclear tunneling effect is important in organic semiconductors, which we showed is absent in both the widely employed Marcus theory and the band-like transport as described by the deformation potential theory. Because the quantum nuclear tunneling tends to favor electron transfer while heavier nuclei decrease the quantum effect, there should occur an isotope effect for carrier mobility. For N,N'-n-bis(n-hexyl)-naphthalene diimide, electron mobility of all-deuteration on alkyls and all (13)C-substitution on the backbone decrease ∼18 and 7%, respectively. Similar isotope effects are found in the N,N'-n-bis(n-octyl)-perylene diimide. However, there is nearly no isotope effect for all-deuterated rubrene or tetracene. We have found that the isotopic effect only occurs when the substituted nuclei contribute actively to vibrations with appreciable charge reorganization energy and coupling with carrier motion. Thus, this prediction can shed light on the current dispute over the hopping versus band-like mechanisms in organic semiconductors. PMID:26279545

  9. Theoretical prediction of silicene as a new candidate for the anode of lithium-ion batteries.

    PubMed

    Seyed-Talebi, Seyedeh Mozhgan; Kazeminezhad, Iraj; Beheshtian, Javad

    2015-11-28

    Using density functional theory calculations, we determine the band structure and DOS of graphene and silicene supercell models. We also study the adsorption mechanism of Li metal atoms and Li-ions onto free-standing silicene (buckled, θ = 101.7°) and compare the results with those of graphene. In contrast to graphene, interactions between Li metal atoms and Li-ions with the silicene surface are quite strong due to its highly reactive buckled hexagonal structure. As a consequence of structural properties the adsorption height, the most stable adsorption site and energy barrier against Li diffusion are also discussed here to outline the prospects of using silicene in electronic devices such as Li ion batteries (LiBs), hydrogen storage and molecular machines. However, in most LiBs, graphene layers are used as anode electrodes. Here, it is shown that graphene has very limited Li storage capacity and low surface area than silicene. As our models are in good agreement with previous predictions, this finding presents a possible avenue for creating better anode materials that can replace graphene for higher capacity and better cycling performance of LiBs.

  10. Chemometric Methods and Theoretical Molecular Descriptors in Predictive QSAR Modeling of the Environmental Behavior of Organic Pollutants

    NASA Astrophysics Data System (ADS)

    Gramatica, Paola

    This chapter surveys the QSAR modeling approaches (developed by the author's research group) for the validated prediction of environmental properties of organic pollutants. Various chemometric methods, based on different theoretical molecular descriptors, have been applied: explorative techniques (such as PCA for ranking, SOM for similarity analysis), modeling approaches by multiple-linear regression (MLR, in particular OLS), and classification methods (mainly k-NN, CART, CP-ANN). The focus of this review is on the main topics of environmental chemistry and ecotoxicology, related to the physico-chemical properties, the reactivity, and biological activity of chemicals of high environmental concern. Thus, the review deals with atmospheric degradation reactions of VOCs by tropospheric oxidants, persistence and long-range transport of POPs, sorption behavior of pesticides (Koc and leaching), bioconcentration, toxicity (acute aquatic toxicity, mutagenicity of PAHs, estrogen binding activity for endocrine disruptors compounds (EDCs)), and finally persistent bioaccumulative and toxic (PBT) behavior for the screening and prioritization of organic pollutants. Common to all the proposed models is the attention paid to model validation for predictive ability (not only internal, but also external for chemicals not participating in the model development) and checking of the chemical domain of applicability. Adherence to such a policy, requested also by the OECD principles, ensures the production of reliable predicted data, useful also in the new European regulation of chemicals, REACH.

  11. Theoretical prediction of phase relations among aqueous solutions and minerals: Salton Sea geothermal system

    NASA Astrophysics Data System (ADS)

    Bird, Dennis K.; Norton, Denis L.

    1981-09-01

    Thermodynamic calculations of compositional relations among aqueous solutions and minerals in the system Na2O-K2O-CaO-MgO-Fe2O3 Al2O3-SiO2-H2O-CO2 HCl at pressures and temperatures corresponding to liquid-vapor equilibrium of H2O permit quantitative description and interpretation of phase relations among rock forming minerals and aqueous solutions in magma-hydrothermal systems. The extensive data base on the Salton Sea geothermal system provides an exemplary case for predicting the chemical characteristics of geothermal fluids associated with metasomatic mineral zones observed in deep drillhole samples. Near the Elmore No. 1 well aqueous species activity ratios of {aNa+}/{aH+} and {aK+}/{aH+} vary several tenths of a log unit with increasing depth and temperature from ∼ 0.6 km and ∼250°C to ∼ 2.2 km and ∼350°C, whereas {aCa2+}/{a2H+} decreases ∼ 2 orders of magnitude for a comparable range in depth and temperature. The fugacity of CO2 gas is ∼1.5-6 bars at ≲ 310°C. Calculated values of aSio2(aq), {aNa+}/{aK+}, {aCa2+}/{aMg2+} and fCO2(g), in the fluid phase coexisting with observed mineralogic phase relations are in remarkably close agreement with measured solute concentrations in geothermal fluids produced from deep drillholes near the Salton Sea. Hydrolysis reactions representing observed phase relations and written with alkali and alkaline earth cations as products have negative standard molal enthalpies (ΔH0P,T,r) and volumes (ΔV0P,T,r) of reactions; consequently, {aNa+}/{aH+}, {aK+}/{aH+}, {aCa2+}/{a2H+}, and {aMg2+}/{a2H+} decrease with increasing temperature at constant pressure, but increase with increasing pressure at constant temperature. An approximate linear relationship exists among these activity ratios and the reciprocal of absolute temperatures because ΔH0P,T,r varies only slightly with increasing temperature at ≲ 250 to 300°C. However, at ≳300°C, ΔH0P,T,r and ΔV0P,T,R decrease dramatically as a consequence of extrema in

  12. Theoretical and experimental {alpha} decay half-lives of the heaviest odd-Z elements and general predictions

    SciTech Connect

    Zhang, H. F.; Royer, G.

    2007-10-15

    Theoretical {alpha} decay half-lives of the heaviest odd-Z nuclei are calculated using the experimental Q{sub {alpha}} value. The barriers in the quasimolecular shape path are determined within a Generalized Liquid Drop Model (GLDM) and the WKB approximation is used. The results are compared with calculations using the Density-Dependent M3Y (DDM3Y) effective interaction and the Viola-Seaborg-Sobiczewski (VSS) formulas. The calculations provide consistent estimates for the half-lives of the {alpha} decay chains of these superheavy elements. The experimental data stand between the GLDM calculations and VSS ones in the most time. Predictions are provided for the {alpha} decay half-lives of other superheavy nuclei within the GLDM and VSS approaches using the recent extrapolated Q{sub {alpha}} of Audi, Wapstra, and Thibault [Nucl. Phys. A729, 337 (2003)], which may be used for future experimental assignment and identification.

  13. Theoretical and experimental α decay half-lives of the heaviest odd-Z elements and general predictions

    NASA Astrophysics Data System (ADS)

    Zhang, H. F.; Royer, G.

    2007-10-01

    Theoretical α decay half-lives of the heaviest odd-Z nuclei are calculated using the experimental Qα value. The barriers in the quasimolecular shape path are determined within a Generalized Liquid Drop Model (GLDM) and the WKB approximation is used. The results are compared with calculations using the Density-Dependent M3Y (DDM3Y) effective interaction and the Viola-Seaborg-Sobiczewski (VSS) formulas. The calculations provide consistent estimates for the half-lives of the α decay chains of these superheavy elements. The experimental data stand between the GLDM calculations and VSS ones in the most time. Predictions are provided for the α decay half-lives of other superheavy nuclei within the GLDM and VSS approaches using the recent extrapolated Qα of Audi, Wapstra, and Thibault [Nucl. Phys. A729, 337 (2003)], which may be used for future experimental assignment and identification.

  14. Toward Relatively General and Accurate Quantum Chemical Predictions of Solid-State 17O NMR Chemical Shifts in Various Biologically Relevant Oxygen-containing Compounds

    PubMed Central

    Rorick, Amber; Michael, Matthew A.; Yang, Liu; Zhang, Yong

    2015-01-01

    Oxygen is an important element in most biologically significant molecules and experimental solid-state 17O NMR studies have provided numerous useful structural probes to study these systems. However, computational predictions of solid-state 17O NMR chemical shift tensor properties are still challenging in many cases and in particular each of the prior computational work is basically limited to one type of oxygen-containing systems. This work provides the first systematic study of the effects of geometry refinement, method and basis sets for metal and non-metal elements in both geometry optimization and NMR property calculations of some biologically relevant oxygen-containing compounds with a good variety of XO bonding groups, X= H, C, N, P, and metal. The experimental range studied is of 1455 ppm, a major part of the reported 17O NMR chemical shifts in organic and organometallic compounds. A number of computational factors towards relatively general and accurate predictions of 17O NMR chemical shifts were studied to provide helpful and detailed suggestions for future work. For the studied various kinds of oxygen-containing compounds, the best computational approach results in a theory-versus-experiment correlation coefficient R2 of 0.9880 and mean absolute deviation of 13 ppm (1.9% of the experimental range) for isotropic NMR shifts and R2 of 0.9926 for all shift tensor properties. These results shall facilitate future computational studies of 17O NMR chemical shifts in many biologically relevant systems, and the high accuracy may also help refinement and determination of active-site structures of some oxygen-containing substrate bound proteins. PMID:26274812

  15. Toward Relatively General and Accurate Quantum Chemical Predictions of Solid-State (17)O NMR Chemical Shifts in Various Biologically Relevant Oxygen-Containing Compounds.

    PubMed

    Rorick, Amber; Michael, Matthew A; Yang, Liu; Zhang, Yong

    2015-09-01

    Oxygen is an important element in most biologically significant molecules, and experimental solid-state (17)O NMR studies have provided numerous useful structural probes to study these systems. However, computational predictions of solid-state (17)O NMR chemical shift tensor properties are still challenging in many cases, and in particular, each of the prior computational works is basically limited to one type of oxygen-containing system. This work provides the first systematic study of the effects of geometry refinement, method, and basis sets for metal and nonmetal elements in both geometry optimization and NMR property calculations of some biologically relevant oxygen-containing compounds with a good variety of XO bonding groups (X = H, C, N, P, and metal). The experimental range studied is of 1455 ppm, a major part of the reported (17)O NMR chemical shifts in organic and organometallic compounds. A number of computational factors toward relatively general and accurate predictions of (17)O NMR chemical shifts were studied to provide helpful and detailed suggestions for future work. For the studied kinds of oxygen-containing compounds, the best computational approach results in a theory-versus-experiment correlation coefficient (R(2)) value of 0.9880 and a mean absolute deviation of 13 ppm (1.9% of the experimental range) for isotropic NMR shifts and an R(2) value of 0.9926 for all shift-tensor properties. These results shall facilitate future computational studies of (17)O NMR chemical shifts in many biologically relevant systems, and the high accuracy may also help the refinement and determination of active-site structures of some oxygen-containing substrate-bound proteins.

  16. Theoretical predictions for spatially-focused heating of magnetic nanoparticles guided by magnetic particle imaging field gradients

    NASA Astrophysics Data System (ADS)

    Dhavalikar, Rohan; Rinaldi, Carlos

    2016-12-01

    Magnetic nanoparticles in alternating magnetic fields (AMFs) transfer some of the field's energy to their surroundings in the form of heat, a property that has attracted significant attention for use in cancer treatment through hyperthermia and in developing magnetic drug carriers that can be actuated to release their cargo externally using magnetic fields. To date, most work in this field has focused on the use of AMFs that actuate heat release by nanoparticles over large regions, without the ability to select specific nanoparticle-loaded regions for heating while leaving other nanoparticle-loaded regions unaffected. In parallel, magnetic particle imaging (MPI) has emerged as a promising approach to image the distribution of magnetic nanoparticle tracers in vivo, with sub-millimeter spatial resolution. The underlying principle in MPI is the application of a selection magnetic field gradient, which defines a small region of low bias field, superimposed with an AMF (of lower frequency and amplitude than those normally used to actuate heating by the nanoparticles) to obtain a signal which is proportional to the concentration of particles in the region of low bias field. Here we extend previous models for estimating the energy dissipation rates of magnetic nanoparticles in uniform AMFs to provide theoretical predictions of how the selection magnetic field gradient used in MPI can be used to selectively actuate heating by magnetic nanoparticles in the low bias field region of the selection magnetic field gradient. Theoretical predictions are given for the spatial decay in energy dissipation rate under magnetic field gradients representative of those that can be achieved with current MPI technology. These results underscore the potential of combining MPI and higher amplitude/frequency actuation AMFs to achieve selective magnetic fluid hyperthermia (MFH) guided by MPI.

  17. Deep vein thrombosis is accurately predicted by comprehensive analysis of the levels of microRNA-96 and plasma D-dimer

    PubMed Central

    Xie, Xuesheng; Liu, Changpeng; Lin, Wei; Zhan, Baoming; Dong, Changjun; Song, Zhen; Wang, Shilei; Qi, Yingguo; Wang, Jiali; Gu, Zengquan

    2016-01-01

    The aim of the present study was to investigate the association between platelet microRNA-96 (miR-96) expression levels and the occurrence of deep vein thrombosis (DVT) in orthopedic patients. A total of consecutive 69 orthopedic patients with DVT and 30 healthy individuals were enrolled. Ultrasonic color Doppler imaging was performed on lower limb veins after orthopedic surgery to determine the occurrence of DVT. An enzyme-linked fluorescent assay was performed to detect the levels of D-dimer in plasma. A quantitative polymerase chain reaction assay was performed to determine the expression levels of miR-96. Expression levels of platelet miR-96 were significantly increased in orthopedic patients after orthopedic surgery. miR-96 expression levels in orthopedic patients with DVT at days 1, 3 and 7 after orthopedic surgery were significantly increased when compared with those in the control group. The increased miR-96 expression levels were correlated with plasma D-dimer levels in orthopedic patients with DVT. However, for the orthopedic patients in the non-DVT group following surgery, miR-96 expression levels were correlated with plasma D-dimer levels. In summary, the present results suggest that the expression levels of miR-96 may be associated with the occurrence of DVT. The occurrence of DVT may be accurately predicted by comprehensive analysis of the levels of miR-96 and plasma D-dimer. PMID:27588107

  18. Theoretical Prediction of Rate Constants for Hydrogen Abstraction by OH, H, O, CH3, and HO2 Radicals from Toluene.

    PubMed

    Li, Shu-Hao; Guo, Jun-Jiang; Li, Rui; Wang, Fan; Li, Xiang-Yuan

    2016-05-26

    Hydrogen abstraction from toluene by OH, H, O, CH3, and HO2 radicals are important reactions in oxidation process of toluene. Geometries and corresponding harmonic frequencies of the reactants, transition states as well as products involved in these reactions are determined at the B3LYP/6-31G(2df,p) level. To achieve highly accurate thermochemical data for these stationary points on the potential energy surfaces, the Gaussian-4(G4) composite method was employed. Torsional motions are treated either as free rotors or hindered rotors in calculating partion functions to determine thermodynamic properties. The obtained standard enthalpies of formation for reactants and some prodcuts are shown to be in excellent agreement with experimental data with the largest error of 0.5 kcal mol(-1). The conventional transition state theory (TST) with tunneling effects was adopted to determine rate constants of these hydrogen abstraction reactions based on results from quantum chemistry calculations. To faciliate its application in kinetic modeling, the obtained rate constants are given in Arrhenius expression: k(T) = AT(n) exp(-EaR/T). The obtained reaction rate constants also agree reasonably well with available expermiental data and previous theoretical values. Branching ratios of these reactions have been determined. The present reaction rates for these reactions have been used in a toluene combustion mechanism, and their effects on some combustion properties are demonstrated. PMID:27164019

  19. Accurate predictions of spectroscopic and molecular properties of 27 Λ-S and 73 Ω states of AsS radical.

    PubMed

    Shi, Deheng; Song, Ziyue; Niu, Xianghong; Sun, Jinfeng; Zhu, Zunlue

    2016-01-15

    The PECs are calculated for the 27 Λ-S states and their corresponding 73 Ω states of AsS radical. Of these Λ-S states, only the 2(2)Δ and 5(4)Π states are replulsive. The 1(2)Σ(+), 2(2)Σ(+), 4(2)Π, 3(4)Δ, 3(4)Σ(+), and 4(4)Π states possess double wells. The 3(2)Σ(+) state possesses three wells. The A(2)Π, 3(2)Π, 1(2)Φ, 2(4)Π, 3(4)Π, 2(4)Δ, 3(4)Δ, 1(6)Σ(+), and 1(6)Π states are inverted with the SO coupling effect included. The 1(4)Σ(+), 2(4)Σ(+), 2(4)Σ(-), 2(4)Δ, 1(4)Φ, 1(6)Σ(+), and 1(6)Π states, the second wells of 1(2)Σ(+), 3(4)Σ(+), 4(2)Π, 4(4)Π, and 3(4)Δ states, and the third well of 3(2)Σ(+) state are very weakly-bound states. The PECs are extrapolated to the CBS limit. The effect of SO coupling on the PECs is discussed. The spectroscopic parameters are evaluated, and compared with available measurements and other theoretical ones. The vibrational properties of several weakly-bound states are determined. The spectroscopic properties reported here can be expected to be reliably predicted ones.

  20. Accurate predictions of spectroscopic and molecular properties of 27 Λ-S and 73 Ω states of AsS radical

    NASA Astrophysics Data System (ADS)

    Shi, Deheng; Song, Ziyue; Niu, Xianghong; Sun, Jinfeng; Zhu, Zunlue

    2016-01-01

    The PECs are calculated for the 27 Λ-S states and their corresponding 73 Ω states of AsS radical. Of these Λ-S states, only the 22Δ and 54Π states are replulsive. The 12Σ+, 22Σ+, 42Π, 34Δ, 34Σ+, and 44Π states possess double wells. The 32Σ+ state possesses three wells. The A2Π, 32Π, 12Φ, 24Π, 34Π, 24Δ, 34Δ, 16Σ+, and 16Π states are inverted with the SO coupling effect included. The 14Σ+, 24Σ+, 24Σ-, 24Δ, 14Φ, 16Σ+, and 16Π states, the second wells of 12Σ+, 34Σ+, 42Π, 44Π, and 34Δ states, and the third well of 32Σ+ state are very weakly-bound states. The PECs are extrapolated to the CBS limit. The effect of SO coupling on the PECs is discussed. The spectroscopic parameters are evaluated, and compared with available measurements and other theoretical ones. The vibrational properties of several weakly-bound states are determined. The spectroscopic properties reported here can be expected to be reliably predicted ones.

  1. Accurate theoretical prediction of vibrational frequencies in an inhomogeneous dynamic environment: A case study of a glutamate molecule in water solution and in a protein-bound form

    NASA Astrophysics Data System (ADS)

    Speranskiy, Kirill; Kurnikova, Maria

    2004-07-01

    We propose a hierarchical approach to model vibrational frequencies of a ligand in a strongly fluctuating inhomogeneous environment such as a liquid solution or when bound to a macromolecule, e.g., a protein. Vibrational frequencies typically measured experimentally are ensemble averaged quantities which result (in part) from the influence of the strongly fluctuating solvent. Solvent fluctuations can be sampled effectively by a classical molecular simulation, which in our model serves as the first, low level of the hierarchy. At the second high level of the hierarchy a small subset of system coordinates is used to construct a patch of the potential surface (ab initio) relevant to the vibration in question. This subset of coordinates is under the influence of an instantaneous external force exerted by the environment. The force is calculated at the lower level of the hierarchy. The proposed methodology is applied to model vibrational frequencies of a glutamate in water and when bound to the Glutamate receptor protein and its mutant. Our results are in close agreement with the experimental values and frequency shifts measured by the Jayaraman group by the Fourier transform infrared spectroscopy [Q. Cheng et al., Biochem. 41, 1602 (2002)]. Our methodology proved useful in successfully reproducing vibrational frequencies of a ligand in such a soft, flexible, and strongly inhomogeneous protein as the Glutamate receptor.

  2. Accurate Prediction of Hyperfine Coupling Constants in Muoniated and Hydrogenated Ethyl Radicals: Ab Initio Path Integral Simulation Study with Density Functional Theory Method.

    PubMed

    Yamada, Kenta; Kawashima, Yukio; Tachikawa, Masanori

    2014-05-13

    We performed ab initio path integral molecular dynamics (PIMD) simulations with a density functional theory (DFT) method to accurately predict hyperfine coupling constants (HFCCs) in the ethyl radical (CβH3-CαH2) and its Mu-substituted (muoniated) compound (CβH2Mu-CαH2). The substitution of a Mu atom, an ultralight isotope of the H atom, with larger nuclear quantum effect is expected to strongly affect the nature of the ethyl radical. The static conventional DFT calculations of CβH3-CαH2 find that the elongation of one Cβ-H bond causes a change in the shape of potential energy curve along the rotational angle via the imbalance of attractive and repulsive interactions between the methyl and methylene groups. Investigation of the methyl-group behavior including the nuclear quantum and thermal effects shows that an unbalanced CβH2Mu group with the elongated Cβ-Mu bond rotates around the Cβ-Cα bond in a muoniated ethyl radical, quite differently from the CβH3 group with the three equivalent Cβ-H bonds in the ethyl radical. These rotations couple with other molecular motions such as the methylene-group rocking motion (inversion), leading to difficulties in reproducing the corresponding barrier heights. Our PIMD simulations successfully predict the barrier heights to be close to the experimental values and provide a significant improvement in muon and proton HFCCs given by the static conventional DFT method. Further investigation reveals that the Cβ-Mu/H stretching motion, methyl-group rotation, methylene-group rocking motion, and HFCC values deeply intertwine with each other. Because these motions are different between the radicals, a proper description of the structural fluctuations reflecting the nuclear quantum and thermal effects is vital to evaluate HFCC values in theory to be comparable to the experimental ones. Accordingly, a fundamental difference in HFCC between the radicals arises from their intrinsic molecular motions at a finite temperature, in

  3. Two-domain description of solute transport in heterogeneous porous media: Comparison between theoretical predictions and numerical experiments

    NASA Astrophysics Data System (ADS)

    Cherblanc, F.; Ahmadi, A.; Quintard, M.

    2007-05-01

    This paper deals with two-equation models describing solute transport in highly heterogeneous porous systems and more particularly dual permeability structures composed of high- and low-permeability regions. A macroscopic two-equation model has been previously proposed in the literature based on the volume averaging technique [Ahmadi A, Quintard M, Whitaker S. Transport in chemically and mechanically heterogeneous porous media V: two-equation model for solute transport with adsorption, Adv Water Resour 1998;22:59-86; Cherblanc F, Ahmadi A, Quintard M. Two-medium description of dispersion in heterogeneous porous media: calculation of macroscopic properties. Water Resour Res 2003;39(6):1154-73]. Through this theoretical upscaling method, both convection and dispersion mechanisms are taken into account in both regions, allowing one to deal with a large range of heterogeneous systems. In this paper, the numerical tools associated with this model are developed in order to test the theory by comparing macroscopic concentration fields to those obtained by Darcy-scale numerical experiments. The heterogeneous structures considered are made up of low-permeability nodules embedded in a continuous high-permeability region. Several permeability ratios are used, leading to very different macroscopic behaviours. Taking advantage of the Darcy-scale simulations, the role of convection and dispersion in the mass exchange between the two regions is investigated. Large-scale averaged concentration fields and elution curves are extracted from the Darcy-scale numerical experiments and compared to the theoretical predictions given by the two-equation model. Very good agreement is found between experimental and theoretical results. A permeability ratio around 100 presents a behaviour characteristic of "mobile-mobile" systems emphasizing the relevance of this two-equation description. Eventually, the theory is used to set-up a criterion for the existence of local equilibrium conditions

  4. Aluminum/hydrocarbon gel propellants: An experimental and theoretical investigation of secondary atomization and predicted rocket engine performance

    NASA Astrophysics Data System (ADS)

    Mueller, Donn Christopher

    1997-12-01

    Experimental and theoretical investigations of aluminum/hydrocarbon gel propellant secondary atomization and its potential effects on rocket engine performance were conducted. In the experimental efforts, a dilute, polydisperse, gel droplet spray was injected into the postflame region of a burner and droplet size distributions was measured as a function of position above the burner using a laser-based sizing/velocimetry technique. The sizing/velocimetry technique was developed to measure droplets in the 10-125 mum size range and avoids size-biased detection through the use of a uniformly illuminated probe volume. The technique was used to determine particle size distributions and velocities at various axial locations above the burner for JP-10, and 50 and 60 wt% aluminum gels. Droplet shell formation models were applied to aluminum/hydrocarbon gels to examine particle size and mass loading effects on the minimum droplet diameter that will permit secondary atomization. This diameter was predicted to be 38.1 and 34.7 mum for the 50 and 60 wt% gels, which is somewhat greater than the experimentally measured 30 and 25 mum diameters. In the theoretical efforts, three models were developed and an existing rocket code was exercised to gain insights into secondary atomization. The first model was designed to predict gel droplet properties and shell stresses after rigid shell formation, while the second, a one-dimensional gel spray combustion model was created to quantify the secondary atomization process. Experimental and numerical comparisons verify that secondary atomization occurs in 10-125 mum diameter particles although an exact model could not be derived. The third model, a one-dimensional gel-fueled rocket combustion chamber, was developed to evaluate secondary atomization effects on various engine performance parameters. Results show that only modest secondary atomization may be required to reduce propellant burnout distance and radiation losses. A solid propellant

  5. Failure-plane angle in Bentheim sandstone subjected to true triaxial stresses: experimental results and theoretical prediction

    NASA Astrophysics Data System (ADS)

    Ma, Xiaodong; Rudnicki, John; Haimson, Bezalel

    2014-05-01

    We conducted true triaxial tests in the high-porosity (n = 24%), quartz-rich (95%), Bentheim sandstone. An important objective was to investigate the dependence of failure-plane angle θ (angle between the normal to the plane and σ1 direction) on the prevailing stress conditions. We employed two distinct loading paths, and seven σ3 magnitudes (between 0 and 150 MPa). In tests using the common loading path, σ2 and σ3 were fixed, while σ1 was raised monotonically to failure. In tests using the novel loading path (which facilitate comparison with theoretical predictions), σ3 was fixed, and the Lode angle, Θ (= tan-1 [(σ1 - 2σ2 + σ3) / 30.5(σ1 - σ3)]) was kept constant by raising σ1 and σ2 simultaneously at a set ratio b [= (σ2 -σ3)/(σ1 -σ3)] until failure occurred. Six stress ratios b (= 0, 1/6, 1/3, 1/2, 3/4, 1), i.e. six Θ (= tan-1 [(1-2b) / 30.5]) values from +π/6 (axisymmetric compression) to -π/6 (axisymmetric extension) were used. In axisymmetric common loading path tests, failure-plane angle θ generally declined as the applied σ3 = σ2 increased from about 80° at σ3 = σ2 = 0 MPa to 0° at σ3 = σ2 = 150 MPa (forming compaction bands). In tests where σ3 ≠ σ2, the resulting failure-plane strike was consistently parallel to σ2 direction. For low σ3, θ typically rose by up to 12° as σ2 rose from σ2 = σ3 to σ2 = σ1. However, the rise in θ with σ2 tended to diminish at higher σ3. A limiting case occurred at σ3 = 150 MPa, where failure plane remained at 0° , regardless of the rise in σ2. In the novel loading path tests, failure-plane angle θ declined monotonically for any given Lode angle Θ, from roughly 80° to 0° , as the mean stress at failure (σoct,f) rose from about 20 MPa to around 220 MPa; for a constant σoct,f, θ typically increased from 10° (at σoct,f = 20 MPa) to 30° (at σoct,f = 220 MPa) as Θ dropped from +π/6 (σ2 = σ3) to -π/6 (σ2 = σ1). We compared the measured θ with that predicted using

  6. Noble-Gas-Inserted Fluoro(sulphido)boron (FNgBS, Ng = Ar, Kr, and Xe): A Theoretical Prediction.

    PubMed

    Ghosh, Ayan; Dey, Sourav; Manna, Debashree; Ghanty, Tapan K

    2015-06-01

    The possibility of the existence of a new series of neutral noble gas compound, FNgBS (where Ng = Ar, Kr, Xe), is explored theoretically through the insertion of a Ng atom into the fluoroborosulfide molecule (FBS). Second-order Møller-Plesset perturbation theory, density functional theory, and coupled cluster theory based methods have been employed to predict the structure, stability, harmonic vibrational frequencies, and charge distribution of FNgBS molecules. Through energetics study, it has been found that the molecules could dissociate into global minima products (Ng + FBS) on the respective singlet potential energy surface via a unimolecular dissociation channel; however, the sufficiently large activation energy barriers provide enough kinetic stability to the predicted molecules, which, in turn, prevent them from dissociating into the global minima products. Moreover, the FNgBS species are thermodynamically stable, owing to very high positive energies with respect to other two two-body dissociation channels, leading to FNg + BS and F(-) + NgBS(+), and two three-body dissociation channels, corresponding to the dissociation into F + Ng + BS and F(-) + Ng + BS(+). Furthermore, the Mulliken and NBO charge analysis together with the AIM results reveal that the Ng-B bond is more of covalent in nature, whereas the F-Ng bond is predominantly ionic in character. Thus, these compounds can be better represented as F(-)[NgBS](+). This fact is also supported by the detail analysis of bond length, bond dissociation energy, and stretching force constant values. All of the calculated results reported in this work clearly indicate that it might be possible to prepare and characterize the FNgBS molecules in cryogenic environment through matrix isolation technique by using a mixture of OCS/BF3 in the presence of large quantity of noble gas under suitable experimental conditions. PMID:25928588

  7. Theoretical predictions of novel superconducting phases of BaGe3 stable at atmospheric and high pressures.

    PubMed

    Zurek, Eva; Yao, Yansun

    2015-03-16

    A series of new superconducting binary silicides and germanides have recently been synthesized under high-pressure high-temperature conditions. A representative member of this group, BaGe3, was theoretically investigated using evolutionary structure searches coupled with structural analogies in the pressure range from 1 atm to 250 GPa, where three new phases were discovered. At 1 atm, in addition to the synthesized P63/mmc phase, we predicted two new phases, I4/mmm and Amm2, to be dynamically stable. The Amm2 structure comprises Ge clusters and triangular prisms intercalated with Ba and Ge atoms, a unique structural motif unknown to this group. The I4/mmm structure has been previously synthesized in binary silicides and is calculated to be thermodynamically stable in BaGe3 between 15.6 and 35.4 GPa. Above 35.4 GPa, two new phases of P6̅m2 and R3̅m symmetry become the global minima and remain so up to the highest pressure considered. These two phases have very similar enthalpies, and both feature layers of double Kagome nets of Ge intercalated with Ba-Ge layers. The predicted phases are suggested to be metallic with itinerant electrons and to be potentially superconducting from the considerable electron-phonon coupling strength. Density functional perturbation calculations combined with the Allen-Dynes-modified McMillan formula were used to estimate the superconducting critical temperatures (Tc) for these new phases, which, with slight pressure variations, are comparable to the experimental Tc measured for the P63/mmc phase.

  8. Metabolic and hemodynamic events following changes in neuronal activity: current hypotheses, theoretical predictions and in vivo NMR experimental findings

    PubMed Central

    Mangia, Silvia; Giove, Federico; Tkáč, Ivan; Logothetis, Nikos K.; Henry, Pierre-Gilles; Olman, Cheryl A.; Maraviglia, Bruno; Di Salle, Francesco; Uğurbil, Kâmil

    2009-01-01

    Unraveling the energy metabolism and the hemodynamic outcomes of excitatory and inhibitory neuronal activity is critical not only for our basic understanding of overall brain function, but also for the understanding of many brain disorders. Methodologies of magnetic resonance spectroscopy (MRS) and magnetic resonance imaging (MRI) are powerful tools for the non-invasive investigation of brain metabolism and physiology. However, the temporal and spatial resolution of in vivo MRS and MRI is not suitable to provide direct evidence for hypotheses that involve metabolic compartmentalization between different cell types, or to untangle the complex neuronal micro-circuitry which results in changes of electrical activity. This review aims at describing how the current models of brain metabolism, mainly built on the basis of in vitro evidence, relate to experimental findings recently obtained in vivo by 1H MRS, 13C MRS and MRI. The hypotheses related to the role of different metabolic substrates, the metabolic neuron-glia interactions, along with the available theoretical predictions of the energy budget of neurotransmission, will be discussed. In addition, the cellular and network mechanisms that characterize different types of increased and suppressed neuronal activity will be considered within the sensitivity-constraints of MRS and MRI. PMID:19002199

  9. Predicting protein subnuclear location with optimized evidence-theoretic K-nearest classifier and pseudo amino acid composition

    SciTech Connect

    Shen Hongbin; Chou Kuochen . E-mail: kchou@san.rr.com

    2005-11-25

    The nucleus is the brain of eukaryotic cells that guides the life processes of the cell by issuing key instructions. For in-depth understanding of the biochemical process of the nucleus, the knowledge of localization of nuclear proteins is very important. With the avalanche of protein sequences generated in the post-genomic era, it is highly desired to develop an automated method for fast annotating the subnuclear locations for numerous newly found nuclear protein sequences so as to be able to timely utilize them for basic research and drug discovery. In view of this, a novel approach is developed for predicting the protein subnuclear location. It is featured by introducing a powerful classifier, the optimized evidence-theoretic K-nearest classifier, and using the pseudo amino acid composition [K.C. Chou, PROTEINS: Structure, Function, and Genetics, 43 (2001) 246], which can incorporate a considerable amount of sequence-order effects, to represent protein samples. As a demonstration, identifications were performed for 370 nuclear proteins among the following 9 subnuclear locations: (1) Cajal body, (2) chromatin, (3) heterochromatin, (4) nuclear diffuse, (5) nuclear pore, (6) nuclear speckle, (7) nucleolus, (8) PcG body, and (9) PML body. The overall success rates thus obtained by both the re-substitution test and jackknife cross-validation test are significantly higher than those by existing classifiers on the same working dataset. It is anticipated that the powerful approach may also become a useful high throughput vehicle to bridge the huge gap occurring in the post-genomic era between the number of gene sequences in databases and the number of gene products that have been functionally characterized. The OET-KNN classifier will be available at www.pami.sjtu.edu.cn/people/hbshen.

  10. Accurate prediction of explicit solvent atom distribution in HIV-1 protease and F-ATP synthase by statistical theory of liquids

    NASA Astrophysics Data System (ADS)

    Sindhikara, Daniel; Yoshida, Norio; Hirata, Fumio

    2012-02-01

    We have created a simple algorithm for automatically predicting the explicit solvent atom distribution of biomolecules. The explicit distribution is coerced from the 3D continuous distribution resulting from a 3D-RISM calculation. This procedure predicts optimal location of solvent molecules and ions given a rigid biomolecular structure. We show examples of predicting water molecules near KNI-275 bound form of HIV-1 protease and predicting both sodium ions and water molecules near the rotor ring of F-ATP synthase. Our results give excellent agreement with experimental structure with an average prediction error of 0.45-0.65 angstroms. Further, unlike experimental methods, this method does not suffer from the partial occupancy limit. Our method can be performed directly on 3D-RISM output within minutes. It is useful not only as a location predictor but also as a convenient method for generating initial structures for MD calculations.

  11. Comparison of theoretically predicted lateral-directional aerodynamic characteristics with full-scale wind tunnel data on the ATLIT airplane

    NASA Technical Reports Server (NTRS)

    Griswold, M.; Roskam, J.

    1980-01-01

    An analytical method is presented for predicting lateral-directional aerodynamic characteristics of light twin engine propeller-driven airplanes. This method is applied to the Advanced Technology Light Twin Engine airplane. The calculated characteristics are correlated against full-scale wind tunnel data. The method predicts the sideslip derivatives fairly well, although angle of attack variations are not well predicted. Spoiler performance was predicted somewhat high but was still reasonable. The rudder derivatives were not well predicted, in particular the effect of angle of attack. The predicted dynamic derivatives could not be correlated due to lack of experimental data.

  12. NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11.

    PubMed

    Lundegaard, Claus; Lamberth, Kasper; Harndahl, Mikkel; Buus, Søren; Lund, Ole; Nielsen, Morten

    2008-07-01

    NetMHC-3.0 is trained on a large number of quantitative peptide data using both affinity data from the Immune Epitope Database and Analysis Resource (IEDB) and elution data from SYFPEITHI. The method generates high-accuracy predictions of major histocompatibility complex (MHC): peptide binding. The predictions are based on artificial neural networks trained on data from 55 MHC alleles (43 Human and 12 non-human), and position-specific scoring matrices (PSSMs) for additional 67 HLA alleles. As only the MHC class I prediction server is available, predictions are possible for peptides of length 8-11 for all 122 alleles. artificial neural network predictions are given as actual IC(50) values whereas PSSM predictions are given as a log-odds likelihood scores. The output is optionally available as download for easy post-processing. The training method underlying the server is the best available, and has been used to predict possible MHC-binding peptides in a series of pathogen viral proteomes including SARS, Influenza and HIV, resulting in an average of 75-80% confirmed MHC binders. Here, the performance is further validated and benchmarked using a large set of newly published affinity data, non-redundant to the training set. The server is free of use and available at: http://www.cbs.dtu.dk/services/NetMHC.

  13. Comparison of theoretical predicted longitudinal aerodynamic characteristics with full-scale wind tunnel data on the ATLIT airplane

    NASA Technical Reports Server (NTRS)

    Vandam, C. P. G.; Griswold, M.; Roskam, J.

    1979-01-01

    An analytical method is presented for predicting the lift coefficient, the pitching moment coefficient, and the drag coefficient of light, twin-engine, propeller-driven airplanes. The method was applied to the Advanced Technology Light Twin-Engine airplane. The calculated characteristics were then correlated against full scale wind tunnel data. The analytical method was found to predict the drag and pitching moment fairly well. However, the lift prediction was extremely poor.

  14. HIGH-TEMPERATURE, SHORT-TIME SULFATION OF CALCIUM- BASED SORBENTS. 2. EXPERIMENTAL DATA AND THEORETICAL MODEL PREDICTIONS

    EPA Science Inventory

    The fundamental processes for injection of CaCO3 and Ca(OH)2 for the removal of SO2 from combustion gases of coal-fired boilers are analyzed on the basis of experimental data and a comprehensive theoretical model. Sulfation data were obtained in a 30-kW isothermal gas-particle t...

  15. Use of quantitative shape-activity relationships to model the photoinduced toxicity of polycyclic aromatic hydrocarbons: Electron density shape features accurately predict toxicity

    SciTech Connect

    Mezey, P.G.; Zimpel, Z.; Warburton, P.; Walker, P.D.; Irvine, D.G.; Huang, X.D.; Dixon, D.G.; Greenberg, B.M.

    1998-07-01

    The quantitative shape-activity relationship (QShAR) methodology, based on accurate three-dimensional electron densities and detailed shape analysis methods, has been applied to a Lemna gibba photoinduced toxicity data set of 16 polycyclic aromatic hydrocarbon (PAH) molecules. In the first phase of the studies, a shape fragment QShAR database of PAHs was developed. The results provide a very good match to toxicity based on a combination of the local shape features of single rings in comparison to the central ring of anthracene and a more global shape feature involving larger molecular fragments. The local shape feature appears as a descriptor of the susceptibility of PAHs to photomodification and the global shape feature is probably related to photosensitization activity.

  16. Use of dose-dependent absorption into target tissues to more accurately predict cancer risk at low oral doses of hexavalent chromium.

    PubMed

    Haney, J

    2015-02-01

    The mouse dose at the lowest water concentration used in the National Toxicology Program hexavalent chromium (CrVI) drinking water study (NTP, 2008) is about 74,500 times higher than the approximate human dose corresponding to the 35-city geometric mean reported in EWG (2010) and over 1000 times higher than that based on the highest reported tap water concentration. With experimental and environmental doses differing greatly, it is a regulatory challenge to extrapolate high-dose results to environmental doses orders of magnitude lower in a meaningful and toxicologically predictive manner. This seems particularly true for the low-dose extrapolation of results for oral CrVI-induced carcinogenesis since dose-dependent differences in the dose fraction absorbed by mouse target tissues are apparent (Kirman et al., 2012). These data can be used for a straightforward adjustment of the USEPA (2010) draft oral slope factor (SFo) to be more predictive of risk at environmentally-relevant doses. More specifically, the evaluation of observed and modeled differences in the fraction of dose absorbed by target tissues at the point-of-departure for the draft SFo calculation versus lower doses suggests that the draft SFo be divided by a dose-specific adjustment factor of at least an order of magnitude to be less over-predictive of risk at more environmentally-relevant doses.

  17. PredPPCrys: Accurate Prediction of Sequence Cloning, Protein Production, Purification and Crystallization Propensity from Protein Sequences Using Multi-Step Heterogeneous Feature Fusion and Selection

    PubMed Central

    Wang, Huilin; Wang, Mingjun; Tan, Hao; Li, Yuan; Zhang, Ziding; Song, Jiangning

    2014-01-01

    X-ray crystallography is the primary approach to solve the three-dimensional structure of a protein. However, a major bottleneck of this method is the failure of multi-step experimental procedures to yield diffraction-quality crystals, including sequence cloning, protein material production, purification, crystallization and ultimately, structural determination. Accordingly, prediction of the propensity of a protein to successfully undergo these experimental procedures based on the protein sequence may help narrow down laborious experimental efforts and facilitate target selection. A number of bioinformatics methods based on protein sequence information have been developed for this purpose. However, our knowledge on the important determinants of propensity for a protein sequence to produce high diffraction-quality crystals remains largely incomplete. In practice, most of the existing methods display poorer performance when evaluated on larger and updated datasets. To address this problem, we constructed an up-to-date dataset as the benchmark, and subsequently developed a new approach termed ‘PredPPCrys’ using the support vector machine (SVM). Using a comprehensive set of multifaceted sequence-derived features in combination with a novel multi-step feature selection strategy, we identified and characterized the relative importance and contribution of each feature type to the prediction performance of five individual experimental steps required for successful crystallization. The resulting optimal candidate features were used as inputs to build the first-level SVM predictor (PredPPCrys I). Next, prediction outputs of PredPPCrys I were used as the input to build second-level SVM classifiers (PredPPCrys II), which led to significantly enhanced prediction performance. Benchmarking experiments indicated that our PredPPCrys method outperforms most existing procedures on both up-to-date and previous datasets. In addition, the predicted crystallization targets of

  18. Normal Tissue Complication Probability Estimation by the Lyman-Kutcher-Burman Method Does Not Accurately Predict Spinal Cord Tolerance to Stereotactic Radiosurgery

    SciTech Connect

    Daly, Megan E.; Luxton, Gary; Choi, Clara Y.H.; Gibbs, Iris C.; Chang, Steven D.; Adler, John R.; Soltys, Scott G.

    2012-04-01

    Purpose: To determine whether normal tissue complication probability (NTCP) analyses of the human spinal cord by use of the Lyman-Kutcher-Burman (LKB) model, supplemented by linear-quadratic modeling to account for the effect of fractionation, predict the risk of myelopathy from stereotactic radiosurgery (SRS). Methods and Materials: From November 2001 to July 2008, 24 spinal hemangioblastomas in 17 patients were treated with SRS. Of the tumors, 17 received 1 fraction with a median dose of 20 Gy (range, 18-30 Gy) and 7 received 20 to 25 Gy in 2 or 3 sessions, with cord maximum doses of 22.7 Gy (range, 17.8-30.9 Gy) and 22.0 Gy (range, 20.2-26.6 Gy), respectively. By use of conventional values for {alpha}/{beta}, volume parameter n, 50% complication probability dose TD{sub 50}, and inverse slope parameter m, a computationally simplified implementation of the LKB model was used to calculate the biologically equivalent uniform dose and NTCP for each treatment. Exploratory calculations were performed with alternate values of {alpha}/{beta} and n. Results: In this study 1 case (4%) of myelopathy occurred. The LKB model using radiobiological parameters from Emami and the logistic model with parameters from Schultheiss overestimated complication rates, predicting 13 complications (54%) and 18 complications (75%), respectively. An increase in the volume parameter (n), to assume greater parallel organization, improved the predictive value of the models. Maximum-likelihood LKB fitting of {alpha}/{beta} and n yielded better predictions (0.7 complications), with n = 0.023 and {alpha}/{beta} = 17.8 Gy. Conclusions: The spinal cord tolerance to the dosimetry of SRS is higher than predicted by the LKB model using any set of accepted parameters. Only a high {alpha}/{beta} value in the LKB model and only a large volume effect in the logistic model with Schultheiss data could explain the low number of complications observed. This finding emphasizes that radiobiological models

  19. Mononuclear nonheme iron(IV)-oxo and manganese(IV)-oxo complexes in oxidation reactions: experimental results prove theoretical prediction.

    PubMed

    Chen, Junying; Cho, Kyung-Bin; Lee, Yong-Min; Kwon, Yoon Hye; Nam, Wonwoo

    2015-08-25

    Reactivities of mononuclear nonheme iron(IV)-oxo and manganese(IV)-oxo complexes bearing a pentadentate N4Py ligand, [M(IV)O(N4Py)](2+) (M = Fe and Mn), are compared in hydrogen atom transfer (HAT) and oxygen atom transfer (OAT) reactions; theoretical and experimental results show that Fe(IV)O is more reactive than Mn(IV)O. The latter is shown to react through excited state reactivity (ESR).

  20. The CUPIC algorithm: an accurate model for the prediction of sustained viral response under telaprevir or boceprevir triple therapy in cirrhotic patients.

    PubMed

    Boursier, J; Ducancelle, A; Vergniol, J; Veillon, P; Moal, V; Dufour, C; Bronowicki, J-P; Larrey, D; Hézode, C; Zoulim, F; Fontaine, H; Canva, V; Poynard, T; Allam, S; De Lédinghen, V

    2015-12-01

    Triple therapy using boceprevir or telaprevir remains the reference treatment for genotype 1 chronic hepatitis C in countries where new interferon-free regimens have not yet become available. Antiviral treatment is highly required in cirrhotic patients, but they represent a difficult-to-treat population. We aimed to develop a simple algorithm for the prediction of sustained viral response (SVR) in cirrhotic patients treated with triple therapy. A total of 484 cirrhotic patients from the ANRS CO20 CUPIC cohort treated with triple therapy were randomly distributed into derivation and validation sets. A total of 52.1% of patients achieved SVR. In the derivation set, a D0 score for the prediction of SVR before treatment initiation included the following independent predictors collected at day 0: prior treatment response, gamma-GT, platelets, telaprevir treatment, viral load. To refine the prediction at the early phase of the treatment, a W4 score included as additional parameter the viral load collected at week 4. The D0 and W4 scores were combined in the CUPIC algorithm defining three subgroups: 'no treatment initiation or early stop at week 4', 'undetermined' and 'SVR highly probable'. In the validation set, the rates of SVR in these three subgroups were, respectively, 11.1%, 50.0% and 82.2% (P < 0.001). By replacing the variable 'prior treatment response' with 'IL28B genotype', another algorithm was derived for treatment-naïve patients with similar results. The CUPIC algorithm is an easy-to-use tool that helps physicians weigh their decision between immediately treating cirrhotic patients using boceprevir/telaprevir triple therapy or waiting for new drugs to become available in their country. PMID:26216230

  1. Ab initio molecular dynamics of liquid water using embedded-fragment second-order many-body perturbation theory towards its accurate property prediction

    PubMed Central

    Willow, Soohaeng Yoo; Salim, Michael A.; Kim, Kwang S.; Hirata, So

    2015-01-01

    A direct, simultaneous calculation of properties of a liquid using an ab initio electron-correlated theory has long been unthinkable. Here we present structural, dynamical, and response properties of liquid water calculated by ab initio molecular dynamics using the embedded-fragment spin-component-scaled second-order many-body perturbation method with the aug-cc-pVDZ basis set. This level of theory is chosen as it accurately and inexpensively reproduces the water dimer potential energy surface from the coupled-cluster singles, doubles, and noniterative triples with the aug-cc-pVQZ basis set, which is nearly exact. The calculated radial distribution function, self-diffusion coefficient, coordinate number, and dipole moment, as well as the infrared and Raman spectra are in excellent agreement with experimental results. The shapes and widths of the OH stretching bands in the infrared and Raman spectra and their isotropic-anisotropic Raman noncoincidence, which reflect the diverse local hydrogen-bond environment, are also reproduced computationally. The simulation also reveals intriguing dynamic features of the environment, which are difficult to probe experimentally, such as a surprisingly large fluctuation in the coordination number and the detailed mechanism by which the hydrogen donating water molecules move across the first and second shells, thereby causing this fluctuation. PMID:26400690

  2. Ab initio molecular dynamics of liquid water using embedded-fragment second-order many-body perturbation theory towards its accurate property prediction.

    PubMed

    Willow, Soohaeng Yoo; Salim, Michael A; Kim, Kwang S; Hirata, So

    2015-01-01

    A direct, simultaneous calculation of properties of a liquid using an ab initio electron-correlated theory has long been unthinkable. Here we present structural, dynamical, and response properties of liquid water calculated by ab initio molecular dynamics using the embedded-fragment spin-component-scaled second-order many-body perturbation method with the aug-cc-pVDZ basis set. This level of theory is chosen as it accurately and inexpensively reproduces the water dimer potential energy surface from the coupled-cluster singles, doubles, and noniterative triples with the aug-cc-pVQZ basis set, which is nearly exact. The calculated radial distribution function, self-diffusion coefficient, coordinate number, and dipole moment, as well as the infrared and Raman spectra are in excellent agreement with experimental results. The shapes and widths of the OH stretching bands in the infrared and Raman spectra and their isotropic-anisotropic Raman noncoincidence, which reflect the diverse local hydrogen-bond environment, are also reproduced computationally. The simulation also reveals intriguing dynamic features of the environment, which are difficult to probe experimentally, such as a surprisingly large fluctuation in the coordination number and the detailed mechanism by which the hydrogen donating water molecules move across the first and second shells, thereby causing this fluctuation.

  3. Stable, high-order SBP-SAT finite difference operators to enable accurate simulation of compressible turbulent flows on curvilinear grids, with application to predicting turbulent jet noise

    NASA Astrophysics Data System (ADS)

    Byun, Jaeseung; Bodony, Daniel; Pantano, Carlos

    2014-11-01

    Improved order-of-accuracy discretizations often require careful consideration of their numerical stability. We report on new high-order finite difference schemes using Summation-By-Parts (SBP) operators along with the Simultaneous-Approximation-Terms (SAT) boundary condition treatment for first and second-order spatial derivatives with variable coefficients. In particular, we present a highly accurate operator for SBP-SAT-based approximations of second-order derivatives with variable coefficients for Dirichlet and Neumann boundary conditions. These terms are responsible for approximating the physical dissipation of kinetic and thermal energy in a simulation, and contain grid metrics when the grid is curvilinear. Analysis using the Laplace transform method shows that strong stability is ensured with Dirichlet boundary conditions while weaker stability is obtained for Neumann boundary conditions. Furthermore, the benefits of the scheme is shown in the direct numerical simulation (DNS) of a Mach 1.5 compressible turbulent supersonic jet using curvilinear grids and skew-symmetric discretization. Particularly, we show that the improved methods allow minimization of the numerical filter often employed in these simulations and we discuss the qualities of the simulation.

  4. Accurate prediction of diradical chemistry from a single-reference density-matrix method: Model application to the bicyclobutane to gauche-1,3-butadiene isomerization

    SciTech Connect

    Bertels, Luke W.; Mazziotti, David A.

    2014-07-28

    Multireference correlation in diradical molecules can be captured by a single-reference 2-electron reduced-density-matrix (2-RDM) calculation with only single and double excitations in the 2-RDM parametrization. The 2-RDM parametrization is determined by N-representability conditions that are non-perturbative in their treatment of the electron correlation. Conventional single-reference wave function methods cannot describe the entanglement within diradical molecules without employing triple- and potentially even higher-order excitations of the mean-field determinant. In the isomerization of bicyclobutane to gauche-1,3-butadiene the parametric 2-RDM (p2-RDM) method predicts that the diradical disrotatory transition state is 58.9 kcal/mol above bicyclobutane. This barrier is in agreement with previous multireference calculations as well as recent Monte Carlo and higher-order coupled cluster calculations. The p2-RDM method predicts the Nth natural-orbital occupation number of the transition state to be 0.635, revealing its diradical character. The optimized geometry from the p2-RDM method differs in important details from the complete-active-space self-consistent-field geometry used in many previous studies including the Monte Carlo calculation.

  5. An equation to estimate the difference between theoretically predicted and SDS PAGE-displayed molecular weights for an acidic peptide.

    PubMed

    Guan, Yihong; Zhu, Qinfang; Huang, Delai; Zhao, Shuyi; Jan Lo, Li; Peng, Jinrong

    2015-01-01

    The molecular weight (MW) of a protein can be predicted based on its amino acids (AA) composition. However, in many cases a non-chemically modified protein shows an SDS PAGE-displayed MW larger than its predicted size. Some reports linked this fact to high content of acidic AA in the protein. However, the exact relationship between the acidic AA composition and the SDS PAGE-displayed MW is not established. Zebrafish nucleolar protein Def is composed of 753 AA and shows an SDS PAGE-displayed MW approximately 13 kDa larger than its predicted MW. The first 188 AA in Def is defined by a glutamate-rich region containing ~35.6% of acidic AA. In this report, we analyzed the relationship between the SDS PAGE-displayed MW of thirteen peptides derived from Def and the AA composition in each peptide. We found that the difference between the predicted and SDS PAGE-displayed MW showed a linear correlation with the percentage of acidic AA that fits the equation y = 276.5x - 31.33 (x represents the percentage of acidic AA, 11.4% ≤ x ≤ 51.1%; y represents the average ΔMW per AA). We demonstrated that this equation could be applied to predict the SDS PAGE-displayed MW for thirteen different natural acidic proteins. PMID:26311515

  6. SNP development from RNA-seq data in a nonmodel fish: how many individuals are needed for accurate allele frequency prediction?

    PubMed

    Schunter, C; Garza, J C; Macpherson, E; Pascual, M

    2014-01-01

    Single nucleotide polymorphisms (SNPs) are rapidly becoming the marker of choice in population genetics due to a variety of advantages relative to other markers, including higher genomic density, data quality, reproducibility and genotyping efficiency, as well as ease of portability between laboratories. Advances in sequencing technology and methodologies to reduce genomic representation have made the isolation of SNPs feasible for nonmodel organisms. RNA-seq is one such technique for the discovery of SNPs and development of markers for large-scale genotyping. Here, we report the development of 192 validated SNP markers for parentage analysis in Tripterygion delaisi (the black-faced blenny), a small rocky-shore fish from the Mediterranean Sea. RNA-seq data for 15 individual samples were used for SNP discovery by applying a series of selection criteria. Genotypes were then collected from 1599 individuals from the same population with the resulting loci. Differences in heterozygosity and allele frequencies were found between the two data sets. Heterozygosity was lower, on average, in the population sample, and the mean difference between the frequencies of particular alleles in the two data sets was 0.135 ± 0.100. We used bootstrap resampling of the sequence data to predict appropriate sample sizes for SNP discovery. As cDNA library production is time-consuming and expensive, we suggest that using seven individuals for RNA sequencing reduces the probability of discarding highly informative SNP loci, due to lack of observed polymorphism, whereas use of more than 12 samples does not considerably improve prediction of true allele frequencies.

  7. Is scoring system of computed tomography based metric parameters can accurately predicts shock wave lithotripsy stone-free rates and aid in the development of treatment strategies?

    PubMed Central

    Badran, Yasser Ali; Abdelaziz, Alsayed Saad; Shehab, Mohamed Ahmed; Mohamed, Hazem Abdelsabour Dief; Emara, Absel-Aziz Ali; Elnabtity, Ali Mohamed Ali; Ghanem, Maged Mohammed; ELHelaly, Hesham Abdel Azim

    2016-01-01

    Objective: The objective was to determine the predicting success of shock wave lithotripsy (SWL) using a combination of computed tomography based metric parameters to improve the treatment plan. Patients and Methods: Consecutive 180 patients with symptomatic upper urinary tract calculi 20 mm or less were enrolled in our study underwent extracorporeal SWL were divided into two main groups, according to the stone size, Group A (92 patients with stone ≤10 mm) and Group B (88 patients with stone >10 mm). Both groups were evaluated, according to the skin to stone distance (SSD) and Hounsfield units (≤500, 500–1000 and >1000 HU). Results: Both groups were comparable in baseline data and stone characteristics. About 92.3% of Group A rendered stone-free, whereas 77.2% were stone-free in Group B (P = 0.001). Furthermore, in both group SWL success rates was a significantly higher for stones with lower attenuation <830 HU than with stones >830 HU (P < 0.034). SSD were statistically differences in SWL outcome (P < 0.02). Simultaneous consideration of three parameters stone size, stone attenuation value, and SSD; we found that stone-free rate (SFR) was 100% for stone attenuation value <830 HU for stone <10 mm or >10 mm but total number SWL sessions and shock waves required for the larger stone group were higher than in the smaller group (P < 0.01). Furthermore, SFR was 83.3% and 37.5% for stone <10 mm, mean HU >830, SSD 90 mm and SSD >120 mm, respectively. On the other hand, SFR was 52.6% and 28.57% for stone >10 mm, mean HU >830, SSD <90 mm and SSD >120 mm, respectively. Conclusion: Stone size, stone density (HU), and SSD is simple to calculate and can be reported by radiologists to applying combined score help to augment predictive power of SWL, reduce cost, and improving of treatment strategies. PMID:27141192

  8. Wind-blown Sand Electrification Inspired Triboelectric Energy Harvesting Based on Homogeneous Inorganic Materials Contact: A Theoretical Study and Prediction

    PubMed Central

    Hu, Wenwen; Wu, Weiwei; Zhou, Hao-miao

    2016-01-01

    Triboelectric nanogenerator (TENG) based on contact electrification between heterogeneous materials has been widely studied. Inspired from wind-blown sand electrification, we design a novel kind of TENG based on size dependent electrification using homogeneous inorganic materials. Based on the asymmetric contact theory between homogeneous material surfaces, a calculation of surface charge density has been carried out. Furthermore, the theoretical output of homogeneous material based TENG has been simulated. Therefore, this work may pave the way of fabricating TENG without the limitation of static sequence. PMID:26817411

  9. Turbulence-induced scintillation on Gaussian-beam waves: theoretical predictions and observations from a laser-illuminated satellite

    NASA Astrophysics Data System (ADS)

    Shelton, John D.

    1995-10-01

    Expressions for the variance and the power spectral density of turbulence-induced log-amplitude fluctuations are derived for Gaussian-beam waves in the regime of weak scattering. This formulation includes effects that are due to turbulence strength variations along the propagation path, offset of the observation point from the beam axis, and sensitivity to focus and beam diameter. Comparison of theoretical results with observed scintillation during experiments with a laser-illuminated satellite reveals good agreement. Copyright (c) 1995 Optical Society of America

  10. Communication: Theoretical prediction of the structure and spectroscopic properties of the tilde{X} and tilde{A} states of hydroxymethyl peroxy (HOCH2OO) radical

    NASA Astrophysics Data System (ADS)

    Delcey, Mickael G.; Lindh, Roland; Linguerri, Roberto; Hochlaf, Majdi; Francisco, Joseph S.

    2013-01-01

    The hydroxymethyl peroxy (HMOO) radical is a radical product from the oxidation of non-methane hydrocarbons. The present study provides theoretical prediction of critical spectroscopic features of this radical that should aid in its experimental characterization. Structure, rotational constants, and harmonic frequencies are presented for the ground and first excited electronic states of HMOO. The adiabatic transition energy for the tilde{A} leftarrow tilde{X} process is 7360 cm-1, suggesting that this transition, occurring in the mid to near infrared, is the most promising candidate for observing the radical spectroscopically. The band origin of the tilde{A} leftarrow tilde{X} transition of HMOO is calibrated and benchmarked with the corresponding state of the HOO radical, which is experimentally and theoretically well characterized.

  11. A Bayesian network model for predicting aquatic toxicity mode of action using two dimensional theoretical molecular descriptors

    EPA Science Inventory

    The mode of toxic action (MoA) has been recognized as a key determinant of chemical toxicity, but development of predictive MoA classification models in aquatic toxicology has been limited. We developed a Bayesian network model to classify aquatic toxicity MoA using a recently pu...

  12. Accurate prediction of hard-sphere virial coefficients B6 to B12 from a compressibility-based equation of state

    NASA Astrophysics Data System (ADS)

    Hansen-Goos, Hendrik

    2016-04-01

    We derive an analytical equation of state for the hard-sphere fluid that is within 0.01% of computer simulations for the whole range of the stable fluid phase. In contrast, the commonly used Carnahan-Starling equation of state deviates by up to 0.3% from simulations. The derivation uses the functional form of the isothermal compressibility from the Percus-Yevick closure of the Ornstein-Zernike relation as a starting point. Two additional degrees of freedom are introduced, which are constrained by requiring the equation of state to (i) recover the exact fourth virial coefficient B4 and (ii) involve only integer coefficients on the level of the ideal gas, while providing best possible agreement with the numerical result for B5. Virial coefficients B6 to B10 obtained from the equation of state are within 0.5% of numerical computations, and coefficients B11 and B12 are within the error of numerical results. We conjecture that even higher virial coefficients are reliably predicted.

  13. Theoretical Prediction of the Ionization Energies of the C₄H₇ Radicals: 1-Methylallyl, 2-Methylallyl, Cyclopropylmethyl, and Cyclobutyl Radicals.

    SciTech Connect

    Lau, Kai Chung; Zheng, Wenxu; Wong, Ning-Bew; Li, Wai-kee

    2007-10-15

    The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The ionization energies (IEs) for the 1-methylallyl, 2-methylallyl, cyclopropylmethyl, and cyclobutyl radicals have been calculated by the wave function based ab initio CCSD(T)/CBS approach, which involves the approximation to the complete basis set (CBS) limit at the coupled cluster level with single and double excitations plus quasiperturbative triple excitation [CCSD(T)]. The zero-point vibrational energy correction, the core-valence electronic correction, and the scalar relativistic effect correction are included in these calculations. The present CCSD(T)/CBS results are then compared with the IEs determined in the photoelectron experiment by Schultz et al. [J. Am. Chem. Soc. 106, 7336 (1984)] The predicted IE value (7.881 eV) of 2-methylallyl radical is found to compare very favorably with the experimental value of 7.90±0.02 eV. Two ionization transitions for cis-1-methylallyl and trans-1-methylallyl radicals have been considered here. The comparison between the predicted IE values and the previous measurements shows that the photoelectron peak observed by Schultz et al. likely corresponds to the adiabatic ionization transition for the trans-1-methylallyl radical to form trans-1-methylallyl cation. Although a precise IE value for the cyclopropylmethyl radical has not been directly determined, the experimental value deduced indirectly using other known energetic data is found to be in good accord with the present CCSD(T)/ CBS prediction. We expect that the Franck-Condon factor for ionization transition of c-C₄H₇ →bicyclobutonium is much less favorable than that for ionization transition of c-C₄H₇ →planar-C₄H₇ +, and the observed IE in the previous

  14. An evaluation of Shuttle Entry Air Data System (SEADS) flight pressures - Comparisons with wind tunnel and theoretical predictions

    NASA Technical Reports Server (NTRS)

    Henry, M. W.; Wolf, H.; Siemers, Paul M., III

    1988-01-01

    The SEADS pressure data obtained from the Shuttle flight 61-C are analyzed in conjunction with the preflight database. Based on wind tunnel data, the sensitivity of the Shuttle Orbiter stagnation region pressure distribution to angle of attack and Mach number is demonstrated. Comparisons are made between flight and wind tunnel SEADS orifice pressure distributions at several points throughout the re-entry. It is concluded that modified Newtonian theory provides a good tool for the design of a flush air data system, furnishing data for determining orifice locations and transducer sizing. Ground-based wind tunnel facilities are capable of providing the correction factors necessary for the derivation of accurate air data parameters from pressure data.

  15. The Value of Accurate Magnetic Resonance Characterization of Posterior Cruciate Ligament Tears in the Setting of Multiligament Knee Injury: Imaging Features Predictive of Early Repair vs Reconstruction.

    PubMed

    Goiney, Christoper C; Porrino, Jack; Twaddle, Bruce; Richardson, Michael L; Mulcahy, Hyojeong; Chew, Felix S

    2016-01-01

    Multiligament knee injury (MLKI) represents a complex set of pathologies treated with a wide variety of surgical approaches. If early surgical intervention is performed, the disrupted posterior cruciate ligament (PCL) can be treated with primary repair or reconstruction. The purpose of our study was to retrospectively identify a critical length of the distal component of the torn PCL on magnetic resonance imaging (MRI) that may predict the ability to perform early proximal femoral repair of the ligament, as opposed to reconstruction. A total of 50 MLKIs were managed at Harborview Medical Center from May 1, 2013, through July 15, 2014, by an orthopedic surgeon. Following exclusions, there were 27 knees with complete disruption of the PCL that underwent either early reattachment to the femoral insertion or reconstruction and were evaluated using preoperative MRI. In a consensus fashion, 2 radiologists measured the proximal and distal fragments of each disrupted PCL using preoperative MRI in multiple planes, as needed. MRI findings were correlated with what was performed at surgery. Those knees with a distal fragment PCL length of ≥41mm were capable of, and underwent, early proximal femoral repair. With repair, the distal stump was attached to the distal femur. Alternatively, those with a distal PCL length of ≤32mm could not undergo repair because of insufficient length and as such, were reconstructed. If early surgical intervention for an MLKI involving disruption of the PCL is considered, attention should be given to the length of the distal PCL fragment on MRI to plan appropriately for proximal femoral reattachment vs reconstruction. If the distal PCL fragment measures ≥41mm, surgical repair is achievable and can be considered as a surgical option.

  16. Mechanism of alkoxy groups substitution by Grignard reagents on aromatic rings and experimental verification of theoretical predictions of anomalous reactions.

    PubMed

    Jiménez-Osés, Gonzalo; Brockway, Anthony J; Shaw, Jared T; Houk, K N

    2013-05-01

    The mechanism of direct displacement of alkoxy groups in vinylogous and aromatic esters by Grignard reagents, a reaction that is not observed with expectedly better tosyloxy leaving groups, is elucidated computationally. The mechanism of this reaction has been determined to proceed through the inner-sphere attack of nucleophilic alkyl groups from magnesium to the reacting carbons via a metalaoxetane transition state. The formation of a strong magnesium chelate with the reacting alkoxy and carbonyl groups dictates the observed reactivity and selectivity. The influence of ester, ketone, and aldehyde substituents was investigated. In some cases, the calculations predicted the formation of products different than those previously reported; these predictions were then verified experimentally. The importance of studying the actual system, and not simplified models as computational systems, is demonstrated. PMID:23601086

  17. Mechanism of Alkoxy Groups Substitution by Grignard Reagents on Aromatic Rings and Experimental Verification of Theoretical Predictions of Anomalous Reactions

    PubMed Central

    Jiménez-Osés, Gonzalo; Brockway, Anthony J.; Shaw, Jared T.; Houk, K. N.

    2013-01-01

    The mechanism of direct displacement of alkoxy groups in vinylogous and aromatic esters by Grignard reagents, a reaction that is not observed with expectedly better tosyloxy leaving groups, is elucidated computationally. The mechanism of this reaction has been determined to proceed through the inner-sphere attack of nucleophilic alkyl groups from magnesium to the reacting carbons via a metalaoxetane transition state. The formation of a strong magnesium chelate with the reacting alkoxy and carbonyl groups dictates the observed reactivity and selectivity. The influence of ester, ketone and aldehyde substituents was investigated. In some cases, the calculations predicted the formation of products different than those previously reported; these predictions were then verified experimentally. The importance of studying the actual system, and not simplified models as computational systems, is demonstrated. PMID:23601086

  18. Comparison between measurements, simulations, and theoretical predictions of the extraction kicker transverse dipole instability in the Spallation Neutron Source

    SciTech Connect

    Cousineau, Sarah M; Danilov, Viatcheslav; Jain, Lalit K

    2011-01-01

    Occasionally it is possible to bring together experiment, theory, and simulation in detail. Such an occasion occurred during a high intensity beam physics study in the Spallation Neutron Source (SNS). A transverse dipole instability in the vertical direction has been observed in the accumulator ring for a coasting beam that was stored for 10000 turns. This instability was observed at a beam intensity of about 12 microcoulombs and was characterized by a frequency spectrum peaking at about 6 MHz. The probable cause of the instability is the impedance of the ring extraction kickers. We carry out here a detailed benchmark of the observed instability, uniting an analysis of the experimental data, a precise ORBIT Code tracking simulation, and a theoretical estimate of the observed beam instability.

  19. Theoretical prediction of Grüneisen parameter for SiO2.TiO2 bulk metallic glasses

    NASA Astrophysics Data System (ADS)

    Singh, Chandra K.; Pandey, Anjani K.; Pandey, Brijesh K.

    2016-05-01

    The Grüneisen parameter (γ) is very important to decide the limitations for the prediction of thermoelastic properties of bulk metallic glasses. It can be defined in terms of microscopic and macroscopic parameters of the material in which former is based on vibrational frequencies of atoms in the material while later is closely related to its thermodynamic properties. Different formulation and equation of states are used by the pioneer researchers of this field to predict the true sense of Gruneisen parameter for BMG but for SiO2.TiO2 very few and insufficient information is available till now. In the present work we have tested the validity of two different isothermal EOS viz. Poirrior-Tarantola EOS and Usual-Tait EOS to predict the true value of Gruneisen parameter for SiO2.TiO2 as a function of compression. Using different thermodynamic limitations related to the material constraints and analyzing obtained result it is concluded that the Poirrior-Tarantola EOS gives better numeric values of Grüneisen parameter (γ) for SiO2.TiO2 BMG.

  20. Predicted levels of Be9 based on a theoretical analysis of neutron double-differential cross sections at En=14.1 and 18 MeV

    NASA Astrophysics Data System (ADS)

    Duan, Junfeng; Zhang, Jingshang; Wu, Haicheng; Sun, Xiaojun

    2009-12-01

    By using the statistical theory for neutron-induced light nucleus reaction, the calculation of the neutron double-differential cross sections for n+Be9 reactions is performed. The secondary outgoing neutrons only coming from the (n,2n)2α reaction channel through six different emission processes are illustrated in detail in this article. Based on the theoretical analysis of neutron double-differential cross sections at En=14.1 and 18 MeV, two predicted levels of Be9, i.e., E(Jπ)Γ=9((5)/(2)+)1000 and 10((5)/(2)+)1000, have been recommended. The calculated results indicate that the fittings would be improved obviously while the predicted levels have been employed.

  1. An Experimental Path to Constraining the Origins of the Jupiter Trojans Using Observations, Theoretical Predictions, and Laboratory Simulants

    NASA Astrophysics Data System (ADS)

    Blacksberg, Jordana; Eiler, John; Brown, Mike; Ehlmann, Bethany; Hand, Kevin; Hodyss, Robert; Mahjoub, Ahmed; Poston, Michael; Liu, Yang; Choukroun, Mathieu; Carey, Elizabeth; Wong, Ian

    2014-11-01

    Hypotheses based on recent dynamical models (e.g. the Nice Model) shape our current understanding of solar system evolution, suggesting radical rearrangement in the first hundreds of millions of years of its history, changing the orbital distances of Jupiter, Saturn, and a large number of small bodies. The goal of this work is to build a methodology to concretely tie individual solar system bodies to dynamical models using observables, providing evidence for their origins and evolutionary pathways. Ultimately, one could imagine identifying a set of chemical or mineralogical signatures that could quantitatively and predictably measure the radial distance at which icy and rocky bodies first accreted. The target of the work presented here is the Jupiter Trojan asteroids, predicted by the Nice Model to have initially formed in the Kuiper belt and later been scattered inward to co-orbit with Jupiter. Here we present our strategy which is fourfold: (1) Generate predictions about the mineralogical, chemical, and isotopic compositions of materials accreted in the early solar system as a function of distance from the Sun. (2) Use temperature and irradiation to simulate evolutionary processing of ices and silicates, and measure the alteration in spectral properties from the UV to mid-IR. (3) Characterize simulants to search for potential fingerprints of origin and processing pathways, and (4) Use telescopic observations to increase our knowledge of the Trojan asteroids, collecting data on populations and using spectroscopy to constrain their compositions. In addition to the overall strategy, we will present preliminary results on compositional modeling, observations, and the synthesis, processing, and characterization of laboratory simulants including ices and silicates. This work has been supported by the Keck Institute for Space Studies (KISS). The research described here was carried out at the Jet Propulsion Laboratory, Caltech, under a contract with the National

  2. Accurate quantum chemical calculations

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

    1989-01-01

    An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.

  3. Predicting breast-feeding intention among low-income pregnant women: a comparison of two theoretical models.

    PubMed

    Kloeblen, A S; Thompson, N J; Miner, K R

    1999-10-01

    This study examined the applicability of the transtheoretical model and a model derived from the theory of reasoned action for predicting breast-feeding intention among low-income pregnant women. Participants completed a 70-item self-report questionnaire assessing their breast-feeding attitudes, intentions, and support. A positive correlation existed between Stages of Change for breast-feeding and the number of Processes of Change used by respondents. A negative correlation existed between Stages of Change for breast-feeding and the number of negative breast-feeding beliefs held by respondents. Furthermore, women's normative beliefs and outcome beliefs were significantly correlated with breast-feeding intention in manners consistent with the model developed from the theory of reasoned action. After accounting for significant sociodemographic and lifestyle factors, the Processes of Change and outcome beliefs remained independently correlated with breast-feeding intention. These models are capable of predicting the intention to breast-feed and might offer an innovative approach for further breast-feeding research and intervention development. PMID:10533172

  4. The improvement of a simple theoretical model for the prediction of the sound insulation of double leaf walls.

    PubMed

    Davy, John L

    2010-02-01

    This paper presents a revised theory for predicting the sound insulation of double leaf cavity walls that removes an approximation, which is usually made when deriving the sound insulation of a double leaf cavity wall above the critical frequencies of the wall leaves due to the airborne transmission across the wall cavity. This revised theory is also used as a correction below the critical frequencies of the wall leaves instead of a correction due to Sewell [(1970). J. Sound Vib. 12, 21-32]. It is found necessary to include the "stud" borne transmission of the window frames when modeling wide air gap double glazed windows. A minimum value of stud transmission is introduced for use with resilient connections such as steel studs. Empirical equations are derived for predicting the effective sound absorption coefficient of wall cavities without sound absorbing material. The theory is compared with experimental results for double glazed windows and gypsum plasterboard cavity walls with and without sound absorbing material in their cavities. The overall mean, standard deviation, maximum, and minimum of the differences between experiment and theory are -0.6 dB, 3.1 dB, 10.9 dB at 1250 Hz, and -14.9 dB at 160 Hz, respectively. PMID:20136207

  5. Predicting breast-feeding intention among low-income pregnant women: a comparison of two theoretical models.

    PubMed

    Kloeblen, A S; Thompson, N J; Miner, K R

    1999-10-01

    This study examined the applicability of the transtheoretical model and a model derived from the theory of reasoned action for predicting breast-feeding intention among low-income pregnant women. Participants completed a 70-item self-report questionnaire assessing their breast-feeding attitudes, intentions, and support. A positive correlation existed between Stages of Change for breast-feeding and the number of Processes of Change used by respondents. A negative correlation existed between Stages of Change for breast-feeding and the number of negative breast-feeding beliefs held by respondents. Furthermore, women's normative beliefs and outcome beliefs were significantly correlated with breast-feeding intention in manners consistent with the model developed from the theory of reasoned action. After accounting for significant sociodemographic and lifestyle factors, the Processes of Change and outcome beliefs remained independently correlated with breast-feeding intention. These models are capable of predicting the intention to breast-feed and might offer an innovative approach for further breast-feeding research and intervention development.

  6. A theoretical prediction of super high-performance thermoelectric materials based on MoS2/WS2 hybrid nanoribbons

    NASA Astrophysics Data System (ADS)

    Zhang, Zhongwei; Xie, Yuee; Peng, Qing; Chen, Yuanping

    2016-02-01

    Modern society is hungry for electrical power. To improve the efficiency of energy harvesting from heat, extensive efforts seek high-performance thermoelectric materials that possess large differences between electronic and thermal conductance. Here we report a super high-performance material of consisting of MoS2/WS2 hybrid nanoribbons discovered from a theoretical investigation using nonequilibrium Green’s function methods combined with first-principles calculations and molecular dynamics simulations. The hybrid nanoribbons show higher efficiency of energy conversion than the MoS2 and WS2 nanoribbons due to the fact that the MoS2/WS2 interface reduces lattice thermal conductivity more than the electron transport. By tuning the number of the MoS2/WS2 interfaces, a figure of merit ZT as high as 5.5 is achieved at a temperature of 600 K. Our results imply that the MoS2/WS2 hybrid nanoribbons have promising applications in thermal energy harvesting.

  7. Cytisine basicity, solvation, logP, and logD theoretical determination as tool for bioavailability prediction.

    PubMed

    Pieńko, Tomasz; Grudzień, Monika; Taciak, Przemysław Paweł; Mazurek, Aleksander Paweł

    2016-01-01

    Cytisine, an α4β2 nicotinic receptor partial agonist, is a plant alkaloid widely used as a smoking cessation agent. Despite long history of use, knowledge on pharmacokinetics of cytisine still demands an extension. This work is aimed at theoretical determination of physicochemical parameters that affect the bioavailability of cytisine. The acidic dissociation constant, Gibbs free energy of solvation in water and n-octanol as well as n-octanol/water partition coefficient and n-octanol/water distribution coefficient of cytisine were calculated as quantities corresponding to its solubility and permeability. Cytisine structure was optimized with several quantum chemical methods-ab initio: HF and MP2, and DFT functionals (B3LYP, B3LYP-D3, CAM-B3LYP, M06-2X, TPSS, VSXC) with 6-311++G(d,p) basis set. Solvation of cytisine in water and n-octanol was determined with the SMD continuum model. It was shown that lipophilicity of cytisine depends on the pH of an environment. Protonated cytisine, the most populated state under acidic conditions, is characterized by enhanced hydrophilicity. Then neutral cytisine, dominating in a basic environment, demonstrates more lipophilic character. It appears that cytisine is very well soluble in the gastrointestinal (GI) tract fluids. Then the distribution of cytisine ought to occur very rapidly. However, permeability of cytisine through the mucous membrane of the GI tract may be limited, leading to the diminished bioavailability.

  8. A theoretical prediction of super high-performance thermoelectric materials based on MoS2/WS2 hybrid nanoribbons

    PubMed Central

    Zhang, Zhongwei; Xie, Yuee; Peng, Qing; Chen, Yuanping

    2016-01-01

    Modern society is hungry for electrical power. To improve the efficiency of energy harvesting from heat, extensive efforts seek high-performance thermoelectric materials that possess large differences between electronic and thermal conductance. Here we report a super high-performance material of consisting of MoS2/WS2 hybrid nanoribbons discovered from a theoretical investigation using nonequilibrium Green’s function methods combined with first-principles calculations and molecular dynamics simulations. The hybrid nanoribbons show higher efficiency of energy conversion than the MoS2 and WS2 nanoribbons due to the fact that the MoS2/WS2 interface reduces lattice thermal conductivity more than the electron transport. By tuning the number of the MoS2/WS2 interfaces, a figure of merit ZT as high as 5.5 is achieved at a temperature of 600 K. Our results imply that the MoS2/WS2 hybrid nanoribbons have promising applications in thermal energy harvesting. PMID:26884123

  9. A theoretical prediction of super high-performance thermoelectric materials based on MoS2/WS2 hybrid nanoribbons.

    PubMed

    Zhang, Zhongwei; Xie, Yuee; Peng, Qing; Chen, Yuanping

    2016-02-17

    Modern society is hungry for electrical power. To improve the efficiency of energy harvesting from heat, extensive efforts seek high-performance thermoelectric materials that possess large differences between electronic and thermal conductance. Here we report a super high-performance material of consisting of MoS2/WS2 hybrid nanoribbons discovered from a theoretical investigation using nonequilibrium Green's function methods combined with first-principles calculations and molecular dynamics simulations. The hybrid nanoribbons show higher efficiency of energy conversion than the MoS2 and WS2 nanoribbons due to the fact that the MoS2/WS2 interface reduces lattice thermal conductivity more than the electron transport. By tuning the number of the MoS2/WS2 interfaces, a figure of merit ZT as high as 5.5 is achieved at a temperature of 600 K. Our results imply that the MoS2/WS2 hybrid nanoribbons have promising applications in thermal energy harvesting.

  10. Biomimetic synthesis of silver nanoparticles by Citrus limon (lemon) aqueous extract and theoretical prediction of particle size.

    PubMed

    Prathna, T C; Chandrasekaran, N; Raichur, Ashok M; Mukherjee, Amitava

    2011-01-01

    In the present study, silver nanoparticles were rapidly synthesized at room temperature by treating silver ions with the Citrus limon (lemon) extract. The effect of various process parameters like the reductant concentration, mixing ratio of the reactants and the concentration of silver nitrate were studied in detail. In the standardized process, 10(-2)M silver nitrate solution was interacted for 4h with lemon juice (2% citric acid concentration and 0.5% ascorbic acid concentration) in the ratio of 1:4 (vol:vol). The formation of silver nanoparticles was confirmed by Surface Plasmon Resonance as determined by UV-Visible spectra in the range of 400-500 nm. X-ray diffraction analysis revealed the distinctive facets (111, 200, 220, 222 and 311 planes) of silver nanoparticles. We found that citric acid was the principal reducing agent for the nanosynthesis process. FT-IR spectral studies demonstrated citric acid as the probable stabilizing agent. Silver nanoparticles below 50 nm with spherical and spheroidal shape were observed from transmission electron microscopy. The correlation between absorption maxima and particle sizes were derived for different UV-Visible absorption maxima (corresponding to different citric acid concentrations) employing "MiePlot v. 3.4". The theoretical particle size corresponding to 2% citric acid concentration was compared to those obtained by various experimental techniques like X-ray diffraction analysis, atomic force microscopy, and transmission electron microscopy.

  11. A Novel Quasi-One-Dimensional Topological Insulator in Bismuth Iodide β-Bi4I4: Theoretical Prediction and Experimental Confirmation

    NASA Astrophysics Data System (ADS)

    Yazyev, Oleg V.; Autès, Gabriel; Isaeva, Anna; Moreschini, Luca; Johannsen, Jens C.; Pisoni, Andrea; Filatova, Taisia G.; Kuznetsov, Alexey N.; Forró, László; van den Broek, Wouter; Kim, Yeongkwan; Denlinger, Jonathan D.; Rotenberg, Eli; Bostwick, Aaron; Grioni, Marco

    2015-03-01

    A new strong Z2 topological insulator is theoretically predicted and experimentally confirmed in the β-phase of quasi-one-dimensional bismuth iodide Bi4I4. According to our first-principles calculations the material is characterized by Z2 invariants (1;110) making it the first representative of this topological class. Importantly, the electronic structure of β-Bi4I4 is in proximity with both the weak topological insulator phase (0;001) and the trivial phase (0;000), suggesting that a high degree of control over the topological electronic properties of this material can be achieved. Experimentally produced samples of this material appears to be practically defect-free, which results in a low concentration of intrinsic charge carriers. By using angle-resolved photoemission spectroscopy (ARPES) on the (001) surface we confirm the theoretical predictions of a highly anisotropic band structure with a small band gap hosting topological surface states centered at the M point, at the boundary of the surface Brillouin zone. We acknowledge support from Swiss NSF, ERC project ``TopoMat'', NCCR-MARVEL, DFG and US DoE. G.A., A.I., L.M. and J.C.J. contributed equally to this work.

  12. Prediction of gas/particle partitioning of polybrominated diphenyl ethers (PBDEs) in global air: a theoretical study

    NASA Astrophysics Data System (ADS)

    Li, Y.-F.; Ma, W.-L.; Yang, M.

    2014-09-01

    Gas/particle (G / P) partitioning for most semivolatile organic compounds (SVOCs) is an important process that primarily governs their atmospheric fate, long-range atmospheric transport potential, and their routs to enter human body. All previous studies on this issue have been hypothetically derived from equilibrium conditions, the results of which do not predict results from monitoring studies well in most cases. In this study, a steady-state model instead of an equilibrium-state model for the investigation of the G / P partitioning behavior for polybrominated diphenyl ethers (PBDEs) was established, and an equation for calculating the partition coefficients under steady state (KPS) for PBDE congeners (log KPS = log KPE + logα) was developed, in which an equilibrium term (log KPE = log KOA + logfOM -11.91, where fOM is organic matter content of the particles) and a nonequilibrium term (logα, mainly caused by dry and wet depositions of particles), both being functions of log KOA (octanol-air partition coefficient), are included, and the equilibrium is a special case of steady state when the nonequilibrium term equals to zero. A criterion to classify the equilibrium and nonequilibrium status for PBDEs was also established using two threshold values of log KOA, log KOA1 and log KOA2, which divide the range of log KOA into 3 domains: equilibrium, nonequilibrium, and maximum partition domains; and accordingly, two threshold values of temperature t, tTH1 when log KOA = log KOA1 and tTH2 when log KOA = log KOA2, were identified, which divide the range of temperature also into the same 3 domains for each BDE congener. We predicted the existence of the maximum partition domain (the values of log KPS reach a maximum constant of -1.53) that every PBDE congener can reach when log KOA ≥ log KOA2, or t ≤ tTH2. The novel equation developed in this study was applied to predict the G / P partition coefficients of PBDEs for the published monitoring data worldwide, including

  13. Prediction of gas/particle partitioning of polybrominated diphenyl ethers (PBDEs) in global air: A theoretical study

    NASA Astrophysics Data System (ADS)

    Li, Y.-F.; Ma, W.-L.; Yang, M.

    2015-02-01

    Gas/particle (G/P) partitioning of semi-volatile organic compounds (SVOCs) is an important process that primarily governs their atmospheric fate, long-range atmospheric transport, and their routes of entering the human body. All previous studies on this issue are hypothetically based on equilibrium conditions, the results of which do not predict results from monitoring studies well in most cases. In this study, a steady-state model instead of an equilibrium-state model for the investigation of the G/P partitioning behavior of polybrominated diphenyl ethers (PBDEs) was established, and an equation for calculating the partition coefficients under steady state (KPS) of PBDEs (log KPS = log KPE + logα) was developed in which an equilibrium term (log KPE = log KOA + logfOM -11.91 where fOM is organic matter content of the particles) and a non-equilibrium term (log α, caused by dry and wet depositions of particles), both being functions of log KOA (octanol-air partition coefficient), are included. It was found that the equilibrium is a special case of steady state when the non-equilibrium term equals zero. A criterion to classify the equilibrium and non-equilibrium status of PBDEs was also established using two threshold values of log KOA, log KOA1, and log KOA2, which divide the range of log KOA into three domains: equilibrium, non-equilibrium, and maximum partition domain. Accordingly, two threshold values of temperature t, tTH1 when log KOA = log KOA1 and tTH2 when log KOA = log KOA2, were identified, which divide the range of temperature also into the same three domains for each PBDE congener. We predicted the existence of the maximum partition domain (the values of log KPS reach a maximum constant of -1.53) that every PBDE congener can reach when log KOA ≥ log KOA2, or t ≤ tTH2. The novel equation developed in this study was applied to predict the G/P partition coefficients of PBDEs for our Chinese persistent organic pollutants (POPs) Soil and Air Monitoring

  14. Thermodynamic Properties of CO{sub 2} Capture Reaction by Solid Sorbents: Theoretical Predictions and Experimental Validations

    SciTech Connect

    Duan, Yuhua; Luebke, David; Pennline, Henry; Li, Liyu; King, David; Zhang,; Keling,; Zhao,; Lifeng,; Xiao, Yunhan

    2012-01-01

    It is generally accepted that current technologies for capturing CO{sub 2} are still too energy intensive. Hence, there is a critical need for development of new materials that can capture CO{sub 2} reversibly with acceptable energy costs. Accordingly, solid sorbents have been proposed to be used for CO{sub 2} capture applications through a reversible chemical transformation. By combining thermodynamic database mining with first principles density functional theory and phonon lattice dynamics calculations, a theoretical screening methodology to identify the most promising CO{sub 2} sorbent candidates from the vast array of possible solid materials has been proposed and validated. The calculated thermodynamic properties of different classes of solid materials versus temperature and pressure changes were further used to evaluate the equilibrium properties for the CO{sub 2} adsorption/desorption cycles. According to the requirements imposed by the pre- and post- combustion technologies and based on our calculated thermodynamic properties for the CO{sub 2} capture reactions by the solids of interest, we were able to screen only those solid materials for which lower capture energy costs are expected at the desired pressure and temperature conditions. These CO{sub 2} sorbent candidates were further considered for experimental validations. In this presentation, we first introduce our screening methodology with validating by solid dataset of alkali and alkaline metal oxides, hydroxides and bicarbonates which thermodynamic properties are available. Then, by studying a series of lithium silicates, we found that by increasing the Li{sub 2}O/SiO{sub 2} ratio in the lithium silicates their corresponding turnover temperatures for CO{sub 2} capture reactions can be increased. Compared to anhydrous K{sub 2}CO{sub 3}, the dehydrated K{sub 2}CO{sub 3}1.5H{sub 2}O can only be applied for post-combustion CO{sub 2} capture technology at temperatures lower than its phase transition (to

  15. Theoretical predictions for the effect of nebular emission on the broad-band photometry of high-redshift galaxies

    NASA Astrophysics Data System (ADS)

    Wilkins, Stephen M.; Coulton, William; Caruana, Joseph; Croft, Rupert; Matteo, Tiziana Di; Khandai, Nishikanta; Feng, Yu; Bunker, Andrew; Elbert, Holly

    2013-11-01

    By combining optical and near-IR observations from the Hubble Space Telescope with near-IR photometry from the Spitzer Space Telescope, it is possible to measure the rest-frame UV-optical colours of galaxies at z = 4-8. The UV-optical spectral energy distribution of star formation dominated galaxies is the result of several different factors. These include the joint distribution of stellar masses, ages and metallicities (solely responsible for the pure stellar spectral energy distribution), and the subsequent reprocessing by dust and gas in the interstellar medium. Using a large cosmological hydrodynamical simulation (MassiveBlack-II), we investigate the predicted spectral energy distributions of galaxies at high redshift with a particular emphasis on assessing the potential contribution of nebular emission. We find that the average (median) pure stellar UV-optical colour correlates with both luminosity and redshift such that galaxies at lower redshift and higher luminosity are typically redder. Assuming that the escape fraction of ionizing photons is close to zero, the effect of nebular emission is to redden the UV-optical 1500 - Vw colour by, on average, 0.4 mag at z = 8 declining to 0.25 mag at z = 4. Young and low-metallicity stellar populations, which typically have bluer pure stellar UV-optical colours, produce larger ionizing luminosities and are thus more strongly affected by the reddening effects of nebular emission. This causes the distribution of 1500 - Vw colours to narrow and the trends with luminosity and redshift to weaken. The strong effect of nebular emission leaves observed-frame colours critically sensitive to the redshift of the source. For example, increasing the redshift by 0.1 can result in observed-frame colours changing by up to ˜0.6. These predictions reinforce the need to include nebular emission when modelling the spectral energy distributions of galaxies at high redshift and also highlight the difficultly in interpreting the observed

  16. Empirical estimates and theoretical predictions of the shorting factor for the THEMIS double-probe electric field instrument

    NASA Astrophysics Data System (ADS)

    Califf, S.; Cully, C. M.

    2016-07-01

    Double-probe electric field measurements on board spacecraft present significant technical challenges, especially in the inner magnetosphere where the ambient plasma characteristics can vary dramatically and alter the behavior of the instrument. We explore the shorting factor for the Time History of Events and Macroscale Interactions during Substorms electric field instrument, which is a scale factor error on the measured electric field due to coupling between the sensing spheres and the long wire booms, using both an empirical technique and through simulations with varying levels of fidelity. The empirical data and simulations both show that there is effectively no shorting when the spacecraft is immersed in high-density plasma deep within the plasmasphere and that shorting becomes more prominent as plasma density decreases and the Debye length increases outside the plasmasphere. However, there is a significant discrepancy between the data and theory for the shorting factor in low-density plasmas: the empirical estimate indicates ~0.7 shorting for long Debye lengths, but the simulations predict a shorting factor of ~0.94. This paper systematically steps through the empirical and modeling methods leading to the disagreement with the intention of motivating further study on the topic.

  17. All-theoretical prediction of cabin noise due to impingement of propeller vortices on a wing structure

    NASA Technical Reports Server (NTRS)

    Martinez, R.; Cole, J. E., III; Martini, K.; Westagard, A.

    1987-01-01

    Reported calculations of structure-borne cabin noise for a small twin engine aircraft powered by tractor propellers rely on the following three-stage methodological breakup of the problem: (1) the unsteady-aerodynamic prediction of wing lift harmonics caused by the whipping action of the vortex system trailed from each propeller; (2) the associated wing/fuselage structural response; (3) the cabin noise field for the computed wall vibration. The first part--the estimate of airloads--skirts a full-fledged aeroelastic situation by assuming the wing to be fixed in space while cancelling the downwash field of the cutting vortices. The model is based on an approximate high-frequency lifting-surface theory justified by the blade rate and flight Mach number of application. Its results drive a finite-element representation of the wing accounting for upper and lower skin surfaces, spars, ribs, and the presence of fuel. The fuselage, modeled as a frame-stiffened cylindrical shell, is bolted to the wing.

  18. Can Selforganizing Maps Accurately Predict Photometric Redshifts?

    NASA Technical Reports Server (NTRS)

    Way, Michael J.; Klose, Christian

    2012-01-01

    We present an unsupervised machine-learning approach that can be employed for estimating photometric redshifts. The proposed method is based on a vector quantization called the self-organizing-map (SOM) approach. A variety of photometrically derived input values were utilized from the Sloan Digital Sky Survey's main galaxy sample, luminous red galaxy, and quasar samples, along with the PHAT0 data set from the Photo-z Accuracy Testing project. Regression results obtained with this new approach were evaluated in terms of root-mean-square error (RMSE) to estimate the accuracy of the photometric redshift estimates. The results demonstrate competitive RMSE and outlier percentages when compared with several other popular approaches, such as artificial neural networks and Gaussian process regression. SOM RMSE results (using delta(z) = z(sub phot) - z(sub spec)) are 0.023 for the main galaxy sample, 0.027 for the luminous red galaxy sample, 0.418 for quasars, and 0.022 for PHAT0 synthetic data. The results demonstrate that there are nonunique solutions for estimating SOM RMSEs. Further research is needed in order to find more robust estimation techniques using SOMs, but the results herein are a positive indication of their capabilities when compared with other well-known methods

  19. The Determination of Predictive Construct of Physical Behavior Change on Osteoporosis Prevention Women Aged 30-50: A Trans-theoretical Method Study

    PubMed Central

    Malekshahi, Farideh; Hidarnia, Alireza; Niknami, Shamseddin; Aminshokravi, Frakhondeh

    2016-01-01

    Osteoporosis is a major public health priority in Iran and throughout the world. The prevention of osteoporosis has recently become the ultimate goal of many health professionals. Behavior change is one of the most powerful strategies to prevent osteoporosis. This study aimed to determine the predictive construct of physical preventive behavior of osteoporosis in women aged 30-50 in Khorramabad, west of Iran. This study included 269 women selected from all the health centers of Khorramabad city according to the inclusion criteria of the study and through random cluster and systematic sampling. The data gathering tools were valid and reliable questionnaires of demographic information, stages of change, decisional balance, self-efficacy, and physical activity. Data were analyzed using descriptive and inferential statistics. The mean of the subjects’ age was 38.72±7.003, and the mean of light weekly physical activity was 38.83±56.400. The results showed that the construct of self-efficacy had the highest predictive power of the preventive behavior. The results also showed that self-efficacy among the constructs of the Trans-theoretical Model was the only predictive construct for osteoporosis prevention behavior. Therefore, the findings of this study can serve as a base for educational interventions in behavioral changes to prevent of osteoporosis by health authorities. PMID:26493413

  20. The Determination of Predictive Construct of Physical Behavior Change on Osteoporosis Prevention Women Aged 30-50: A Trans-Theoretical Method Study.

    PubMed

    Malekshahi, Farideh; Hidarnia, Alirezad; Niknami, Shamseddin; Aminshokravi, Frakhondeh

    2016-01-01

    Osteoporosis is a major public health priority in Iran and throughout the world. The prevention of osteoporosis has recently become the ultimate goal of many health professionals. Behavior change is one of the most powerful strategies to prevent osteoporosis. This study aimed to determine the predictive construct of physical preventive behavior of osteoporosis in women aged 30-50 in Khorramabad, west of Iran. This study included 269 women selected from all the health centers of Khorramabad city according to the inclusion criteria of the study and through random cluster and systematic sampling. The data gathering tools were valid and reliable questionnaires of demographic information, stages of change, decisional balance, self-efficacy, and physical activity. Data were analyzed using descriptive and inferential statistics. The mean of the subjects' age was 38.72±7.003, and the mean of light weekly physical activity was 38.83±56.400. The results showed that the construct of self-efficacy had the highest predictive power of the preventive behavior. The results also showed that self-efficacy among the constructs of the Trans-theoretical Model was the only predictive construct for osteoporosis prevention behavior. Therefore, the findings of this study can serve as a base for educational interventions in behavioral changes to prevent of osteoporosis by health authorities.

  1. Statistical analysis of accurate prediction of local atmospheric optical attenuation with a new model according to weather together with beam wandering compensation system: a season-wise experimental investigation

    NASA Astrophysics Data System (ADS)

    Arockia Bazil Raj, A.; Padmavathi, S.

    2016-07-01

    Atmospheric parameters strongly affect the performance of Free Space Optical Communication (FSOC) system when the optical wave is propagating through the inhomogeneous turbulent medium. Developing a model to get an accurate prediction of optical attenuation according to meteorological parameters becomes significant to understand the behaviour of FSOC channel during different seasons. A dedicated free space optical link experimental set-up is developed for the range of 0.5 km at an altitude of 15.25 m. The diurnal profile of received power and corresponding meteorological parameters are continuously measured using the developed optoelectronic assembly and weather station, respectively, and stored in a data logging computer. Measured meteorological parameters (as input factors) and optical attenuation (as response factor) of size [177147 × 4] are used for linear regression analysis and to design the mathematical model that is more suitable to predict the atmospheric optical attenuation at our test field. A model that exhibits the R2 value of 98.76% and average percentage deviation of 1.59% is considered for practical implementation. The prediction accuracy of the proposed model is investigated along with the comparative results obtained from some of the existing models in terms of Root Mean Square Error (RMSE) during different local seasons in one-year period. The average RMSE value of 0.043-dB/km is obtained in the longer range dynamic of meteorological parameters variations.

  2. Theoretical technique for predicting the cumulative impact of iron and manganese oxidation in streams receiving discharge from coal mines

    USGS Publications Warehouse

    Bobay, Keith E.

    1986-01-01

    Two U.S. Geological Survey computer programs are modified and linked to predict the cumulative impact of iron and manganese oxidation in coal-mine discharge water on the dissolved chemical quality of a receiving stream. The coupled programs calculate the changes in dissolved iron, dissolved manganese, and dissolved oxygen concentrations; alkalinity; and, pH of surface water downstream from the point of discharge. First, the one-dimensional, stead-state stream, water quality program uses a dissolved oxygen model to calculate the changes in concentration of elements as a function of the chemical reaction rates and time-of-travel. Second, a program (PHREEQE) combining pH, reduction-oxidation potential, and equilibrium equations uses an aqueous-ion association model to determine the saturation indices and to calculate pH; it then mixes the discharge with a receiving stream. The kinetic processes of the first program dominate the system, whereas the equilibrium thermodynamics of the second define the limits of the reactions. A comprehensive test of the technique was not possible because a complete set of data was unavailable. However, the cumulative impact of representative discharges from several coal mines on stream quality in a small watershed in southwestern Indiana was simulated to illustrate the operation of the technique and to determine its sensitivity to changes in physical, chemical, and kinetic parameters. Mine discharges averaged 2 cu ft/sec, with a pH of 6.0, and concentrations of 7.0 mg/L dissolved iron, 4.0 mg/L dissolved manganese, and 8.08 mg/L dissolved oxygen. The receiving stream discharge was 2 cu ft/sec, with a pH of 7.0, and concentrations of 0.1 mg/L dissolved iron, 0.1 mg/L dissolved manganese, and 8.70 mg/L dissolved oxygen. Results of the simulations indicated the following cumulative impact on the receiving stream from five discharges as compared with the effect from one discharge: 0.30 unit decrease in pH, 1.82 mg/L increase in dissolved

  3. A statistical rain attenuation prediction model with application to the advanced communication technology satellite project. 1: Theoretical development and application to yearly predictions for selected cities in the United States

    NASA Technical Reports Server (NTRS)

    Manning, Robert M.

    1986-01-01

    A rain attenuation prediction model is described for use in calculating satellite communication link availability for any specific location in the world that is characterized by an extended record of rainfall. Such a formalism is necessary for the accurate assessment of such availability predictions in the case of the small user-terminal concept of the Advanced Communication Technology Satellite (ACTS) Project. The model employs the theory of extreme value statistics to generate the necessary statistical rainrate parameters from rain data in the form compiled by the National Weather Service. These location dependent rain statistics are then applied to a rain attenuation model to obtain a yearly prediction of the occurrence of attenuation on any satellite link at that location. The predictions of this model are compared to those of the Crane Two-Component Rain Model and some empirical data and found to be very good. The model is then used to calculate rain attenuation statistics at 59 locations in the United States (including Alaska and Hawaii) for the 20 GHz downlinks and 30 GHz uplinks of the proposed ACTS system. The flexibility of this modeling formalism is such that it allows a complete and unified treatment of the temporal aspects of rain attenuation that leads to the design of an optimum stochastic power control algorithm, the purpose of which is to efficiently counter such rain fades on a satellite link.

  4. Accurate method of modeling cluster scaling relations in modified gravity

    NASA Astrophysics Data System (ADS)

    He, Jian-hua; Li, Baojiu

    2016-06-01

    We propose a new method to model cluster scaling relations in modified gravity. Using a suite of nonradiative hydrodynamical simulations, we show that the scaling relations of accumulated gas quantities, such as the Sunyaev-Zel'dovich effect (Compton-y parameter) and the x-ray Compton-y parameter, can be accurately predicted using the known results in the Λ CDM model with a precision of ˜3 % . This method provides a reliable way to analyze the gas physics in modified gravity using the less demanding and much more efficient pure cold dark matter simulations. Our results therefore have important theoretical and practical implications in constraining gravity using cluster surveys.

  5. Prediction of {sup 2}D Rydberg energy levels of {sup 6}Li and {sup 7}Li based on very accurate quantum mechanical calculations performed with explicitly correlated Gaussian functions

    SciTech Connect

    Bubin, Sergiy; Sharkey, Keeper L.; Adamowicz, Ludwik

    2013-04-28

    Very accurate variational nonrelativistic finite-nuclear-mass calculations employing all-electron explicitly correlated Gaussian basis functions are carried out for six Rydberg {sup 2}D states (1s{sup 2}nd, n= 6, Horizontal-Ellipsis , 11) of the {sup 7}Li and {sup 6}Li isotopes. The exponential parameters of the Gaussian functions are optimized using the variational method with the aid of the analytical energy gradient determined with respect to these parameters. The experimental results for the lower states (n= 3, Horizontal-Ellipsis , 6) and the calculated results for the higher states (n= 7, Horizontal-Ellipsis , 11) fitted with quantum-defect-like formulas are used to predict the energies of {sup 2}D 1s{sup 2}nd states for {sup 7}Li and {sup 6}Li with n up to 30.

  6. Field theoretical Lie symmetry analysis: The Möbius group, exact solutions of conformal autonomous systems, and predictive model-building

    NASA Astrophysics Data System (ADS)

    Christodoulides, Kyriakos

    2014-07-01

    We study single and coupled first-order differential equations (ODEs) that admit symmetries with tangent vector fields, which satisfy the N-dimensional Cauchy-Riemann equations. In the two-dimensional case, classes of first-order ODEs which are invariant under Möbius transformations are explored. In the N dimensional case we outline a symmetry analysis method for constructing exact solutions for conformal autonomous systems. A very important aspect of this work is that we propose to extend the traditional technical usage of Lie groups to one that could provide testable predictions and guidelines for model-building and model-validation. The Lie symmetries in this paper are constrained and classified by field theoretical considerations and their phenomenological implications. Our results indicate that conformal transformations are appropriate for elucidating a variety of linear and nonlinear systems which could be used for, or inspire, future applications. The presentation is pragmatic and it is addressed to a wide audience.

  7. Theoretical geology

    NASA Astrophysics Data System (ADS)

    Mikeš, Daniel

    2010-05-01

    Theoretical geology Present day geology is mostly empirical of nature. I claim that geology is by nature complex and that the empirical approach is bound to fail. Let's consider the input to be the set of ambient conditions and the output to be the sedimentary rock record. I claim that the output can only be deduced from the input if the relation from input to output be known. The fundamental question is therefore the following: Can one predict the output from the input or can one predict the behaviour of a sedimentary system? If one can, than the empirical/deductive method has changes, if one can't than that method is bound to fail. The fundamental problem to solve is therefore the following: How to predict the behaviour of a sedimentary system? It is interesting to observe that this question is never asked and many a study is conducted by the empirical/deductive method; it seems that the empirical method has been accepted as being appropriate without question. It is, however, easy to argument that a sedimentary system is by nature complex and that several input parameters vary at the same time and that they can create similar output in the rock record. It follows trivially from these first principles that in such a case the deductive solution cannot be unique. At the same time several geological methods depart precisely from the assumption, that one particular variable is the dictator/driver and that the others are constant, even though the data do not support such an assumption. The method of "sequence stratigraphy" is a typical example of such a dogma. It can be easily argued that all the interpretation resulting from a method that is built on uncertain or wrong assumptions is erroneous. Still, this method has survived for many years, nonwithstanding all the critics it has received. This is just one example of the present day geological world and is not unique. Even the alternative methods criticising sequence stratigraphy actually depart from the same

  8. Experimental and theoretical studies into the formation of C4-C6 products in partially chlorinated hydrocarbon pyrolysis systems: a probabilistic approach to congener-specific yield predictions.

    PubMed

    McIntosh, Grant J; Russell, Douglas K

    2014-09-25

    This work presents a study of the pyrolytic formation of vinylacetylene and benzene congeners formed from chlorinated hydrocarbon precursors, a complex, multipath polymerization system formed in a monomer-rich environment. (Co-)pyrolyses of dichloro- and trichloroethylene yield a rich array of products, and assuming a single dominant underlying growth mechanism, this (on comparing expected and observed products) allows a number of potentially competing channels to C4 and C6 products to be ruled out. Poor congener/isomer descriptions rule out even-carbon radical routes, and the absence of C3 and C5 products rule out odd-carbon processes. Vinylidenes appear unable to describe the increased reactivity of acetylenes with chlorination noted in our experiments, leaving molecular acetylene dimerization processes and, in C6 systems, the closely related Diels-Alder cyclization as the likely reaction mechanism. The feasibility of these routes is further supported by ab initio calculations. However, some of the most persuasive evidence is provided by congener-specific yield predictions enabled by the construction of a probability tree analogue of kinetic modeling. This approach is relatively quick to construct, provides surprisingly accurate predictions, and may be a very useful tool in screening for important reaction channels in poorly understood congener- or isomer-rich reaction systems.

  9. Identification of Two New Electronic States of NiCl Using Intracavity Laser Spectroscopy and the Correlation Between Theoretical Predictions and Experimental Observations

    NASA Astrophysics Data System (ADS)

    Harms, Jack C.; Grames, Ethan M.; Han, Shu; O'Brien, Leah C.; O'Brien, James J.

    2016-06-01

    The near-infrared spectrum of NiCl has been recorded in high resolution in the 13,200-13,500 wn and 13,600-13,750 wn regions using Intracavity Laser Spectroscopy (ILS). The NiCl Molecules were produced in the plasma discharge of a Ni-lined copper hollow cathode with 0.3-0.6 torr of argon as the sputter gas, and a trace amount of CCl_4. The hollow cathode was located within the laser cavity of a Verdi V-10 pumped Ti:sapphire system. A generation of 90 μsec resulted in an effective pathlength of approximately 700 m for the absorption measurements. Several transitions were observed, including 3 transitions involving 2 previously unreported electronic states. The (0,0) and (1,0) bands of the [13.5] 2Φ7/2-[0.16] A 2Δ5/2 transition were observed near 13,709 wn and 13,318 wn, respectively. The (0,0) band of the [13.8] 2Π1/2 - [0.38] X 2Π1/2 transition was observed near 13,480 wn. With the analysis of these transitions, molecular constants have been obtained for 9 of the 12 doublet states of NiCl predicted by Zou and Lou in 2006. Analysis of these transitions and a comparison between the experimentally observed transitions and the theoretically predicted states of NiCl will be presented.

  10. Predicting the potential distribution of invasive exotic species using GIS and information-theoretic approaches: A case of ragweed (Ambrosia artemisiifolia L.) distribution in China

    USGS Publications Warehouse

    Chen, H.; Chen, L.; Albright, T.P.

    2007-01-01

    Invasive exotic species pose a growing threat to the economy, public health, and ecological integrity of nations worldwide. Explaining and predicting the spatial distribution of invasive exotic species is of great importance to prevention and early warning efforts. We are investigating the potential distribution of invasive exotic species, the environmental factors that influence these distributions, and the ability to predict them using statistical and information-theoretic approaches. For some species, detailed presence/absence occurrence data are available, allowing the use of a variety of standard statistical techniques. However, for most species, absence data are not available. Presented with the challenge of developing a model based on presence-only information, we developed an improved logistic regression approach using Information Theory and Frequency Statistics to produce a relative suitability map. This paper generated a variety of distributions of ragweed (Ambrosia artemisiifolia L.) from logistic regression models applied to herbarium specimen location data and a suite of GIS layers including climatic, topographic, and land cover information. Our logistic regression model was based on Akaike's Information Criterion (AIC) from a suite of ecologically reasonable predictor variables. Based on the results we provided a new Frequency Statistical method to compartmentalize habitat-suitability in the native range. Finally, we used the model and the compartmentalized criterion developed in native ranges to "project" a potential distribution onto the exotic ranges to build habitat-suitability maps. ?? Science in China Press 2007.

  11. Density functional theory based tight binding study on theoretical prediction of low-density nanoporous phases ZnO semiconductor materials

    NASA Astrophysics Data System (ADS)

    Tuoc, Vu Ngoc; Doan Huan, Tran; Viet Minh, Nguyen; Thi Thao, Nguyen

    2016-06-01

    Polymorphs or phases - different inorganic solids structures of the same composition usually have widely differing properties and applications, thereby synthesizing or predicting new classes of polymorphs for a certain compound is of great significance and has been gaining considerable interest. Herein, we perform a density functional theory based tight binding (DFTB) study on theoretical prediction of several new phases series of II-VI semiconductor material ZnO nanoporous phases from their bottom-up building blocks. Among these, three phases are reported for the first time, which could greatly expand the family of II- VI compound nanoporous phases. We also show that all these generally can be categorized similarly to the aluminosilicate zeolites inorganic open-framework materials. The hollow cage structure of the corresponding building block ZnkOk (k= 9, 12, 16) is well preserved in all of them, which leads to their low-density nanoporous and high flexibility. Additionally the electronic wide-energy gap of the individual ZnkOk is also retained. Our study reveals that they are all semiconductor materials with a large band gap. Further, this study is likely to be the common for II-VI semiconductor compounds and will be helpful for extending their range of properties and applications.

  12. Superheavies:. Theoretical Incitements and Predictions

    NASA Astrophysics Data System (ADS)

    Zagrebaev, V. I.; Karpov, A. V.; Mishustin, I. N.; Greiner, Walter

    2012-01-01

    It is well known that in fusion reactions one may get only neutron deficient superheavy nuclei located far from the island of stability. The multi-nucleon transfer reactions allow one to produce more neutron enriched new heavy nuclei but the corresponding cross sections are rather low. Neutron capture process is considered here as alternative method for production of long-lived neutron rich superheavy nuclei. Strong neutron fluxes might be provided by nuclear reactors and nuclear explosions in laboratory frame and by supernova explosions in nature. All these cases are discussed in the paper.

  13. Theoretical prediction of vibrational spectra

    NASA Astrophysics Data System (ADS)

    Niu, Zefu; Dunn, Kevin M.; Boggs, James E.

    The complete harmonic force field and the diagonal and first off-diagonal cubic constants of aniline have been calculated ab initio using a 4-21 basis set augmented by addition of d functions to the nitrogen atom. The force constants were then scaled using scale factors optimized previously to give the best fit to the similarly computed vibrational spectra of benzene and its deuterated isotopomers. The vibrational spectra of aniline, aniline-NHD, and aniline-ND2 were then calculated from this scaled quantum mechanical (SQM) force field and compared with experimentally observed spectra. Several corrections were made to previously proposed empirical spectral assignments. Because of computational difficulties, no definitive statement can be made about the torsion or inversion modes of the amino group. Aside from these and the C-H stretching frequencies for which the detailed assignment is still quite uncertain, the average deviation between the observed frequencies and those obtained entirely from the scaled computed force field is 9·1 cm-1. Dipole moment derivatives and infrared absorption intensities were also calculated, but these are of lower accuracy.

  14. Esr Spectra of Alkali-Metal Atoms on Helium Nanodroplets: a Theoretical Model for the Prediction of Helium Induced Hyperfine Structure Shifts

    NASA Astrophysics Data System (ADS)

    Hauser, Reas W.; Filatov, Michael; Ernst, Wolfgang E.

    2013-06-01

    We predict He-droplet-induced changes of the isotropic HFS constant a_{HFS} of the alkali-metal atoms M = Li, Na, K and Rb on the basis of a model description. Optically detected electron spin resonance spectroscopy has allowed high resolution measurements that show the influence of the helium droplet and its size on the unpaired electron spin density at the alkali nucleus. Our theoretical approach to describe this dependence is based on a combination of two well established techniques: Results of relativistic coupled-cluster calculations on the alkali-He dimers (energy and HFS constant as functions of the binding length) are mapped onto the doped-droplet-situation with the help of helium-density functional theory. We simulate doped droplets He_{N} with N ranging from 50 to 10000, using the diatomic alkali-He-potential energy curves as input. From the obtained density profiles we evaluate average distances between the dopant atom and its direct helium neighborhood. The distances are then set in relation to the variation of the HFS constant with binding length in the simplified alkali-He-dimer model picture. This method yields reliable relative shifts but involves a systematic absolute error. Hence, the absolute values of the shifts are tied to one experimentally determined HFS constant for ^{85}Rb-He_{N = 2000}. With this parameter choice we obtain results in good agreement with the available experimental data for Rb and K^{a,b} confirming the predicted 1/N trend of the functional dependence^{c}. M. Koch, G. Auböck, C. Callegari, and W. E. Ernst, Phys. Rev. Lett. 103, 035302-1-4 (2009) M. Koch, C. Callegari, and W. E. Ernst, Mol. Phys. 108 (7), 1005-1011 (2010) A. W. Hauser, T. Gruber, M. Filatov, and W. E. Ernst, ChemPhysChem (2013) online DOI: 10.1002/cphc.201200697

  15. Using a theoretical predictive tool for the analysis of recent health department inspections at outbreak restaurants and relation of this information to foodborne illness likelihood.

    PubMed

    Petran, Ruth L; White, Bruce W; Hedberg, Craig W

    2012-11-01

    Because U.S. restaurants are inspected at least annually against criteria in the U.S. Food and Drug Administration Model Food Code, large amounts of data are generated and should be systematically reviewed. The purpose of this study was to determine the relationships among the data obtained through health department inspections, the contributing factors to foodborne illness identified by the Centers for Disease Control and Prevention, and the risks of outbreaks of norovirus, Salmonella, and Clostridium perfringens infection associated with a specific restaurant. These agents were chosen for the analysis because they cause the majority of foodborne illnesses. A theoretical predictive assessment tool was built that extracts data from routine health department inspection reports for specific restaurants to establish a risk profile for each restaurant and identify the likelihood of a norovirus, Salmonella, or C. perfringens outbreak at that restaurant. The tool was used to examine inspection reports from restaurants known to have had confirmed norovirus, Salmonella, and C. perfringens outbreaks. Although evaluation of an extensive data set revealed lack of an overall association between outbreak inspection scores and routine inspection scores obtained at outbreak restaurant locations, certain specific violations were significantly more likely to be recorded. Significant differences in types of violations recorded during outbreak and routine inspections were determined. When risks based on violation type can be identified, targeted actions may be able to be prioritized and implemented to help decrease illnesses.

  16. Accurate theoretical and experimental characterization of optical grating coupler.

    PubMed

    Fesharaki, Faezeh; Hossain, Nadir; Vigne, Sebastien; Chaker, Mohamed; Wu, Ke

    2016-09-01

    Periodic structures, acting as reflectors, filters, and couplers, are a fundamental building block section in many optical devices. In this paper, a three-dimensional simulation of a grating coupler, a well-known periodic structure, is conducted. Guided waves and leakage characteristics of an out-of-plane grating coupler are studied in detail, and its coupling efficiency is examined. Furthermore, a numerical calibration analysis is applied through a commercial software package on the basis of a full-wave finite-element method to calculate the complex propagation constant of the structure and to evaluate the radiation pattern. For experimental evaluation, an optimized grating coupler is fabricated using electron-beam lithography technique and plasma etching. An excellent agreement between simulations and measurements is observed, thereby validating the demonstrated method. PMID:27607706

  17. Accurate thermoelastic tensor and acoustic velocities of NaCl

    NASA Astrophysics Data System (ADS)

    Marcondes, Michel L.; Shukla, Gaurav; da Silveira, Pedro; Wentzcovitch, Renata M.

    2015-12-01

    Despite the importance of thermoelastic properties of minerals in geology and geophysics, their measurement at high pressures and temperatures are still challenging. Thus, ab initio calculations are an essential tool for predicting these properties at extreme conditions. Owing to the approximate description of the exchange-correlation energy, approximations used in calculations of vibrational effects, and numerical/methodological approximations, these methods produce systematic deviations. Hybrid schemes combining experimental data and theoretical results have emerged as a way to reconcile available information and offer more reliable predictions at experimentally inaccessible thermodynamics conditions. Here we introduce a method to improve the calculated thermoelastic tensor by using highly accurate thermal equation of state (EoS). The corrective scheme is general, applicable to crystalline solids with any symmetry, and can produce accurate results at conditions where experimental data may not exist. We apply it to rock-salt-type NaCl, a material whose structural properties have been challenging to describe accurately by standard ab initio methods and whose acoustic/seismic properties are important for the gas and oil industry.

  18. Accurate thermoelastic tensor and acoustic velocities of NaCl

    SciTech Connect

    Marcondes, Michel L.; Shukla, Gaurav; Silveira, Pedro da; Wentzcovitch, Renata M.

    2015-12-15

    Despite the importance of thermoelastic properties of minerals in geology and geophysics, their measurement at high pressures and temperatures are still challenging. Thus, ab initio calculations are an essential tool for predicting these properties at extreme conditions. Owing to the approximate description of the exchange-correlation energy, approximations used in calculations of vibrational effects, and numerical/methodological approximations, these methods produce systematic deviations. Hybrid schemes combining experimental data and theoretical results have emerged as a way to reconcile available information and offer more reliable predictions at experimentally inaccessible thermodynamics conditions. Here we introduce a method to improve the calculated thermoelastic tensor by using highly accurate thermal equation of state (EoS). The corrective scheme is general, applicable to crystalline solids with any symmetry, and can produce accurate results at conditions where experimental data may not exist. We apply it to rock-salt-type NaCl, a material whose structural properties have been challenging to describe accurately by standard ab initio methods and whose acoustic/seismic properties are important for the gas and oil industry.

  19. Prognosis Can Be Predicted More Accurately Using Pre- and Postchemoradiotherapy Carcinoembryonic Antigen Levels Compared to Only Prechemoradiotherapy Carcinoembryonic Antigen Level in Locally Advanced Rectal Cancer Patients Who Received Neoadjuvant Chemoradiotherapy

    PubMed Central

    Sung, SooYoon; Son, Seok Hyun; Kay, Chul Seung; Lee, Yoon Suk

    2016-01-01

    Abstract We aimed to evaluate the prognostic value of a change in the carcinoembryonic antigen (CEA) level during neoadjuvant chemoradiotherapy (nCRT) in patients with locally advanced rectal cancer. A total of 110 patients with clinical T3/T4 or node-positive disease underwent nCRT and curative total mesorectal resection from February 2006 to December 2013. Serum CEA level was measured before nCRT, after nCRT, and then again after surgery. A cut-off value for CEA level to predict prognosis was determined using the maximally selected log-rank test. According to the test, patients were classified into 3 groups, based on their CEA levels (Group A: pre-CRT CEA ≤3.2; Group B: pre-CRT CEA level >3.2 and post-CRT CEA ≤2.8; and Group C: pre-CRT CEA >3.2 and post-CRT CEA >2.8). The median follow-up time was 31.1 months. The 3-year disease-free survival (DFS) rates of Group A and Group B were similar, while Group C showed a significantly lower 3-year DFS rate (82.5% vs. 89.5% vs. 55.1%, respectively, P = 0.001). Other clinicopathological factors that showed statistical significance on univariate analysis were pre-CRT CEA, post-CRT CEA, tumor distance from the anal verge, surgery type, downstage, pathologic N stage, margin status and perineural invasion. The CEA group (P = 0.001) and tumor distance from the anal verge (P = 0.044) were significant prognostic factors for DFS on multivariate analysis. Post-CRT CEA level may be a useful prognostic factor in patients whose prognosis cannot be predicted exactly by pre-CRT CEA levels alone in the neoadjuvant treatment era. Combined pre-CRT CEA and post-CRT CEA levels enable us to predict prognosis more accurately and determine treatment and follow-up policies. Further large-scale studies are necessary to validate the prognostic value of CEA levels. PMID:26962798

  20. Accurate lineshape spectroscopy and the Boltzmann constant

    PubMed Central

    Truong, G.-W.; Anstie, J. D.; May, E. F.; Stace, T. M.; Luiten, A. N.

    2015-01-01

    Spectroscopy has an illustrious history delivering serendipitous discoveries and providing a stringent testbed for new physical predictions, including applications from trace materials detection, to understanding the atmospheres of stars and planets, and even constraining cosmological models. Reaching fundamental-noise limits permits optimal extraction of spectroscopic information from an absorption measurement. Here, we demonstrate a quantum-limited spectrometer that delivers high-precision measurements of the absorption lineshape. These measurements yield a very accurate measurement of the excited-state (6P1/2) hyperfine splitting in Cs, and reveals a breakdown in the well-known Voigt spectral profile. We develop a theoretical model that accounts for this breakdown, explaining the observations to within the shot-noise limit. Our model enables us to infer the thermal velocity dispersion of the Cs vapour with an uncertainty of 35 p.p.m. within an hour. This allows us to determine a value for Boltzmann's constant with a precision of 6 p.p.m., and an uncertainty of 71 p.p.m. PMID:26465085

  1. Accurate adiabatic correction in the hydrogen molecule

    NASA Astrophysics Data System (ADS)

    Pachucki, Krzysztof; Komasa, Jacek

    2014-12-01

    A new formalism for the accurate treatment of adiabatic effects in the hydrogen molecule is presented, in which the electronic wave function is expanded in the James-Coolidge basis functions. Systematic increase in the size of the basis set permits estimation of the accuracy. Numerical results for the adiabatic correction to the Born-Oppenheimer interaction energy reveal a relative precision of 10-12 at an arbitrary internuclear distance. Such calculations have been performed for 88 internuclear distances in the range of 0 < R ⩽ 12 bohrs to construct the adiabatic correction potential and to solve the nuclear Schrödinger equation. Finally, the adiabatic correction to the dissociation energies of all rovibrational levels in H2, HD, HT, D2, DT, and T2 has been determined. For the ground state of H2 the estimated precision is 3 × 10-7 cm-1, which is almost three orders of magnitude higher than that of the best previous result. The achieved accuracy removes the adiabatic contribution from the overall error budget of the present day theoretical predictions for the rovibrational levels.

  2. Accurate adiabatic correction in the hydrogen molecule

    SciTech Connect

    Pachucki, Krzysztof; Komasa, Jacek

    2014-12-14

    A new formalism for the accurate treatment of adiabatic effects in the hydrogen molecule is presented, in which the electronic wave function is expanded in the James-Coolidge basis functions. Systematic increase in the size of the basis set permits estimation of the accuracy. Numerical results for the adiabatic correction to the Born-Oppenheimer interaction energy reveal a relative precision of 10{sup −12} at an arbitrary internuclear distance. Such calculations have been performed for 88 internuclear distances in the range of 0 < R ⩽ 12 bohrs to construct the adiabatic correction potential and to solve the nuclear Schrödinger equation. Finally, the adiabatic correction to the dissociation energies of all rovibrational levels in H{sub 2}, HD, HT, D{sub 2}, DT, and T{sub 2} has been determined. For the ground state of H{sub 2} the estimated precision is 3 × 10{sup −7} cm{sup −1}, which is almost three orders of magnitude higher than that of the best previous result. The achieved accuracy removes the adiabatic contribution from the overall error budget of the present day theoretical predictions for the rovibrational levels.

  3. Accurate adiabatic correction in the hydrogen molecule.

    PubMed

    Pachucki, Krzysztof; Komasa, Jacek

    2014-12-14

    A new formalism for the accurate treatment of adiabatic effects in the hydrogen molecule is presented, in which the electronic wave function is expanded in the James-Coolidge basis functions. Systematic increase in the size of the basis set permits estimation of the accuracy. Numerical results for the adiabatic correction to the Born-Oppenheimer interaction energy reveal a relative precision of 10(-12) at an arbitrary internuclear distance. Such calculations have been performed for 88 internuclear distances in the range of 0 < R ⩽ 12 bohrs to construct the adiabatic correction potential and to solve the nuclear Schrödinger equation. Finally, the adiabatic correction to the dissociation energies of all rovibrational levels in H2, HD, HT, D2, DT, and T2 has been determined. For the ground state of H2 the estimated precision is 3 × 10(-7) cm(-1), which is almost three orders of magnitude higher than that of the best previous result. The achieved accuracy removes the adiabatic contribution from the overall error budget of the present day theoretical predictions for the rovibrational levels. PMID:25494728

  4. Does safety climate predict safety performance in Italy and the USA? Cross-cultural validation of a theoretical model of safety climate.

    PubMed

    Barbaranelli, Claudio; Petitta, Laura; Probst, Tahira M

    2015-04-01

    Previous studies have acknowledged the relevance of assessing the measurement equivalence of safety related measures across different groups, and demonstrating whether the existence of disparities in safety perceptions might impair direct group comparisons. The Griffin and Neal (2000) model of safety climate, and the accompanying measure (Neal et al. [NGH], 2000), are both widely cited and utilized. Yet neither the model in its entirety nor the measure have been previously validated across different national contexts. The current study is the first to examine the NGH measurement equivalence by testing whether their model of safety climate predicting safety performance is tenable in both English speaking and non-English speaking countries. The study involved 616 employees from 21 organizations in the US, and 738 employees from 20 organizations in Italy. A multi-group confirmatory factor analytic approach was used to assess the equivalence of the measures across the two countries. Similarly, the structural model of relations among the NGH variables was examined in order to demonstrate its cross-country invariance. Results substantially support strict invariance across groups for the NGH safety scales. Moreover, the invariance across countries is also demonstrated for the effects of safety climate on safety knowledge and motivation, which in turn positively relate to both compliance and participation. Our findings have relevant theoretical implications by establishing measurement and relational equivalence of the NGH model. Practical implications are discussed for managers and practitioners dealing with multi-national organizational contexts. Future research should continue to investigate potential differences in safety related perceptions across additional non-English speaking countries.

  5. Theoretical study on the transition-metal oxoboryl complex: M-BO bonding nature, mechanism of the formation reaction, and prediction of a new oxoboryl complex.

    PubMed

    Zeng, Guixiang; Sakaki, Shigeyoshi

    2012-04-16

    The Pt-BO bonding nature and the formation reaction of the experimentally reported platinum(II) oxoboryl complex, simplified to PtBr(BO)(PMe(3))(2), were theoretically investigated with the density functional theory method. The BO(-) ligand was quantitatively demonstrated to have extremely strong σ-donation but very weak d(π)-electron-accepting abilities. Therefore, it exhibits a strong trans influence. The formation reaction occurs through a four-center transition state, in which the B(δ+)-Br(δ-) polarization and the Br → Si and O p(π) → B p(π) charge-transfer interactions play key roles. The Gibbs activation energy (ΔG°(++)) and Gibbs reaction energy (ΔG°) of the formation reaction are 32.2 and -6.1 kcal/mol, respectively. The electron-donating bulky phosphine ligand is found to be favorable for lowering both ΔG°(++) and ΔG°. In addition, the metal effect is examined with the nickel and palladium analogues and MBrCl[BBr(OSiMe(3))](CO)(PR(3))(2) (M = Ir and Rh). By a comparison of the ΔG°(++) and ΔG° values, the M-BO (M = Ni, Pd, Ir, and Rh) bonding nature, and the interaction energy between [MBrCl(CO)(PR(3))(2)](+) and BO(-) with those of the platinum system, MBrCl(BO)(CO)(PR(3))(2) (M = Ir and Rh) is predicted to be a good candidate for a stable oxoboryl complex. PMID:22458310

  6. Accurate monotone cubic interpolation

    NASA Technical Reports Server (NTRS)

    Huynh, Hung T.

    1991-01-01

    Monotone piecewise cubic interpolants are simple and effective. They are generally third-order accurate, except near strict local extrema where accuracy degenerates to second-order due to the monotonicity constraint. Algorithms for piecewise cubic interpolants, which preserve monotonicity as well as uniform third and fourth-order accuracy are presented. The gain of accuracy is obtained by relaxing the monotonicity constraint in a geometric framework in which the median function plays a crucial role.

  7. Accurate Finite Difference Algorithms

    NASA Technical Reports Server (NTRS)

    Goodrich, John W.

    1996-01-01

    Two families of finite difference algorithms for computational aeroacoustics are presented and compared. All of the algorithms are single step explicit methods, they have the same order of accuracy in both space and time, with examples up to eleventh order, and they have multidimensional extensions. One of the algorithm families has spectral like high resolution. Propagation with high order and high resolution algorithms can produce accurate results after O(10(exp 6)) periods of propagation with eight grid points per wavelength.

  8. Feedback about More Accurate versus Less Accurate Trials: Differential Effects on Self-Confidence and Activation

    ERIC Educational Resources Information Center

    Badami, Rokhsareh; VaezMousavi, Mohammad; Wulf, Gabriele; Namazizadeh, Mahdi

    2012-01-01

    One purpose of the present study was to examine whether self-confidence or anxiety would be differentially affected by feedback from more accurate rather than less accurate trials. The second purpose was to determine whether arousal variations (activation) would predict performance. On Day 1, participants performed a golf putting task under one of…

  9. Theoretical predictions of source rates for exospheric CO 2 on icy satellites of the outer planets due to sublimation of deep subsurface CO 2 ice

    NASA Astrophysics Data System (ADS)

    Wood, Stephen E.

    2016-10-01

    The abundances of CO2 observed in the exospheres of Callisto and, more recently, Rhea and Dione are difficult to explain. The previously proposed sources for the CO2 either have production rates well below the expected rates of escape/destruction or should produce other species (e.g. CO) that are not observed.We consider a potential source that has not been previously investigated – CO2 vapor originating from crustal CO2 ice and driven upward by the endogenic heat flux – and have developed a model to make quantitative estimates of the corresponding global subsurface vapor flux.Our model is based on previous theoretical work by Clifford (1993) and Mellon et al. (1997) for equatorial ground ice on Mars, who showed that in times or places where subsurface pore ice is undergoing long-term sublimation and diffusive loss, the ice table (the shallowest depth where any pore ice exists) will not continue to recede indefinitely. Beyond a certain, predictable depth, the linear diffusive profile of vapor density between the ice table and the surface will become supersaturated with respect to the local temperature and recondense as pore ice. This is true for any planetary body with a non-negligible interior heat source (e.g. radiogenic, tidal, etc) and is due to the fact that, while the ice temperature increases ~linearly with depth, the corresponding equilibrium vapor density increases exponentially.Once this occurs, a steady-state profile of ice volume fraction, f_ice(z), develops, with net mass loss only occurring from the retreating pore-filling ice layer. The rate of vapor flux to the surface is then determined only by the vapor density and temperature gradient at the ice table depth. We use a 1-D thermal model coupled with an analytic physical model for regolith thermal conductivity (including its depth- and T-dependence), to calculate the zonally-integrated global CO2 vapor flux corresponding to the range of expected heat flow values. Our preliminary results show

  10. Vibrations of twisted cantilever plates - A comparison of theoretical results

    NASA Technical Reports Server (NTRS)

    Kielb, R. E.; Leissa, A. W.; Macbain, J. C.

    1985-01-01

    As a result of significant differences in the published results for various methods of analysis involving the use of finite element techniques, there are now some questions regarding the adequacy of these methods to predict accurately the vibratory characteristics of highly twisted cantilever plates. In an attempt to help in a resolution of the arising problems, a joint government/industry/university research effort was initiated. The primary objective of the present paper is to summarize the theoretical methods used in the study and show samples of the obtained results. The study provided 19 sets of theoretical results which are derived from beam theory, shell theory, and finite element methods.

  11. Theoretical Modeling for Hepatic Microwave Ablation

    PubMed Central

    Prakash, Punit

    2010-01-01

    Thermal tissue ablation is an interventional procedure increasingly being used for treatment of diverse medical conditions. Microwave ablation is emerging as an attractive modality for thermal therapy of large soft tissue targets in short periods of time, making it particularly suitable for ablation of hepatic and other tumors. Theoretical models of the ablation process are a powerful tool for predicting the temperature profile in tissue and resultant tissue damage created by ablation devices. These models play an important role in the design and optimization of devices for microwave tissue ablation. Furthermore, they are a useful tool for exploring and planning treatment delivery strategies. This review describes the status of theoretical models developed for microwave tissue ablation. It also reviews current challenges, research trends and progress towards development of accurate models for high temperature microwave tissue ablation. PMID:20309393

  12. Accurate Cross Sections for Microanalysis

    PubMed Central

    Rez, Peter

    2002-01-01

    To calculate the intensity of x-ray emission in electron beam microanalysis requires a knowledge of the energy distribution of the electrons in the solid, the energy variation of the ionization cross section of the relevant subshell, the fraction of ionizations events producing x rays of interest and the absorption coefficient of the x rays on the path to the detector. The theoretical predictions and experimental data available for ionization cross sections are limited mainly to K shells of a few elements. Results of systematic plane wave Born approximation calculations with exchange for K, L, and M shell ionization cross sections over the range of electron energies used in microanalysis are presented. Comparisons are made with experimental measurement for selected K shells and it is shown that the plane wave theory is not appropriate for overvoltages less than 2.5 V. PMID:27446747

  13. TAD- THEORETICAL AERODYNAMICS PROGRAM

    NASA Technical Reports Server (NTRS)

    Barrowman, J.

    1994-01-01

    This theoretical aerodynamics program, TAD, was developed to predict the aerodynamic characteristics of vehicles with sounding rocket configurations. These slender, axisymmetric finned vehicle configurations have a wide range of aeronautical applications from rockets to high speed armament. Over a given range of Mach numbers, TAD will compute the normal force coefficient derivative, the center-of-pressure, the roll forcing moment coefficient derivative, the roll damping moment coefficient derivative, and the pitch damping moment coefficient derivative of a sounding rocket configured vehicle. The vehicle may consist of a sharp pointed nose of cone or tangent ogive shape, up to nine other body divisions of conical shoulder, conical boattail, or circular cylinder shape, and fins of trapezoid planform shape with constant cross section and either three or four fins per fin set. The characteristics computed by TAD have been shown to be accurate to within ten percent of experimental data in the supersonic region. The TAD program calculates the characteristics of separate portions of the vehicle, calculates the interference between separate portions of the vehicle, and then combines the results to form a total vehicle solution. Also, TAD can be used to calculate the characteristics of the body or fins separately as an aid in the design process. Input to the TAD program consists of simple descriptions of the body and fin geometries and the Mach range of interest. Output includes the aerodynamic characteristics of the total vehicle, or user-selected portions, at specified points over the mach range. The TAD program is written in FORTRAN IV for batch execution and has been implemented on an IBM 360 computer with a central memory requirement of approximately 123K of 8 bit bytes. The TAD program was originally developed in 1967 and last updated in 1972.

  14. Fast and accurate determination of modularity and its effect size

    NASA Astrophysics Data System (ADS)

    Treviño, Santiago, III; Nyberg, Amy; Del Genio, Charo I.; Bassler, Kevin E.

    2015-02-01

    We present a fast spectral algorithm for community detection in complex networks. Our method searches for the partition with the maximum value of the modularity via the interplay of several refinement steps that include both agglomeration and division. We validate the accuracy of the algorithm by applying it to several real-world benchmark networks. On all these, our algorithm performs as well or better than any other known polynomial scheme. This allows us to extensively study the modularity distribution in ensembles of Erdős-Rényi networks, producing theoretical predictions for means and variances inclusive of finite-size corrections. Our work provides a way to accurately estimate the effect size of modularity, providing a z-score measure of it and enabling a more informative comparison of networks with different numbers of nodes and links.

  15. Future missions studies: Combining Schatten's solar activity prediction model with a chaotic prediction model

    NASA Technical Reports Server (NTRS)

    Ashrafi, S.

    1991-01-01

    K. Schatten (1991) recently developed a method for combining his prediction model with our chaotic model. The philosophy behind this combined model and his method of combination is explained. Because the Schatten solar prediction model (KS) uses a dynamo to mimic solar dynamics, accurate prediction is limited to long-term solar behavior (10 to 20 years). The Chaotic prediction model (SA) uses the recently developed techniques of nonlinear dynamics to predict solar activity. It can be used to predict activity only up to the horizon. In theory, the chaotic prediction should be several orders of magnitude better than statistical predictions up to that horizon; beyond the horizon, chaotic predictions would theoretically be just as good as statistical predictions. Therefore, chaos theory puts a fundamental limit on predictability.

  16. Dicopper(II) metallacyclophanes with oligo(p-phenylene-ethynylene) spacers: experimental foundations and theoretical predictions on potential molecular magnetic wires.

    PubMed

    Castellano, María; Fortea-Pérez, Francisco R; Bentama, Abdeslem; Stiriba, Salah-Eddine; Julve, Miguel; Lloret, Francesc; De Munno, Giovanni; Armentano, Donatella; Li, Yangling; Ruiz-García, Rafael; Cano, Joan

    2013-07-01

    absorption spectra of 1 and 2 [λ1 = 308 (1) and 316 nm (2)]. In the series of orthogonal model complexes 1-5 with linear oligo(p-phenylene-ethynylene) (OPE) spacers, -C6H4(C≡CC6H4)n- (n = 1-5), a linear increase of the IL π-π* transition energy with the reciprocal of the intermetallic distance is theoretically predicted [νmax = 1.99 × 10(4) + 2.15 × 10(5) (1/r) (S = 0) or ν = 2.01 × 10(4) + 2.18 × 10(5) (1/r) (S = 1)], which clearly indicates that the effective π-conjugation length increases with the number of phenylethyne repeating units. This is accompanied by an exponential decay of the antiferromagnetic coupling with the intermetallic distance [-J = 1.08 × 10(3) exp(-0.31r)], which supports the ability of the extended π-conjugated OPEs to mediate the exchange interaction between the unpaired electrons of the two Cu(II) centers with intermetallic distances in the range of 1.5-4.3 nm. Further developments may be then envisaged for this new family of oxamato-based dicopper(II) oligo-p-phenylethynophanes on the basis of the unique ligand capacity to act as a molecular antiferromagnetic wire.

  17. Accurate Optical Reference Catalogs

    NASA Astrophysics Data System (ADS)

    Zacharias, N.

    2006-08-01

    Current and near future all-sky astrometric catalogs on the ICRF are reviewed with the emphasis on reference star data at optical wavelengths for user applications. The standard error of a Hipparcos Catalogue star position is now about 15 mas per coordinate. For the Tycho-2 data it is typically 20 to 100 mas, depending on magnitude. The USNO CCD Astrograph Catalog (UCAC) observing program was completed in 2004 and reductions toward the final UCAC3 release are in progress. This all-sky reference catalogue will have positional errors of 15 to 70 mas for stars in the 10 to 16 mag range, with a high degree of completeness. Proper motions for the about 60 million UCAC stars will be derived by combining UCAC astrometry with available early epoch data, including yet unpublished scans of the complete set of AGK2, Hamburg Zone astrograph and USNO Black Birch programs. Accurate positional and proper motion data are combined in the Naval Observatory Merged Astrometric Dataset (NOMAD) which includes Hipparcos, Tycho-2, UCAC2, USNO-B1, NPM+SPM plate scan data for astrometry, and is supplemented by multi-band optical photometry as well as 2MASS near infrared photometry. The Milli-Arcsecond Pathfinder Survey (MAPS) mission is currently being planned at USNO. This is a micro-satellite to obtain 1 mas positions, parallaxes, and 1 mas/yr proper motions for all bright stars down to about 15th magnitude. This program will be supplemented by a ground-based program to reach 18th magnitude on the 5 mas level.

  18. Feedback about more accurate versus less accurate trials: differential effects on self-confidence and activation.

    PubMed

    Badami, Rokhsareh; VaezMousavi, Mohammad; Wulf, Gabriele; Namazizadeh, Mahdi

    2012-06-01

    One purpose of the present study was to examine whether self-confidence or anxiety would be differentially affected byfeedback from more accurate rather than less accurate trials. The second purpose was to determine whether arousal variations (activation) would predict performance. On day 1, participants performed a golf putting task under one of two conditions: one group received feedback on the most accurate trials, whereas another group received feedback on the least accurate trials. On day 2, participants completed an anxiety questionnaire and performed a retention test. Shin conductance level, as a measure of arousal, was determined. The results indicated that feedback about more accurate trials resulted in more effective learning as well as increased self-confidence. Also, activation was a predictor of performance. PMID:22808705

  19. Predicting Noninsulin Antidiabetic Drug Adherence Using a Theoretical Framework Based on the Theory of Planned Behavior in Adults With Type 2 Diabetes: A Prospective Study.

    PubMed

    Zomahoun, Hervé Tchala Vignon; Moisan, Jocelyne; Lauzier, Sophie; Guillaumie, Laurence; Grégoire, Jean-Pierre; Guénette, Line

    2016-04-01

    Understanding the process behind noninsulin antidiabetic drug (NIAD) nonadherence is necessary for designing effective interventions to resolve this problem. This study aimed to explore the ability of the theory of planned behavior (TPB), which is known as a good predictor of behaviors, to predict the future NIAD adherence in adults with type 2 diabetes. We conducted a prospective study of adults with type 2 diabetes. They completed a questionnaire on TPB variables and external variables. Linear regression was used to explore the TPB's ability to predict future NIAD adherence, which was prospectively measured as the proportion of days covered by at least 1 NIAD using pharmacy claims data. The interaction between past NIAD adherence and intention was tested. The sample included 340 people. There was an interaction between past NIAD adherence and intention to adhere to the NIAD (P = 0.032). Intention did not predict future NIAD adherence in the past adherers and nonadherers groups, but its association measure was high among past nonadherers (β = 5.686, 95% confidence interval [CI] -10.174, 21.546). In contrast, intention was mainly predicted by perceived behavioral control both in the past adherers (β = 0.900, 95% CI 0.796, 1.004) and nonadherers groups (β = 0.760, 95% CI 0.555, 0.966). The present study suggests that TPB is a good tool to predict intention to adhere and future NIAD adherence. However, there was a gap between intention to adhere and actual adherence to the NIAD, which is partly explained by the past adherence level in adults with type 2 diabetes.

  20. Predicting Noninsulin Antidiabetic Drug Adherence Using a Theoretical Framework Based on the Theory of Planned Behavior in Adults With Type 2 Diabetes

    PubMed Central

    Zomahoun, Hervé Tchala Vignon; Moisan, Jocelyne; Lauzier, Sophie; Guillaumie, Laurence; Grégoire, Jean-Pierre; Guénette, Line

    2016-01-01

    Abstract Understanding the process behind noninsulin antidiabetic drug (NIAD) nonadherence is necessary for designing effective interventions to resolve this problem. This study aimed to explore the ability of the theory of planned behavior (TPB), which is known as a good predictor of behaviors, to predict the future NIAD adherence in adults with type 2 diabetes. We conducted a prospective study of adults with type 2 diabetes. They completed a questionnaire on TPB variables and external variables. Linear regression was used to explore the TPB's ability to predict future NIAD adherence, which was prospectively measured as the proportion of days covered by at least 1 NIAD using pharmacy claims data. The interaction between past NIAD adherence and intention was tested. The sample included 340 people. There was an interaction between past NIAD adherence and intention to adhere to the NIAD (P = 0.032). Intention did not predict future NIAD adherence in the past adherers and nonadherers groups, but its association measure was high among past nonadherers (β = 5.686, 95% confidence interval [CI] −10.174, 21.546). In contrast, intention was mainly predicted by perceived behavioral control both in the past adherers (β = 0.900, 95% CI 0.796, 1.004) and nonadherers groups (β = 0.760, 95% CI 0.555, 0.966). The present study suggests that TPB is a good tool to predict intention to adhere and future NIAD adherence. However, there was a gap between intention to adhere and actual adherence to the NIAD, which is partly explained by the past adherence level in adults with type 2 diabetes. PMID:27082543

  1. Predicting Noninsulin Antidiabetic Drug Adherence Using a Theoretical Framework Based on the Theory of Planned Behavior in Adults With Type 2 Diabetes: A Prospective Study.

    PubMed

    Zomahoun, Hervé Tchala Vignon; Moisan, Jocelyne; Lauzier, Sophie; Guillaumie, Laurence; Grégoire, Jean-Pierre; Guénette, Line

    2016-04-01

    Understanding the process behind noninsulin antidiabetic drug (NIAD) nonadherence is necessary for designing effective interventions to resolve this problem. This study aimed to explore the ability of the theory of planned behavior (TPB), which is known as a good predictor of behaviors, to predict the future NIAD adherence in adults with type 2 diabetes. We conducted a prospective study of adults with type 2 diabetes. They completed a questionnaire on TPB variables and external variables. Linear regression was used to explore the TPB's ability to predict future NIAD adherence, which was prospectively measured as the proportion of days covered by at least 1 NIAD using pharmacy claims data. The interaction between past NIAD adherence and intention was tested. The sample included 340 people. There was an interaction between past NIAD adherence and intention to adhere to the NIAD (P = 0.032). Intention did not predict future NIAD adherence in the past adherers and nonadherers groups, but its association measure was high among past nonadherers (β = 5.686, 95% confidence interval [CI] -10.174, 21.546). In contrast, intention was mainly predicted by perceived behavioral control both in the past adherers (β = 0.900, 95% CI 0.796, 1.004) and nonadherers groups (β = 0.760, 95% CI 0.555, 0.966). The present study suggests that TPB is a good tool to predict intention to adhere and future NIAD adherence. However, there was a gap between intention to adhere and actual adherence to the NIAD, which is partly explained by the past adherence level in adults with type 2 diabetes. PMID:27082543

  2. Theoretical Issues

    SciTech Connect

    Marc Vanderhaeghen

    2007-04-01

    The theoretical issues in the interpretation of the precision measurements of the nucleon-to-Delta transition by means of electromagnetic probes are highlighted. The results of these measurements are confronted with the state-of-the-art calculations based on chiral effective-field theories (EFT), lattice QCD, large-Nc relations, perturbative QCD, and QCD-inspired models. The link of the nucleon-to-Delta form factors to generalized parton distributions (GPDs) is also discussed.

  3. Theoretical prediction of the ionization energies of the C4H7 radicals: 1-methylallyl, 2-methylallyl, cyclopropylmethyl, and cyclobutyl radicals.

    PubMed

    Lau, Kai-Chung; Zheng, Wenxu; Wong, Ning-Bew; Li, Wai-Kee

    2007-10-21

    The ionization energies (IEs) for the 1-methylallyl, 2-methylallyl, cyclopropylmethyl, and cyclobutyl radicals have been calculated by the wave function based ab initio CCSD(T)/CBS approach, which involves the approximation to the complete basis set (CBS) limit at the coupled cluster level with single and double excitations plus quasiperturbative triple excitation [CCSD(T)]. The zero-point vibrational energy correction, the core-valence electronic correction, and the scalar relativistic effect correction are included in these calculations. The present CCSD(T)/CBS results are then compared with the IEs determined in the photoelectron experiment by Schultz et al. [J. Am. Chem. Soc. 106, 7336 (1984)] The predicted IE value (7.881 eV) of 2-methylallyl radical is found to compare very favorably with the experimental value of 7.90+/-0.02 eV. Two ionization transitions for cis-1-methylallyl and trans-1-methylallyl radicals have been considered here. The comparison between the predicted IE values and the previous measurements shows that the photoelectron peak observed by Schultz et al. likely corresponds to the adiabatic ionization transition for the trans-1-methylallyl radical to form trans-1-methylallyl cation. Although a precise IE value for the cyclopropylmethyl radical has not been directly determined, the experimental value deduced indirectly using other known energetic data is found to be in good accord with the present CCSD(T)/CBS prediction. We expect that the Franck-Condon factor for ionization transition of c-C4H7-->bicyclobutonium is much less favorable than that for ionization transition of c-C4H7-->planar-C4H7+, and the observed IE in the previous photoelectron experiment is likely due to the ionization transition for c-C4H7-->planar-C4H7+. Based on our CCSD(T)/CBS prediction, the ionization transition of c-C4H7-->bicyclobutonium with an IE value around 6.92 eV should be taken as the adiabatic ionization transition for the cyclobutyl radical. The present

  4. A comparison of the results of dynamic wind-tunnel tests with theoretical predictions for an aeromechanical gust-alleviation system for light airplanes

    NASA Technical Reports Server (NTRS)

    Stewart, E. C.; Redd, L. T.

    1977-01-01

    Dynamic wind tunnel tests have been conducted on a 1/6-scale model of a general aviation airplane equipped with an all-mechanical gust alleviation system which uses auxiliary aerodynamic surfaces to drive the flaps. The longitudinal short period motions were studied under simulated gust conditions in order to verify the mathematical model used in a previous study to predict the performance of the full scale system and determine the amount of normal acceleration alleviation which could be attained. The model responses were measured for different configurations with the system active and without the system active for comparison. The tests confirmed the general relationships between the experimental variables and the model responses predicted by the mathematical model, but there were significant differences in the magnitudes of the responses. The experimental results for the model were used to estimate a reduction of 30 percent in the rms normal acceleration response of a similar full scale airplane in atmospheric turbulence.

  5. A theoretical comparison of the near-optimum design and predicted performance of n/p and p/n indium phosphide homojunction solar cells

    NASA Technical Reports Server (NTRS)

    Goradia, Chandra; Thesling, William; Weinberg, Irving

    1991-01-01

    Using a detailed simulation model of p(+)nn(+) and n(+)pp(+) indium phosphide (InP) homojunction solar cells, extensive parametric variation computer simulation runs were performed to aid in making near-optimum designs for these two solar cell configurations. The values of all the geometrical and material parameters corresponding to the near-optimal designs of both these configurations are presented. The results of parametric variation runs are presented for each configuration showing how the performance parameters J(sub sc), V(sub oc), and eta vary with each of the cell design parameters for the near-optimally designed cell. Finally, the theoretically obtained results are discussed, and the relative merits and drawbacks of the two configurations are compared.

  6. Theoretical prediction of the effect of heat transfer parameters on cooling rates of liquid-filled plastic straws used for cryopreservation of spermatozoa.

    PubMed

    Sansinen, M; Santos, M V; Zaritzky, N; Baez, R; Chirife, J

    2010-01-01

    Heat transfer plays a key role in cryopreservation of liquid semen in plastic straws. The effect of several parameters on the cooling rate of a liquid-filled polypropylene straw when plunged into liquid nitrogen was investigated using a theoretical model. The geometry of the straw containing the liquid was assimilated as two concentric finite cylinders of different materials: the fluid and the straw; the unsteady-state heat conduction equation for concentric cylinders was numerically solved. Parameters studied include external (convection) heat transfer coefficient (h), the thermal properties of straw manufacturing material and wall thickness. It was concluded that the single most important parameter affecting the cooling rate of a liquid column contained in a straw is the external heat transfer coefficient in LN2. Consequently, in order to attain maximum cooling rates, conditions have to be designed to obtain the highest possible heat transfer coefficient when the plastic straw is plunged in liquid nitrogen.

  7. Predicting hydration Gibbs energies of alkyl-aromatics using molecular simulation: a comparison of current force fields and the development of a new parameter set for accurate solvation data.

    PubMed

    Garrido, Nuno M; Jorge, Miguel; Queimada, António J;