Sample records for accurate experimental potential

  1. Development of accurate potentials to explore the structure of water on 2D materials

    NASA Astrophysics Data System (ADS)

    Bejagam, Karteek; Singh, Samrendra; Deshmukh, Sanket; Deshmkuh Group Team; Samrendra Group Collaboration

    Water play an important role in many biological and non-biological process. Thus structure of water at various interfaces and under confinement has always been the topic of immense interest. 2-D materials have shown great potential in surface coating applications and nanofluidic devices. However, the exact atomic level understanding of the wettability of single layer of these 2-D materials is still lacking mainly due to lack of experimental techniques and computational methodologies including accurate force-field potentials and algorithms to measure the contact angle of water. In the present study, we have developed a new algorithm to measure the accurate contact angle between water and 2-D materials. The algorithm is based on fitting the best sphere to the shape of the droplet. This novel spherical fitting method accounts for every individual molecule of the droplet, rather than those at the surface only. We employ this method of contact angle measurements to develop the accurate non-bonded potentials between water and 2-D materials including graphene and boron nitride (BN) to reproduce the experimentally observed contact angle of water on these 2-D materials. Different water models such as SPC, SPC/Fw, and TIP3P were used to study the structure of water at the interfaces.

  2. The importance of accurate interaction potentials in the melting of argon nanoclusters

    NASA Astrophysics Data System (ADS)

    Pahl, E.; Calvo, F.; Schwerdtfeger, P.

    The melting temperatures of argon clusters ArN (N = 13, 55, 147, 309, 561, and 923) and of bulk argon have been obtained from exchange Monte Carlo simulations and are compared using different two-body interaction potentials, namely the standard Lennard-Jones (LJ), Aziz and extended Lennard-Jones (ELJ) potentials. The latter potential has many advantages: while maintaining the computational efficiency of the commonly used LJ potential, it is as accurate as the Aziz potential but the computer time scales more favorably with increasing cluster size. By applying the ELJ form and extrapolating the cluster data to the infinite system, we are able to extract the melting point of argon already in good agreement with experimental measurements. By considering the additional Axilrod-Teller three-body contribution as well, we calculate a melting temperature of T meltELJ = 84.7 K compared to the experimental value of T meltexp = 83.85 K, whereas the LJ potential underestimates the melting point by more than 7 K. Thus melting temperatures within 1 K accuracy are now feasible.

  3. Water trimer torsional spectrum from accurate ab initio and semiempirical potentials

    NASA Astrophysics Data System (ADS)

    van der Avoird, Ad; Szalewicz, Krzysztof

    2008-01-01

    The torsional levels of (H2O)3 and (D2O)3 were calculated in a restricted dimensionality (three-dimensional) model with several recently proposed water potentials. Comparison with the experimental data provides a critical test, not only of the pair interactions that have already been probed on the water dimer spectra, but also of the nonadditive three-body contributions to the potential. The purely ab initio CC-pol and HBB potentials that were previously shown to yield very accurate water dimer levels, also reproduce the trimer levels well when supplemented with an appropriate three-body interaction potential. The TTM2.1 potential gives considerably less good agreement with experiment. Also the semiempirical VRT(ASP-W)III potential, fitted to the water dimer vibration-rotation-tunneling levels, gives substantial disagreement with the measured water trimer levels, which shows that the latter probe the potential for geometries other than those probed by the dimer spectrum. Although the three-body nonadditive interactions significantly increase the stability of the water trimer, their effect on the torsional energy barriers and vibration-tunneling frequencies is less significant.

  4. Accurate potential drop sheet resistance measurements of laser-doped areas in semiconductors

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Heinrich, Martin, E-mail: mh.seris@gmail.com; NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore 117456; Kluska, Sven

    2014-10-07

    It is investigated how potential drop sheet resistance measurements of areas formed by laser-assisted doping in crystalline Si wafers are affected by typically occurring experimental factors like sample size, inhomogeneities, surface roughness, or coatings. Measurements are obtained with a collinear four point probe setup and a modified transfer length measurement setup to measure sheet resistances of laser-doped lines. Inhomogeneities in doping depth are observed from scanning electron microscope images and electron beam induced current measurements. It is observed that influences from sample size, inhomogeneities, surface roughness, and coatings can be neglected if certain preconditions are met. Guidelines are given onmore » how to obtain accurate potential drop sheet resistance measurements on laser-doped regions.« less

  5. Low-dimensional, morphologically accurate models of subthreshold membrane potential

    PubMed Central

    Kellems, Anthony R.; Roos, Derrick; Xiao, Nan; Cox, Steven J.

    2009-01-01

    The accurate simulation of a neuron’s ability to integrate distributed synaptic input typically requires the simultaneous solution of tens of thousands of ordinary differential equations. For, in order to understand how a cell distinguishes between input patterns we apparently need a model that is biophysically accurate down to the space scale of a single spine, i.e., 1 μm. We argue here that one can retain this highly detailed input structure while dramatically reducing the overall system dimension if one is content to accurately reproduce the associated membrane potential at a small number of places, e.g., at the site of action potential initiation, under subthreshold stimulation. The latter hypothesis permits us to approximate the active cell model with an associated quasi-active model, which in turn we reduce by both time-domain (Balanced Truncation) and frequency-domain (ℋ2 approximation of the transfer function) methods. We apply and contrast these methods on a suite of typical cells, achieving up to four orders of magnitude in dimension reduction and an associated speed-up in the simulation of dendritic democratization and resonance. We also append a threshold mechanism and indicate that this reduction has the potential to deliver an accurate quasi-integrate and fire model. PMID:19172386

  6. Accurate Valence Ionization Energies from Kohn-Sham Eigenvalues with the Help of Potential Adjustors.

    PubMed

    Thierbach, Adrian; Neiss, Christian; Gallandi, Lukas; Marom, Noa; Körzdörfer, Thomas; Görling, Andreas

    2017-10-10

    An accurate yet computationally very efficient and formally well justified approach to calculate molecular ionization potentials is presented and tested. The first as well as higher ionization potentials are obtained as the negatives of the Kohn-Sham eigenvalues of the neutral molecule after adjusting the eigenvalues by a recently [ Görling Phys. Rev. B 2015 , 91 , 245120 ] introduced potential adjustor for exchange-correlation potentials. Technically the method is very simple. Besides a Kohn-Sham calculation of the neutral molecule, only a second Kohn-Sham calculation of the cation is required. The eigenvalue spectrum of the neutral molecule is shifted such that the negative of the eigenvalue of the highest occupied molecular orbital equals the energy difference of the total electronic energies of the cation minus the neutral molecule. For the first ionization potential this simply amounts to a ΔSCF calculation. Then, the higher ionization potentials are obtained as the negatives of the correspondingly shifted Kohn-Sham eigenvalues. Importantly, this shift of the Kohn-Sham eigenvalue spectrum is not just ad hoc. In fact, it is formally necessary for the physically correct energetic adjustment of the eigenvalue spectrum as it results from ensemble density-functional theory. An analogous approach for electron affinities is equally well obtained and justified. To illustrate the practical benefits of the approach, we calculate the valence ionization energies of test sets of small- and medium-sized molecules and photoelectron spectra of medium-sized electron acceptor molecules using a typical semilocal (PBE) and two typical global hybrid functionals (B3LYP and PBE0). The potential adjusted B3LYP and PBE0 eigenvalues yield valence ionization potentials that are in very good agreement with experimental values, reaching an accuracy that is as good as the best G 0 W 0 methods, however, at much lower computational costs. The potential adjusted PBE eigenvalues result in

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Shvab, I.; Sadus, Richard J., E-mail: rsadus@swin.edu.au

    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.more » 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.« less

  8. Latency correction of event-related potentials between different experimental protocols

    NASA Astrophysics Data System (ADS)

    Iturrate, I.; Chavarriaga, R.; Montesano, L.; Minguez, J.; Millán, JdR

    2014-06-01

    Objective. A fundamental issue in EEG event-related potentials (ERPs) studies is the amount of data required to have an accurate ERP model. This also impacts the time required to train a classifier for a brain-computer interface (BCI). This issue is mainly due to the poor signal-to-noise ratio and the large fluctuations of the EEG caused by several sources of variability. One of these sources is directly related to the experimental protocol or application designed, and may affect the amplitude or latency of ERPs. This usually prevents BCI classifiers from generalizing among different experimental protocols. In this paper, we analyze the effect of the amplitude and the latency variations among different experimental protocols based on the same type of ERP. Approach. We present a method to analyze and compensate for the latency variations in BCI applications. The algorithm has been tested on two widely used ERPs (P300 and observation error potentials), in three experimental protocols in each case. We report the ERP analysis and single-trial classification. Main results. The results obtained show that the designed experimental protocols significantly affect the latency of the recorded potentials but not the amplitudes. Significance. These results show how the use of latency-corrected data can be used to generalize the BCIs, reducing the calibration time when facing a new experimental protocol.

  9. Experimental and Theoretical Reduction Potentials of Some Biologically Active ortho-Carbonyl para-Quinones.

    PubMed

    Martínez-Cifuentes, Maximiliano; Salazar, Ricardo; Ramírez-Rodríguez, Oney; Weiss-López, Boris; Araya-Maturana, Ramiro

    2017-04-04

    The rational design of quinones with specific redox properties is an issue of great interest because of their applications in pharmaceutical and material sciences. In this work, the electrochemical behavior of a series of four p -quinones was studied experimentally and theoretically. The first and second one-electron reduction potentials of the quinones were determined using cyclic voltammetry and correlated with those calculated by density functional theory (DFT) using three different functionals, BHandHLYP, M06-2x and PBE0. The differences among the experimental reduction potentials were explained in terms of structural effects on the stabilities of the formed species. DFT calculations accurately reproduced the first one-electron experimental reduction potentials with R ² higher than 0.94. The BHandHLYP functional presented the best fit to the experimental values ( R ² = 0.957), followed by M06-2x ( R ² = 0.947) and PBE0 ( R ² = 0.942).

  10. A highly accurate ab initio potential energy surface for methane.

    PubMed

    Owens, Alec; Yurchenko, Sergei N; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter

    2016-09-14

    A new nine-dimensional potential energy surface (PES) for methane has been generated using state-of-the-art ab initio theory. The PES is based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set limit and incorporates a range of higher-level additive energy corrections. These include core-valence electron correlation, higher-order coupled cluster terms beyond perturbative triples, scalar relativistic effects, and the diagonal Born-Oppenheimer correction. Sub-wavenumber accuracy is achieved for the majority of experimentally known vibrational energy levels with the four fundamentals of (12)CH4 reproduced with a root-mean-square error of 0.70 cm(-1). The computed ab initio equilibrium C-H bond length is in excellent agreement with previous values despite pure rotational energies displaying minor systematic errors as J (rotational excitation) increases. It is shown that these errors can be significantly reduced by adjusting the equilibrium geometry. The PES represents the most accurate ab initio surface to date and will serve as a good starting point for empirical refinement.

  11. Highly accurate potential energy surface for the He-H2 dimer

    NASA Astrophysics Data System (ADS)

    Bakr, Brandon W.; Smith, Daniel G. A.; Patkowski, Konrad

    2013-10-01

    A new highly accurate interaction potential is constructed for the He-H2 van der Waals complex. This potential is fitted to 1900 ab initio energies computed at the very large-basis coupled-cluster level and augmented by corrections for higher-order excitations (up to full configuration interaction level) and the diagonal Born-Oppenheimer correction. At the vibrationally averaged H-H bond length of 1.448736 bohrs, the well depth of our potential, 15.870 ± 0.065 K, is nearly 1 K larger than the most accurate previous studies have indicated. In addition to constructing our own three-dimensional potential in the van der Waals region, we present a reparameterization of the Boothroyd-Martin-Peterson potential surface [A. I. Boothroyd, P. G. Martin, and M. R. Peterson, J. Chem. Phys. 119, 3187 (2003)] that is suitable for all configurations of the triatomic system. Finally, we use the newly developed potentials to compute the properties of the lone bound states of 4He-H2 and 3He-H2 and the interaction second virial coefficient of the hydrogen-helium mixture.

  12. The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures.

    PubMed

    Holton, James M; Classen, Scott; Frankel, Kenneth A; Tainer, John A

    2014-09-01

    In macromolecular crystallography, the agreement between observed and predicted structure factors (Rcryst and Rfree ) is seldom better than 20%. This is much larger than the estimate of experimental error (Rmerge ). The difference between Rcryst and Rmerge is the R-factor gap. There is no such gap in small-molecule crystallography, for which calculated structure factors are generally considered more accurate than the experimental measurements. Perhaps the true noise level of macromolecular data is higher than expected? Or is the gap caused by inaccurate phases that trap refined models in local minima? By generating simulated diffraction patterns using the program MLFSOM, and including every conceivable source of experimental error, we show that neither is the case. Processing our simulated data yielded values that were indistinguishable from those of real data for all crystallographic statistics except the final Rcryst and Rfree . These values decreased to 3.8% and 5.5% for simulated data, suggesting that the reason for high R-factors in macromolecular crystallography is neither experimental error nor phase bias, but rather an underlying inadequacy in the models used to explain our observations. The present inability to accurately represent the entire macromolecule with both its flexibility and its protein-solvent interface may be improved by synergies between small-angle X-ray scattering, computational chemistry and crystallography. The exciting implication of our finding is that macromolecular data contain substantial hidden and untapped potential to resolve ambiguities in the true nature of the nanoscale, a task that the second century of crystallography promises to fulfill. Coordinates and structure factors for the real data have been submitted to the Protein Data Bank under accession 4tws. © 2014 The Authors. FEBS Journal published by John Wiley & Sons Ltd on behalf of FEBS.

  13. Experimental and theoretical oscillator strengths of Mg I for accurate abundance analysis

    NASA Astrophysics Data System (ADS)

    Pehlivan Rhodin, A.; Hartman, H.; Nilsson, H.; Jönsson, P.

    2017-02-01

    Context. With the aid of stellar abundance analysis, it is possible to study the galactic formation and evolution. Magnesium is an important element to trace the α-element evolution in our Galaxy. For chemical abundance analysis, such as magnesium abundance, accurate and complete atomic data are essential. Inaccurate atomic data lead to uncertain abundances and prevent discrimination between different evolution models. Aims: We study the spectrum of neutral magnesium from laboratory measurements and theoretical calculations. Our aim is to improve the oscillator strengths (f-values) of Mg I lines and to create a complete set of accurate atomic data, particularly for the near-IR region. Methods: We derived oscillator strengths by combining the experimental branching fractions with radiative lifetimes reported in the literature and computed in this work. A hollow cathode discharge lamp was used to produce free atoms in the plasma and a Fourier transform spectrometer recorded the intensity-calibrated high-resolution spectra. In addition, we performed theoretical calculations using the multiconfiguration Hartree-Fock program ATSP2K. Results: This project provides a set of experimental and theoretical oscillator strengths. We derived 34 experimental oscillator strengths. Except from the Mg I optical triplet lines (3p 3P°0,1,2-4s 3S1), these oscillator strengths are measured for the first time. The theoretical oscillator strengths are in very good agreement with the experimental data and complement the missing transitions of the experimental data up to n = 7 from even and odd parity terms. We present an evaluated set of oscillator strengths, gf, with uncertainties as small as 5%. The new values of the Mg I optical triplet line (3p 3P°0,1,2-4s 3S1) oscillator strength values are 0.08 dex larger than the previous measurements.

  14. Evaluation of New Reference Genes in Papaya for Accurate Transcript Normalization under Different Experimental Conditions

    PubMed Central

    Chen, Weixin; Chen, Jianye; Lu, Wangjin; Chen, Lei; Fu, Danwen

    2012-01-01

    Real-time reverse transcription PCR (RT-qPCR) is a preferred method for rapid and accurate quantification of gene expression studies. Appropriate application of RT-qPCR requires accurate normalization though the use of reference genes. As no single reference gene is universally suitable for all experiments, thus reference gene(s) validation under different experimental conditions is crucial for RT-qPCR analysis. To date, only a few studies on reference genes have been done in other plants but none in papaya. In the present work, we selected 21 candidate reference genes, and evaluated their expression stability in 246 papaya fruit samples using three algorithms, geNorm, NormFinder and RefFinder. The samples consisted of 13 sets collected under different experimental conditions, including various tissues, different storage temperatures, different cultivars, developmental stages, postharvest ripening, modified atmosphere packaging, 1-methylcyclopropene (1-MCP) treatment, hot water treatment, biotic stress and hormone treatment. Our results demonstrated that expression stability varied greatly between reference genes and that different suitable reference gene(s) or combination of reference genes for normalization should be validated according to the experimental conditions. In general, the internal reference genes EIF (Eukaryotic initiation factor 4A), TBP1 (TATA binding protein 1) and TBP2 (TATA binding protein 2) genes had a good performance under most experimental conditions, whereas the most widely present used reference genes, ACTIN (Actin 2), 18S rRNA (18S ribosomal RNA) and GAPDH (Glyceraldehyde-3-phosphate dehydrogenase) were not suitable in many experimental conditions. In addition, two commonly used programs, geNorm and Normfinder, were proved sufficient for the validation. This work provides the first systematic analysis for the selection of superior reference genes for accurate transcript normalization in papaya under different experimental conditions. PMID

  15. Kinetic determinations of accurate relative oxidation potentials of amines with reactive radical cations.

    PubMed

    Gould, Ian R; Wosinska, Zofia M; Farid, Samir

    2006-01-01

    Accurate oxidation potentials for organic compounds are critical for the evaluation of thermodynamic and kinetic properties of their radical cations. Except when using a specialized apparatus, electrochemical oxidation of molecules with reactive radical cations is usually an irreversible process, providing peak potentials, E(p), rather than thermodynamically meaningful oxidation potentials, E(ox). In a previous study on amines with radical cations that underwent rapid decarboxylation, we estimated E(ox) by correcting the E(p) from cyclic voltammetry with rate constants for decarboxylation obtained using laser flash photolysis. Here we use redox equilibration experiments to determine accurate relative oxidation potentials for the same amines. We also describe an extension of these experiments to show how relative oxidation potentials can be obtained in the absence of equilibrium, from a complete kinetic analysis of the reversible redox kinetics. The results provide support for the previous cyclic voltammetry/laser flash photolysis method for determining oxidation potentials.

  16. Development and application of accurate analytical models for single active electron potentials

    NASA Astrophysics Data System (ADS)

    Miller, Michelle; Jaron-Becker, Agnieszka; Becker, Andreas

    2015-05-01

    The single active electron (SAE) approximation is a theoretical model frequently employed to study scenarios in which inner-shell electrons may productively be treated as frozen spectators to a physical process of interest, and accurate analytical approximations for these potentials are sought as a useful simulation tool. Density function theory is often used to construct a SAE potential, requiring that a further approximation for the exchange correlation functional be enacted. In this study, we employ the Krieger, Li, and Iafrate (KLI) modification to the optimized-effective-potential (OEP) method to reduce the complexity of the problem to the straightforward solution of a system of linear equations through simple arguments regarding the behavior of the exchange-correlation potential in regions where a single orbital dominates. We employ this method for the solution of atomic and molecular potentials, and use the resultant curve to devise a systematic construction for highly accurate and useful analytical approximations for several systems. Supported by the U.S. Department of Energy (Grant No. DE-FG02-09ER16103), and the U.S. National Science Foundation (Graduate Research Fellowship, Grants No. PHY-1125844 and No. PHY-1068706).

  17. Accurate complex scaling of three dimensional numerical potentials

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Cerioni, Alessandro; Genovese, Luigi; Duchemin, Ivan

    2013-05-28

    The complex scaling method, which consists in continuing spatial coordinates into the complex plane, is a well-established method that allows to compute resonant eigenfunctions of the time-independent Schroedinger operator. Whenever it is desirable to apply the complex scaling to investigate resonances in physical systems defined on numerical discrete grids, the most direct approach relies on the application of a similarity transformation to the original, unscaled Hamiltonian. We show that such an approach can be conveniently implemented in the Daubechies wavelet basis set, featuring a very promising level of generality, high accuracy, and no need for artificial convergence parameters. Complex scalingmore » of three dimensional numerical potentials can be efficiently and accurately performed. By carrying out an illustrative resonant state computation in the case of a one-dimensional model potential, we then show that our wavelet-based approach may disclose new exciting opportunities in the field of computational non-Hermitian quantum mechanics.« less

  18. Ab Initio Potential Energy Surfaces and the Calculation of Accurate Vibrational Frequencies

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Dateo, Christopher E.; Martin, Jan M. L.; Taylor, Peter R.; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    Due to advances in quantum mechanical methods over the last few years, it is now possible to determine ab initio potential energy surfaces in which fundamental vibrational frequencies are accurate to within plus or minus 8 cm(exp -1) on average, and molecular bond distances are accurate to within plus or minus 0.001-0.003 Angstroms, depending on the nature of the bond. That is, the potential energy surfaces have not been scaled or empirically adjusted in any way, showing that theoretical methods have progressed to the point of being useful in analyzing spectra that are not from a tightly controlled laboratory environment, such as vibrational spectra from the interstellar medium. Some recent examples demonstrating this accuracy will be presented and discussed. These include the HNO, CH4, C2H4, and ClCN molecules. The HNO molecule is interesting due to the very large H-N anharmonicity, while ClCN has a very large Fermi resonance. The ab initio studies for the CH4 and C2H4 molecules present the first accurate full quartic force fields of any kind (i.e., whether theoretical or empirical) for a five-atom and six-atom system, respectively.

  19. Accurate potential energy, dipole moment curves, and lifetimes of vibrational states of heteronuclear alkali dimers

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Fedorov, Dmitry A.; Varganov, Sergey A., E-mail: svarganov@unr.edu; Derevianko, Andrei

    2014-05-14

    We calculate the potential energy curves, the permanent dipole moment curves, and the lifetimes of the ground and excited vibrational states of the heteronuclear alkali dimers XY (X, Y = Li, Na, K, Rb, Cs) in the X{sup 1}Σ{sup +} electronic state using the coupled cluster with singles doubles and triples method. All-electron quadruple-ζ basis sets with additional core functions are used for Li and Na, and small-core relativistic effective core potentials with quadruple-ζ quality basis sets are used for K, Rb, and Cs. The inclusion of the coupled cluster non-perturbative triple excitations is shown to be crucial for obtainingmore » the accurate potential energy curves. A large one-electron basis set with additional core functions is needed for the accurate prediction of permanent dipole moments. The dissociation energies are overestimated by only 14 cm{sup −1} for LiNa and by no more than 114 cm{sup −1} for the other molecules. The discrepancies between the experimental and calculated harmonic vibrational frequencies are less than 1.7 cm{sup −1}, and the discrepancies for the anharmonic correction are less than 0.1 cm{sup −1}. We show that correlation between atomic electronegativity differences and permanent dipole moment of heteronuclear alkali dimers is not perfect. To obtain the vibrational energies and wave functions the vibrational Schrödinger equation is solved with the B-spline basis set method. The transition dipole moments between all vibrational states, the Einstein coefficients, and the lifetimes of the vibrational states are calculated. We analyze the decay rates of the vibrational states in terms of spontaneous emission, and stimulated emission and absorption induced by black body radiation. In all studied heteronuclear alkali dimers the ground vibrational states have much longer lifetimes than any excited states.« less

  20. Accurate double many-body expansion potential energy surface for the 2(1)A' state of N2O.

    PubMed

    Li, Jing; Varandas, António J C

    2014-08-28

    An accurate double many-body expansion potential energy surface is reported for the 2(1)A' state of N2O. The new double many-body expansion (DMBE) form has been fitted to a wealth of ab initio points that have been calculated at the multi-reference configuration interaction level using the full-valence-complete-active-space wave function as reference and the cc-pVQZ basis set, and subsequently corrected semiempirically via double many-body expansion-scaled external correlation method to extrapolate the calculated energies to the limit of a complete basis set and, most importantly, the limit of an infinite configuration interaction expansion. The topographical features of the novel potential energy surface are then examined in detail and compared with corresponding attributes of other potential functions available in the literature. Exploratory trajectories have also been run on this DMBE form with the quasiclassical trajectory method, with the thermal rate constant so determined at room temperature significantly enhancing agreement with experimental data.

  1. A knowledge-based potential with an accurate description of local interactions improves discrimination between native and near-native protein conformations.

    PubMed

    Ferrada, Evandro; Vergara, Ismael A; Melo, Francisco

    2007-01-01

    The correct discrimination between native and near-native protein conformations is essential for achieving accurate computer-based protein structure prediction. However, this has proven to be a difficult task, since currently available physical energy functions, empirical potentials and statistical scoring functions are still limited in achieving this goal consistently. In this work, we assess and compare the ability of different full atom knowledge-based potentials to discriminate between native protein structures and near-native protein conformations generated by comparative modeling. Using a benchmark of 152 near-native protein models and their corresponding native structures that encompass several different folds, we demonstrate that the incorporation of close non-bonded pairwise atom terms improves the discriminating power of the empirical potentials. Since the direct and unbiased derivation of close non-bonded terms from current experimental data is not possible, we obtained and used those terms from the corresponding pseudo-energy functions of a non-local knowledge-based potential. It is shown that this methodology significantly improves the discrimination between native and near-native protein conformations, suggesting that a proper description of close non-bonded terms is important to achieve a more complete and accurate description of native protein conformations. Some external knowledge-based energy functions that are widely used in model assessment performed poorly, indicating that the benchmark of models and the specific discrimination task tested in this work constitutes a difficult challenge.

  2. Time-Accurate Solutions of Incompressible Navier-Stokes Equations for Potential Turbopump Applications

    NASA Technical Reports Server (NTRS)

    Kiris, Cetin; Kwak, Dochan

    2001-01-01

    Two numerical procedures, one based on artificial compressibility method and the other pressure projection method, are outlined for obtaining time-accurate solutions of the incompressible Navier-Stokes equations. The performance of the two method are compared by obtaining unsteady solutions for the evolution of twin vortices behind a at plate. Calculated results are compared with experimental and other numerical results. For an un- steady ow which requires small physical time step, pressure projection method was found to be computationally efficient since it does not require any subiterations procedure. It was observed that the artificial compressibility method requires a fast convergence scheme at each physical time step in order to satisfy incompressibility condition. This was obtained by using a GMRES-ILU(0) solver in our computations. When a line-relaxation scheme was used, the time accuracy was degraded and time-accurate computations became very expensive.

  3. Accurate double many-body expansion potential energy surface of HS2A2A‧) by scaling the external correlation

    NASA Astrophysics Data System (ADS)

    Lu-Lu, Zhang; Yu-Zhi, Song; Shou-Bao, Gao; Yuan, Zhang; Qing-Tian, Meng

    2016-05-01

    A globally accurate single-sheeted double many-body expansion potential energy surface is reported for the first excited state of HS2 by fitting the accurate ab initio energies, which are calculated at the multireference configuration interaction level with the aug-cc-pVQZ basis set. By using the double many-body expansion-scaled external correlation method, such calculated ab initio energies are then slightly corrected by scaling their dynamical correlation. A grid of 2767 ab initio energies is used in the least-square fitting procedure with the total root-mean square deviation being 1.406 kcal·mol-1. The topographical features of the HS2(A2A‧) global potential energy surface are examined in detail. The attributes of the stationary points are presented and compared with the corresponding ab initio results as well as experimental and other theoretical data, showing good agreement. The resulting potential energy surface of HS2(A2A‧) can be used as a building block for constructing the global potential energy surfaces of larger S/H molecular systems and recommended for dynamic studies on the title molecular system. Project supported by the National Natural Science Foundation of China (Grant No. 11304185), the Taishan Scholar Project of Shandong Province, China, the Shandong Provincial Natural Science Foundation, China (Grant No. ZR2014AM022), the Shandong Province Higher Educational Science and Technology Program, China (Grant No. J15LJ03), the China Postdoctoral Science Foundation (Grant No. 2014M561957), and the Post-doctoral Innovation Project of Shandong Province, China (Grant No. 201402013).

  4. Technical Note: Using experimentally determined proton spot scanning timing parameters to accurately model beam delivery time.

    PubMed

    Shen, Jiajian; Tryggestad, Erik; Younkin, James E; Keole, Sameer R; Furutani, Keith M; Kang, Yixiu; Herman, Michael G; Bues, Martin

    2017-10-01

    To accurately model the beam delivery time (BDT) for a synchrotron-based proton spot scanning system using experimentally determined beam parameters. A model to simulate the proton spot delivery sequences was constructed, and BDT was calculated by summing times for layer switch, spot switch, and spot delivery. Test plans were designed to isolate and quantify the relevant beam parameters in the operation cycle of the proton beam therapy delivery system. These parameters included the layer switch time, magnet preparation and verification time, average beam scanning speeds in x- and y-directions, proton spill rate, and maximum charge and maximum extraction time for each spill. The experimentally determined parameters, as well as the nominal values initially provided by the vendor, served as inputs to the model to predict BDTs for 602 clinical proton beam deliveries. The calculated BDTs (T BDT ) were compared with the BDTs recorded in the treatment delivery log files (T Log ): ∆t = T Log -T BDT . The experimentally determined average layer switch time for all 97 energies was 1.91 s (ranging from 1.9 to 2.0 s for beam energies from 71.3 to 228.8 MeV), average magnet preparation and verification time was 1.93 ms, the average scanning speeds were 5.9 m/s in x-direction and 19.3 m/s in y-direction, the proton spill rate was 8.7 MU/s, and the maximum proton charge available for one acceleration is 2.0 ± 0.4 nC. Some of the measured parameters differed from the nominal values provided by the vendor. The calculated BDTs using experimentally determined parameters matched the recorded BDTs of 602 beam deliveries (∆t = -0.49 ± 1.44 s), which were significantly more accurate than BDTs calculated using nominal timing parameters (∆t = -7.48 ± 6.97 s). An accurate model for BDT prediction was achieved by using the experimentally determined proton beam therapy delivery parameters, which may be useful in modeling the interplay effect and patient throughput. The model may

  5. Communication: An accurate global potential energy surface for the ground electronic state of ozone

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Dawes, Richard, E-mail: dawesr@mst.edu, E-mail: hguo@unm.edu; Lolur, Phalgun; Li, Anyang

    We report a new full-dimensional and global potential energy surface (PES) for the O + O{sub 2} → O{sub 3} ozone forming reaction based on explicitly correlated multireference configuration interaction (MRCI-F12) data. It extends our previous [R. Dawes, P. Lolur, J. Ma, and H. Guo, J. Chem. Phys. 135, 081102 (2011)] dynamically weighted multistate MRCI calculations of the asymptotic region which showed the widely found submerged reef along the minimum energy path to be the spurious result of an avoided crossing with an excited state. A spin-orbit correction was added and the PES tends asymptotically to the recently developed long-rangemore » electrostatic model of Lepers et al. [J. Chem. Phys. 137, 234305 (2012)]. This PES features: (1) excellent equilibrium structural parameters, (2) good agreement with experimental vibrational levels, (3) accurate dissociation energy, and (4) most-notably, a transition region without a spurious reef. The new PES is expected to allow insight into the still unresolved issues surrounding the kinetics, dynamics, and isotope signature of ozone.« less

  6. Accurate atomistic potentials and training sets for boron-nitride nanostructures

    NASA Astrophysics Data System (ADS)

    Tamblyn, Isaac

    Boron nitride nanotubes exhibit exceptional structural, mechanical, and thermal properties. They are optically transparent and have high thermal stability, suggesting a wide range of opportunities for structural reinforcement of materials. Modeling can play an important role in determining the optimal approach to integrating nanotubes into a supporting matrix. Developing accurate, atomistic scale models of such nanoscale interfaces embedded within composites is challenging, however, due to the mismatch of length scales involved. Typical nanotube diameters range from 5-50 nm, with a length as large as a micron (i.e. a relevant length-scale for structural reinforcement). Unlike their carbon-based counterparts, well tested and transferable interatomic force fields are not common for BNNT. In light of this, we have developed an extensive training database of BN rich materials, under conditions relevant for BNNT synthesis and composites based on extensive first principles molecular dynamics simulations. Using this data, we have produced an artificial neural network potential capable of reproducing the accuracy of first principles data at significantly reduced computational cost, allowing for accurate simulation at the much larger length scales needed for composite design.

  7. Energy-switching potential energy surface for the water molecule revisited: A highly accurate singled-sheeted form.

    PubMed

    Galvão, B R L; Rodrigues, S P J; Varandas, A J C

    2008-07-28

    A global ab initio potential energy surface is proposed for the water molecule by energy-switching/merging a highly accurate isotope-dependent local potential function reported by Polyansky et al. [Science 299, 539 (2003)] with a global form of the many-body expansion type suitably adapted to account explicitly for the dynamical correlation and parametrized from extensive accurate multireference configuration interaction energies extrapolated to the complete basis set limit. The new function mimics also the complicated Sigma/Pi crossing that arises at linear geometries of the water molecule.

  8. Constructing simple yet accurate potentials for describing the solvation of HCl/water clusters in bulk helium and nanodroplets.

    PubMed

    Boese, A Daniel; Forbert, Harald; Masia, Marco; Tekin, Adem; Marx, Dominik; Jansen, Georg

    2011-08-28

    The infrared spectroscopy of molecules, complexes, and molecular aggregates dissolved in superfluid helium clusters, commonly called HElium NanoDroplet Isolation (HENDI) spectroscopy, is an established, powerful experimental technique for extracting high resolution ro-vibrational spectra at ultra-low temperatures. Realistic quantum simulations of such systems, in particular in cases where the solute is undergoing a chemical reaction, require accurate solute-helium potentials which are also simple enough to be efficiently evaluated over the vast number of steps required in typical Monte Carlo or molecular dynamics sampling. This precludes using global potential energy surfaces as often parameterized for small complexes in the realm of high-resolution spectroscopic investigations that, in view of the computational effort imposed, are focused on the intermolecular interaction of rigid molecules with helium. Simple Lennard-Jones-like pair potentials, on the other hand, fall short in providing the required flexibility and accuracy in order to account for chemical reactions of the solute molecule. Here, a general scheme of constructing sufficiently accurate site-site potentials for use in typical quantum simulations is presented. This scheme employs atom-based grids, accounts for local and global minima, and is applied to the special case of a HCl(H(2)O)(4) cluster solvated by helium. As a first step, accurate interaction energies of a helium atom with a set of representative configurations sampled from a trajectory following the dissociation of the HCl(H(2)O)(4) cluster were computed using an efficient combination of density functional theory and symmetry-adapted perturbation theory, i.e. the DFT-SAPT approach. For each of the sampled cluster configurations, a helium atom was placed at several hundred positions distributed in space, leading to an overall number of about 400,000 such quantum chemical calculations. The resulting total interaction energies, decomposed into

  9. An accurate and efficient experimental approach for characterization of the complex oral microbiota.

    PubMed

    Zheng, Wei; Tsompana, Maria; Ruscitto, Angela; Sharma, Ashu; Genco, Robert; Sun, Yijun; Buck, Michael J

    2015-10-05

    Currently, taxonomic interrogation of microbiota is based on amplification of 16S rRNA gene sequences in clinical and scientific settings. Accurate evaluation of the microbiota depends heavily on the primers used, and genus/species resolution bias can arise with amplification of non-representative genomic regions. The latest Illumina MiSeq sequencing chemistry has extended the read length to 300 bp, enabling deep profiling of large number of samples in a single paired-end reaction at a fraction of the cost. An increasingly large number of researchers have adopted this technology for various microbiome studies targeting the 16S rRNA V3-V4 hypervariable region. To expand the applicability of this powerful platform for further descriptive and functional microbiome studies, we standardized and tested an efficient, reliable, and straightforward workflow for the amplification, library construction, and sequencing of the 16S V1-V3 hypervariable region using the new 2 × 300 MiSeq platform. Our analysis involved 11 subgingival plaque samples from diabetic and non-diabetic human subjects suffering from periodontitis. The efficiency and reliability of our experimental protocol was compared to 16S V3-V4 sequencing data from the same samples. Comparisons were based on measures of observed taxonomic richness and species evenness, along with Procrustes analyses using beta(β)-diversity distance metrics. As an experimental control, we also analyzed a total of eight technical replicates for the V1-V3 and V3-V4 regions from a synthetic community with known bacterial species operon counts. We show that our experimental protocol accurately measures true bacterial community composition. Procrustes analyses based on unweighted UniFrac β-diversity metrics depicted significant correlation between oral bacterial composition for the V1-V3 and V3-V4 regions. However, measures of phylotype richness were higher for the V1-V3 region, suggesting that V1-V3 offers a deeper assessment of

  10. Experimental Influences in the Accurate Measurement of Cartilage Thickness in MRI.

    PubMed

    Wang, Nian; Badar, Farid; Xia, Yang

    2018-01-01

    Objective To study the experimental influences to the measurement of cartilage thickness by magnetic resonance imaging (MRI). Design The complete thicknesses of healthy and trypsin-degraded cartilage were measured at high-resolution MRI under different conditions, using two intensity-based imaging sequences (ultra-short echo [UTE] and multislice-multiecho [MSME]) and 3 quantitative relaxation imaging sequences (T 1 , T 2 , and T 1 ρ). Other variables included different orientations in the magnet, 2 soaking solutions (saline and phosphate buffered saline [PBS]), and external loading. Results With cartilage soaked in saline, UTE and T 1 methods yielded complete and consistent measurement of cartilage thickness, while the thickness measurement by T 2 , T 1 ρ, and MSME methods were orientation dependent. The effect of external loading on cartilage thickness is also sequence and orientation dependent. All variations in cartilage thickness in MRI could be eliminated with the use of a 100 mM PBS or imaged by UTE sequence. Conclusions The appearance of articular cartilage and the measurement accuracy of cartilage thickness in MRI can be influenced by a number of experimental factors in ex vivo MRI, from the use of various pulse sequences and soaking solutions to the health of the tissue. T 2 -based imaging sequence, both proton-intensity sequence and quantitative relaxation sequence, similarly produced the largest variations. With adequate resolution, the accurate measurement of whole cartilage tissue in clinical MRI could be utilized to detect differences between healthy and osteoarthritic cartilage after compression.

  11. An accurate potential model for the a3Σu+ state of the alkali dimers Na2, K2, Rb2, and Cs2

    NASA Astrophysics Data System (ADS)

    Lau, Jascha A.; Toennies, J. Peter; Tang, K. T.

    2016-11-01

    A modified semi-empirical Tang-Toennies potential model is used to describe the a3Σu+ potentials of the alkali dimers. These potentials are currently of interest in connection with the laser manipulation of the ultracold alkali gases. The fully analytical model is based on three experimental parameters, the well depth De, well location Re, and the harmonic vibrational frequency ωe of which the latter is only slightly optimized within the range of the literature values. Comparison with the latest spectroscopic data shows good agreement for Na2, K2, Rb2, and Cs2, comparable to that found with published potential models with up to 55 parameters. The differences between the reduced potential of Li2 and the conformal reduced potentials of the heavier dimers are analyzed together with why the model describes Li2 less accurately. The new model potential provides a test of the principle of corresponding states and an excellent first order approximation for further optimization to improve the fits to the spectroscopic data and describe the scattering lengths and Feshbach resonances at ultra-low temperatures.

  12. Accurate virial coefficients of gaseous krypton from state-of-the-art ab initio potential and polarizability of the krypton dimer

    NASA Astrophysics Data System (ADS)

    Song, Bo; Waldrop, Jonathan M.; Wang, Xiaopo; Patkowski, Konrad

    2018-01-01

    We have developed a new krypton-krypton interaction-induced isotropic dipole polarizability curve based on high-level ab initio methods. The determination was carried out using the coupled-cluster singles and doubles plus perturbative triples method with very large basis sets up to augmented correlation-consistent sextuple zeta as well as the corrections for core-core and core-valence correlation and relativistic effects. The analytical function of polarizability and our recently constructed reference interatomic potential [J. M. Waldrop et al., J. Chem. Phys. 142, 204307 (2015)] were used to predict the thermophysical and electromagnetic properties of krypton gas. The second pressure, acoustic, and dielectric virial coefficients were computed for the temperature range of 116 K-5000 K using classical statistical mechanics supplemented with high-order quantum corrections. The virial coefficients calculated were compared with the generally less precise available experimental data as well as with values computed from other potentials in the literature {in particular, the recent highly accurate potential of Jäger et al. [J. Chem. Phys. 144, 114304 (2016)]}. The detailed examination in this work suggests that the present theoretical prediction can be applied as reference values in disciplines involving thermophysical and electromagnetic properties of krypton gas.

  13. Competitive Abilities in Experimental Microcosms Are Accurately Predicted by a Demographic Index for R*

    PubMed Central

    Murrell, Ebony G.; Juliano, Steven A.

    2012-01-01

    Resource competition theory predicts that R*, the equilibrium resource amount yielding zero growth of a consumer population, should predict species' competitive abilities for that resource. This concept has been supported for unicellular organisms, but has not been well-tested for metazoans, probably due to the difficulty of raising experimental populations to equilibrium and measuring population growth rates for species with long or complex life cycles. We developed an index (Rindex) of R* based on demography of one insect cohort, growing from egg to adult in a non-equilibrium setting, and tested whether Rindex yielded accurate predictions of competitive abilities using mosquitoes as a model system. We estimated finite rate of increase (λ′) from demographic data for cohorts of three mosquito species raised with different detritus amounts, and estimated each species' Rindex using nonlinear regressions of λ′ vs. initial detritus amount. All three species' Rindex differed significantly, and accurately predicted competitive hierarchy of the species determined in simultaneous pairwise competition experiments. Our Rindex could provide estimates and rigorous statistical comparisons of competitive ability for organisms for which typical chemostat methods and equilibrium population conditions are impractical. PMID:22970128

  14. Temperature dependent effective potential method for accurate free energy calculations of solids

    NASA Astrophysics Data System (ADS)

    Hellman, Olle; Steneteg, Peter; Abrikosov, I. A.; Simak, S. I.

    2013-03-01

    We have developed a thorough and accurate method of determining anharmonic free energies, the temperature dependent effective potential technique (TDEP). It is based on ab initio molecular dynamics followed by a mapping onto a model Hamiltonian that describes the lattice dynamics. The formalism and the numerical aspects of the technique are described in detail. A number of practical examples are given, and results are presented, which confirm the usefulness of TDEP within ab initio and classical molecular dynamics frameworks. In particular, we examine from first principles the behavior of force constants upon the dynamical stabilization of the body centered phase of Zr, and show that they become more localized. We also calculate the phase diagram for 4He modeled with the Aziz potential and obtain results which are in favorable agreement both with respect to experiment and established techniques.

  15. Atomistic simulations of materials: Methods for accurate potentials and realistic time scales

    NASA Astrophysics Data System (ADS)

    Tiwary, Pratyush

    This thesis deals with achieving more realistic atomistic simulations of materials, by developing accurate and robust force-fields, and algorithms for practical time scales. I develop a formalism for generating interatomic potentials for simulating atomistic phenomena occurring at energy scales ranging from lattice vibrations to crystal defects to high-energy collisions. This is done by fitting against an extensive database of ab initio results, as well as to experimental measurements for mixed oxide nuclear fuels. The applicability of these interactions to a variety of mixed environments beyond the fitting domain is also assessed. The employed formalism makes these potentials applicable across all interatomic distances without the need for any ambiguous splining to the well-established short-range Ziegler-Biersack-Littmark universal pair potential. We expect these to be reliable potentials for carrying out damage simulations (and molecular dynamics simulations in general) in nuclear fuels of varying compositions for all relevant atomic collision energies. A hybrid stochastic and deterministic algorithm is proposed that while maintaining fully atomistic resolution, allows one to achieve milliseconds and longer time scales for several thousands of atoms. The method exploits the rare event nature of the dynamics like other such methods, but goes beyond them by (i) not having to pick a scheme for biasing the energy landscape, (ii) providing control on the accuracy of the boosted time scale, (iii) not assuming any harmonic transition state theory (HTST), and (iv) not having to identify collective coordinates or interesting degrees of freedom. The method is validated by calculating diffusion constants for vacancy-mediated diffusion in iron metal at low temperatures, and comparing against brute-force high temperature molecular dynamics. We also calculate diffusion constants for vacancy diffusion in tantalum metal, where we compare against low-temperature HTST as well

  16. ACCURATE SPECTROSCOPIC CHARACTERIZATION OF PROTONATED OXIRANE: A POTENTIAL PREBIOTIC SPECIES IN TITAN'S ATMOSPHERE.

    PubMed

    Puzzarini, Cristina; Ali, Ashraf; Biczysko, Malgorzata; Barone, Vincenzo

    2014-09-10

    An accurate spectroscopic characterization of protonated oxirane has been carried out by means of state-of-the-art computational methods and approaches. The calculated spectroscopic parameters from our recent computational investigation of oxirane together with the corresponding experimental data available were used to assess the accuracy of our predicted rotational and IR spectra of protonated oxirane. We found an accuracy of about 10 cm -1 for vibrational transitions (fundamentals as well as overtones and combination bands) and, in relative terms, of 0.1% for rotational transitions. We are therefore confident that the spectroscopic data provided herein are a valuable support for the detection of protonated oxirane not only in Titan's atmosphere but also in the interstellar medium.

  17. Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Thompson, Aidan P.; Swiler, Laura P.; Trott, Christian R.

    2015-03-15

    Here, we present a new interatomic potential for solids and liquids called Spectral Neighbor Analysis Potential (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected onto a basis of hyperspherical harmonics in four dimensions. The bispectrum components are the same bond-orientational order parameters employed by the GAP potential [1].more » The SNAP potential, unlike GAP, assumes a linear relationship between atom energy and bispectrum components. The linear SNAP coefficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. We demonstrate that a previously unnoticed symmetry property can be exploited to reduce the computational cost of the force calculations by more than one order of magnitude. We present results for a SNAP potential for tantalum, showing that it accurately reproduces a range of commonly calculated properties of both the crystalline solid and the liquid phases. In addition, unlike simpler existing potentials, SNAP correctly predicts the energy barrier for screw dislocation migration in BCC tantalum.« less

  18. Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Thompson, A.P., E-mail: athomps@sandia.gov; Swiler, L.P., E-mail: lpswile@sandia.gov; Trott, C.R., E-mail: crtrott@sandia.gov

    2015-03-15

    We present a new interatomic potential for solids and liquids called Spectral Neighbor Analysis Potential (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected onto a basis of hyperspherical harmonics in four dimensions. The bispectrum components are the same bond-orientational order parameters employed by the GAP potential [1]. Themore » SNAP potential, unlike GAP, assumes a linear relationship between atom energy and bispectrum components. The linear SNAP coefficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. We demonstrate that a previously unnoticed symmetry property can be exploited to reduce the computational cost of the force calculations by more than one order of magnitude. We present results for a SNAP potential for tantalum, showing that it accurately reproduces a range of commonly calculated properties of both the crystalline solid and the liquid phases. In addition, unlike simpler existing potentials, SNAP correctly predicts the energy barrier for screw dislocation migration in BCC tantalum.« less

  19. Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials

    NASA Astrophysics Data System (ADS)

    Thompson, A. P.; Swiler, L. P.; Trott, C. R.; Foiles, S. M.; Tucker, G. J.

    2015-03-01

    We present a new interatomic potential for solids and liquids called Spectral Neighbor Analysis Potential (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected onto a basis of hyperspherical harmonics in four dimensions. The bispectrum components are the same bond-orientational order parameters employed by the GAP potential [1]. The SNAP potential, unlike GAP, assumes a linear relationship between atom energy and bispectrum components. The linear SNAP coefficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. We demonstrate that a previously unnoticed symmetry property can be exploited to reduce the computational cost of the force calculations by more than one order of magnitude. We present results for a SNAP potential for tantalum, showing that it accurately reproduces a range of commonly calculated properties of both the crystalline solid and the liquid phases. In addition, unlike simpler existing potentials, SNAP correctly predicts the energy barrier for screw dislocation migration in BCC tantalum.

  20. Dynamics of the O(3P) + CHD3(vCH = 0,1) reactions on an accurate ab initio potential energy surface

    PubMed Central

    Czakó, Gábor; Bowman, Joel M.

    2012-01-01

    Recent experimental and theoretical studies on the dynamics of the reactions of methane with F and Cl atoms have modified our understanding of mode-selective chemical reactivity. The O + methane reaction is also an important candidate to extend our knowledge on the rules of reactivity. Here, we report a unique full-dimensional ab initio potential energy surface for the O(3P) + methane reaction, which opens the door for accurate dynamics calculations using this surface. Quasiclassical trajectory calculations of the angular and vibrational distributions for the ground state and CH stretching excited O + CHD3(v1 = 0,1) → OH + CD3 reactions are in excellent agreement with the experiment. Our theory confirms what was proposed experimentally: The mechanistic origin of the vibrational enhancement is that the CH-stretching excitation enlarges the reactive cone of acceptance. PMID:22566657

  1. Automated generation of quantum-accurate classical interatomic potentials for metals and semiconductors

    NASA Astrophysics Data System (ADS)

    Thompson, Aidan; Foiles, Stephen; Schultz, Peter; Swiler, Laura; Trott, Christian; Tucker, Garritt

    2013-03-01

    Molecular dynamics (MD) is a powerful condensed matter simulation tool for bridging between macroscopic continuum models and quantum models (QM) treating a few hundred atoms, but is limited by the accuracy of available interatomic potentials. Sound physical and chemical understanding of these interactions have resulted in a variety of concise potentials for certain systems, but it is difficult to extend them to new materials and properties. The growing availability of large QM data sets has made it possible to use more automated machine-learning approaches. Bartók et al. demonstrated that the bispectrum of the local neighbor density provides good regression surrogates for QM models. We adopt a similar bispectrum representation within a linear regression scheme. We have produced potentials for silicon and tantalum, and we are currently extending the method to III-V compounds. Results will be presented demonstrating the accuracy of these potentials relative to the training data, as well as their ability to accurately predict material properties not explicitly included in the training data. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Dept. of Energy Nat. Nuclear Security Admin. under Contract DE-AC04-94AL85000.

  2. Rib biomechanical properties exhibit diagnostic potential for accurate ageing in forensic investigations

    PubMed Central

    Bonicelli, Andrea; Xhemali, Bledar; Kranioti, Elena F.

    2017-01-01

    Age estimation remains one of the most challenging tasks in forensic practice when establishing a biological profile of unknown skeletonised remains. Morphological methods based on developmental markers of bones can provide accurate age estimates at a young age, but become highly unreliable for ages over 35 when all developmental markers disappear. This study explores the changes in the biomechanical properties of bone tissue and matrix, which continue to change with age even after skeletal maturity, and their potential value for age estimation. As a proof of concept we investigated the relationship of 28 variables at the macroscopic and microscopic level in rib autopsy samples from 24 individuals. Stepwise regression analysis produced a number of equations one of which with seven variables showed an R2 = 0.949; a mean residual error of 2.13 yrs ±0.4 (SD) and a maximum residual error value of 2.88 yrs. For forensic purposes, by using only bench top machines in tests which can be carried out within 36 hrs, a set of just 3 variables produced an equation with an R2 = 0.902 a mean residual error of 3.38 yrs ±2.6 (SD) and a maximum observed residual error 9.26yrs. This method outstrips all existing age-at-death methods based on ribs, thus providing a novel lab based accurate tool in the forensic investigation of human remains. The present application is optimised for fresh (uncompromised by taphonomic conditions) remains, but the potential of the principle and method is vast once the trends of the biomechanical variables are established for other environmental conditions and circumstances. PMID:28520764

  3. Accurate Determination of Tunneling-Affected Rate Coefficients: Theory Assessing Experiment.

    PubMed

    Zuo, Junxiang; Xie, Changjian; Guo, Hua; Xie, Daiqian

    2017-07-20

    The thermal rate coefficients of a prototypical bimolecular reaction are determined on an accurate ab initio potential energy surface (PES) using ring polymer molecular dynamics (RPMD). It is shown that quantum effects such as tunneling and zero-point energy (ZPE) are of critical importance for the HCl + OH reaction at low temperatures, while the heavier deuterium substitution renders tunneling less facile in the DCl + OH reaction. The calculated RPMD rate coefficients are in excellent agreement with experimental data for the HCl + OH reaction in the entire temperature range of 200-1000 K, confirming the accuracy of the PES. On the other hand, the RPMD rate coefficients for the DCl + OH reaction agree with some, but not all, experimental values. The self-consistency of the theoretical results thus allows a quality assessment of the experimental data.

  4. Toward Hamiltonian Adaptive QM/MM: Accurate Solvent Structures Using Many-Body Potentials.

    PubMed

    Boereboom, Jelle M; Potestio, Raffaello; Donadio, Davide; Bulo, Rosa E

    2016-08-09

    Adaptive quantum mechanical (QM)/molecular mechanical (MM) methods enable efficient molecular simulations of chemistry in solution. Reactive subregions are modeled with an accurate QM potential energy expression while the rest of the system is described in a more approximate manner (MM). As solvent molecules diffuse in and out of the reactive region, they are gradually included into (and excluded from) the QM expression. It would be desirable to model such a system with a single adaptive Hamiltonian, but thus far this has resulted in distorted structures at the boundary between the two regions. Solving this long outstanding problem will allow microcanonical adaptive QM/MM simulations that can be used to obtain vibrational spectra and dynamical properties. The difficulty lies in the complex QM potential energy expression, with a many-body expansion that contains higher order terms. Here, we outline a Hamiltonian adaptive multiscale scheme within the framework of many-body potentials. The adaptive expressions are entirely general, and complementary to all standard (nonadaptive) QM/MM embedding schemes available. We demonstrate the merit of our approach on a molecular system defined by two different MM potentials (MM/MM'). For the long-range interactions a numerical scheme is used (particle mesh Ewald), which yields energy expressions that are many-body in nature. Our Hamiltonian approach is the first to provide both energy conservation and the correct solvent structure everywhere in this system.

  5. Accurate quantum wave packet calculations for the F + HCl → Cl + HF reaction on the ground 1(2)A' potential energy surface.

    PubMed

    Bulut, Niyazi; Kłos, Jacek; Alexander, Millard H

    2012-03-14

    We present converged exact quantum wave packet calculations of reaction probabilities, integral cross sections, and thermal rate coefficients for the title reaction. Calculations have been carried out on the ground 1(2)A' global adiabatic potential energy surface of Deskevich et al. [J. Chem. Phys. 124, 224303 (2006)]. Converged wave packet reaction probabilities at selected values of the total angular momentum up to a partial wave of J = 140 with the HCl reagent initially selected in the v = 0, j = 0-16 rovibrational states have been obtained for the collision energy range from threshold up to 0.8 eV. The present calculations confirm an important enhancement of reactivity with rotational excitation of the HCl molecule. First, accurate integral cross sections and rate constants have been calculated and compared with the available experimental data.

  6. Noniterative accurate algorithm for the exact exchange potential of density-functional theory

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Cinal, M.; Holas, A.

    2007-10-15

    An algorithm for determination of the exchange potential is constructed and tested. It represents a one-step procedure based on the equations derived by Krieger, Li, and Iafrate (KLI) [Phys. Rev. A 46, 5453 (1992)], implemented already as an iterative procedure by Kuemmel and Perdew [Phys. Rev. Lett. 90, 043004 (2003)]. Due to suitable transformation of the KLI equations, we can solve them avoiding iterations. Our algorithm is applied to the closed-shell atoms, from Be up to Kr, within the DFT exchange-only approximation. Using pseudospectral techniques for representing orbitals, we obtain extremely accurate values of total and orbital energies with errorsmore » at least four orders of magnitude smaller than known in the literature.« less

  7. Programmable Potentials: Approximate N-body potentials from coarse-level logic.

    PubMed

    Thakur, Gunjan S; Mohr, Ryan; Mezić, Igor

    2016-09-27

    This paper gives a systematic method for constructing an N-body potential, approximating the true potential, that accurately captures meso-scale behavior of the chemical or biological system using pairwise potentials coming from experimental data or ab initio methods. The meso-scale behavior is translated into logic rules for the dynamics. Each pairwise potential has an associated logic function that is constructed using the logic rules, a class of elementary logic functions, and AND, OR, and NOT gates. The effect of each logic function is to turn its associated potential on and off. The N-body potential is constructed as linear combination of the pairwise potentials, where the "coefficients" of the potentials are smoothed versions of the associated logic functions. These potentials allow a potentially low-dimensional description of complex processes while still accurately capturing the relevant physics at the meso-scale. We present the proposed formalism to construct coarse-grained potential models for three examples: an inhibitor molecular system, bond breaking in chemical reactions, and DNA transcription from biology. The method can potentially be used in reverse for design of molecular processes by specifying properties of molecules that can carry them out.

  8. Programmable Potentials: Approximate N-body potentials from coarse-level logic

    NASA Astrophysics Data System (ADS)

    Thakur, Gunjan S.; Mohr, Ryan; Mezić, Igor

    2016-09-01

    This paper gives a systematic method for constructing an N-body potential, approximating the true potential, that accurately captures meso-scale behavior of the chemical or biological system using pairwise potentials coming from experimental data or ab initio methods. The meso-scale behavior is translated into logic rules for the dynamics. Each pairwise potential has an associated logic function that is constructed using the logic rules, a class of elementary logic functions, and AND, OR, and NOT gates. The effect of each logic function is to turn its associated potential on and off. The N-body potential is constructed as linear combination of the pairwise potentials, where the “coefficients” of the potentials are smoothed versions of the associated logic functions. These potentials allow a potentially low-dimensional description of complex processes while still accurately capturing the relevant physics at the meso-scale. We present the proposed formalism to construct coarse-grained potential models for three examples: an inhibitor molecular system, bond breaking in chemical reactions, and DNA transcription from biology. The method can potentially be used in reverse for design of molecular processes by specifying properties of molecules that can carry them out.

  9. Programmable Potentials: Approximate N-body potentials from coarse-level logic

    PubMed Central

    Thakur, Gunjan S.; Mohr, Ryan; Mezić, Igor

    2016-01-01

    This paper gives a systematic method for constructing an N-body potential, approximating the true potential, that accurately captures meso-scale behavior of the chemical or biological system using pairwise potentials coming from experimental data or ab initio methods. The meso-scale behavior is translated into logic rules for the dynamics. Each pairwise potential has an associated logic function that is constructed using the logic rules, a class of elementary logic functions, and AND, OR, and NOT gates. The effect of each logic function is to turn its associated potential on and off. The N-body potential is constructed as linear combination of the pairwise potentials, where the “coefficients” of the potentials are smoothed versions of the associated logic functions. These potentials allow a potentially low-dimensional description of complex processes while still accurately capturing the relevant physics at the meso-scale. We present the proposed formalism to construct coarse-grained potential models for three examples: an inhibitor molecular system, bond breaking in chemical reactions, and DNA transcription from biology. The method can potentially be used in reverse for design of molecular processes by specifying properties of molecules that can carry them out. PMID:27671683

  10. Toward Accurate and Quantitative Comparative Metagenomics

    PubMed Central

    Nayfach, Stephen; Pollard, Katherine S.

    2016-01-01

    Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. PMID:27565341

  11. An Accurate New Potential Function for Ground-State X{e}_2 from UV and Virial Coefficient Data

    NASA Astrophysics Data System (ADS)

    Le Roy, Robert J.; Mackie, J. Cameron; Chandrasekhar, Pragna

    2011-06-01

    Determining accurate analytic pair potentials for rare gas dimers has been a longstanding goal in molecular physics. However, most potential energy functions reported to date fail to optimally represent the available spectroscopic data, in spite of the fact that such data provide constraints of unparalleled precision on the attractive potential energy wells of these species. A recent study of ArXe showed that it is a straightforward matter to combine multi-isotopologue spectroscopic data (in that case, microwave, and high resolution UV measurements) and virial coefficients in a direct fit to obtain a flexible analytic potential function that incorporates the theoretically predicted damped inverse-power long-range behaviour. The present work reports the application of this approach to Xe_2, with a direct fit to high resolution rotationally resolved UV emission data for v''=0 and 1, band head data for v''=0-9, and virial coefficient data for T=165-950 K being used to obtain an accurate new potential energy function for the ground state of this Van der Waals molecule. Analogous results for other rare-gas pairs will also be presented, as time permits. L. Piticco, F. Merkt, A.A. Cholewinski, F.R. McCourt and R.J. Le Roy, J. Mol. Spectrosc. 264, 83 (2010). A. Wüest and K.G. Bruin and F. Merkt, Can. J. Chem. 82, 750 (2004). D.E. Freeman, K. Yoshino, and Y. Tanaka, J. Chem. Phys. 61, 4880 (1974). J.H. Dymond, K.N. Marsh, R.C. Wilhoit and K.C. Wong, in Landold-Börnstein, New Series, Group IV, edited by M. Frenkel and K.N. Marsh, Vol. 21 (2003).

  12. Experimental demonstration of cheap and accurate phase estimation

    NASA Astrophysics Data System (ADS)

    Rudinger, Kenneth; Kimmel, Shelby; Lobser, Daniel; Maunz, Peter

    We demonstrate experimental implementation of robust phase estimation (RPE) to learn the phases of X and Y rotations on a trapped Yb+ ion qubit.. Unlike many other phase estimation protocols, RPE does not require ancillae nor near-perfect state preparation and measurement operations. Additionally, its computational requirements are minimal. Via RPE, using only 352 experimental samples per phase, we estimate phases of implemented gates with errors as small as 10-4 radians, as validated using gate set tomography. We also demonstrate that these estimates exhibit Heisenberg scaling in accuracy. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  13. Predicting vapor-liquid phase equilibria with augmented ab initio interatomic potentials

    NASA Astrophysics Data System (ADS)

    Vlasiuk, Maryna; Sadus, Richard J.

    2017-06-01

    The ability of ab initio interatomic potentials to accurately predict vapor-liquid phase equilibria is investigated. Monte Carlo simulations are reported for the vapor-liquid equilibria of argon and krypton using recently developed accurate ab initio interatomic potentials. Seventeen interatomic potentials are studied, formulated from different combinations of two-body plus three-body terms. The simulation results are compared to either experimental or reference data for conditions ranging from the triple point to the critical point. It is demonstrated that the use of ab initio potentials enables systematic improvements to the accuracy of predictions via the addition of theoretically based terms. The contribution of three-body interactions is accounted for using the Axilrod-Teller-Muto plus other multipole contributions and the effective Marcelli-Wang-Sadus potentials. The results indicate that the predictive ability of recent interatomic potentials, obtained from quantum chemical calculations, is comparable to that of accurate empirical models. It is demonstrated that the Marcelli-Wang-Sadus potential can be used in combination with accurate two-body ab initio models for the computationally inexpensive and accurate estimation of vapor-liquid phase equilibria.

  14. Predicting vapor-liquid phase equilibria with augmented ab initio interatomic potentials.

    PubMed

    Vlasiuk, Maryna; Sadus, Richard J

    2017-06-28

    The ability of ab initio interatomic potentials to accurately predict vapor-liquid phase equilibria is investigated. Monte Carlo simulations are reported for the vapor-liquid equilibria of argon and krypton using recently developed accurate ab initio interatomic potentials. Seventeen interatomic potentials are studied, formulated from different combinations of two-body plus three-body terms. The simulation results are compared to either experimental or reference data for conditions ranging from the triple point to the critical point. It is demonstrated that the use of ab initio potentials enables systematic improvements to the accuracy of predictions via the addition of theoretically based terms. The contribution of three-body interactions is accounted for using the Axilrod-Teller-Muto plus other multipole contributions and the effective Marcelli-Wang-Sadus potentials. The results indicate that the predictive ability of recent interatomic potentials, obtained from quantum chemical calculations, is comparable to that of accurate empirical models. It is demonstrated that the Marcelli-Wang-Sadus potential can be used in combination with accurate two-body ab initio models for the computationally inexpensive and accurate estimation of vapor-liquid phase equilibria.

  15. Mixed Potentials: Experimental Illustrations of an Important Concept in Practical Electrochemistry.

    ERIC Educational Resources Information Center

    Power, G. P.; Ritchie, I. M.

    1983-01-01

    Presents a largely experimental approach to the concept of mixed potentials, pointing out the close parallel that exists between equilibrium potentials. Describes several important examples of mixed potentials, providing current-voltage and polarization curves and half reactions as examples. Includes a discussion of corrosion reactions and…

  16. Toward Accurate and Quantitative Comparative Metagenomics.

    PubMed

    Nayfach, Stephen; Pollard, Katherine S

    2016-08-25

    Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. Copyright © 2016 Elsevier Inc. All rights reserved.

  17. Accurate thermoelastic tensor and acoustic velocities of NaCl

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Marcondes, Michel L., E-mail: michel@if.usp.br; Chemical Engineering and Material Science, University of Minnesota, Minneapolis, 55455; Shukla, Gaurav, E-mail: shukla@physics.umn.edu

    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 bymore » 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.« less

  18. Experimental Demonstration of a Cheap and Accurate Phase Estimation

    DOE PAGES

    Rudinger, Kenneth; Kimmel, Shelby; Lobser, Daniel; ...

    2017-05-11

    We demonstrate an experimental implementation of robust phase estimation (RPE) to learn the phase of a single-qubit rotation on a trapped Yb + ion qubit. Here, we show this phase can be estimated with an uncertainty below 4 × 10 -4 rad using as few as 176 total experimental samples, and our estimates exhibit Heisenberg scaling. Unlike standard phase estimation protocols, RPE neither assumes perfect state preparation and measurement, nor requires access to ancillae. We crossvalidate the results of RPE with the more resource-intensive protocol of gate set tomography.

  19. Prediction of Reduction Potentials of Copper Proteins with Continuum Electrostatics and Density Functional Theory

    PubMed Central

    Fowler, Nicholas J.; Blanford, Christopher F.

    2017-01-01

    Abstract Blue copper proteins, such as azurin, show dramatic changes in Cu2+/Cu+ reduction potential upon mutation over the full physiological range. Hence, they have important functions in electron transfer and oxidation chemistry and have applications in industrial biotechnology. The details of what determines these reduction potential changes upon mutation are still unclear. Moreover, it has been difficult to model and predict the reduction potential of azurin mutants and currently no unique procedure or workflow pattern exists. Furthermore, high‐level computational methods can be accurate but are too time consuming for practical use. In this work, a novel approach for calculating reduction potentials of azurin mutants is shown, based on a combination of continuum electrostatics, density functional theory and empirical hydrophobicity factors. Our method accurately reproduces experimental reduction potential changes of 30 mutants with respect to wildtype within experimental error and highlights the factors contributing to the reduction potential change. Finally, reduction potentials are predicted for a series of 124 new mutants that have not yet been investigated experimentally. Several mutants are identified that are located well over 10 Å from the copper center that change the reduction potential by more than 85 mV. The work shows that secondary coordination sphere mutations mostly lead to long‐range electrostatic changes and hence can be modeled accurately with continuum electrostatics. PMID:28815759

  20. A rabbit ventricular action potential model replicating cardiac dynamics at rapid heart rates.

    PubMed

    Mahajan, Aman; Shiferaw, Yohannes; Sato, Daisuke; Baher, Ali; Olcese, Riccardo; Xie, Lai-Hua; Yang, Ming-Jim; Chen, Peng-Sheng; Restrepo, Juan G; Karma, Alain; Garfinkel, Alan; Qu, Zhilin; Weiss, James N

    2008-01-15

    Mathematical modeling of the cardiac action potential has proven to be a powerful tool for illuminating various aspects of cardiac function, including cardiac arrhythmias. However, no currently available detailed action potential model accurately reproduces the dynamics of the cardiac action potential and intracellular calcium (Ca(i)) cycling at rapid heart rates relevant to ventricular tachycardia and fibrillation. The aim of this study was to develop such a model. Using an existing rabbit ventricular action potential model, we modified the L-type calcium (Ca) current (I(Ca,L)) and Ca(i) cycling formulations based on new experimental patch-clamp data obtained in isolated rabbit ventricular myocytes, using the perforated patch configuration at 35-37 degrees C. Incorporating a minimal seven-state Markovian model of I(Ca,L) that reproduced Ca- and voltage-dependent kinetics in combination with our previously published dynamic Ca(i) cycling model, the new model replicates experimentally observed action potential duration and Ca(i) transient alternans at rapid heart rates, and accurately reproduces experimental action potential duration restitution curves obtained by either dynamic or S1S2 pacing.

  1. Accurate prediction of secondary metabolite gene clusters in filamentous fungi.

    PubMed

    Andersen, Mikael R; Nielsen, Jakob B; Klitgaard, Andreas; Petersen, Lene M; Zachariasen, Mia; Hansen, Tilde J; Blicher, Lene H; Gotfredsen, Charlotte H; Larsen, Thomas O; Nielsen, Kristian F; Mortensen, Uffe H

    2013-01-02

    Biosynthetic pathways of secondary metabolites from fungi are currently subject to an intense effort to elucidate the genetic basis for these compounds due to their large potential within pharmaceutics and synthetic biochemistry. The preferred method is methodical gene deletions to identify supporting enzymes for key synthases one cluster at a time. In this study, we design and apply a DNA expression array for Aspergillus nidulans in combination with legacy data to form a comprehensive gene expression compendium. We apply a guilt-by-association-based analysis to predict the extent of the biosynthetic clusters for the 58 synthases active in our set of experimental conditions. A comparison with legacy data shows the method to be accurate in 13 of 16 known clusters and nearly accurate for the remaining 3 clusters. Furthermore, we apply a data clustering approach, which identifies cross-chemistry between physically separate gene clusters (superclusters), and validate this both with legacy data and experimentally by prediction and verification of a supercluster consisting of the synthase AN1242 and the prenyltransferase AN11080, as well as identification of the product compound nidulanin A. We have used A. nidulans for our method development and validation due to the wealth of available biochemical data, but the method can be applied to any fungus with a sequenced and assembled genome, thus supporting further secondary metabolite pathway elucidation in the fungal kingdom.

  2. Efficacy of clavulanate-potentiated amoxycillin in experimental and clinical skin infections.

    PubMed

    Bywater, R J; Hewett, G R; Marshall, A B; West, B

    1985-02-16

    The efficacy of clavulanate-potentiated amoxycillin was compared with amoxycillin alone in experimental staphylococcal infection in dogs and in a controlled trial in clinical cases of skin infection in dogs and cats. The experimental infection was produced by subdermal inoculation with beta-lactamase producing (amoxycillin resistant) staphylococci absorbed in cotton dust. This produced discrete, localised lesions with no systemic involvement. In a cross over study, six animals were randomly allocated to treatment with either amoxycillin alone (10 mg/kg, dosed twice daily) or a formulation of clavulanate-potentiated amoxycillin (12.5 mg/kg, of a 1:4 ratio, dosed twice daily). The lesions of the animals treated with clavulanate-potentiated amoxycillin resolved more quickly than those treated with amoxycillin alone. The difference was significant (P less than 0.05) for both lesion diameter and inflammation score after day 6 of treatment. A trial was carried out in clinical cases of skin disease which were randomly allocated to twice daily treatment with either amoxycillin alone (10 or 20 mg/kg), or with clavulanate-potentiated amoxycillin (12.5 or 25 mg/kg of a 1:4 ratio). The required duration of treatment was shorter (P less than 0.5) for the potentiated amoxycillin treatments, and the success rate (judged by cure or substantial improvement) was higher (P less than 0.05) for this group, especially (P less than 0.01) where amoxycillin resistant organisms were isolated. It was concluded that clavulanate-potentiated amoxycillin was an effective treatment of skin infections both under experimental and clinical conditions.

  3. Accurate structural and spectroscopic characterization of prebiotic molecules: The neutral and cationic acetyl cyanide and their related species.

    PubMed

    Bellili, A; Linguerri, R; Hochlaf, M; Puzzarini, C

    2015-11-14

    In an effort to provide an accurate structural and spectroscopic characterization of acetyl cyanide, its two enolic isomers and the corresponding cationic species, state-of-the-art computational methods, and approaches have been employed. The coupled-cluster theory including single and double excitations together with a perturbative treatment of triples has been used as starting point in composite schemes accounting for extrapolation to the complete basis-set limit as well as core-valence correlation effects to determine highly accurate molecular structures, fundamental vibrational frequencies, and rotational parameters. The available experimental data for acetyl cyanide allowed us to assess the reliability of our computations: structural, energetic, and spectroscopic properties have been obtained with an overall accuracy of about, or better than, 0.001 Å, 2 kcal/mol, 1-10 MHz, and 11 cm(-1) for bond distances, adiabatic ionization potentials, rotational constants, and fundamental vibrational frequencies, respectively. We are therefore confident that the highly accurate spectroscopic data provided herein can be useful for guiding future experimental investigations and/or astronomical observations.

  4. Ensemble MD simulations restrained via crystallographic data: Accurate structure leads to accurate dynamics

    PubMed Central

    Xue, Yi; Skrynnikov, Nikolai R

    2014-01-01

    Currently, the best existing molecular dynamics (MD) force fields cannot accurately reproduce the global free-energy minimum which realizes the experimental protein structure. As a result, long MD trajectories tend to drift away from the starting coordinates (e.g., crystallographic structures). To address this problem, we have devised a new simulation strategy aimed at protein crystals. An MD simulation of protein crystal is essentially an ensemble simulation involving multiple protein molecules in a crystal unit cell (or a block of unit cells). To ensure that average protein coordinates remain correct during the simulation, we introduced crystallography-based restraints into the MD protocol. Because these restraints are aimed at the ensemble-average structure, they have only minimal impact on conformational dynamics of the individual protein molecules. So long as the average structure remains reasonable, the proteins move in a native-like fashion as dictated by the original force field. To validate this approach, we have used the data from solid-state NMR spectroscopy, which is the orthogonal experimental technique uniquely sensitive to protein local dynamics. The new method has been tested on the well-established model protein, ubiquitin. The ensemble-restrained MD simulations produced lower crystallographic R factors than conventional simulations; they also led to more accurate predictions for crystallographic temperature factors, solid-state chemical shifts, and backbone order parameters. The predictions for 15N R1 relaxation rates are at least as accurate as those obtained from conventional simulations. Taken together, these results suggest that the presented trajectories may be among the most realistic protein MD simulations ever reported. In this context, the ensemble restraints based on high-resolution crystallographic data can be viewed as protein-specific empirical corrections to the standard force fields. PMID:24452989

  5. Prediction of Reduction Potentials of Copper Proteins with Continuum Electrostatics and Density Functional Theory.

    PubMed

    Fowler, Nicholas J; Blanford, Christopher F; Warwicker, Jim; de Visser, Sam P

    2017-11-02

    Blue copper proteins, such as azurin, show dramatic changes in Cu 2+ /Cu + reduction potential upon mutation over the full physiological range. Hence, they have important functions in electron transfer and oxidation chemistry and have applications in industrial biotechnology. The details of what determines these reduction potential changes upon mutation are still unclear. Moreover, it has been difficult to model and predict the reduction potential of azurin mutants and currently no unique procedure or workflow pattern exists. Furthermore, high-level computational methods can be accurate but are too time consuming for practical use. In this work, a novel approach for calculating reduction potentials of azurin mutants is shown, based on a combination of continuum electrostatics, density functional theory and empirical hydrophobicity factors. Our method accurately reproduces experimental reduction potential changes of 30 mutants with respect to wildtype within experimental error and highlights the factors contributing to the reduction potential change. Finally, reduction potentials are predicted for a series of 124 new mutants that have not yet been investigated experimentally. Several mutants are identified that are located well over 10 Å from the copper center that change the reduction potential by more than 85 mV. The work shows that secondary coordination sphere mutations mostly lead to long-range electrostatic changes and hence can be modeled accurately with continuum electrostatics. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  6. Development of a machine learning potential for graphene

    NASA Astrophysics Data System (ADS)

    Rowe, Patrick; Csányi, Gábor; Alfè, Dario; Michaelides, Angelos

    2018-02-01

    We present an accurate interatomic potential for graphene, constructed using the Gaussian approximation potential (GAP) machine learning methodology. This GAP model obtains a faithful representation of a density functional theory (DFT) potential energy surface, facilitating highly accurate (approaching the accuracy of ab initio methods) molecular dynamics simulations. This is achieved at a computational cost which is orders of magnitude lower than that of comparable calculations which directly invoke electronic structure methods. We evaluate the accuracy of our machine learning model alongside that of a number of popular empirical and bond-order potentials, using both experimental and ab initio data as references. We find that whilst significant discrepancies exist between the empirical interatomic potentials and the reference data—and amongst the empirical potentials themselves—the machine learning model introduced here provides exemplary performance in all of the tested areas. The calculated properties include: graphene phonon dispersion curves at 0 K (which we predict with sub-meV accuracy), phonon spectra at finite temperature, in-plane thermal expansion up to 2500 K as compared to NPT ab initio molecular dynamics simulations and a comparison of the thermally induced dispersion of graphene Raman bands to experimental observations. We have made our potential freely available online at [http://www.libatoms.org].

  7. Accurate Monitoring and Fault Detection in Wind Measuring Devices through Wireless Sensor Networks

    PubMed Central

    Khan, Komal Saifullah; Tariq, Muhammad

    2014-01-01

    Many wind energy projects report poor performance as low as 60% of the predicted performance. The reason for this is poor resource assessment and the use of new untested technologies and systems in remote locations. Predictions about the potential of an area for wind energy projects (through simulated models) may vary from the actual potential of the area. Hence, introducing accurate site assessment techniques will lead to accurate predictions of energy production from a particular area. We solve this problem by installing a Wireless Sensor Network (WSN) to periodically analyze the data from anemometers installed in that area. After comparative analysis of the acquired data, the anemometers transmit their readings through a WSN to the sink node for analysis. The sink node uses an iterative algorithm which sequentially detects any faulty anemometer and passes the details of the fault to the central system or main station. We apply the proposed technique in simulation as well as in practical implementation and study its accuracy by comparing the simulation results with experimental results to analyze the variation in the results obtained from both simulation model and implemented model. Simulation results show that the algorithm indicates faulty anemometers with high accuracy and low false alarm rate when as many as 25% of the anemometers become faulty. Experimental analysis shows that anemometers incorporating this solution are better assessed and performance level of implemented projects is increased above 86% of the simulated models. PMID:25421739

  8. Toward spectroscopically accurate global ab initio potential energy surface for the acetylene-vinylidene isomerization

    NASA Astrophysics Data System (ADS)

    Han, Huixian; Li, Anyang; Guo, Hua

    2014-12-01

    A new full-dimensional global potential energy surface (PES) for the acetylene-vinylidene isomerization on the ground (S0) electronic state has been constructed by fitting ˜37 000 high-level ab initio points using the permutation invariant polynomial-neural network method with a root mean square error of 9.54 cm-1. The geometries and harmonic vibrational frequencies of acetylene, vinylidene, and all other stationary points (two distinct transition states and one secondary minimum in between) have been determined on this PES. Furthermore, acetylene vibrational energy levels have been calculated using the Lanczos algorithm with an exact (J = 0) Hamiltonian. The vibrational energies up to 12 700 cm-1 above the zero-point energy are in excellent agreement with the experimentally derived effective Hamiltonians, suggesting that the PES is approaching spectroscopic accuracy. In addition, analyses of the wavefunctions confirm the experimentally observed emergence of the local bending and counter-rotational modes in the highly excited bending vibrational states. The reproduction of the experimentally derived effective Hamiltonians for highly excited bending states signals the coming of age for the ab initio based PES, which can now be trusted for studying the isomerization reaction.

  9. Accurate Vibrational-Rotational Parameters and Infrared Intensities of 1-Bromo-1-fluoroethene: A Joint Experimental Analysis and Ab Initio Study.

    PubMed

    Pietropolli Charmet, Andrea; Stoppa, Paolo; Giorgianni, Santi; Bloino, Julien; Tasinato, Nicola; Carnimeo, Ivan; Biczysko, Malgorzata; Puzzarini, Cristina

    2017-05-04

    The medium-resolution gas-phase infrared (IR) spectra of 1-bromo-1-fluoroethene (BrFC═CH 2 , 1,1-C 2 H 2 BrF) were investigated in the range 300-6500 cm -1 , and the vibrational analysis led to the assignment of all fundamentals as well as many overtone and combination bands up to three quanta, thus giving an accurate description of its vibrational structure. Integrated band intensity data were determined with high precision from the measurements of their corresponding absorption cross sections. The vibrational analysis was supported by high-level ab initio investigations. CCSD(T) computations accounting for extrapolation to the complete basis set and core correlation effects were employed to accurately determine the molecular structure and harmonic force field. The latter was then coupled to B2PLYP and MP2 computations in order to account for mechanical and electrical anharmonicities. Second-order perturbative vibrational theory was then applied to the thus obtained hybrid force fields to support the experimental assignment of the IR spectra.

  10. Excitation energies from particle-particle random phase approximation with accurate optimized effective potentials

    NASA Astrophysics Data System (ADS)

    Jin, Ye; Yang, Yang; Zhang, Du; Peng, Degao; Yang, Weitao

    2017-10-01

    The optimized effective potential (OEP) that gives accurate Kohn-Sham (KS) orbitals and orbital energies can be obtained from a given reference electron density. These OEP-KS orbitals and orbital energies are used here for calculating electronic excited states with the particle-particle random phase approximation (pp-RPA). Our calculations allow the examination of pp-RPA excitation energies with the exact KS density functional theory (DFT). Various input densities are investigated. Specifically, the excitation energies using the OEP with the electron densities from the coupled-cluster singles and doubles method display the lowest mean absolute error from the reference data for the low-lying excited states. This study probes into the theoretical limit of the pp-RPA excitation energies with the exact KS-DFT orbitals and orbital energies. We believe that higher-order correlation contributions beyond the pp-RPA bare Coulomb kernel are needed in order to achieve even higher accuracy in excitation energy calculations.

  11. Correlative imaging across microscopy platforms using the fast and accurate relocation of microscopic experimental regions (FARMER) method

    NASA Astrophysics Data System (ADS)

    Huynh, Toan; Daddysman, Matthew K.; Bao, Ying; Selewa, Alan; Kuznetsov, Andrey; Philipson, Louis H.; Scherer, Norbert F.

    2017-05-01

    Imaging specific regions of interest (ROIs) of nanomaterials or biological samples with different imaging modalities (e.g., light and electron microscopy) or at subsequent time points (e.g., before and after off-microscope procedures) requires relocating the ROIs. Unfortunately, relocation is typically difficult and very time consuming to achieve. Previously developed techniques involve the fabrication of arrays of features, the procedures for which are complex, and the added features can interfere with imaging the ROIs. We report the Fast and Accurate Relocation of Microscopic Experimental Regions (FARMER) method, which only requires determining the coordinates of 3 (or more) conspicuous reference points (REFs) and employs an algorithm based on geometric operators to relocate ROIs in subsequent imaging sessions. The 3 REFs can be quickly added to various regions of a sample using simple tools (e.g., permanent markers or conductive pens) and do not interfere with the ROIs. The coordinates of the REFs and the ROIs are obtained in the first imaging session (on a particular microscope platform) using an accurate and precise encoded motorized stage. In subsequent imaging sessions, the FARMER algorithm finds the new coordinates of the ROIs (on the same or different platforms), using the coordinates of the manually located REFs and the previously recorded coordinates. FARMER is convenient, fast (3-15 min/session, at least 10-fold faster than manual searches), accurate (4.4 μm average error on a microscope with a 100x objective), and precise (almost all errors are <8 μm), even with deliberate rotating and tilting of the sample well beyond normal repositioning accuracy. We demonstrate this versatility by imaging and re-imaging a diverse set of samples and imaging methods: live mammalian cells at different time points; fixed bacterial cells on two microscopes with different imaging modalities; and nanostructures on optical and electron microscopes. FARMER can be readily

  12. Accurate simulations of helium pick-up experiments using a rejection-free Monte Carlo method

    NASA Astrophysics Data System (ADS)

    Dutra, Matthew; Hinde, Robert

    2018-04-01

    In this paper, we present Monte Carlo simulations of helium droplet pick-up experiments with the intention of developing a robust and accurate theoretical approach for interpreting experimental helium droplet calorimetry data. Our approach is capable of capturing the evaporative behavior of helium droplets following dopant acquisition, allowing for a more realistic description of the pick-up process. Furthermore, we circumvent the traditional assumption of bulk helium behavior by utilizing density functional calculations of the size-dependent helium droplet chemical potential. The results of this new Monte Carlo technique are compared to commonly used Poisson pick-up statistics for simulations that reflect a broad range of experimental parameters. We conclude by offering an assessment of both of these theoretical approaches in the context of our observed results.

  13. Toward spectroscopically accurate global ab initio potential energy surface for the acetylene-vinylidene isomerization

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Han, Huixian; School of Physics, Northwest University, Xi’an, Shaanxi 710069; Li, Anyang

    2014-12-28

    A new full-dimensional global potential energy surface (PES) for the acetylene-vinylidene isomerization on the ground (S{sub 0}) electronic state has been constructed by fitting ∼37 000 high-level ab initio points using the permutation invariant polynomial-neural network method with a root mean square error of 9.54 cm{sup −1}. The geometries and harmonic vibrational frequencies of acetylene, vinylidene, and all other stationary points (two distinct transition states and one secondary minimum in between) have been determined on this PES. Furthermore, acetylene vibrational energy levels have been calculated using the Lanczos algorithm with an exact (J = 0) Hamiltonian. The vibrational energies upmore » to 12 700 cm{sup −1} above the zero-point energy are in excellent agreement with the experimentally derived effective Hamiltonians, suggesting that the PES is approaching spectroscopic accuracy. In addition, analyses of the wavefunctions confirm the experimentally observed emergence of the local bending and counter-rotational modes in the highly excited bending vibrational states. The reproduction of the experimentally derived effective Hamiltonians for highly excited bending states signals the coming of age for the ab initio based PES, which can now be trusted for studying the isomerization reaction.« less

  14. An Accurate Potential Energy Surface for H2O

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.; Partridge, Harry; Langhoff, Stephen R. (Technical Monitor)

    1997-01-01

    We have carried out extensive high quality ab initio electronic structure calculations of the ground state potential energy surface (PES) and dipole moment function (DMF) for H2O. A small adjustment is made to the PES to improve the agreement of line positions from theory and experiment. The theoretical line positions are obtained from variational ro-vibrational calculations using the exact kinetic energy operator. For the lines being fitted, the root-mean-square error was reduced from 6.9 to 0.08 /cm. We were then able to match 30,092 of the 30,117 lines from the HITRAN 96 data base to theoretical lines, and 80% of the line positions differed less than 0.1 /cm. About 3% of the line positions in the experimental data base appear to be incorrect. Theory predicts the existence of many additional weak lines with intensities above the cutoff used in the data base. To obtain results of similar accuracy for HDO, a mass dependent correction to the PH is introduced and is parameterized by simultaneously fitting line positions for HDO and D2O. The mass dependent PH has good predictive value for T2O and HTO. Nonadiabatic effects are not explicitly included. Line strengths for vibrational bands summed over rotational levels usually agree well between theory and experiment, but individual line strengths can differ greatly. A high temperature line list containing about 380 million lines has been generated using the present PES and DMF

  15. Prevention of hepatocellular carcinoma: potential targets, experimental models, and clinical challenges

    PubMed Central

    Hoshida, Yujin; Fuchs, Bryan C.; Tanabe, Kenneth K.

    2013-01-01

    Chronic fibrotic liver diseases such as viral hepatitis eventually develop liver cirrhosis, which causes occurrence of hepatocellular carcinoma (HCC). Given the limited therapeutic efficacy in advanced HCC, prevention of HCC development could be an effective strategy for improving patient prognosis. However, there is still no established therapy to meet the goal. Studies have elucidated a wide variety of molecular mechanisms and signaling pathways involved in HCC development. Genetically-engineered or chemically-treated experimental models of cirrhosis and HCC have been developed and shown their potential value in investigating molecular therapeutic targets and diagnostic biomarkers for HCC prevention. In this review, we overview potential targets of prevention and currently available experimental models, and discuss strategies to translate the findings into clinical practice. PMID:22873223

  16. Nonexposure Accurate Location K-Anonymity Algorithm in LBS

    PubMed Central

    2014-01-01

    This paper tackles location privacy protection in current location-based services (LBS) where mobile users have to report their exact location information to an LBS provider in order to obtain their desired services. Location cloaking has been proposed and well studied to protect user privacy. It blurs the user's accurate coordinate and replaces it with a well-shaped cloaked region. However, to obtain such an anonymous spatial region (ASR), nearly all existent cloaking algorithms require knowing the accurate locations of all users. Therefore, location cloaking without exposing the user's accurate location to any party is urgently needed. In this paper, we present such two nonexposure accurate location cloaking algorithms. They are designed for K-anonymity, and cloaking is performed based on the identifications (IDs) of the grid areas which were reported by all the users, instead of directly on their accurate coordinates. Experimental results show that our algorithms are more secure than the existent cloaking algorithms, need not have all the users reporting their locations all the time, and can generate smaller ASR. PMID:24605060

  17. Theoretical and experimental prediction of the redox potentials of metallocene compounds

    NASA Astrophysics Data System (ADS)

    Li, Ya-Ping; Liu, Hai-Bo; Liu, Tao; Yu, Zhang-Yu

    2017-11-01

    The standard redox electrode potential ( E°) values of metallocene compounds are obtained theoretically with density functional theory (DFT) method at B3LYP/6-311++G( d, p) level and experimentally with cyclic voltammetry (CV). The theoretical E° values of metallocene compounds are in good agreement with experimental ones. We investigate the substituent effects on the redox properties of metallocene compounds. Among the four metallocene compounds, the E° values is largest for titanocene dichloride and smallest for ferrocene.

  18. Work function measurements by the field emission retarding potential method.

    NASA Technical Reports Server (NTRS)

    Strayer, R. W.; Mackie, W.; Swanson, L. W.

    1973-01-01

    Description of the theoretical foundation of the field electron retarding potential method, and review of its experimental application to the measurement of single crystal face work functions. The results obtained from several substrates are discussed. An interesting and useful fallout from the experimental approach described is the ability to accurately measure the elastic and inelastic reflection coefficient for impinging electrons to near zero-volt energy.

  19. Ab initio interatomic potentials and the thermodynamic properties of fluids

    NASA Astrophysics Data System (ADS)

    Vlasiuk, Maryna; Sadus, Richard J.

    2017-07-01

    Monte Carlo simulations with accurate ab initio interatomic potentials are used to investigate the key thermodynamic properties of argon and krypton in both vapor and liquid phases. Data are reported for the isochoric and isobaric heat capacities, the Joule-Thomson coefficient, and the speed of sound calculated using various two-body interatomic potentials and different combinations of two-body plus three-body terms. The results are compared to either experimental or reference data at state points between the triple and critical points. Using accurate two-body ab initio potentials, combined with three-body interaction terms such as the Axilrod-Teller-Muto and Marcelli-Wang-Sadus potentials, yields systematic improvements to the accuracy of thermodynamic predictions. The effect of three-body interactions is to lower the isochoric and isobaric heat capacities and increase both the Joule-Thomson coefficient and speed of sound. The Marcelli-Wang-Sadus potential is a computationally inexpensive way to utilize accurate two-body ab initio potentials for the prediction of thermodynamic properties. In particular, it provides a very effective way of extending two-body ab initio potentials to liquid phase properties.

  20. Ab initio interatomic potentials and the thermodynamic properties of fluids.

    PubMed

    Vlasiuk, Maryna; Sadus, Richard J

    2017-07-14

    Monte Carlo simulations with accurate ab initio interatomic potentials are used to investigate the key thermodynamic properties of argon and krypton in both vapor and liquid phases. Data are reported for the isochoric and isobaric heat capacities, the Joule-Thomson coefficient, and the speed of sound calculated using various two-body interatomic potentials and different combinations of two-body plus three-body terms. The results are compared to either experimental or reference data at state points between the triple and critical points. Using accurate two-body ab initio potentials, combined with three-body interaction terms such as the Axilrod-Teller-Muto and Marcelli-Wang-Sadus potentials, yields systematic improvements to the accuracy of thermodynamic predictions. The effect of three-body interactions is to lower the isochoric and isobaric heat capacities and increase both the Joule-Thomson coefficient and speed of sound. The Marcelli-Wang-Sadus potential is a computationally inexpensive way to utilize accurate two-body ab initio potentials for the prediction of thermodynamic properties. In particular, it provides a very effective way of extending two-body ab initio potentials to liquid phase properties.

  1. Ab initio study of the CO-N2 complex: a new highly accurate intermolecular potential energy surface and rovibrational spectrum.

    PubMed

    Cybulski, Hubert; Henriksen, Christian; Dawes, Richard; Wang, Xiao-Gang; Bora, Neha; Avila, Gustavo; Carrington, Tucker; Fernández, Berta

    2018-05-09

    A new, highly accurate ab initio ground-state intermolecular potential-energy surface (IPES) for the CO-N2 complex is presented. Thousands of interaction energies calculated with the CCSD(T) method and Dunning's aug-cc-pVQZ basis set extended with midbond functions were fitted to an analytical function. The global minimum of the potential is characterized by an almost T-shaped structure and has an energy of -118.2 cm-1. The symmetry-adapted Lanczos algorithm was used to compute rovibrational energies (up to J = 20) on the new IPES. The RMSE with respect to experiment was found to be on the order of 0.038 cm-1 which confirms the very high accuracy of the potential. This level of agreement is among the best reported in the literature for weakly bound systems and considerably improves on those of previously published potentials.

  2. Z-scan theoretical and experimental studies for accurate measurements of the nonlinear refractive index and absorption of optical glasses near damage threshold

    NASA Astrophysics Data System (ADS)

    Olivier, Thomas; Billard, Franck; Akhouayri, Hassan

    2004-06-01

    Self-focusing is one of the dramatic phenomena that may occur during the propagation of a high power laser beam in a nonlinear material. This phenomenon leads to a degradation of the wave front and may also lead to a photoinduced damage of the material. Realistic simulations of the propagation of high power laser beams require an accurate knowledge of the nonlinear refractive index γ. In the particular case of fused silica and in the nanosecond regime, it seems that electronic mechanisms as well as electrostriction and thermal effects can lead to a significant refractive index variation. Compared to the different methods used to measure this parmeter, the Z-scan method is simple, offers a good sensitivity and may give absolute measurements if the incident beam is accurately studied. However, this method requires a very good knowledge of the incident beam and of its propagation inside a nonlinear sample. We used a split-step propagation algorithm to simlate Z-scan curves for arbitrary beam shape, sample thickness and nonlinear phase shift. According to our simulations and a rigorous analysis of the Z-scan measured signal, it appears that some abusive approximations lead to very important errors. Thus, by reducing possible errors on the interpretation of Z-scan experimental studies, we performed accurate measurements of the nonlinear refractive index of fused silica that show the significant contribution of nanosecond mechanisms.

  3. Accurate experimental and theoretical comparisons between superconductor-insulator-superconductor mixers showing weak and strong quantum effects

    NASA Technical Reports Server (NTRS)

    Mcgrath, W. R.; Richards, P. L.; Face, D. W.; Prober, D. E.; Lloyd, F. L.

    1988-01-01

    A systematic study of the gain and noise in superconductor-insulator-superconductor mixers employing Ta based, Nb based, and Pb-alloy based tunnel junctions was made. These junctions displayed both weak and strong quantum effects at a signal frequency of 33 GHz. The effects of energy gap sharpness and subgap current were investigated and are quantitatively related to mixer performance. Detailed comparisons are made of the mixing results with the predictions of a three-port model approximation to the Tucker theory. Mixer performance was measured with a novel test apparatus which is accurate enough to allow for the first quantitative tests of theoretical noise predictions. It is found that the three-port model of the Tucker theory underestimates the mixer noise temperature by a factor of about 2 for all of the mixers. In addition, predicted values of available mixer gain are in reasonable agreement with experiment when quantum effects are weak. However, as quantum effects become strong, the predicted available gain diverges to infinity, which is in sharp contrast to the experimental results. Predictions of coupled gain do not always show such divergences.

  4. Simple optimized Brenner potential for thermodynamic properties of diamond

    NASA Astrophysics Data System (ADS)

    Liu, F.; Tang, Q. H.; Shang, B. S.; Wang, T. C.

    2012-02-01

    We have examined the commonly used Brenner potentials in the context of the thermodynamic properties of diamond. A simple optimized Brenner potential is proposed that provides very good predictions of the thermodynamic properties of diamond. It is shown that, compared to the experimental data, the lattice wave theory of molecular dynamics (LWT) with this optimized Brenner potential can accurately predict the temperature dependence of specific heat, lattice constant, Grüneisen parameters and coefficient of thermal expansion (CTE) of diamond.

  5. The gradational step test for assessing cardiorespiratory capacity : an experimental evaluation of treadmill and step test procedures.

    DOT National Transportation Integrated Search

    1964-01-01

    "Physical fitness" - the potential capacity for making adequate functional adjustments to increased metabolic demands - is most meaningful and accurately assessed in the laboratory by making physiological measurements on the experimental subject whil...

  6. Classical Trajectory Study of Collision Energy Transfer between Ne and C2H2 on a Full Dimensional Accurate Potential Energy Surface.

    PubMed

    Liu, Yang; Huang, Yin; Ma, Jianyi; Li, Jun

    2018-02-15

    Collision energy transfer plays an important role in gas phase reaction kinetics and relaxation of excited molecules. However, empirical treatments are generally adopted for the collisional energy transfer in the master equation based approach. In this work, classical trajectory approach is employed to investigate the collision energy transfer dynamics in the C 2 H 2 -Ne system. The entire potential energy surface is described as the sum of the C 2 H 2 potential and interaction potential between C 2 H 2 and Ne. It is highlighted that both parts of the entire potential are highly accurate. In particular, the interaction potential is fit to ∼41 300 configurations determined at the level of CCSD(T)-F12a/cc-pCVTZ-F12 with the counterpoise correction. Collision energy transfer dynamics are then carried out on this benchmark potential and the widely used Lennard-Jones and Buckingham interaction potentials. Energy transfers and related probability densities at different collisional energies are reported and discussed.

  7. Topological Quantum Phase Transition in Synthetic Non-Abelian Gauge Potential: Gauge Invariance and Experimental Detections

    PubMed Central

    Sun, Fadi; Yu, Xiao-Lu; Ye, Jinwu; Fan, Heng; Liu, Wu-Ming

    2013-01-01

    The method of synthetic gauge potentials opens up a new avenue for our understanding and discovering novel quantum states of matter. We investigate the topological quantum phase transition of Fermi gases trapped in a honeycomb lattice in the presence of a synthetic non-Abelian gauge potential. We develop a systematic fermionic effective field theory to describe a topological quantum phase transition tuned by the non-Abelian gauge potential and explore its various important experimental consequences. Numerical calculations on lattice scales are performed to compare with the results achieved by the fermionic effective field theory. Several possible experimental detection methods of topological quantum phase transition are proposed. In contrast to condensed matter experiments where only gauge invariant quantities can be measured, both gauge invariant and non-gauge invariant quantities can be measured by experimentally generating various non-Abelian gauges corresponding to the same set of Wilson loops. PMID:23846153

  8. New optimization scheme to obtain interaction potentials for oxide glasses

    NASA Astrophysics Data System (ADS)

    Sundararaman, Siddharth; Huang, Liping; Ispas, Simona; Kob, Walter

    2018-05-01

    We propose a new scheme to parameterize effective potentials that can be used to simulate atomic systems such as oxide glasses. As input data for the optimization, we use the radial distribution functions of the liquid and the vibrational density of state of the glass, both obtained from ab initio simulations, as well as experimental data on the pressure dependence of the density of the glass. For the case of silica, we find that this new scheme facilitates finding pair potentials that are significantly more accurate than the previous ones even if the functional form is the same, thus demonstrating that even simple two-body potentials can be superior to more complex three-body potentials. We have tested the new potential by calculating the pressure dependence of the elastic moduli and found a good agreement with the corresponding experimental data.

  9. Accurate ab initio binding energies of the benzene dimer.

    PubMed

    Park, Young Choon; Lee, Jae Shin

    2006-04-20

    Accurate binding energies of the benzene dimer at the T and parallel displaced (PD) configurations were determined using the single- and double-coupled cluster method with perturbative triple correction (CCSD(T)) with correlation-consistent basis sets and an effective basis set extrapolation scheme recently devised. The difference between the estimated CCSD(T) basis set limit electronic binding energies for the T and PD shapes appears to amount to more than 0.3 kcal/mol, indicating the PD shape is a more stable configuration than the T shape for this dimer in the gas phase. This conclusion is further strengthened when a vibrational zero-point correction to the electronic binding energies of this dimer is made, which increases the difference between the two configurations to 0.4-0.5 kcal/mol. The binding energies of 2.4 and 2.8 kcal/mol for the T and PD configurations are in good accord with the previous experimental result from ionization potential measurement.

  10. Accurate mass measurement: terminology and treatment of data.

    PubMed

    Brenton, A Gareth; Godfrey, A Ruth

    2010-11-01

    High-resolution mass spectrometry has become ever more accessible with improvements in instrumentation, such as modern FT-ICR and Orbitrap mass spectrometers. This has resulted in an increase in the number of articles submitted for publication quoting accurate mass data. There is a plethora of terms related to accurate mass analysis that are in current usage, many employed incorrectly or inconsistently. This article is based on a set of notes prepared by the authors for research students and staff in our laboratories as a guide to the correct terminology and basic statistical procedures to apply in relation to mass measurement, particularly for accurate mass measurement. It elaborates on the editorial by Gross in 1994 regarding the use of accurate masses for structure confirmation. We have presented and defined the main terms in use with reference to the International Union of Pure and Applied Chemistry (IUPAC) recommendations for nomenclature and symbolism for mass spectrometry. The correct use of statistics and treatment of data is illustrated as a guide to new and existing mass spectrometry users with a series of examples as well as statistical methods to compare different experimental methods and datasets. Copyright © 2010. Published by Elsevier Inc.

  11. Experimental results on the ω- and η'-nucleus potential - on the way to mesic states

    NASA Astrophysics Data System (ADS)

    Nanova, Mariana

    2015-06-01

    Different experimental approaches to determine the meson-nucleus optical potential are discussed. The experiments have been performed with the Crystal Barrel/TAPS detector system at the ELSA accelerator in Bonn and the Crystal Ball/TAPS at the MAMI accelerator in Mainz. Experimental results about the real and imaginary part of the η'- and ω-nucleus optical potential are presented. The imaginary part of the meson-nucleus optical potential is determined from the in-medium width of the meson by the measurement of the transparency ratio. Information on the real part of the optical potential is deduced from measurements of the excitation function and momentum distribution which are sensitive to the sign and depth of the potential. The results are discussed and compared to theoretical predictions. The data for both mesons are consistent with a weakly attractive potential. The formation and population of ω-nucleus and η'-nucleus bound states is additionally discussed.

  12. Laser diode absorption spectroscopy for accurate CO(2) line parameters at 2 microm: consequences for space-based DIAL measurements and potential biases.

    PubMed

    Joly, Lilian; Marnas, Fabien; Gibert, Fabien; Bruneau, Didier; Grouiez, Bruno; Flamant, Pierre H; Durry, Georges; Dumelie, Nicolas; Parvitte, Bertrand; Zéninari, Virginie

    2009-10-10

    Space-based active sensing of CO(2) concentration is a very promising technique for the derivation of CO(2) surface fluxes. There is a need for accurate spectroscopic parameters to enable accurate space-based measurements to address global climatic issues. New spectroscopic measurements using laser diode absorption spectroscopy are presented for the preselected R30 CO(2) absorption line ((20(0)1)(III)<--(000) band) and four others. The line strength, air-broadening halfwidth, and its temperature dependence have been investigated. The results exhibit significant improvement for the R30 CO(2) absorption line: 0.4% on the line strength, 0.15% on the air-broadening coefficient, and 0.45% on its temperature dependence. Analysis of potential biases of space-based DIAL CO(2) mixing ratio measurements associated to spectroscopic parameter uncertainties are presented.

  13. New experimental methodology, setup and LabView program for accurate absolute thermoelectric power and electrical resistivity measurements between 25 and 1600 K: application to pure copper, platinum, tungsten, and nickel at very high temperatures.

    PubMed

    Abadlia, L; Gasser, F; Khalouk, K; Mayoufi, M; Gasser, J G

    2014-09-01

    In this paper we describe an experimental setup designed to measure simultaneously and very accurately the resistivity and the absolute thermoelectric power, also called absolute thermopower or absolute Seebeck coefficient, of solid and liquid conductors/semiconductors over a wide range of temperatures (room temperature to 1600 K in present work). A careful analysis of the existing experimental data allowed us to extend the absolute thermoelectric power scale of platinum to the range 0-1800 K with two new polynomial expressions. The experimental device is controlled by a LabView program. A detailed description of the accurate dynamic measurement methodology is given in this paper. We measure the absolute thermoelectric power and the electrical resistivity and deduce with a good accuracy the thermal conductivity using the relations between the three electronic transport coefficients, going beyond the classical Wiedemann-Franz law. We use this experimental setup and methodology to give new very accurate results for pure copper, platinum, and nickel especially at very high temperatures. But resistivity and absolute thermopower measurement can be more than an objective in itself. Resistivity characterizes the bulk of a material while absolute thermoelectric power characterizes the material at the point where the electrical contact is established with a couple of metallic elements (forming a thermocouple). In a forthcoming paper we will show that the measurement of resistivity and absolute thermoelectric power characterizes advantageously the (change of) phase, probably as well as DSC (if not better), since the change of phases can be easily followed during several hours/days at constant temperature.

  14. New experimental methodology, setup and LabView program for accurate absolute thermoelectric power and electrical resistivity measurements between 25 and 1600 K: Application to pure copper, platinum, tungsten, and nickel at very high temperatures

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Abadlia, L.; Mayoufi, M.; Gasser, F.

    2014-09-15

    In this paper we describe an experimental setup designed to measure simultaneously and very accurately the resistivity and the absolute thermoelectric power, also called absolute thermopower or absolute Seebeck coefficient, of solid and liquid conductors/semiconductors over a wide range of temperatures (room temperature to 1600 K in present work). A careful analysis of the existing experimental data allowed us to extend the absolute thermoelectric power scale of platinum to the range 0-1800 K with two new polynomial expressions. The experimental device is controlled by a LabView program. A detailed description of the accurate dynamic measurement methodology is given in thismore » paper. We measure the absolute thermoelectric power and the electrical resistivity and deduce with a good accuracy the thermal conductivity using the relations between the three electronic transport coefficients, going beyond the classical Wiedemann-Franz law. We use this experimental setup and methodology to give new very accurate results for pure copper, platinum, and nickel especially at very high temperatures. But resistivity and absolute thermopower measurement can be more than an objective in itself. Resistivity characterizes the bulk of a material while absolute thermoelectric power characterizes the material at the point where the electrical contact is established with a couple of metallic elements (forming a thermocouple). In a forthcoming paper we will show that the measurement of resistivity and absolute thermoelectric power characterizes advantageously the (change of) phase, probably as well as DSC (if not better), since the change of phases can be easily followed during several hours/days at constant temperature.« less

  15. A gauged finite-element potential formulation for accurate inductive and galvanic modelling of 3-D electromagnetic problems

    NASA Astrophysics Data System (ADS)

    Ansari, S. M.; Farquharson, C. G.; MacLachlan, S. P.

    2017-07-01

    In this paper, a new finite-element solution to the potential formulation of the geophysical electromagnetic (EM) problem that explicitly implements the Coulomb gauge, and that accurately computes the potentials and hence inductive and galvanic components, is proposed. The modelling scheme is based on using unstructured tetrahedral meshes for domain subdivision, which enables both realistic Earth models of complex geometries to be considered and efficient spatially variable refinement of the mesh to be done. For the finite-element discretization edge and nodal elements are used for approximating the vector and scalar potentials respectively. The issue of non-unique, incorrect potentials from the numerical solution of the usual incomplete-gauged potential system is demonstrated for a benchmark model from the literature that uses an electric-type EM source, through investigating the interface continuity conditions for both the normal and tangential components of the potential vectors, and by showing inconsistent results obtained from iterative and direct linear equation solvers. By explicitly introducing the Coulomb gauge condition as an extra equation, and by augmenting the Helmholtz equation with the gradient of a Lagrange multiplier, an explicitly gauged system for the potential formulation is formed. The solution to the discretized form of this system is validated for the above-mentioned example and for another classic example that uses a magnetic EM source. In order to stabilize the iterative solution of the gauged system, a block diagonal pre-conditioning scheme that is based upon the Schur complement of the potential system is used. For all examples, both the iterative and direct solvers produce the same responses for the potentials, demonstrating the uniqueness of the numerical solution for the potentials and fixing the problems with the interface conditions between cells observed for the incomplete-gauged system. These solutions of the gauged system also

  16. Theory of bi-molecular association dynamics in 2D for accurate model and experimental parameterization of binding rates

    PubMed Central

    Yogurtcu, Osman N.; Johnson, Margaret E.

    2015-01-01

    The dynamics of association between diffusing and reacting molecular species are routinely quantified using simple rate-equation kinetics that assume both well-mixed concentrations of species and a single rate constant for parameterizing the binding rate. In two-dimensions (2D), however, even when systems are well-mixed, the assumption of a single characteristic rate constant for describing association is not generally accurate, due to the properties of diffusional searching in dimensions d ≤ 2. Establishing rigorous bounds for discriminating between 2D reactive systems that will be accurately described by rate equations with a single rate constant, and those that will not, is critical for both modeling and experimentally parameterizing binding reactions restricted to surfaces such as cellular membranes. We show here that in regimes of intrinsic reaction rate (ka) and diffusion (D) parameters ka/D > 0.05, a single rate constant cannot be fit to the dynamics of concentrations of associating species independently of the initial conditions. Instead, a more sophisticated multi-parametric description than rate-equations is necessary to robustly characterize bimolecular reactions from experiment. Our quantitative bounds derive from our new analysis of 2D rate-behavior predicted from Smoluchowski theory. Using a recently developed single particle reaction-diffusion algorithm we extend here to 2D, we are able to test and validate the predictions of Smoluchowski theory and several other theories of reversible reaction dynamics in 2D for the first time. Finally, our results also mean that simulations of reactive systems in 2D using rate equations must be undertaken with caution when reactions have ka/D > 0.05, regardless of the simulation volume. We introduce here a simple formula for an adaptive concentration dependent rate constant for these chemical kinetics simulations which improves on existing formulas to better capture non-equilibrium reaction dynamics from dilute

  17. Toward more accurate loss tangent measurements in reentrant cavities

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Moyer, R. D.

    1980-05-01

    Karpova has described an absolute method for measurement of dielectric properties of a solid in a coaxial reentrant cavity. His cavity resonance equation yields very accurate results for dielectric constants. However, he presented only approximate expressions for the loss tangent. This report presents more exact expressions for that quantity and summarizes some experimental results.

  18. Highly accurate nephelometric titrimetry.

    PubMed

    Zhan, Xiancheng; Li, Chengrong; Li, Zhiyi; Yang, Xiucen; Zhong, Shuguang; Yi, Tao

    2004-02-01

    A method that accurately indicates the end-point of precipitation reactions by the measurement of the relative intensity of the scattered light in the titrate is presented. A new nephelometric titrator with an internal nephelometric sensor has been devised. The work of the titrator including the sensor and change in the turbidity of the titrate and intensity of the scattered light are described. The accuracy of the nephelometric titrimetry is discussed theoretically. The titration of NaCl with AgNO(3) serves as a model. A relative error as well as deviation is within 0.2% under the experimental conditions. The applicability of the titrimetry in pharmaceutical analyses, for example, phenytoin sodium and procaine hydrochloride, is generally illustrated. Copyright 2004 Wiley-Liss, Inc. and the American Pharmacists Association

  19. Experimental constraints on the damp peridotite solidus and oceanic mantle potential temperature

    NASA Astrophysics Data System (ADS)

    Sarafian, Emily; Gaetani, Glenn A.; Hauri, Erik H.; Sarafian, Adam R.

    2017-03-01

    Decompression of hot mantle rock upwelling beneath oceanic spreading centers causes it to exceed the melting point (solidus), producing magmas that ascend to form basaltic crust ~6 to 7 kilometers thick. The oceanic upper mantle contains ~50 to 200 micrograms per gram of water (H2O) dissolved in nominally anhydrous minerals, which—relative to its low concentration—has a disproportionate effect on the solidus that has not been quantified experimentally. Here, we present results from an experimental determination of the peridotite solidus containing known amounts of dissolved hydrogen. Our data reveal that the H2O-undersaturated peridotite solidus is hotter than previously thought. Reconciling geophysical observations of the melting regime beneath the East Pacific Rise with our experimental results requires that existing estimates for the oceanic upper mantle potential temperature be adjusted upward by about 60°C.

  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. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Accurate lithography simulation model based on convolutional neural networks

    NASA Astrophysics Data System (ADS)

    Watanabe, Yuki; Kimura, Taiki; Matsunawa, Tetsuaki; Nojima, Shigeki

    2017-07-01

    Lithography simulation is an essential technique for today's semiconductor manufacturing process. In order to calculate an entire chip in realistic time, compact resist model is commonly used. The model is established for faster calculation. To have accurate compact resist model, it is necessary to fix a complicated non-linear model function. However, it is difficult to decide an appropriate function manually because there are many options. This paper proposes a new compact resist model using CNN (Convolutional Neural Networks) which is one of deep learning techniques. CNN model makes it possible to determine an appropriate model function and achieve accurate simulation. Experimental results show CNN model can reduce CD prediction errors by 70% compared with the conventional model.

  2. Accurate Critical Stress Intensity Factor Griffith Crack Theory Measurements by Numerical Techniques

    PubMed Central

    Petersen, Richard C.

    2014-01-01

    Critical stress intensity factor (KIc) has been an approximation for fracture toughness using only load-cell measurements. However, artificial man-made cracks several orders of magnitude longer and wider than natural flaws have required a correction factor term (Y) that can be up to about 3 times the recorded experimental value [1-3]. In fact, over 30 years ago a National Academy of Sciences advisory board stated that empirical KIc testing was of serious concern and further requested that an accurate bulk fracture toughness method be found [4]. Now that fracture toughness can be calculated accurately by numerical integration from the load/deflection curve as resilience, work of fracture (WOF) and strain energy release (SIc) [5, 6], KIc appears to be unnecessary. However, the large body of previous KIc experimental test results found in the literature offer the opportunity for continued meta analysis with other more practical and accurate fracture toughness results using energy methods and numerical integration. Therefore, KIc is derived from the classical Griffith Crack Theory [6] to include SIc as a more accurate term for strain energy release rate (𝒢Ic), along with crack surface energy (γ), crack length (a), modulus (E), applied stress (σ), Y, crack-tip plastic zone defect region (rp) and yield strength (σys) that can all be determined from load and deflection data. Polymer matrix discontinuous quartz fiber-reinforced composites to accentuate toughness differences were prepared for flexural mechanical testing comprising of 3 mm fibers at different volume percentages from 0-54.0 vol% and at 28.2 vol% with different fiber lengths from 0.0-6.0 mm. Results provided a new correction factor and regression analyses between several numerical integration fracture toughness test methods to support KIc results. Further, bulk KIc accurate experimental values are compared with empirical test results found in literature. Also, several fracture toughness mechanisms

  3. Hypoglycemic and antioxidant potential of coconut water in experimental diabetes.

    PubMed

    Preetha, P P; Devi, V Girija; Rajamohan, T

    2012-07-01

    Coconut water is a natural nutritious beverage that contains several biologically active compounds. The present study aims to evaluate the hypoglycemic and antioxidant effects of mature coconut water (MCW) on alloxan-induced diabetes in experimental rats. The experimental animals were divided into four groups - normal control, normal rats treated with MCW, diabetic control and diabetic rats treated with MCW. The blood glucose, plasma insulin, hemoglobin, glycated hemoglobin, activities of the various antioxidant enzymes (catalase, superoxide dismutase, glutathione peroxidase and glutathione reductase) and lipid peroxidation markers (malondialdehyde, hydroperoxides and conjugated dienes) were evaluated in all the groups. The results indicate that the diabetic animals treated with MCW had decreased blood glucose levels and reduced oxidative stress induced by alloxan, which was evident from the increased activities of the antioxidant enzymes and the decreased levels of the lipid peroxidation products. The overall results indicate that MCW significantly attenuated hyperglycemia and oxidative stress in alloxan-induced diabetic rats, indicating the therapeutic potential of MCW.

  4. Descriptive and Experimental Analyses of Potential Precursors to Problem Behavior

    PubMed Central

    Borrero, Carrie S.W; Borrero, John C

    2008-01-01

    We conducted descriptive observations of severe problem behavior for 2 individuals with autism to identify precursors to problem behavior. Several comparative probability analyses were conducted in addition to lag-sequential analyses using the descriptive data. Results of the descriptive analyses showed that the probability of the potential precursor was greater given problem behavior compared to the unconditional probability of the potential precursor. Results of the lag-sequential analyses showed a marked increase in the probability of a potential precursor in the 1-s intervals immediately preceding an instance of problem behavior, and that the probability of problem behavior was highest in the 1-s intervals immediately following an instance of the precursor. We then conducted separate functional analyses of problem behavior and the precursor to identify respective operant functions. Results of the functional analyses showed that both problem behavior and the precursor served the same operant functions. These results replicate prior experimental analyses on the relation between problem behavior and precursors and extend prior research by illustrating a quantitative method to identify precursors to more severe problem behavior. PMID:18468281

  5. Accurate radiation temperature and chemical potential from quantitative photoluminescence analysis of hot carrier populations.

    PubMed

    Gibelli, François; Lombez, Laurent; Guillemoles, Jean-François

    2017-02-15

    In order to characterize hot carrier populations in semiconductors, photoluminescence measurement is a convenient tool, enabling us to probe the carrier thermodynamical properties in a contactless way. However, the analysis of the photoluminescence spectra is based on some assumptions which will be discussed in this work. We especially emphasize the importance of the variation of the material absorptivity that should be considered to access accurate thermodynamical properties of the carriers, especially by varying the excitation power. The proposed method enables us to obtain more accurate results of thermodynamical properties by taking into account a rigorous physical description and finds direct application in investigating hot carrier solar cells, which are an adequate concept for achieving high conversion efficiencies with a relatively simple device architecture.

  6. Experimental Potential Energy Curve for the 43 Π Electronic State of NaCs

    NASA Astrophysics Data System (ADS)

    Steely, Andrew; Cooper, Hannah; Zain, Hareem; Whipp, Ciara; Faust, Carl; Kortyna, Andrew; Huennekens, John

    2017-04-01

    We present results from experimental studies of the 43 Π electronic state of the NaCs molecule. This electronic state is interesting in that its potential energy curve likely exhibits a double minimum. As a result, interference effects are observed in the resolved bound-free fluorescence spectra. The optical-optical double resonance method was used to obtain Doppler-free excitation spectra for the 43 Π state. This dataset of measured level energies was expanded largely by observing fluorescence from levels populated by collisions. To aid in level assignments, simulations of resolved bound-free fluorescence spectra were calculated using the BCONT program (R. J. Le Roy, University of Waterloo). Spectroscopic constants were determined to summarize data belonging to inner well, outer well, and above barrier regions of the electronic state. Current work focuses on using the IPA method to construct an experimental potential energy curve. Work supported by NSF and Susquehanna University.

  7. An experimental setup to characterize MR switched gradient-induced potentials.

    PubMed

    Fokapu, Odette; El-Tatar, Aziz

    2013-06-01

    We have developed an experimental setup as an in vitro research tool for studying the contamination of electrophysiological signals (EPS) by MRI environment; particularly, when due to the switched gradient-induced potentials. The system is composed of: 1) a MRI compatible module for the transmission of the EPS into the MRI tunnel, 2) a gelatin-based tissue-mimicking phantom, placed inside the tunnel, in which EPS is injected, 3) a detection module composed of a five input channel MRI compatible transmitter placed inside the tunnel, allowing an on-site pre-amplification of the bio-potentials and their transmission, via an optical fiber cable, to a four filtered output per channel receiver (350 Hz, 160 Hz, 80 Hz, and 40 Hz, for a total of 20 channels) placed in the control room, and 4) a signal processing algorithm used to analyze the generated induced potentials. A set of tests were performed to validate the electronic performances of the setup. We also present in this work an interesting application of the setup, i.e., the acquisition and analysis of the induced potentials with respect of the slice orientation for a given MRI sequence. Significant modifications of the time and frequency characteristics were observed with respect to axial, coronal or sagittal orientations.

  8. The determination of accurate dipole polarizabilities alpha and gamma for the noble gases

    NASA Technical Reports Server (NTRS)

    Rice, Julia E.; Taylor, Peter R.; Lee, Timothy J.; Almlof, Jan

    1991-01-01

    Accurate static dipole polarizabilities alpha and gamma of the noble gases He through Xe were determined using wave functions of similar quality for each system. Good agreement with experimental data for the static polarizability gamma was obtained for Ne and Xe, but not for Ar and Kr. Calculations suggest that the experimental values for these latter ions are too low.

  9. How accurately does the Brief Job Stress Questionnaire identify workers with or without potential psychological distress?

    PubMed

    Tsutsumi, Akizumi; Inoue, Akiomi; Eguchi, Hisashi

    2017-07-27

    The manual for the Japanese Stress Check Program recommends use of the Brief Job Stress Questionnaire (BJSQ) from among the program's instruments and proposes criteria for defining "high-stress" workers. This study aimed to examine how accurately the BJSQ identifies workers with or without potential psychological distress. We used an online survey to administer the BJSQ with a psychological distress scale (K6) to randomly selected workers (n=1,650). We conducted receiver operating characteristics curve analyses to estimate the screening performance of the cutoff points that the Stress Check Program manual recommends for the BJSQ. Prevalence of workers with potential psychological distress defined as K6 score ≥13 was 13%. Prevalence of "high-risk" workers defined using criteria recommended by the program manual was 16.7% for the original version of the BJSQ. The estimated values were as follows: sensitivity, 60.5%; specificity, 88.9%; Youden index, 0.504; positive predictive value, 47.3%; negative predictive value, 93.8%; positive likelihood ratio, 6.0; and negative likelihood ratio, 0.4. Analyses based on the simplified BJSQ indicated lower sensitivity compared with the original version, although we expected roughly the same screening performance for the best scenario using the original version. Our analyses in which psychological distress measured by K6 was set as the target condition indicate less than half of the identified "high-stress" workers warrant consideration for secondary screening for psychological distress.

  10. Accurate Mapping of Multilevel Rydberg Atoms on Interacting Spin-1 /2 Particles for the Quantum Simulation of Ising Models

    NASA Astrophysics Data System (ADS)

    de Léséleuc, Sylvain; Weber, Sebastian; Lienhard, Vincent; Barredo, Daniel; Büchler, Hans Peter; Lahaye, Thierry; Browaeys, Antoine

    2018-03-01

    We study a system of atoms that are laser driven to n D3 /2 Rydberg states and assess how accurately they can be mapped onto spin-1 /2 particles for the quantum simulation of anisotropic Ising magnets. Using nonperturbative calculations of the pair potentials between two atoms in the presence of electric and magnetic fields, we emphasize the importance of a careful selection of experimental parameters in order to maintain the Rydberg blockade and avoid excitation of unwanted Rydberg states. We benchmark these theoretical observations against experiments using two atoms. Finally, we show that in these conditions, the experimental dynamics observed after a quench is in good agreement with numerical simulations of spin-1 /2 Ising models in systems with up to 49 spins, for which numerical simulations become intractable.

  11. Design and experimentation of an empirical multistructure framework for accurate, sharp and reliable hydrological ensembles

    NASA Astrophysics Data System (ADS)

    Seiller, G.; Anctil, F.; Roy, R.

    2017-09-01

    This paper outlines the design and experimentation of an Empirical Multistructure Framework (EMF) for lumped conceptual hydrological modeling. This concept is inspired from modular frameworks, empirical model development, and multimodel applications, and encompasses the overproduce and select paradigm. The EMF concept aims to reduce subjectivity in conceptual hydrological modeling practice and includes model selection in the optimisation steps, reducing initial assumptions on the prior perception of the dominant rainfall-runoff transformation processes. EMF generates thousands of new modeling options from, for now, twelve parent models that share their functional components and parameters. Optimisation resorts to ensemble calibration, ranking and selection of individual child time series based on optimal bias and reliability trade-offs, as well as accuracy and sharpness improvement of the ensemble. Results on 37 snow-dominated Canadian catchments and 20 climatically-diversified American catchments reveal the excellent potential of the EMF in generating new individual model alternatives, with high respective performance values, that may be pooled efficiently into ensembles of seven to sixty constitutive members, with low bias and high accuracy, sharpness, and reliability. A group of 1446 new models is highlighted to offer good potential on other catchments or applications, based on their individual and collective interests. An analysis of the preferred functional components reveals the importance of the production and total flow elements. Overall, results from this research confirm the added value of ensemble and flexible approaches for hydrological applications, especially in uncertain contexts, and open up new modeling possibilities.

  12. New analytical model for the ozone electronic ground state potential surface and accurate ab initio vibrational predictions at high energy range.

    PubMed

    Tyuterev, Vladimir G; Kochanov, Roman V; Tashkun, Sergey A; Holka, Filip; Szalay, Péter G

    2013-10-07

    An accurate description of the complicated shape of the potential energy surface (PES) and that of the highly excited vibration states is of crucial importance for various unsolved issues in the spectroscopy and dynamics of ozone and remains a challenge for the theory. In this work a new analytical representation is proposed for the PES of the ground electronic state of the ozone molecule in the range covering the main potential well and the transition state towards the dissociation. This model accounts for particular features specific to the ozone PES for large variations of nuclear displacements along the minimum energy path. The impact of the shape of the PES near the transition state (existence of the "reef structure") on vibration energy levels was studied for the first time. The major purpose of this work was to provide accurate theoretical predictions for ozone vibrational band centres at the energy range near the dissociation threshold, which would be helpful for understanding the very complicated high-resolution spectra and its analyses currently in progress. Extended ab initio electronic structure calculations were carried out enabling the determination of the parameters of a minimum energy path PES model resulting in a new set of theoretical vibrational levels of ozone. A comparison with recent high-resolution spectroscopic data on the vibrational levels gives the root-mean-square deviations below 1 cm(-1) for ozone band centres up to 90% of the dissociation energy. New ab initio vibrational predictions represent a significant improvement with respect to all previously available calculations.

  13. A machine learning method for fast and accurate characterization of depth-of-interaction gamma cameras

    NASA Astrophysics Data System (ADS)

    Pedemonte, Stefano; Pierce, Larry; Van Leemput, Koen

    2017-11-01

    Measuring the depth-of-interaction (DOI) of gamma photons enables increasing the resolution of emission imaging systems. Several design variants of DOI-sensitive detectors have been recently introduced to improve the performance of scanners for positron emission tomography (PET). However, the accurate characterization of the response of DOI detectors, necessary to accurately measure the DOI, remains an unsolved problem. Numerical simulations are, at the state of the art, imprecise, while measuring directly the characteristics of DOI detectors experimentally is hindered by the impossibility to impose the depth-of-interaction in an experimental set-up. In this article we introduce a machine learning approach for extracting accurate forward models of gamma imaging devices from simple pencil-beam measurements, using a nonlinear dimensionality reduction technique in combination with a finite mixture model. The method is purely data-driven, not requiring simulations, and is applicable to a wide range of detector types. The proposed method was evaluated both in a simulation study and with data acquired using a monolithic gamma camera designed for PET (the cMiCE detector), demonstrating the accurate recovery of the DOI characteristics. The combination of the proposed calibration technique with maximum- a posteriori estimation of the coordinates of interaction provided a depth resolution of  ≈1.14 mm for the simulated PET detector and  ≈1.74 mm for the cMiCE detector. The software and experimental data are made available at http://occiput.mgh.harvard.edu/depthembedding/.

  14. All optical experimental design for neuron excitation, inhibition, and action potential detection

    NASA Astrophysics Data System (ADS)

    Walsh, Alex J.; Tolstykh, Gleb; Martens, Stacey; Sedelnikova, Anna; Ibey, Bennett L.; Beier, Hope T.

    2016-03-01

    Recently, infrared light has been shown to both stimulate and inhibit excitatory cells. However, studies of infrared light for excitatory cell inhibition have been constrained by the use of invasive and cumbersome electrodes for cell excitation and action potential recording. Here, we present an all optical experimental design for neuronal excitation, inhibition, and action potential detection. Primary rat neurons were transfected with plasmids containing the light sensitive ion channel CheRiff. CheRiff has a peak excitation around 450 nm, allowing excitation of transfected neurons with pulsed blue light. Additionally, primary neurons were transfected with QuasAr2, a fast and sensitive fluorescent voltage indicator. QuasAr2 is excited with yellow or red light and therefore does not spectrally overlap CheRiff, enabling imaging and action potential activation, simultaneously. Using an optic fiber, neurons were exposed to blue light sequentially to generate controlled action potentials. A second optic fiber delivered a single pulse of 1869nm light to the neuron causing inhibition of the evoked action potentials (by the blue light). When used in concert, these optical techniques enable electrode free neuron excitation, inhibition, and action potential recording, allowing research into neuronal behaviors with high spatial fidelity.

  15. Multimodal Spatial Calibration for Accurately Registering EEG Sensor Positions

    PubMed Central

    Chen, Shengyong; Xiao, Gang; Li, Xiaoli

    2014-01-01

    This paper proposes a fast and accurate calibration method to calibrate multiple multimodal sensors using a novel photogrammetry system for fast localization of EEG sensors. The EEG sensors are placed on human head and multimodal sensors are installed around the head to simultaneously obtain all EEG sensor positions. A multiple views' calibration process is implemented to obtain the transformations of multiple views. We first develop an efficient local repair algorithm to improve the depth map, and then a special calibration body is designed. Based on them, accurate and robust calibration results can be achieved. We evaluate the proposed method by corners of a chessboard calibration plate. Experimental results demonstrate that the proposed method can achieve good performance, which can be further applied to EEG source localization applications on human brain. PMID:24803954

  16. Microbial Potential for Ecosystem N Loss Is Increased by Experimental N Deposition

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Freedman, Zachary B.; Upchurch, Rima A.; Zak, Donald R.

    Fossil fuel combustion and fertilizer use has increased the amount of biologically available N entering terrestrial ecosystems. Nonetheless, our understanding of how anthropogenic N may alter the physiological mechanisms by which soil microorganisms cycle N in soil is still developing. Here, we applied shotgun metagenomics to a replicated long-term field experiment to determine how two decades of experimental N deposition, at a rate expected by mid-century, has affected the genetic potential of the soil microbial community to cycle N in soils. Experimental N deposition lead to a significant and persistent increase in functional assemblages mediating N cycle transformations associated withmore » ecosystem N loss (i.e., denitrification and nitrification), whereas functional assemblages associated with N input and retention (i.e., N fixation and microbial N assimilation) were less positively affected. Furthermore, the abundance and composition of microbial taxa, as well as functional assemblages involved in housekeeping functions (i.e., DNA replication) were unaffected by experimental N deposition. Here taken together, our results suggest that functional genes and gene pathways associated with ecosystem N loss have been favored by experimental N deposition, which may represent a genetic mechanism fostering increased N loss as anthropogenic N deposition increases in the future.« less

  17. Microbial Potential for Ecosystem N Loss Is Increased by Experimental N Deposition

    DOE PAGES

    Freedman, Zachary B.; Upchurch, Rima A.; Zak, Donald R.; ...

    2016-10-13

    Fossil fuel combustion and fertilizer use has increased the amount of biologically available N entering terrestrial ecosystems. Nonetheless, our understanding of how anthropogenic N may alter the physiological mechanisms by which soil microorganisms cycle N in soil is still developing. Here, we applied shotgun metagenomics to a replicated long-term field experiment to determine how two decades of experimental N deposition, at a rate expected by mid-century, has affected the genetic potential of the soil microbial community to cycle N in soils. Experimental N deposition lead to a significant and persistent increase in functional assemblages mediating N cycle transformations associated withmore » ecosystem N loss (i.e., denitrification and nitrification), whereas functional assemblages associated with N input and retention (i.e., N fixation and microbial N assimilation) were less positively affected. Furthermore, the abundance and composition of microbial taxa, as well as functional assemblages involved in housekeeping functions (i.e., DNA replication) were unaffected by experimental N deposition. Here taken together, our results suggest that functional genes and gene pathways associated with ecosystem N loss have been favored by experimental N deposition, which may represent a genetic mechanism fostering increased N loss as anthropogenic N deposition increases in the future.« less

  18. A relativistic coupled-cluster interaction potential and rovibrational constants for the xenon dimer

    NASA Astrophysics Data System (ADS)

    Jerabek, Paul; Smits, Odile; Pahl, Elke; Schwerdtfeger, Peter

    2018-01-01

    An accurate potential energy curve has been derived for the xenon dimer using state-of-the-art relativistic coupled-cluster theory up to quadruple excitations accounting for both basis set superposition and incompleteness errors. The data obtained is fitted to a computationally efficient extended Lennard-Jones potential form and to a modified Tang-Toennies potential function treating the short- and long-range part separately. The vibrational spectrum of Xe2 obtained from a numerical solution of the rovibrational Schrödinger equation and subsequently derived spectroscopic constants are in excellent agreement with experimental values. We further present solid-state calculations for xenon using a static many-body expansion up to fourth-order in the xenon interaction potential including dynamic effects within the Einstein approximation. Again we find very good agreement with the experimental (face-centred cubic) lattice constant and cohesive energy.

  19. Reliable and accurate extraction of Hamaker constants from surface force measurements.

    PubMed

    Miklavcic, S J

    2018-08-15

    A simple and accurate closed-form expression for the Hamaker constant that best represents experimental surface force data is presented. Numerical comparisons are made with the current standard least squares approach, which falsely assumes error-free separation measurements, and a nonlinear version assuming independent measurements of force and separation are subject to error. The comparisons demonstrate that not only is the proposed formula easily implemented it is also considerably more accurate. This option is appropriate for any value of Hamaker constant, high or low, and certainly for any interacting system exhibiting an inverse square distance dependent van der Waals force. Copyright © 2018 Elsevier Inc. All rights reserved.

  20. Validation of reference genes for quantitative gene expression analysis in experimental epilepsy.

    PubMed

    Sadangi, Chinmaya; Rosenow, Felix; Norwood, Braxton A

    2017-12-01

    To grasp the molecular mechanisms and pathophysiology underlying epilepsy development (epileptogenesis) and epilepsy itself, it is important to understand the gene expression changes that occur during these phases. Quantitative real-time polymerase chain reaction (qPCR) is a technique that rapidly and accurately determines gene expression changes. It is crucial, however, that stable reference genes are selected for each experimental condition to ensure that accurate values are obtained for genes of interest. If reference genes are unstably expressed, this can lead to inaccurate data and erroneous conclusions. To date, epilepsy studies have used mostly single, nonvalidated reference genes. This is the first study to systematically evaluate reference genes in male Sprague-Dawley rat models of epilepsy. We assessed 15 potential reference genes in hippocampal tissue obtained from 2 different models during epileptogenesis, 1 model during chronic epilepsy, and a model of noninjurious seizures. Reference gene ranking varied between models and also differed between epileptogenesis and chronic epilepsy time points. There was also some variance between the four mathematical models used to rank reference genes. Notably, we found novel reference genes to be more stably expressed than those most often used in experimental epilepsy studies. The consequence of these findings is that reference genes suitable for one epilepsy model may not be appropriate for others and that reference genes can change over time. It is, therefore, critically important to validate potential reference genes before using them as normalizing factors in expression analysis in order to ensure accurate, valid results. © 2017 Wiley Periodicals, Inc.

  1. Experimental realization of a subwavelength optical potential based on atomic dark state

    NASA Astrophysics Data System (ADS)

    Wang, Yang; Subhankar, Sarthak; Rolston, Steven; Porto, James

    2017-04-01

    As a well-established tool optical lattice (OL) provides the unique opportunity to exploit the rich manybody physics. However, ``traditional'' OL, either via laser beam interference or direct projection with spatial light modulator, has a length scale around the wavelength (0.1 10 λ) that is set by diffraction, a fundamental limit from the wave nature of the light. Recent theoretical proposals suggest an alternative route, where the geometric potential, stemming from light-atom interaction, can be engineered to generate a much finer potential landscape which is essentially limited by the wave nature of the slow moving cold atoms. We report on the progress towards an experimental realization of these ideas using degenerate fermionic ytterbium atoms. Such subwavelength optical potential could open the gate to study physics beyond currently available parameter regimes, such as enhanced super-exchange coupling, magnetic dipolar coupling, and tunnel junction in atomtronics.

  2. A compact and accurate semi-global potential energy surface for malonaldehyde from constrained least squares regression

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Mizukami, Wataru, E-mail: wataru.mizukami@bristol.ac.uk; Tew, David P., E-mail: david.tew@bristol.ac.uk; Habershon, Scott, E-mail: S.Habershon@warwick.ac.uk

    2014-10-14

    We present a new approach to semi-global potential energy surface fitting that uses the least absolute shrinkage and selection operator (LASSO) constrained least squares procedure to exploit an extremely flexible form for the potential function, while at the same time controlling the risk of overfitting and avoiding the introduction of unphysical features such as divergences or high-frequency oscillations. Drawing from a massively redundant set of overlapping distributed multi-dimensional Gaussian functions of inter-atomic separations we build a compact full-dimensional surface for malonaldehyde, fit to explicitly correlated coupled cluster CCSD(T)(F12*) energies with a root mean square deviations accuracy of 0.3%–0.5% up tomore » 25 000 cm{sup −1} above equilibrium. Importance-sampled diffusion Monte Carlo calculations predict zero point energies for malonaldehyde and its deuterated isotopologue of 14 715.4(2) and 13 997.9(2) cm{sup −1} and hydrogen transfer tunnelling splittings of 21.0(4) and 3.2(4) cm{sup −1}, respectively, which are in excellent agreement with the experimental values of 21.583 and 2.915(4) cm{sup −1}.« less

  3. Accurate and Efficient Approximation to the Optimized Effective Potential for Exchange

    NASA Astrophysics Data System (ADS)

    Ryabinkin, Ilya G.; Kananenka, Alexei A.; Staroverov, Viktor N.

    2013-07-01

    We devise an efficient practical method for computing the Kohn-Sham exchange-correlation potential corresponding to a Hartree-Fock electron density. This potential is almost indistinguishable from the exact-exchange optimized effective potential (OEP) and, when used as an approximation to the OEP, is vastly better than all existing models. Using our method one can obtain unambiguous, nearly exact OEPs for any reasonable finite one-electron basis set at the same low cost as the Krieger-Li-Iafrate and Becke-Johnson potentials. For all practical purposes, this solves the long-standing problem of black-box construction of OEPs in exact-exchange calculations.

  4. Numerical and experimental investigations of human swimming motions.

    PubMed

    Takagi, Hideki; Nakashima, Motomu; Sato, Yohei; Matsuuchi, Kazuo; Sanders, Ross H

    2016-08-01

    This paper reviews unsteady flow conditions in human swimming and identifies the limitations and future potential of the current methods of analysing unsteady flow. The capability of computational fluid dynamics (CFD) has been extended from approaches assuming steady-state conditions to consideration of unsteady/transient conditions associated with the body motion of a swimmer. However, to predict hydrodynamic forces and the swimmer's potential speeds accurately, more robust and efficient numerical methods are necessary, coupled with validation procedures, requiring detailed experimental data reflecting local flow. Experimental data obtained by particle image velocimetry (PIV) in this area are limited, because at present observations are restricted to a two-dimensional 1.0 m(2) area, though this could be improved if the output range of the associated laser sheet increased. Simulations of human swimming are expected to improve competitive swimming, and our review has identified two important advances relating to understanding the flow conditions affecting performance in front crawl swimming: one is a mechanism for generating unsteady fluid forces, and the other is a theory relating to increased speed and efficiency.

  5. Numerical and experimental investigations of human swimming motions

    PubMed Central

    Takagi, Hideki; Nakashima, Motomu; Sato, Yohei; Matsuuchi, Kazuo; Sanders, Ross H.

    2016-01-01

    ABSTRACT This paper reviews unsteady flow conditions in human swimming and identifies the limitations and future potential of the current methods of analysing unsteady flow. The capability of computational fluid dynamics (CFD) has been extended from approaches assuming steady-state conditions to consideration of unsteady/transient conditions associated with the body motion of a swimmer. However, to predict hydrodynamic forces and the swimmer’s potential speeds accurately, more robust and efficient numerical methods are necessary, coupled with validation procedures, requiring detailed experimental data reflecting local flow. Experimental data obtained by particle image velocimetry (PIV) in this area are limited, because at present observations are restricted to a two-dimensional 1.0 m2 area, though this could be improved if the output range of the associated laser sheet increased. Simulations of human swimming are expected to improve competitive swimming, and our review has identified two important advances relating to understanding the flow conditions affecting performance in front crawl swimming: one is a mechanism for generating unsteady fluid forces, and the other is a theory relating to increased speed and efficiency. PMID:26699925

  6. Accurate Phylogenetic Tree Reconstruction from Quartets: A Heuristic Approach

    PubMed Central

    Reaz, Rezwana; Bayzid, Md. Shamsuzzoha; Rahman, M. Sohel

    2014-01-01

    Supertree methods construct trees on a set of taxa (species) combining many smaller trees on the overlapping subsets of the entire set of taxa. A ‘quartet’ is an unrooted tree over taxa, hence the quartet-based supertree methods combine many -taxon unrooted trees into a single and coherent tree over the complete set of taxa. Quartet-based phylogeny reconstruction methods have been receiving considerable attentions in the recent years. An accurate and efficient quartet-based method might be competitive with the current best phylogenetic tree reconstruction methods (such as maximum likelihood or Bayesian MCMC analyses), without being as computationally intensive. In this paper, we present a novel and highly accurate quartet-based phylogenetic tree reconstruction method. We performed an extensive experimental study to evaluate the accuracy and scalability of our approach on both simulated and biological datasets. PMID:25117474

  7. Light Field Imaging Based Accurate Image Specular Highlight Removal

    PubMed Central

    Wang, Haoqian; Xu, Chenxue; Wang, Xingzheng; Zhang, Yongbing; Peng, Bo

    2016-01-01

    Specular reflection removal is indispensable to many computer vision tasks. However, most existing methods fail or degrade in complex real scenarios for their individual drawbacks. Benefiting from the light field imaging technology, this paper proposes a novel and accurate approach to remove specularity and improve image quality. We first capture images with specularity by the light field camera (Lytro ILLUM). After accurately estimating the image depth, a simple and concise threshold strategy is adopted to cluster the specular pixels into “unsaturated” and “saturated” category. Finally, a color variance analysis of multiple views and a local color refinement are individually conducted on the two categories to recover diffuse color information. Experimental evaluation by comparison with existed methods based on our light field dataset together with Stanford light field archive verifies the effectiveness of our proposed algorithm. PMID:27253083

  8. Accurately estimating PSF with straight lines detected by Hough transform

    NASA Astrophysics Data System (ADS)

    Wang, Ruichen; Xu, Liangpeng; Fan, Chunxiao; Li, Yong

    2018-04-01

    This paper presents an approach to estimating point spread function (PSF) from low resolution (LR) images. Existing techniques usually rely on accurate detection of ending points of the profile normal to edges. In practice however, it is often a great challenge to accurately localize profiles of edges from a LR image, which hence leads to a poor PSF estimation of the lens taking the LR image. For precisely estimating the PSF, this paper proposes firstly estimating a 1-D PSF kernel with straight lines, and then robustly obtaining the 2-D PSF from the 1-D kernel by least squares techniques and random sample consensus. Canny operator is applied to the LR image for obtaining edges and then Hough transform is utilized to extract straight lines of all orientations. Estimating 1-D PSF kernel with straight lines effectively alleviates the influence of the inaccurate edge detection on PSF estimation. The proposed method is investigated on both natural and synthetic images for estimating PSF. Experimental results show that the proposed method outperforms the state-ofthe- art and does not rely on accurate edge detection.

  9. Robust and accurate vectorization of line drawings.

    PubMed

    Hilaire, Xavier; Tombre, Karl

    2006-06-01

    This paper presents a method for vectorizing the graphical parts of paper-based line drawings. The method consists of separating the input binary image into layers of homogeneous thickness, skeletonizing each layer, segmenting the skeleton by a method based on random sampling, and simplifying the result. The segmentation method is robust with a best bound of 50 percent noise reached for indefinitely long primitives. Accurate estimation of the recognized vector's parameters is enabled by explicitly computing their feasibility domains. Theoretical performance analysis and expression of the complexity of the segmentation method are derived. Experimental results and comparisons with other vectorization systems are also provided.

  10. Accurate Identification of Fear Facial Expressions Predicts Prosocial Behavior

    PubMed Central

    Marsh, Abigail A.; Kozak, Megan N.; Ambady, Nalini

    2009-01-01

    The fear facial expression is a distress cue that is associated with the provision of help and prosocial behavior. Prior psychiatric studies have found deficits in the recognition of this expression by individuals with antisocial tendencies. However, no prior study has shown accuracy for recognition of fear to predict actual prosocial or antisocial behavior in an experimental setting. In 3 studies, the authors tested the prediction that individuals who recognize fear more accurately will behave more prosocially. In Study 1, participants who identified fear more accurately also donated more money and time to a victim in a classic altruism paradigm. In Studies 2 and 3, participants’ ability to identify the fear expression predicted prosocial behavior in a novel task designed to control for confounding variables. In Study 3, accuracy for recognizing fear proved a better predictor of prosocial behavior than gender, mood, or scores on an empathy scale. PMID:17516803

  11. Accurate identification of fear facial expressions predicts prosocial behavior.

    PubMed

    Marsh, Abigail A; Kozak, Megan N; Ambady, Nalini

    2007-05-01

    The fear facial expression is a distress cue that is associated with the provision of help and prosocial behavior. Prior psychiatric studies have found deficits in the recognition of this expression by individuals with antisocial tendencies. However, no prior study has shown accuracy for recognition of fear to predict actual prosocial or antisocial behavior in an experimental setting. In 3 studies, the authors tested the prediction that individuals who recognize fear more accurately will behave more prosocially. In Study 1, participants who identified fear more accurately also donated more money and time to a victim in a classic altruism paradigm. In Studies 2 and 3, participants' ability to identify the fear expression predicted prosocial behavior in a novel task designed to control for confounding variables. In Study 3, accuracy for recognizing fear proved a better predictor of prosocial behavior than gender, mood, or scores on an empathy scale.

  12. Accurate experimental determination of the isotope effects on the triple point temperature of water. I. Dependence on the 2H abundance

    NASA Astrophysics Data System (ADS)

    Faghihi, V.; Peruzzi, A.; Aerts-Bijma, A. T.; Jansen, H. G.; Spriensma, J. J.; van Geel, J.; Meijer, H. A. J.

    2015-12-01

    Variation in the isotopic composition of water is one of the major contributors to uncertainty in the realization of the triple point of water (TPW). Although the dependence of the TPW on the isotopic composition of the water has been known for years, there is still a lack of a detailed and accurate experimental determination of the values for the correction constants. This paper is the first of two articles (Part I and Part II) that address quantification of isotope abundance effects on the triple point temperature of water. In this paper, we describe our experimental assessment of the 2H isotope effect. We manufactured five triple point cells with prepared water mixtures with a range of 2H isotopic abundances encompassing widely the natural abundance range, while the 18O and 17O isotopic abundance were kept approximately constant and the 18O  -  17O ratio was close to the Meijer-Li relationship for natural waters. The selected range of 2H isotopic abundances led to cells that realised TPW temperatures between approximately  -140 μK to  +2500 μK with respect to the TPW temperature as realized by VSMOW (Vienna Standard Mean Ocean Water). Our experiment led to determination of the value for the δ2H correction parameter of A2H  =  673 μK / (‰ deviation of δ2H from VSMOW) with a combined uncertainty of 4 μK (k  =  1, or 1σ).

  13. Accurate deuterium spectroscopy for fundamental studies

    NASA Astrophysics Data System (ADS)

    Wcisło, P.; Thibault, F.; Zaborowski, M.; Wójtewicz, S.; Cygan, A.; Kowzan, G.; Masłowski, P.; Komasa, J.; Puchalski, M.; Pachucki, K.; Ciuryło, R.; Lisak, D.

    2018-07-01

    We present an accurate measurement of the weak quadrupole S(2) 2-0 line in self-perturbed D2 and theoretical ab initio calculations of both collisional line-shape effects and energy of this rovibrational transition. The spectra were collected at the 247-984 Torr pressure range with a frequency-stabilized cavity ring-down spectrometer linked to an optical frequency comb (OFC) referenced to a primary time standard. Our line-shape modeling employed quantum calculations of molecular scattering (the pressure broadening and shift and their speed dependencies were calculated, while the complex frequency of optical velocity-changing collisions was fitted to experimental spectra). The velocity-changing collisions are handled with the hard-sphere collisional kernel. The experimental and theoretical pressure broadening and shift are consistent within 5% and 27%, respectively (the discrepancy for shift is 8% when referred not to the speed averaged value, which is close to zero, but to the range of variability of the speed-dependent shift). We use our high pressure measurement to determine the energy, ν0, of the S(2) 2-0 transition. The ab initio line-shape calculations allowed us to mitigate the expected collisional systematics reaching the 410 kHz accuracy of ν0. We report theoretical determination of ν0 taking into account relativistic and QED corrections up to α5. Our estimation of the accuracy of the theoretical ν0 is 1.3 MHz. We observe 3.4σ discrepancy between experimental and theoretical ν0.

  14. A sEMG model with experimentally based simulation parameters.

    PubMed

    Wheeler, Katherine A; Shimada, Hiroshima; Kumar, Dinesh K; Arjunan, Sridhar P

    2010-01-01

    A differential, time-invariant, surface electromyogram (sEMG) model has been implemented. While it is based on existing EMG models, the novelty of this implementation is that it assigns more accurate distributions of variables to create realistic motor unit (MU) characteristics. Variables such as muscle fibre conduction velocity, jitter (the change in the interpulse interval between subsequent action potential firings) and motor unit size have been considered to follow normal distributions about an experimentally obtained mean. In addition, motor unit firing frequencies have been considered to have non-linear and type based distributions that are in accordance with experimental results. Motor unit recruitment thresholds have been considered to be related to the MU type. The model has been used to simulate single channel differential sEMG signals from voluntary, isometric contractions of the biceps brachii muscle. The model has been experimentally verified by conducting experiments on three subjects. Comparison between simulated signals and experimental recordings shows that the Root Mean Square (RMS) increases linearly with force in both cases. The simulated signals also show similar values and rates of change of RMS to the experimental signals.

  15. Accurate respiration measurement using DC-coupled continuous-wave radar sensor for motion-adaptive cancer radiotherapy.

    PubMed

    Gu, Changzhan; Li, Ruijiang; Zhang, Hualiang; Fung, Albert Y C; Torres, Carlos; Jiang, Steve B; Li, Changzhi

    2012-11-01

    Accurate respiration measurement is crucial in motion-adaptive cancer radiotherapy. Conventional methods for respiration measurement are undesirable because they are either invasive to the patient or do not have sufficient accuracy. In addition, measurement of external respiration signal based on conventional approaches requires close patient contact to the physical device which often causes patient discomfort and undesirable motion during radiation dose delivery. In this paper, a dc-coupled continuous-wave radar sensor was presented to provide a noncontact and noninvasive approach for respiration measurement. The radar sensor was designed with dc-coupled adaptive tuning architectures that include RF coarse-tuning and baseband fine-tuning, which allows the radar sensor to precisely measure movement with stationary moment and always work with the maximum dynamic range. The accuracy of respiration measurement with the proposed radar sensor was experimentally evaluated using a physical phantom, human subject, and moving plate in a radiotherapy environment. It was shown that respiration measurement with radar sensor while the radiation beam is on is feasible and the measurement has a submillimeter accuracy when compared with a commercial respiration monitoring system which requires patient contact. The proposed radar sensor provides accurate, noninvasive, and noncontact respiration measurement and therefore has a great potential in motion-adaptive radiotherapy.

  16. Improvement of experimental testing and network training conditions with genome-wide microarrays for more accurate predictions of drug gene targets

    PubMed Central

    2014-01-01

    Background Genome-wide microarrays have been useful for predicting chemical-genetic interactions at the gene level. However, interpreting genome-wide microarray results can be overwhelming due to the vast output of gene expression data combined with off-target transcriptional responses many times induced by a drug treatment. This study demonstrates how experimental and computational methods can interact with each other, to arrive at more accurate predictions of drug-induced perturbations. We present a two-stage strategy that links microarray experimental testing and network training conditions to predict gene perturbations for a drug with a known mechanism of action in a well-studied organism. Results S. cerevisiae cells were treated with the antifungal, fluconazole, and expression profiling was conducted under different biological conditions using Affymetrix genome-wide microarrays. Transcripts were filtered with a formal network-based method, sparse simultaneous equation models and Lasso regression (SSEM-Lasso), under different network training conditions. Gene expression results were evaluated using both gene set and single gene target analyses, and the drug’s transcriptional effects were narrowed first by pathway and then by individual genes. Variables included: (i) Testing conditions – exposure time and concentration and (ii) Network training conditions – training compendium modifications. Two analyses of SSEM-Lasso output – gene set and single gene – were conducted to gain a better understanding of how SSEM-Lasso predicts perturbation targets. Conclusions This study demonstrates that genome-wide microarrays can be optimized using a two-stage strategy for a more in-depth understanding of how a cell manifests biological reactions to a drug treatment at the transcription level. Additionally, a more detailed understanding of how the statistical model, SSEM-Lasso, propagates perturbations through a network of gene regulatory interactions is achieved

  17. Calibration-quality adiabatic potential energy surfaces for H3(+) and its isotopologues.

    PubMed

    Pavanello, Michele; Adamowicz, Ludwik; Alijah, Alexander; Zobov, Nikolai F; Mizus, Irina I; Polyansky, Oleg L; Tennyson, Jonathan; Szidarovszky, Tamás; Császár, Attila G

    2012-05-14

    Calibration-quality ab initio adiabatic potential energy surfaces (PES) have been determined for all isotopologues of the molecular ion H(3)(+). The underlying Born-Oppenheimer electronic structure computations used optimized explicitly correlated shifted Gaussian functions. The surfaces include diagonal Born-Oppenheimer corrections computed from the accurate electronic wave functions. A fit to the 41,655 ab initio points is presented which gives a standard deviation better than 0.1 cm(-1) when restricted to the points up to 6000 cm(-1) above the first dissociation asymptote. Nuclear motion calculations utilizing this PES, called GLH3P, and an exact kinetic energy operator given in orthogonal internal coordinates are presented. The ro-vibrational transition frequencies for H(3)(+), H(2)D(+), and HD(2)(+) are compared with high resolution measurements. The most sophisticated and complete procedure employed to compute ro-vibrational energy levels, which makes explicit allowance for the inclusion of non-adiabatic effects, reproduces all the known ro-vibrational levels of the H(3)(+) isotopologues considered to better than 0.2 cm(-1). This represents a significant (order-of-magnitude) improvement compared to previous studies of transitions in the visible. Careful treatment of linear geometries is important for high frequency transitions and leads to new assignments for some of the previously observed lines. Prospects for further investigations of non-adiabatic effects in the H(3)(+) isotopologues are discussed. In short, the paper presents (a) an extremely accurate global potential energy surface of H(3)(+) resulting from high accuracy ab initio computations and global fit, (b) very accurate nuclear motion calculations of all available experimental line data up to 16,000 cm(-1), and (c) results suggest that we can predict accurately the lines of H(3)(+) towards dissociation and thus facilitate their experimental observation.

  18. Calibration-quality adiabatic potential energy surfaces for H3+ and its isotopologues

    NASA Astrophysics Data System (ADS)

    Pavanello, Michele; Adamowicz, Ludwik; Alijah, Alexander; Zobov, Nikolai F.; Mizus, Irina I.; Polyansky, Oleg L.; Tennyson, Jonathan; Szidarovszky, Tamás; Császár, Attila G.

    2012-05-01

    Calibration-quality ab initio adiabatic potential energy surfaces (PES) have been determined for all isotopologues of the molecular ion H_3^+. The underlying Born-Oppenheimer electronic structure computations used optimized explicitly correlated shifted Gaussian functions. The surfaces include diagonal Born-Oppenheimer corrections computed from the accurate electronic wave functions. A fit to the 41 655 ab initio points is presented which gives a standard deviation better than 0.1 cm-1 when restricted to the points up to 6000 cm-1 above the first dissociation asymptote. Nuclear motion calculations utilizing this PES, called GLH3P, and an exact kinetic energy operator given in orthogonal internal coordinates are presented. The ro-vibrational transition frequencies for H_3^+, H2D+, and HD_2^+ are compared with high resolution measurements. The most sophisticated and complete procedure employed to compute ro-vibrational energy levels, which makes explicit allowance for the inclusion of non-adiabatic effects, reproduces all the known ro-vibrational levels of the H_3^+ isotopologues considered to better than 0.2 cm-1. This represents a significant (order-of-magnitude) improvement compared to previous studies of transitions in the visible. Careful treatment of linear geometries is important for high frequency transitions and leads to new assignments for some of the previously observed lines. Prospects for further investigations of non-adiabatic effects in the H_3^+ isotopologues are discussed. In short, the paper presents (a) an extremely accurate global potential energy surface of H_3^+ resulting from high accuracy ab initio computations and global fit, (b) very accurate nuclear motion calculations of all available experimental line data up to 16 000 cm-1, and (c) results suggest that we can predict accurately the lines of H_3^+ towards dissociation and thus facilitate their experimental observation.

  19. Experimental investigation to evaluate the potential environmental hazards of photovoltaic panels.

    PubMed

    Tammaro, Marco; Salluzzo, Antonio; Rimauro, Juri; Schiavo, Simona; Manzo, Sonia

    2016-04-05

    Recently the potential environmental hazard of photovoltaic modules together with their management as waste has attracted the attention of scientists. Particular concern is aroused by the several metals contained in photovoltaic panels whose potential release in the environment were scarcely investigated. Here, for the first time, the potential environmental hazard of panels produced in the last 30 years was investigated through the assessment of up to 18 releasable metals. Besides, the corresponding ecotoxicological effects were also evaluated. Experimental data were compared with the current European and Italian law limits for drinking water, discharge on soil and landfill inert disposal in order to understand the actual pollution load. Results showed that less than 3% of the samples respected all law limits and around 21% was not ecotoxic. By considering the technological evolutions in manufacturing, we have shown that during the years crystalline silicon panels have lower tendency to release hazardous metals with respect to thin film panels. In addition, a prediction of the amounts of lead, chromium, cadmium and nickel releasable from next photovoltaic waste was performed. The prevision up to 2050 showed high amounts of lead (30t) and cadmium (2.9t) releasable from crystalline and thin film panels respectively. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. Experimental evidence for non-Abelian gauge potentials in twisted graphene bilayers

    NASA Astrophysics Data System (ADS)

    Yin, Long-Jing; Qiao, Jia-Bin; Zuo, Wei-Jie; Li, Wen-Tian; He, Lin

    2015-08-01

    Non-Abelian gauge potentials are quite relevant in subatomic physics, but they are relatively rare in a condensed matter context. Here we report the experimental evidence for non-Abelian gauge potentials in twisted graphene bilayers by scanning tunneling microscopy and spectroscopy. At a magic twisted angle, θ ≈(1.11±0.05 ) ∘ , a pronounced sharp peak, which arises from the nondispersive flat bands at the charge neutrality point, is observed in the tunneling density of states due to the action of the non-Abelian gauge fields. Moreover, we observe confined electronic states in the twisted bilayer, as manifested by regularly spaced tunneling peaks with energy spacing δ E ≈vF/D ≈70 meV (here vF is the Fermi velocity of graphene and D is the period of the moiré patterns). This indicates that the non-Abelian gauge potentials in twisted graphene bilayers confine low-energy electrons into a triangular array of quantum dots following the modulation of the moiré patterns. Our results also directly demonstrate that the Fermi velocity in twisted bilayers can be tuned from about 106m /s to zero by simply reducing the twisted angle of about 2∘.

  1. Accurate acoustic power measurement for low-intensity focused ultrasound using focal axial vibration velocity

    NASA Astrophysics Data System (ADS)

    Tao, Chenyang; Guo, Gepu; Ma, Qingyu; Tu, Juan; Zhang, Dong; Hu, Jimin

    2017-07-01

    Low-intensity focused ultrasound is a form of therapy that can have reversible acoustothermal effects on biological tissue, depending on the exposure parameters. The acoustic power (AP) should be chosen with caution for the sake of safety. To recover the energy of counteracted radial vibrations at the focal point, an accurate AP measurement method using the focal axial vibration velocity (FAVV) is proposed in explicit formulae and is demonstrated experimentally using a laser vibrometer. The experimental APs for two transducers agree well with theoretical calculations and numerical simulations, showing that AP is proportional to the square of the FAVV, with a fixed power gain determined by the physical parameters of the transducers. The favorable results suggest that the FAVV can be used as a valuable parameter for non-contact AP measurement, providing a new strategy for accurate power control for low-intensity focused ultrasound in biomedical engineering.

  2. Assessment of empirical potential for MOX nuclear fuels and thermomechanical properties

    NASA Astrophysics Data System (ADS)

    Balboa, Hector; Van Brutzel, Laurent; Chartier, Alain; Le Bouar, Yann

    2017-11-01

    We assess five empirical interatomic potentials in the approximation of rigid ions and pair interactions for the (U1-y,Puy)O solid solution. The assessment compares available experimental data and Fink's recommendation with simulations on: the structural, thermodynamics, and mechanical properties over the full range of plutonium composition, from pure UO2 to pure PuO2 and for temperatures ranging from 300 K to the melting point. The best results are obtained by potentials referred as Cooper and Potashnikov potentials. The first one reproduces more accurately recommendations for the thermodynamics and mechanical properties exhibiting ductile-like behaviour during crack propagation, while the second one gives brittle behaviour at low temperature.

  3. Evaluating the use of electronegativity in band alignment models through the experimental slope parameter of lanthanum aluminate heterostructures

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Liu, Z. Q.; Chim, W. K.; Chiam, S. Y

    2011-11-01

    In this work, photoelectron spectroscopy is used to characterize the band alignment of lanthanum aluminate heterostructures which possess a wide range of potential applications. It is found that our experimental slope parameter agrees with theory using the metal-induced gap states model while the interface induced gap states (IFIGS) model yields unsatisfactory results. We show that this discrepancy can be attributed to the correlation between the dielectric work function and the electronegativity in the IFIGS model. It is found that the original trend, as established largely by metals, may not be accurate for larger band gap materials. By using a newmore » correlation, our experimental data shows good agreement of the slope parameter using the IFIGS model. This correlation, therefore, plays a crucial role in heterostructures involving wider bandgap materials for accurate band alignment prediction using the IFIGS model.« less

  4. Accurate modelling of unsteady flows in collapsible tubes.

    PubMed

    Marchandise, Emilie; Flaud, Patrice

    2010-01-01

    The context of this paper is the development of a general and efficient numerical haemodynamic tool to help clinicians and researchers in understanding of physiological flow phenomena. We propose an accurate one-dimensional Runge-Kutta discontinuous Galerkin (RK-DG) method coupled with lumped parameter models for the boundary conditions. The suggested model has already been successfully applied to haemodynamics in arteries and is now extended for the flow in collapsible tubes such as veins. The main difference with cardiovascular simulations is that the flow may become supercritical and elastic jumps may appear with the numerical consequence that scheme may not remain monotone if no limiting procedure is introduced. We show that our second-order RK-DG method equipped with an approximate Roe's Riemann solver and a slope-limiting procedure allows us to capture elastic jumps accurately. Moreover, this paper demonstrates that the complex physics associated with such flows is more accurately modelled than with traditional methods such as finite difference methods or finite volumes. We present various benchmark problems that show the flexibility and applicability of the numerical method. Our solutions are compared with analytical solutions when they are available and with solutions obtained using other numerical methods. Finally, to illustrate the clinical interest, we study the emptying process in a calf vein squeezed by contracting skeletal muscle in a normal and pathological subject. We compare our results with experimental simulations and discuss the sensitivity to parameters of our model.

  5. An accurate computational method for the diffusion regime verification

    NASA Astrophysics Data System (ADS)

    Zhokh, Alexey A.; Strizhak, Peter E.

    2018-04-01

    The diffusion regime (sub-diffusive, standard, or super-diffusive) is defined by the order of the derivative in the corresponding transport equation. We develop an accurate computational method for the direct estimation of the diffusion regime. The method is based on the derivative order estimation using the asymptotic analytic solutions of the diffusion equation with the integer order and the time-fractional derivatives. The robustness and the computational cheapness of the proposed method are verified using the experimental methane and methyl alcohol transport kinetics through the catalyst pellet.

  6. Accurate determinations of alpha(s) from realistic lattice QCD.

    PubMed

    Mason, Q; Trottier, H D; Davies, C T H; Foley, K; Gray, A; Lepage, G P; Nobes, M; Shigemitsu, J

    2005-07-29

    We obtain a new value for the QCD coupling constant by combining lattice QCD simulations with experimental data for hadron masses. Our lattice analysis is the first to (1) include vacuum polarization effects from all three light-quark flavors (using MILC configurations), (2) include third-order terms in perturbation theory, (3) systematically estimate fourth and higher-order terms, (4) use an unambiguous lattice spacing, and (5) use an [symbol: see text](a2)-accurate QCD action. We use 28 different (but related) short-distance quantities to obtain alpha((5)/(MS))(M(Z)) = 0.1170(12).

  7. Experimental and Theoretical Study of Heat Conduction for Air up to 5000 K

    NASA Technical Reports Server (NTRS)

    Peng, Tzy-Cheng; Ahtye, Warren F.

    1961-01-01

    The theoretical value of the integral of thermal conductivity is compared with the experimental values from shock-tube measurements. The particular case considered is the one-dimensional nonsteady flow of heat through air at constant pressure. This approach has been previously described in NASA TR R-27. experiment was uncertain because of the large scatter in the experimental data. In this paper, an attempt is made to improve the correlation by use of a more refined calculation of the integral of thermal conductivity, and by use of improved experimental techniques and instrumentation. As a result of these changes, a much closer correlation is shown between the experimental and theoretical heat-flux potentials. This indicates that the predicted values of the coefficient of thermal conductivity for high-temperature air may be suitably accurate for many engineering needs, up to the limits of the test (4600 K).

  8. A novel method for the accurate evaluation of Poisson's ratio of soft polymer materials.

    PubMed

    Lee, Jae-Hoon; Lee, Sang-Soo; Chang, Jun-Dong; Thompson, Mark S; Kang, Dong-Joong; Park, Sungchan; Park, Seonghun

    2013-01-01

    A new method with a simple algorithm was developed to accurately measure Poisson's ratio of soft materials such as polyvinyl alcohol hydrogel (PVA-H) with a custom experimental apparatus consisting of a tension device, a micro X-Y stage, an optical microscope, and a charge-coupled device camera. In the proposed method, the initial positions of the four vertices of an arbitrarily selected quadrilateral from the sample surface were first measured to generate a 2D 1st-order 4-node quadrilateral element for finite element numerical analysis. Next, minimum and maximum principal strains were calculated from differences between the initial and deformed shapes of the quadrilateral under tension. Finally, Poisson's ratio of PVA-H was determined by the ratio of minimum principal strain to maximum principal strain. This novel method has an advantage in the accurate evaluation of Poisson's ratio despite misalignment between specimens and experimental devices. In this study, Poisson's ratio of PVA-H was 0.44 ± 0.025 (n = 6) for 2.6-47.0% elongations with a tendency to decrease with increasing elongation. The current evaluation method of Poisson's ratio with a simple measurement system can be employed to a real-time automated vision-tracking system which is used to accurately evaluate the material properties of various soft materials.

  9. Highly Accurate Quantitative Analysis Of Enantiomeric Mixtures from Spatially Frequency Encoded 1H NMR Spectra.

    PubMed

    Plainchont, Bertrand; Pitoux, Daisy; Cyrille, Mathieu; Giraud, Nicolas

    2018-02-06

    We propose an original concept to measure accurately enantiomeric excesses on proton NMR spectra, which combines high-resolution techniques based on a spatial encoding of the sample, with the use of optically active weakly orienting solvents. We show that it is possible to simulate accurately dipolar edited spectra of enantiomers dissolved in a chiral liquid crystalline phase, and to use these simulations to calibrate integrations that can be measured on experimental data, in order to perform a quantitative chiral analysis. This approach is demonstrated on a chemical intermediate for which optical purity is an essential criterion. We find that there is a very good correlation between the experimental and calculated integration ratios extracted from G-SERF spectra, which paves the way to a general method of determination of enantiomeric excesses based on the observation of 1 H nuclei.

  10. Accurate radiative transfer calculations for layered media.

    PubMed

    Selden, Adrian C

    2016-07-01

    Simple yet accurate results for radiative transfer in layered media with discontinuous refractive index are obtained by the method of K-integrals. These are certain weighted integrals applied to the angular intensity distribution at the refracting boundaries. The radiative intensity is expressed as the sum of the asymptotic angular intensity distribution valid in the depth of the scattering medium and a transient term valid near the boundary. Integrated boundary equations are obtained, yielding simple linear equations for the intensity coefficients, enabling the angular emission intensity and the diffuse reflectance (albedo) and transmittance of the scattering layer to be calculated without solving the radiative transfer equation directly. Examples are given of half-space, slab, interface, and double-layer calculations, and extensions to multilayer systems are indicated. The K-integral method is orders of magnitude more accurate than diffusion theory and can be applied to layered scattering media with a wide range of scattering albedos, with potential applications to biomedical and ocean optics.

  11. Magnetohydrodynamic generator experimental studies

    NASA Technical Reports Server (NTRS)

    Pierson, E. S.

    1972-01-01

    The results for an experimental study of a one wavelength MHD induction generator operating on a liquid flow are presented. First the design philosophy and the experimental generator design are summarized, including a description of the flow loop and instrumentation. Next a Fourier series method of treating the fact that the magnetic flux density produced by the stator is not a pure traveling sinusoid is described and some results summarized. This approach appears to be of interest after revisions are made, but the initial results are not accurate. Finally, some of the experimental data is summarized for various methods of excitation.

  12. Accurate Determination of the Frequency Response Function of Submerged and Confined Structures by Using PZT-Patches†.

    PubMed

    Presas, Alexandre; Valentin, David; Egusquiza, Eduard; Valero, Carme; Egusquiza, Mònica; Bossio, Matias

    2017-03-22

    To accurately determine the dynamic response of a structure is of relevant interest in many engineering applications. Particularly, it is of paramount importance to determine the Frequency Response Function (FRF) for structures subjected to dynamic loads in order to avoid resonance and fatigue problems that can drastically reduce their useful life. One challenging case is the experimental determination of the FRF of submerged and confined structures, such as hydraulic turbines, which are greatly affected by dynamic problems as reported in many cases in the past. The utilization of classical and calibrated exciters such as instrumented hammers or shakers to determine the FRF in such structures can be very complex due to the confinement of the structure and because their use can disturb the boundary conditions affecting the experimental results. For such cases, Piezoelectric Patches (PZTs), which are very light, thin and small, could be a very good option. Nevertheless, the main drawback of these exciters is that the calibration as dynamic force transducers (relationship voltage/force) has not been successfully obtained in the past. Therefore, in this paper, a method to accurately determine the FRF of submerged and confined structures by using PZTs is developed and validated. The method consists of experimentally determining some characteristic parameters that define the FRF, with an uncalibrated PZT exciting the structure. These parameters, which have been experimentally determined, are then introduced in a validated numerical model of the tested structure. In this way, the FRF of the structure can be estimated with good accuracy. With respect to previous studies, where only the natural frequencies and mode shapes were considered, this paper discuss and experimentally proves the best excitation characteristic to obtain also the damping ratios and proposes a procedure to fully determine the FRF. The method proposed here has been validated for the structure vibrating

  13. In vitro osteogenic/dentinogenic potential of an experimental calcium aluminosilicate cement

    PubMed Central

    Eid, Ashraf A.; Niu, Li-na; Primus, Carolyn M.; Opperman, Lynne A.; Watanabe, Ikuya; Pashley, David H.; Tay, Franklin R.

    2013-01-01

    Introduction Calcium aluminosilicate cements are fast-setting, acid-resistant, bioactive cements that may be used as root-repair materials. This study examined the osteogenic/dentinogenic potential of an experimental calcium aluminosilicate cement (Quick-Set) using a murine odontoblast-like cell model. Methods Quick-Set and white ProRoot MTA (WMTA) were mixed with the proprietary gel or deionized water, allowed to set completely in 100% relative humidity and aged in complete growth medium for 2 weeks until rendered non-cytotoxic. Similarly-aged Teflon discs were used as negative control. The MDPC-23 cell-line was used for evaluating changes in mRNA expressions of genes associated with osteogenic/dentinogenic differentiation and mineralization (qRT-PCR) alkaline phosphatase enzyme production and extracellular matrix mineralization (Alizarin red-S staining). Results After MDPC-23 cells were incubated with the materials in osteogenic differentiation medium for 1 week, both cements showed upregulation in ALP and DSPP expression. Fold increases in these two genes were not significantly different between Quick-Set and WMTA. Both cements showed no statistically significant upregulation/downregulation in RUNX2, OCN, BSP and DMP1 gene expression compared with Teflon. Alkaline phosphatase activity of cells cultured on Quick-Set and WMTA were not significantly different at 1 week or 2 weeks, but were significantly higher (p<0.05) than Teflon in both weeks. Both cements showed significantly higher calcium deposition compared with Teflon after 3 weeks of incubation in mineralizing medium (p<0.001). Differences between Quick-Set and WMTA were not statistically significant. Conclusions The experimental calcium aluminosilicate cement exhibits similar osteogenic/dentinogenic properties to WMTA and may be a potential substitute for commercially-available tricalcium silicate cements. PMID:23953291

  14. Accurate Construction of Photoactivated Localization Microscopy (PALM) Images for Quantitative Measurements

    PubMed Central

    Coltharp, Carla; Kessler, Rene P.; Xiao, Jie

    2012-01-01

    Localization-based superresolution microscopy techniques such as Photoactivated Localization Microscopy (PALM) and Stochastic Optical Reconstruction Microscopy (STORM) have allowed investigations of cellular structures with unprecedented optical resolutions. One major obstacle to interpreting superresolution images, however, is the overcounting of molecule numbers caused by fluorophore photoblinking. Using both experimental and simulated images, we determined the effects of photoblinking on the accurate reconstruction of superresolution images and on quantitative measurements of structural dimension and molecule density made from those images. We found that structural dimension and relative density measurements can be made reliably from images that contain photoblinking-related overcounting, but accurate absolute density measurements, and consequently faithful representations of molecule counts and positions in cellular structures, require the application of a clustering algorithm to group localizations that originate from the same molecule. We analyzed how applying a simple algorithm with different clustering thresholds (tThresh and dThresh) affects the accuracy of reconstructed images, and developed an easy method to select optimal thresholds. We also identified an empirical criterion to evaluate whether an imaging condition is appropriate for accurate superresolution image reconstruction with the clustering algorithm. Both the threshold selection method and imaging condition criterion are easy to implement within existing PALM clustering algorithms and experimental conditions. The main advantage of our method is that it generates a superresolution image and molecule position list that faithfully represents molecule counts and positions within a cellular structure, rather than only summarizing structural properties into ensemble parameters. This feature makes it particularly useful for cellular structures of heterogeneous densities and irregular geometries, and

  15. Image Capture with Synchronized Multiple-Cameras for Extraction of Accurate Geometries

    NASA Astrophysics Data System (ADS)

    Koehl, M.; Delacourt, T.; Boutry, C.

    2016-06-01

    This paper presents a project of recording and modelling tunnels, traffic circles and roads from multiple sensors. The aim is the representation and the accurate 3D modelling of a selection of road infrastructures as dense point clouds in order to extract profiles and metrics from it. Indeed, these models will be used for the sizing of infrastructures in order to simulate exceptional convoy truck routes. The objective is to extract directly from the point clouds the heights, widths and lengths of bridges and tunnels, the diameter of gyrating and to highlight potential obstacles for a convoy. Light, mobile and fast acquisition approaches based on images and videos from a set of synchronized sensors have been tested in order to obtain useable point clouds. The presented solution is based on a combination of multiple low-cost cameras designed on an on-boarded device allowing dynamic captures. The experimental device containing GoPro Hero4 cameras has been set up and used for tests in static or mobile acquisitions. That way, various configurations have been tested by using multiple synchronized cameras. These configurations are discussed in order to highlight the best operational configuration according to the shape of the acquired objects. As the precise calibration of each sensor and its optics are major factors in the process of creation of accurate dense point clouds, and in order to reach the best quality available from such cameras, the estimation of the internal parameters of fisheye lenses of the cameras has been processed. Reference measures were also realized by using a 3D TLS (Faro Focus 3D) to allow the accuracy assessment.

  16. Band-structure calculations of noble-gas and alkali halide solids using accurate Kohn-Sham potentials with self-interaction correction

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Li, Y.; Krieger, J.B.; Norman, M.R.

    1991-11-15

    The optimized-effective-potential (OEP) method and a method developed recently by Krieger, Li, and Iafrate (KLI) are applied to the band-structure calculations of noble-gas and alkali halide solids employing the self-interaction-corrected (SIC) local-spin-density (LSD) approximation for the exchange-correlation energy functional. The resulting band gaps from both calculations are found to be in fair agreement with the experimental values. The discrepancies are typically within a few percent with results that are nearly the same as those of previously published orbital-dependent multipotential SIC calculations, whereas the LSD results underestimate the band gaps by as much as 40%. As in the LSD---and it ismore » believed to be the case even for the exact Kohn-Sham potential---both the OEP and KLI predict valence-band widths which are narrower than those of experiment. In all cases, the KLI method yields essentially the same results as the OEP.« less

  17. 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.

  18. An entropy correction method for unsteady full potential flows with strong shocks

    NASA Technical Reports Server (NTRS)

    Whitlow, W., Jr.; Hafez, M. M.; Osher, S. J.

    1986-01-01

    An entropy correction method for the unsteady full potential equation is presented. The unsteady potential equation is modified to account for entropy jumps across shock waves. The conservative form of the modified equation is solved in generalized coordinates using an implicit, approximate factorization method. A flux-biasing differencing method, which generates the proper amounts of artificial viscosity in supersonic regions, is used to discretize the flow equations in space. Comparisons between the present method and solutions of the Euler equations and between the present method and experimental data are presented. The comparisons show that the present method more accurately models solutions of the Euler equations and experiment than does the isentropic potential formulation.

  19. A simplified approach to characterizing a kilovoltage source spectrum for accurate dose computation.

    PubMed

    Poirier, Yannick; Kouznetsov, Alexei; Tambasco, Mauro

    2012-06-01

    To investigate and validate the clinical feasibility of using half-value layer (HVL) and peak tube potential (kVp) for characterizing a kilovoltage (kV) source spectrum for the purpose of computing kV x-ray dose accrued from imaging procedures. To use this approach to characterize a Varian® On-Board Imager® (OBI) source and perform experimental validation of a novel in-house hybrid dose computation algorithm for kV x-rays. We characterized the spectrum of an imaging kV x-ray source using the HVL and the kVp as the sole beam quality identifiers using third-party freeware Spektr to generate the spectra. We studied the sensitivity of our dose computation algorithm to uncertainties in the beam's HVL and kVp by systematically varying these spectral parameters. To validate our approach experimentally, we characterized the spectrum of a Varian® OBI system by measuring the HVL using a Farmer-type Capintec ion chamber (0.06 cc) in air and compared dose calculations using our computationally validated in-house kV dose calculation code to measured percent depth-dose and transverse dose profiles for 80, 100, and 125 kVp open beams in a homogeneous phantom and a heterogeneous phantom comprising tissue, lung, and bone equivalent materials. The sensitivity analysis of the beam quality parameters (i.e., HVL, kVp, and field size) on dose computation accuracy shows that typical measurement uncertainties in the HVL and kVp (±0.2 mm Al and ±2 kVp, respectively) source characterization parameters lead to dose computation errors of less than 2%. Furthermore, for an open beam with no added filtration, HVL variations affect dose computation accuracy by less than 1% for a 125 kVp beam when field size is varied from 5 × 5 cm(2) to 40 × 40 cm(2). The central axis depth dose calculations and experimental measurements for the 80, 100, and 125 kVp energies agreed within 2% for the homogeneous and heterogeneous block phantoms, and agreement for the transverse dose profiles was within 6

  20. Zeta potential of microfluidic substrates: 1. Theory, experimental techniques, and effects on separations.

    PubMed

    Kirby, Brian J; Hasselbrink, Ernest F

    2004-01-01

    This paper summarizes theory, experimental techniques, and the reported data pertaining to the zeta potential of silica and silicon with attention to use as microfluidic substrate materials, particularly for microchip chemical separations. Dependence on cation concentration, buffer and cation type, pH, cation valency, and temperature are discussed. The Debye-Hückel limit, which is often correctly treated as a good approximation for describing the ion concentration in the double layer, can lead to serious errors if it is extended to predict the dependence of zeta potential on the counterion concentration. For indifferent univalent electrolytes (e.g., sodium and potassium), two simple scalings for the dependence of zeta potential on counterion concentration can be derived in high- and low-zeta limits of the nonlinear Poisson-Boltzman equation solution in the double layer. It is shown that for most situations relevant to microchip separations, the high-zeta limit is most applicable, leading to the conclusion that the zeta potential on silica substrates is approximately proportional to the logarithm of the molar counterion concentration. The zeta vs. pH dependence measurements from several experiments are compared by normalizing the zeta based on concentration.

  1. A fast, time-accurate unsteady full potential scheme

    NASA Technical Reports Server (NTRS)

    Shankar, V.; Ide, H.; Gorski, J.; Osher, S.

    1985-01-01

    The unsteady form of the full potential equation is solved in conservation form by an implicit method based on approximate factorization. At each time level, internal Newton iterations are performed to achieve time accuracy and computational efficiency. A local time linearization procedure is introduced to provide a good initial guess for the Newton iteration. A novel flux-biasing technique is applied to generate proper forms of the artificial viscosity to treat hyperbolic regions with shocks and sonic lines present. The wake is properly modeled by accounting not only for jumps in phi, but also for jumps in higher derivatives of phi, obtained by imposing the density to be continuous across the wake. The far field is modeled using the Riemann invariants to simulate nonreflecting boundary conditions. The resulting unsteady method performs well which, even at low reduced frequency levels of 0.1 or less, requires fewer than 100 time steps per cycle at transonic Mach numbers. The code is fully vectorized for the CRAY-XMP and the VPS-32 computers.

  2. An Accurately Controlled Antagonistic Shape Memory Alloy Actuator with Self-Sensing

    PubMed Central

    Wang, Tian-Miao; Shi, Zhen-Yun; Liu, Da; Ma, Chen; Zhang, Zhen-Hua

    2012-01-01

    With the progress of miniaturization, shape memory alloy (SMA) actuators exhibit high energy density, self-sensing ability and ease of fabrication, which make them well suited for practical applications. This paper presents a self-sensing controlled actuator drive that was designed using antagonistic pairs of SMA wires. Under a certain pre-strain and duty cycle, the stress between two wires becomes constant. Meanwhile, the strain to resistance curve can minimize the hysteresis gap between the heating and the cooling paths. The curves of both wires are then modeled by fitting polynomials such that the measured resistance can be used directly to determine the difference between the testing values and the target strain. The hysteresis model of strains to duty cycle difference has been used as compensation. Accurate control is demonstrated through step response and sinusoidal tracking. The experimental results show that, under a combination control program, the root-mean-square error can be reduced to 1.093%. The limited bandwidth of the frequency is estimated to be 0.15 Hz. Two sets of instruments with three degrees of freedom are illustrated to show how this type actuator could be potentially implemented. PMID:22969368

  3. Experimental measurements of thermoelectric and electrochemical potentials in sandstones saturated with NaCl electrolyte

    NASA Astrophysics Data System (ADS)

    Leinov, E.; Jackson, M.

    2013-12-01

    Measurements of the self-potential (SP) have been used to characterize subsurface flow in numerous settings, including volcanoes, earthquake zones, and geothermal fields. Thermoelectric (TE) and electrochemical (EC) potentials contribute to the measured SP if gradients in temperature and/or concentration are present, yet few experimental measurements of EC and TE potentials in natural porous media have been reported. Each is the sum of a diffusion and exclusion potential: the former arises when ions of contrasting mobility migrate at different rates down a temperature or concentration gradient; the latter arises when there is a temperature or concentration gradient across an electrically charged porous medium in which co-ions of the same polarity have been excluded from the pore-space. Here we report measurements of the SP arising from temperature or concentration gradients across clean (clay-free) sandstone samples saturated with NaCl electrolyte over the salinity range 5x10-5 to 1M. Electrical potentials are measured using non-polarizing Ag/AgCl electrodes, and temperature or salinity gradients are induced by placing the saturated samples in contact with electrolyte reservoirs of contrasting temperature or concentration. Our experimental methodology accounts for the temperature- and concentration-dependent electrode response. We find that the TE potential responds linearly to the applied temperature difference, allowing a TE potential coupling coefficient to be determined; the value of this decreases as the electrolyte concentration increases, from +0.056mV/K at 10-4 M to -0.126mV/K at 1M. The EC potential increases as the concentration ratio increases, from a minimum of 1.8mV at a salinity ratio of 1.13, to a maximum of 24.8mV at salinity ratio of 102, before decreasing to 19.5mV at salinity ratio of 103. In both cases, at high values of concentration (>0.01M) the measured potential is diffusion dominated, while at lower concentration the exclusion potential is

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

    DOE PAGES

    Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; ...

    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

  5. 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

  6. Accurately predicting the structure, density, and hydrostatic compression of crystalline β-1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane based on its wave-function-based potential

    NASA Astrophysics Data System (ADS)

    Song, H.-J.; Huang, F.

    2011-09-01

    A wave-function-based intermolecular potential of the β phase 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane (HMX) molecule has been constructed from first principles using the Williams-Stone-Misquitta method and the symmetry-adapted perturbation theory. Using the potential and its derivatives, we have accurately predicted not only the structure and lattice energy of the crystalline β-HMX at 0 K, but also its densities at temperatures of 0-403 K within an accuracy of 1% of density. The calculated densities at pressures within 0-6 GPa excellently agree with the results from the experiments on hydrostatic compression.

  7. Convergence in parameters and predictions using computational experimental design.

    PubMed

    Hagen, David R; White, Jacob K; Tidor, Bruce

    2013-08-06

    Typically, biological models fitted to experimental data suffer from significant parameter uncertainty, which can lead to inaccurate or uncertain predictions. One school of thought holds that accurate estimation of the true parameters of a biological system is inherently problematic. Recent work, however, suggests that optimal experimental design techniques can select sets of experiments whose members probe complementary aspects of a biochemical network that together can account for its full behaviour. Here, we implemented an experimental design approach for selecting sets of experiments that constrain parameter uncertainty. We demonstrated with a model of the epidermal growth factor-nerve growth factor pathway that, after synthetically performing a handful of optimal experiments, the uncertainty in all 48 parameters converged below 10 per cent. Furthermore, the fitted parameters converged to their true values with a small error consistent with the residual uncertainty. When untested experimental conditions were simulated with the fitted models, the predicted species concentrations converged to their true values with errors that were consistent with the residual uncertainty. This paper suggests that accurate parameter estimation is achievable with complementary experiments specifically designed for the task, and that the resulting parametrized models are capable of accurate predictions.

  8. Kinetics and dynamics of the C(3P) + H2O reaction on a full-dimensional accurate triplet state potential energy surface.

    PubMed

    Li, Jun; Xie, Changjian; Guo, Hua

    2017-08-30

    A full dimensional accurate potential energy surface (PES) for the C( 3 P) and H 2 O reaction is developed based on ∼34 000 data points calculated at the level of the explicitly correlated unrestricted coupled cluster method with single, double, and perturbative triple excitations with the augmented correlation-consistent polarized triple zeta basis set (CCSD(T)-F12a/AVTZ). The PES is invariant with respect to the permutation of the two hydrogen atoms and the total root mean square error (RMSE) of the fit is only 0.31 kcal mol -1 . The PES features two barriers in the entrance channel and several potential minima, as well as multiple product channels. The rate coefficients of this reaction calculated using a transition-state theory and quasi-classical trajectory (QCT) method are small near room temperature, consistent with experiments. The reaction dynamics is also investigated with QCT on the new PES, which found that the reactivity is constrained by the entrance barriers and the final product branching is not statistical.

  9. Baseline experimental investigation of an electrohydrodynamically assisted heat pipe

    NASA Technical Reports Server (NTRS)

    Duncan, A. B.

    1995-01-01

    The increases in power demand and associated thermal management requirements of future space programs such as potential Lunar/Mars missions will require enhancing the operating efficiencies of thermal management devices. Currently, the use of electrohydrodynamically (EHD) assisted thermal control devices is under consideration as a potential method of increasing thermal management system capacity. The objectives of the currently described investigation included completing build-up of the EHD-Assisted Heat Pipe Test bed, developing test procedures for an experimental evaluation of the unassisted heat pipe, developing an analytical model capable of predicting the performance limits of the unassisted heat pipe, and obtaining experimental data which would define the performance characteristics of the unassisted heat pipe. The information obtained in the currently proposed study will be used in order to provide extensive comparisons with the EHD-assisted performance observations to be obtained during the continuing investigation of EHD-Assisted heat transfer devices. Through comparisons of the baseline test bed data and the EHD assisted test bed data, accurate insight into the performance enhancing characteristics of EHD augmentation may be obtained. This may lead to optimization, development, and implementation of EHD technology for future space programs.

  10. Derivation of an optical potential for statically deformed rare-earth nuclei from a global spherical potential

    DOE PAGES

    Nobre, G. P. A.; Palumbo, A.; Herman, M.; ...

    2015-02-25

    The coupled-channel theory is a natural way of treating nonelastic channels, in particular those arising from collective excitations characterized by nuclear deformations. A proper treatment of such excitations is often essential to the accurate description of experimental nuclear-reaction data and to the prediction of a wide variety of scattering observables. Stimulated by recent work substantiating the near validity of the adiabatic approximation in coupled-channel calculations for scattering on statically deformed nuclei, we explore the possibility of generalizing a global spherical optical model potential (OMP) to make it usable in coupled-channel calculations on this class of nuclei. To do this, wemore » have deformed the Koning-Delaroche global spherical potential for neutrons, coupling a sufficient number of states of the ground state band to ensure convergence. We present an extensive study of the effects of collective couplings and nuclear deformations on integrated cross sections as well as on angular distributions for neutron-induced reactions on statically deformed nuclei in the rare-earth region. We choose isotopes of three rare-earth elements (Gd, Ho, W), which are known to be nearly perfect rotors, to exemplify the results of the proposed method. Predictions from our model for total, elastic and inelastic cross sections, as well as for elastic and inelastic angular distributions, are in reasonable agreement with measured experimental data. In conclusion, these results suggest that the deformed Koning-Delaroche potential provides a useful regional neutron optical potential for the statically deformed rare earth nuclei.« less

  11. Fast and Accurate Circuit Design Automation through Hierarchical Model Switching.

    PubMed

    Huynh, Linh; Tagkopoulos, Ilias

    2015-08-21

    In computer-aided biological design, the trifecta of characterized part libraries, accurate models and optimal design parameters is crucial for producing reliable designs. As the number of parts and model complexity increase, however, it becomes exponentially more difficult for any optimization method to search the solution space, hence creating a trade-off that hampers efficient design. To address this issue, we present a hierarchical computer-aided design architecture that uses a two-step approach for biological design. First, a simple model of low computational complexity is used to predict circuit behavior and assess candidate circuit branches through branch-and-bound methods. Then, a complex, nonlinear circuit model is used for a fine-grained search of the reduced solution space, thus achieving more accurate results. Evaluation with a benchmark of 11 circuits and a library of 102 experimental designs with known characterization parameters demonstrates a speed-up of 3 orders of magnitude when compared to other design methods that provide optimality guarantees.

  12. Accurate color synthesis of three-dimensional objects in an image

    NASA Astrophysics Data System (ADS)

    Xin, John H.; Shen, Hui-Liang

    2004-05-01

    Our study deals with color synthesis of a three-dimensional object in an image; i.e., given a single image, a target color can be accurately mapped onto the object such that the color appearance of the synthesized object closely resembles that of the actual one. As it is almost impossible to acquire the complete geometric description of the surfaces of an object in an image, this study attempted to recover the implicit description of geometry for the color synthesis. The description was obtained from either a series of spectral reflectances or the RGB signals at different surface positions on the basis of the dichromatic reflection model. The experimental results showed that this implicit image-based representation is related to the object geometry and is sufficient for accurate color synthesis of three-dimensional objects in an image. The method established is applicable to the color synthesis of both rigid and deformable objects and should contribute to color fidelity in virtual design, manufacturing, and retailing.

  13. Viscous/potential flow about multi-element two-dimensional and infinite-span swept wings: Theory and experiment

    NASA Technical Reports Server (NTRS)

    Olson, L. E.; Dvorak, F. A.

    1975-01-01

    The viscous subsonic flow past two-dimensional and infinite-span swept multi-component airfoils is studied theoretically and experimentally. The computerized analysis is based on iteratively coupled boundary layer and potential flow analysis. The method, which is restricted to flows with only slight separation, gives surface pressure distribution, chordwise and spanwise boundary layer characteristics, lift, drag, and pitching moment for airfoil configurations with up to four elements. Merging confluent boundary layers are treated. Theoretical predictions are compared with an exact theoretical potential flow solution and with experimental measures made in the Ames 40- by 80-Foot Wind Tunnel for both two-dimensional and infinite-span swept wing configurations. Section lift characteristics are accurately predicted for zero and moderate sweep angles where flow separation effects are negligible.

  14. An Accurate Temperature Correction Model for Thermocouple Hygrometers 1

    PubMed Central

    Savage, Michael J.; Cass, Alfred; de Jager, James M.

    1982-01-01

    Numerous water relation studies have used thermocouple hygrometers routinely. However, the accurate temperature correction of hygrometer calibration curve slopes seems to have been largely neglected in both psychrometric and dewpoint techniques. In the case of thermocouple psychrometers, two temperature correction models are proposed, each based on measurement of the thermojunction radius and calculation of the theoretical voltage sensitivity to changes in water potential. The first model relies on calibration at a single temperature and the second at two temperatures. Both these models were more accurate than the temperature correction models currently in use for four psychrometers calibrated over a range of temperatures (15-38°C). The model based on calibration at two temperatures is superior to that based on only one calibration. The model proposed for dewpoint hygrometers is similar to that for psychrometers. It is based on the theoretical voltage sensitivity to changes in water potential. Comparison with empirical data from three dewpoint hygrometers calibrated at four different temperatures indicates that these instruments need only be calibrated at, e.g. 25°C, if the calibration slopes are corrected for temperature. PMID:16662241

  15. Machine Learning of Accurate Energy-Conserving Molecular Force Fields

    NASA Astrophysics Data System (ADS)

    Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel; Poltavsky, Igor; Schütt, Kristof; Müller, Klaus-Robert; GDML Collaboration

    Efficient and accurate access to the Born-Oppenheimer potential energy surface (PES) is essential for long time scale molecular dynamics (MD) simulations. Using conservation of energy - a fundamental property of closed classical and quantum mechanical systems - we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio MD trajectories (AIMD). The GDML implementation is able to reproduce global potential-energy surfaces of intermediate-size molecules with an accuracy of 0.3 kcal/mol for energies and 1 kcal/mol/Å for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, malonaldehyde, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative MD simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods.

  16. Accurate Determination of the Frequency Response Function of Submerged and Confined Structures by Using PZT-Patches †

    PubMed Central

    Presas, Alexandre; Valentin, David; Egusquiza, Eduard; Valero, Carme; Egusquiza, Mònica; Bossio, Matias

    2017-01-01

    To accurately determine the dynamic response of a structure is of relevant interest in many engineering applications. Particularly, it is of paramount importance to determine the Frequency Response Function (FRF) for structures subjected to dynamic loads in order to avoid resonance and fatigue problems that can drastically reduce their useful life. One challenging case is the experimental determination of the FRF of submerged and confined structures, such as hydraulic turbines, which are greatly affected by dynamic problems as reported in many cases in the past. The utilization of classical and calibrated exciters such as instrumented hammers or shakers to determine the FRF in such structures can be very complex due to the confinement of the structure and because their use can disturb the boundary conditions affecting the experimental results. For such cases, Piezoelectric Patches (PZTs), which are very light, thin and small, could be a very good option. Nevertheless, the main drawback of these exciters is that the calibration as dynamic force transducers (relationship voltage/force) has not been successfully obtained in the past. Therefore, in this paper, a method to accurately determine the FRF of submerged and confined structures by using PZTs is developed and validated. The method consists of experimentally determining some characteristic parameters that define the FRF, with an uncalibrated PZT exciting the structure. These parameters, which have been experimentally determined, are then introduced in a validated numerical model of the tested structure. In this way, the FRF of the structure can be estimated with good accuracy. With respect to previous studies, where only the natural frequencies and mode shapes were considered, this paper discuss and experimentally proves the best excitation characteristic to obtain also the damping ratios and proposes a procedure to fully determine the FRF. The method proposed here has been validated for the structure vibrating

  17. A tungsten-rhenium interatomic potential for point defect studies

    NASA Astrophysics Data System (ADS)

    Setyawan, Wahyu; Gao, Ning; Kurtz, Richard J.

    2018-05-01

    A tungsten-rhenium (W-Re) classical interatomic potential is developed within the embedded atom method interaction framework. A force-matching method is employed to fit the potential to ab initio forces, energies, and stresses. Simulated annealing is combined with the conjugate gradient technique to search for an optimum potential from over 1000 initial trial sets. The potential is designed for studying point defects in W-Re systems. It gives good predictions of the formation energies of Re defects in W and the binding energies of W self-interstitial clusters with Re. The potential is further evaluated for describing the formation energy of structures in the σ and χ intermetallic phases. The predicted convex-hulls of formation energy are in excellent agreement with ab initio data. In pure Re, the potential can reproduce the formation energies of vacancies and self-interstitial defects sufficiently accurately and gives the correct ground state self-interstitial configuration. Furthermore, by including liquid structures in the fit, the potential yields a Re melting temperature (3130 K) that is close to the experimental value (3459 K).

  18. Experimental Studies on role of pH, potential and concentration of buffer solution for chemical bath deposition technique

    NASA Astrophysics Data System (ADS)

    Suresha, B. L.; Sumantha, H. S.; Salman, K. Mohammed; Pramod, N. G.; Abhiram, J.

    2018-04-01

    The ionization potential is usually found to be less in acid and more in base. The experiment proves that the ionization potential increases on dilution of acid to base and reduces from base to acid. The potential can be tailored according to the desired properties based on our choice of acid or base. The experimental study establishes a direct relationship between pH and electric potential. This work provides theoretical insights on the need for a basic media of pH 10 in chemical thin film growth techniques called Chemical Bath Deposition Techniques.

  19. Apparatus for use in rapid and accurate controlled-potential coulometric analysis

    DOEpatents

    Frazzini, Thomas L.; Holland, Michael K.; Pietri, Charles E.; Weiss, Jon R.

    1981-01-01

    An apparatus for controlled-potential coulometric analysis of a solution includes a cell to contain the solution to be analyzed and a plurality of electrodes to contact the solution in the cell. Means are provided to stir the solution and to control the atmosphere above it. A potentiostat connected to the electrodes controls potential differences among the electrodes. An electronic circuit connected to the potentiostat provides analog-to-digital conversion and displays a precise count of charge transfer during a desired chemical process. This count provides a measure of the amount of an unknown substance in the solution.

  20. Highly Accurate Potential Energy Surface, Dipole Moment Surface, Rovibrational Energy Levels, and Infrared Line List for (32)S(16)O2 up to 8000 cm(exp -1)

    NASA Technical Reports Server (NTRS)

    Huang, Xinchuan; Schwenke, David W.; Lee, Timothy J.

    2014-01-01

    A purely ab initio potential energy surface (PES) was refined with selected (32)S(16)O2 HITRAN data. Compared to HITRAN, the root-mean-squares error (RMS) error for all J=0-80 rovibrational energy levels computed on the refined PES (denoted Ames-1) is 0.013 cm(exp -1). Combined with a CCSD(T)/aug-cc-pV(Q+d)Z dipole moment surface (DMS), an infrared (IR) line list (denoted Ames-296K) has been computed at 296K and covers up to 8,000 cm(exp -1). Compared to the HITRAN and CDMS databases, the intensity agreement for most vibrational bands is better than 85-90%. Our predictions for (34)S(16)O2 band origins, higher energy (32)S(16)O2 band origins and missing (32)S(16)O2 IR bands have been verified by most recent experiments and available HITRAN data. We conclude that the Ames-1 PES is able to predict (32/34)S(16)O2 band origins below 5500 cm(exp -1) with 0.01-0.03 cm(exp -1) uncertainties, and the Ames-296K line list provides continuous, reliable and accurate IR simulations. The Ka-dependence of both line position and line intensity errors is discussed. The line list will greatly facilitate SO2 IR spectral experimental analysis, as well as elimination of SO2 lines in high-resolution astronomical observations.

  1. The extraction of accurate coordinates of images on photographic plates by means of a scanning type measuring machine

    NASA Technical Reports Server (NTRS)

    Ross, B. E.

    1971-01-01

    The Moire method experimental stress analysis is similar to a problem encountered in astrometry. It is necessary to extract accurate coordinates from images on photographic plates. The solution to the mutual problem found applicable to the field of experimental stress analysis is presented to outline the measurement problem. A discussion of the photo-reading device developed to make the measurements follows.

  2. Accurate potential energy surface for the 1(2)A' state of NH(2): scaling of external correlation versus extrapolation to the complete basis set limit.

    PubMed

    Li, Y Q; Varandas, A J C

    2010-09-16

    An accurate single-sheeted double many-body expansion potential energy surface is reported for the title system which is suitable for dynamics and kinetics studies of the reactions of N(2D) + H2(X1Sigmag+) NH(a1Delta) + H(2S) and their isotopomeric variants. It is obtained by fitting ab initio energies calculated at the multireference configuration interaction level with the aug-cc-pVQZ basis set, after slightly correcting semiempirically the dynamical correlation using the double many-body expansion-scaled external correlation method. The function so obtained is compared in detail with a potential energy surface of the same family obtained by extrapolating the calculated raw energies to the complete basis set limit. The topographical features of the novel global potential energy surface are examined in detail and found to be in general good agreement with those calculated directly from the raw ab initio energies, as well as previous calculations available in the literature. The novel function has been built so as to become degenerate at linear geometries with the ground-state potential energy surface of A'' symmetry reported by our group, where both form a Renner-Teller pair.

  3. Full-Dimensional Quantum Calculations of Vibrational Levels of NH4(+) and Isotopomers on An Accurate Ab Initio Potential Energy Surface.

    PubMed

    Yu, Hua-Gen; Han, Huixian; Guo, Hua

    2016-04-14

    Vibrational energy levels of the ammonium cation (NH4(+)) and its deuterated isotopomers are calculated using a numerically exact kinetic energy operator on a recently developed nine-dimensional permutation invariant semiglobal potential energy surface fitted to a large number of high-level ab initio points. Like CH4, the vibrational levels of NH4(+) and ND4(+) exhibit a polyad structure, characterized by a collective quantum number P = 2(v1 + v3) + v2 + v4. The low-lying vibrational levels of all isotopomers are assigned and the agreement with available experimental data is better than 1 cm(-1).

  4. Accurate simulation of backscattering spectra in the presence of sharp resonances

    NASA Astrophysics Data System (ADS)

    Barradas, N. P.; Alves, E.; Jeynes, C.; Tosaki, M.

    2006-06-01

    In elastic backscattering spectrometry, the shape of the observed spectrum due to resonances in the nuclear scattering cross-section is influenced by many factors. If the energy spread of the beam before interaction is larger than the resonance width, then a simple convolution with the energy spread on exit and with the detection system resolution will lead to a calculated spectrum with a resonance much sharper than the observed signal. Also, the yield from a thin layer will not be calculated accurately. We have developed an algorithm for the accurate simulation of backscattering spectra in the presence of sharp resonances. Albeit approximate, the algorithm leads to dramatic improvements in the quality and accuracy of the simulations. It is simple to implement and leads to only small increases of the calculation time, being thus suitable for routine data analysis. We show different experimental examples, including samples with roughness and porosity.

  5. Estimations of global warming potentials from computational chemistry calculations for CH(2)F(2) and other fluorinated methyl species verified by comparison to experiment.

    PubMed

    Blowers, Paul; Hollingshead, Kyle

    2009-05-21

    In this work, the global warming potential (GWP) of methylene fluoride (CH(2)F(2)), or HFC-32, is estimated through computational chemistry methods. We find our computational chemistry approach reproduces well all phenomena important for predicting global warming potentials. Geometries predicted using the B3LYP/6-311g** method were in good agreement with experiment, although some other computational methods performed slightly better. Frequencies needed for both partition function calculations in transition-state theory and infrared intensities needed for radiative forcing estimates agreed well with experiment compared to other computational methods. A modified CBS-RAD method used to obtain energies led to superior results to all other previous heat of reaction estimates and most barrier height calculations when the B3LYP/6-311g** optimized geometry was used as the base structure. Use of the small-curvature tunneling correction and a hindered rotor treatment where appropriate led to accurate reaction rate constants and radiative forcing estimates without requiring any experimental data. Atmospheric lifetimes from theory at 277 K were indistinguishable from experimental results, as were the final global warming potentials compared to experiment. This is the first time entirely computational methods have been applied to estimate a global warming potential for a chemical, and we have found the approach to be robust, inexpensive, and accurate compared to prior experimental results. This methodology was subsequently used to estimate GWPs for three additional species [methane (CH(4)); fluoromethane (CH(3)F), or HFC-41; and fluoroform (CHF(3)), or HFC-23], where estimations also compare favorably to experimental values.

  6. Determining potential 30/20 GHZ domestic satellite system concepts and establishment of a suitable experimental configuration

    NASA Technical Reports Server (NTRS)

    Stevens, G. H.; Anzic, G.

    1979-01-01

    NASA is conducting a series of millimeter wave satellite communication systems and market studies to: (1) determine potential domestic 30/20 GHz satellite concepts and market potential, and (2) establish the requirements for a suitable technology verification payload which, although intended to be modest in capacity, would sufficiently demonstrate key technologies and experimentally address key operational issues. Preliminary results and critical issues of the current contracted effort are described. Also included is a description of a NASA-developed multibeam satellite payload configuration which may be representative of concepts utilized in a technology flight verification program.

  7. COSMOS: accurate detection of somatic structural variations through asymmetric comparison between tumor and normal samples

    PubMed Central

    Yamagata, Koichi; Yamanishi, Ayako; Kokubu, Chikara; Takeda, Junji; Sese, Jun

    2016-01-01

    An important challenge in cancer genomics is precise detection of structural variations (SVs) by high-throughput short-read sequencing, which is hampered by the high false discovery rates of existing analysis tools. Here, we propose an accurate SV detection method named COSMOS, which compares the statistics of the mapped read pairs in tumor samples with isogenic normal control samples in a distinct asymmetric manner. COSMOS also prioritizes the candidate SVs using strand-specific read-depth information. Performance tests on modeled tumor genomes revealed that COSMOS outperformed existing methods in terms of F-measure. We also applied COSMOS to an experimental mouse cell-based model, in which SVs were induced by genome engineering and gamma-ray irradiation, followed by polymerase chain reaction-based confirmation. The precision of COSMOS was 84.5%, while the next best existing method was 70.4%. Moreover, the sensitivity of COSMOS was the highest, indicating that COSMOS has great potential for cancer genome analysis. PMID:26833260

  8. Large divalent cations and electrostatic potentials adjacent to membranes. Experimental results with hexamethonium.

    PubMed Central

    Alvarez, O; Brodwick, M; Latorre, R; McLaughlin, A; McLaughlin, S; Szabo, G

    1983-01-01

    A simple extension of the Gouy-Chapman theory predicts that the ability of a divalent cation to screen charges at a membrane-solution interface decreases significantly if the distance between the charges on the cation is comparable with the Debye length. We tested this prediction by investigating the effect of hexamethonium on the electrostatic potential adjacent to negatively charged phospholipid bilayer membranes. The distance between the two charges of an extended hexamethonium molecule is approximately 1 nm, which is the Debye length in the 0.1 M monovalent salt solutions used in these experiments. Six different experimental approaches were utilized. We measured the electrophoretic mobility of multilamellar vesicles to determine the zeta potential, the line width of the 31P nuclear magnetic resonance (NMR) signal from sonicated vesicles to calculate the change in potential at the phosphodiester moiety of the lipid, and the conductance of planar bilayer membranes exposed to either carriers (nonactin) or pore formers (gramicidin) to estimate the change in potential within the membrane. We also measured directly the effect of hexamethonium on the potential above a monolayer formed from negative lipids, and attempted to calculate the change in the surface potential of a bilayer membrane from capacitance measurements. With the exception of the capacitance calculations, each of the techniques gave comparable results: hexamethonium exerts a smaller effect on the potential than that predicted by the classic screening theory. The results are consistent with the predictions of the extended Gouy-Chapman theory and are relevant to the interpretation of physiological and pharmacological experiments that utilize hexamethonium and other large divalent cations. PMID:6198001

  9. A Dual-Mode Large-Arrayed CMOS ISFET Sensor for Accurate and High-Throughput pH Sensing in Biomedical Diagnosis.

    PubMed

    Huang, Xiwei; Yu, Hao; Liu, Xu; Jiang, Yu; Yan, Mei; Wu, Dongping

    2015-09-01

    The existing ISFET-based DNA sequencing detects hydrogen ions released during the polymerization of DNA strands on microbeads, which are scattered into microwell array above the ISFET sensor with unknown distribution. However, false pH detection happens at empty microwells due to crosstalk from neighboring microbeads. In this paper, a dual-mode CMOS ISFET sensor is proposed to have accurate pH detection toward DNA sequencing. Dual-mode sensing, optical and chemical modes, is realized by integrating a CMOS image sensor (CIS) with ISFET pH sensor, and is fabricated in a standard 0.18-μm CIS process. With accurate determination of microbead physical locations with CIS pixel by contact imaging, the dual-mode sensor can correlate local pH for one DNA slice at one location-determined microbead, which can result in improved pH detection accuracy. Moreover, toward a high-throughput DNA sequencing, a correlated-double-sampling readout that supports large array for both modes is deployed to reduce pixel-to-pixel nonuniformity such as threshold voltage mismatch. The proposed CMOS dual-mode sensor is experimentally examined to show a well correlated pH map and optical image for microbeads with a pH sensitivity of 26.2 mV/pH, a fixed pattern noise (FPN) reduction from 4% to 0.3%, and a readout speed of 1200 frames/s. A dual-mode CMOS ISFET sensor with suppressed FPN for accurate large-arrayed pH sensing is proposed and demonstrated with state-of-the-art measured results toward accurate and high-throughput DNA sequencing. The developed dual-mode CMOS ISFET sensor has great potential for future personal genome diagnostics with high accuracy and low cost.

  10. PyVCI: A flexible open-source code for calculating accurate molecular infrared spectra

    NASA Astrophysics Data System (ADS)

    Sibaev, Marat; Crittenden, Deborah L.

    2016-06-01

    The PyVCI program package is a general purpose open-source code for simulating accurate molecular spectra, based upon force field expansions of the potential energy surface in normal mode coordinates. It includes harmonic normal coordinate analysis and vibrational configuration interaction (VCI) algorithms, implemented primarily in Python for accessibility but with time-consuming routines written in C. Coriolis coupling terms may be optionally included in the vibrational Hamiltonian. Non-negligible VCI matrix elements are stored in sparse matrix format to alleviate the diagonalization problem. CPU and memory requirements may be further controlled by algorithmic choices and/or numerical screening procedures, and recommended values are established by benchmarking using a test set of 44 molecules for which accurate analytical potential energy surfaces are available. Force fields in normal mode coordinates are obtained from the PyPES library of high quality analytical potential energy surfaces (to 6th order) or by numerical differentiation of analytic second derivatives generated using the GAMESS quantum chemical program package (to 4th order).

  11. Accurate modeling of high-repetition rate ultrashort pulse amplification in optical fibers

    PubMed Central

    Lindberg, Robert; Zeil, Peter; Malmström, Mikael; Laurell, Fredrik; Pasiskevicius, Valdas

    2016-01-01

    A numerical model for amplification of ultrashort pulses with high repetition rates in fiber amplifiers is presented. The pulse propagation is modeled by jointly solving the steady-state rate equations and the generalized nonlinear Schrödinger equation, which allows accurate treatment of nonlinear and dispersive effects whilst considering arbitrary spatial and spectral gain dependencies. Comparison of data acquired by using the developed model and experimental results prove to be in good agreement. PMID:27713496

  12. Evaluation of copper, aluminum, and nickel interatomic potentials on predicting the elastic properties

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Rassoulinejad-Mousavi, Seyed Moein; Mao, Yijin; Zhang, Yuwen, E-mail: zhangyu@missouri.edu

    Choice of appropriate force field is one of the main concerns of any atomistic simulation that needs to be seriously considered in order to yield reliable results. Since investigations on the mechanical behavior of materials at micro/nanoscale have been becoming much more widespread, it is necessary to determine an adequate potential which accurately models the interaction of the atoms for desired applications. In this framework, reliability of multiple embedded atom method based interatomic potentials for predicting the elastic properties was investigated. Assessments were carried out for different copper, aluminum, and nickel interatomic potentials at room temperature which is considered asmore » the most applicable case. Examined force fields for the three species were taken from online repositories of National Institute of Standards and Technology, as well as the Sandia National Laboratories, the LAMMPS database. Using molecular dynamic simulations, the three independent elastic constants, C{sub 11}, C{sub 12}, and C{sub 44}, were found for Cu, Al, and Ni cubic single crystals. Voigt-Reuss-Hill approximation was then implemented to convert elastic constants of the single crystals into isotropic polycrystalline elastic moduli including bulk modulus, shear modulus, and Young's modulus as well as Poisson's ratio. Simulation results from massive molecular dynamic were compared with available experimental data in the literature to justify the robustness of each potential for each species. Eventually, accurate interatomic potentials have been recommended for finding each of the elastic properties of the pure species. Exactitude of the elastic properties was found to be sensitive to the choice of the force fields. Those potentials that were fitted for a specific compound may not necessarily work accurately for all the existing pure species. Tabulated results in this paper might be used as a benchmark to increase assurance of using the interatomic potential that was

  13. Evaluation of copper, aluminum, and nickel interatomic potentials on predicting the elastic properties

    NASA Astrophysics Data System (ADS)

    Rassoulinejad-Mousavi, Seyed Moein; Mao, Yijin; Zhang, Yuwen

    2016-06-01

    Choice of appropriate force field is one of the main concerns of any atomistic simulation that needs to be seriously considered in order to yield reliable results. Since investigations on the mechanical behavior of materials at micro/nanoscale have been becoming much more widespread, it is necessary to determine an adequate potential which accurately models the interaction of the atoms for desired applications. In this framework, reliability of multiple embedded atom method based interatomic potentials for predicting the elastic properties was investigated. Assessments were carried out for different copper, aluminum, and nickel interatomic potentials at room temperature which is considered as the most applicable case. Examined force fields for the three species were taken from online repositories of National Institute of Standards and Technology, as well as the Sandia National Laboratories, the LAMMPS database. Using molecular dynamic simulations, the three independent elastic constants, C11, C12, and C44, were found for Cu, Al, and Ni cubic single crystals. Voigt-Reuss-Hill approximation was then implemented to convert elastic constants of the single crystals into isotropic polycrystalline elastic moduli including bulk modulus, shear modulus, and Young's modulus as well as Poisson's ratio. Simulation results from massive molecular dynamic were compared with available experimental data in the literature to justify the robustness of each potential for each species. Eventually, accurate interatomic potentials have been recommended for finding each of the elastic properties of the pure species. Exactitude of the elastic properties was found to be sensitive to the choice of the force fields. Those potentials that were fitted for a specific compound may not necessarily work accurately for all the existing pure species. Tabulated results in this paper might be used as a benchmark to increase assurance of using the interatomic potential that was designated for a problem.

  14. Oil well flow assurance through static electric potential: An experimental investigation

    NASA Astrophysics Data System (ADS)

    Hashmi, Muhammad Ihtsham Asmat

    Flow assurance technology deals with the deposition of organic and inorganic solids in the oil flow path, which results in constriction of the production tubing and surface flow lines and drastically reduces the kinetic energy of the fluid. The major contributors to this flow restriction are inorganic scales, asphaltene, wax and gas hydrates, in addition to minor contribution from formation fines and corrosion products. Some of these materials (particularly asphaltene and inorganic scales) carry surface charges on their nuclei and seen to be attracted by electrode having opposite charge. The focus of the present research is to find the possibilities of inhibiting the deposition of asphaltene and inorganic scales in the production tubing by applying static electrical potential. With this objective, two flow set ups were made; one for asphaltene and the other for scale deposition studies, attached with precision pumps, pressure recording system and DC power supply. In each set up there were two flow loops, one was converted as Anode and the other as Cathode. A series of flow studies were conducted using the flow set ups, in which oil-dilution ratio, temperature and most importantly DC potential difference was varied and the deposition behavior of the asphaltene aggregates and calcium carbonate scale to the walls of the test loops were observed through rise of differential pressure across the loop due to possible deposition and constriction of the flow path. Two different sets of flow studies; one without oil dilution and other with the diluted oil (with n-heptane), were performed. Both experiments were investigated under the influence of static potential applied across the two test loops. Experimental results indicated that asphaltene deposition in the cathode can be retarded or stopped by applying a suitable negative potential; an increase in the static potential resulted in enhanced control over the asphaltene aggregation and hence the deposition. In the second

  15. An experimental comparison between the continuum and single jump descriptions of nonactin-mediated potassium transport through black lipid membranes.

    PubMed Central

    van Dijk, C; de Levie, R

    1985-01-01

    The continuum and single jump treatments of ion transport through black lipid membranes predict experimentally distinguishable results, even when the same mechanistic assumptions are made and the same potential-distance profile is used. On the basis of steady-state current-voltage curves for nonactin-mediated transport of potassium ions, we find that the continuum model describes the data accurately, whereas the single jump model fails to do so, for all cases investigated in which capacitance measurements indicate that the membrane thickness varies little with applied potential. PMID:3839420

  16. Equation of motion coupled cluster methods for electron attachment and ionization potential in polyacenes

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bhaskaran-Nair, Kiran; Kowalski, Karol; Jarrell, Mark

    2015-11-05

    Polyacenes have attracted considerable attention due to their use in organic based optoelectronic materials. Polyacenes are polycyclic aromatic hydrocarbons composed of fused benzene rings. Key to understanding and design of new functional materials is an understanding of their excited state properties starting with their electron affinity (EA) and ionization potential (IP). We have developed a highly accurate and com- putationally e*fficient EA/IP equation of motion coupled cluster singles and doubles (EA/IP-EOMCCSD) method that is capable of treating large systems and large basis set. In this study we employ the EA/IP-EOMCCSD method to calculate the electron affinity and ionization potential ofmore » naphthalene, anthracene, tetracene, pentacene, hex- acene and heptacene. We have compared our results with other previous theoretical studies and experimental data. Our EA/IP results are in very good agreement with experiment and when compared with the other theoretical investigations our results represent the most accurate calculations as compared to experiment.« less

  17. Accurately controlled sequential self-folding structures by polystyrene film

    NASA Astrophysics Data System (ADS)

    Deng, Dongping; Yang, Yang; Chen, Yong; Lan, Xing; Tice, Jesse

    2017-08-01

    Four-dimensional (4D) printing overcomes the traditional fabrication limitations by designing heterogeneous materials to enable the printed structures evolve over time (the fourth dimension) under external stimuli. Here, we present a simple 4D printing of self-folding structures that can be sequentially and accurately folded. When heated above their glass transition temperature pre-strained polystyrene films shrink along the XY plane. In our process silver ink traces printed on the film are used to provide heat stimuli by conducting current to trigger the self-folding behavior. The parameters affecting the folding process are studied and discussed. Sequential folding and accurately controlled folding angles are achieved by using printed ink traces and angle lock design. Theoretical analyses are done to guide the design of the folding processes. Programmable structures such as a lock and a three-dimensional antenna are achieved to test the feasibility and potential applications of this method. These self-folding structures change their shapes after fabrication under controlled stimuli (electric current) and have potential applications in the fields of electronics, consumer devices, and robotics. Our design and fabrication method provides an easy way by using silver ink printed on polystyrene films to 4D print self-folding structures for electrically induced sequential folding with angular control.

  18. Comparison of methods for accurate end-point detection of potentiometric titrations

    NASA Astrophysics Data System (ADS)

    Villela, R. L. A.; Borges, P. P.; Vyskočil, L.

    2015-01-01

    Detection of the end point in potentiometric titrations has wide application on experiments that demand very low measurement uncertainties mainly for certifying reference materials. Simulations of experimental coulometric titration data and consequential error analysis of the end-point values were conducted using a programming code. These simulations revealed that the Levenberg-Marquardt method is in general more accurate than the traditional second derivative technique used currently as end-point detection for potentiometric titrations. Performance of the methods will be compared and presented in this paper.

  19. Systematic Validation of Protein Force Fields against Experimental Data

    PubMed Central

    Eastwood, Michael P.; Dror, Ron O.; Shaw, David E.

    2012-01-01

    Molecular dynamics simulations provide a vehicle for capturing the structures, motions, and interactions of biological macromolecules in full atomic detail. The accuracy of such simulations, however, is critically dependent on the force field—the mathematical model used to approximate the atomic-level forces acting on the simulated molecular system. Here we present a systematic and extensive evaluation of eight different protein force fields based on comparisons of experimental data with molecular dynamics simulations that reach a previously inaccessible timescale. First, through extensive comparisons with experimental NMR data, we examined the force fields' abilities to describe the structure and fluctuations of folded proteins. Second, we quantified potential biases towards different secondary structure types by comparing experimental and simulation data for small peptides that preferentially populate either helical or sheet-like structures. Third, we tested the force fields' abilities to fold two small proteins—one α-helical, the other with β-sheet structure. The results suggest that force fields have improved over time, and that the most recent versions, while not perfect, provide an accurate description of many structural and dynamical properties of proteins. PMID:22384157

  20. The accurate assessment of small-angle X-ray scattering data

    DOE PAGES

    Grant, Thomas D.; Luft, Joseph R.; Carter, Lester G.; ...

    2015-01-23

    Small-angle X-ray scattering (SAXS) has grown in popularity in recent times with the advent of bright synchrotron X-ray sources, powerful computational resources and algorithms enabling the calculation of increasingly complex models. However, the lack of standardized data-quality metrics presents difficulties for the growing user community in accurately assessing the quality of experimental SAXS data. Here, a series of metrics to quantitatively describe SAXS data in an objective manner using statistical evaluations are defined. These metrics are applied to identify the effects of radiation damage, concentration dependence and interparticle interactions on SAXS data from a set of 27 previously described targetsmore » for which high-resolution structures have been determined via X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. Studies show that these metrics are sufficient to characterize SAXS data quality on a small sample set with statistical rigor and sensitivity similar to or better than manual analysis. The development of data-quality analysis strategies such as these initial efforts is needed to enable the accurate and unbiased assessment of SAXS data quality.« less

  1. Quasi-experimental study designs series-paper 13: realizing the full potential of quasi-experiments for health research.

    PubMed

    Rockers, Peter C; Tugwell, Peter; Røttingen, John-Arne; Bärnighausen, Till

    2017-09-01

    Although the number of quasi-experiments conducted by health researchers has increased in recent years, there clearly remains unrealized potential for using these methods for causal evaluation of health policies and programs globally. This article proposes five prescriptions for capturing the full value of quasi-experiments for health research. First, new funding opportunities targeting proposals that use quasi-experimental methods should be made available to a broad pool of health researchers. Second, administrative data from health programs, often amenable to quasi-experimental analysis, should be made more accessible to researchers. Third, training in quasi-experimental methods should be integrated into existing health science graduate programs to increase global capacity to use these methods. Fourth, clear guidelines for primary research and synthesis of evidence from quasi-experiments should be developed. Fifth, strategic investments should be made to continue to develop new innovations in quasi-experimental methodologies. Tremendous opportunities exist to expand the use of quasi-experimental methods to increase our understanding of which health programs and policies work and which do not. Health researchers should continue to expand their commitment to rigorous causal evaluation with quasi-experimental methods, and international institutions should increase their support for these efforts. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Full-dimensional quantum calculations of vibrational levels of NH 4 + and isotopomers on an accurate ab initio potential energy surface

    DOE PAGES

    Hua -Gen Yu; Han, Huixian; Guo, Hua

    2016-03-29

    Vibrational energy levels of the ammonium cation (NH 4 +) and its deuterated isotopomers are calculated using a numerically exact kinetic energy operator on a recently developed nine-dimensional permutation invariant semiglobal potential energy surface fitted to a large number of high-level ab initio points. Like CH4, the vibrational levels of NH 4 + and ND 4 + exhibit a polyad structure, characterized by a collective quantum number P = 2(v 1 + v 3) + v 2 + v 4. As a result, the low-lying vibrational levels of all isotopomers are assigned and the agreement with available experimental data ismore » better than 1 cm –1.« less

  3. Accurate potential energy functions, non-adiabatic and spin-orbit couplings in the ZnH(+) system.

    PubMed

    Liang, Guiying; Liu, Xiaoting; Zhang, Xiaomei; Xu, Haifeng; Yan, Bing

    2016-03-05

    A high-level ab initio calculation on the ZnH(+) cation has been carried out with the multi-reference configuration interaction method plus Davison correction (MRCI+Q). The scalar relativistic effect is included by using the Douglas-Kroll-Hess (DKH) method. The calculated potential energy curves (PECs) of the 7 Λ-S states are associated with the dissociation limits of Zn(+)((2)Sg)+H((2)Sg), Zn((1)Sg)+H(+)((1)Sg), and Zn(+)((2)Pu)+H((2)Sg), respectively (The Λ-S state is labeled as (2S+1)Λ, in which Λ is the quantum number for the projection along the internuclear axis of the total electronic orbital angular momentum and S is the total electron spin). The spectroscopic constants of the bound states are determined and in good agreement with the available theoretical and experimental results. The permanent dipole moments (PDMs) of Λ-S states and the spin-orbit (SO) matrix elements between Λ-S states are also computed. The results show that the abrupt changes of the PDMs and SO matrix elements come into being for the reason of the avoided crossing between the states with the same symmetry. In addition, the non-adiabatic couplings matrix elements between Λ-S states are also evaluated. Finally, the spin-orbit couplings (SOCs) for the low-lying states are considered with Breit-Pauli operator. The SOC effect makes the 7 Λ-S states of the ZnH(+) cation split into 12 Ω states (Ω=Λ+Sz, in which Sz is projection of the total electron spin S along the internuclear Z-axis). For the (3)0(+) state, the two energy minima exhibit in the potential, which could be attributed to the formation of the new avoided crossing point. The transition dipole moments (TDMs), Franck-Condon factors, and the radiative lifetimes of the selected transitions (2)0(+)-X0(+), (3)0(+)-X0(+), (2)1-X0(+) and (3)1-X0(+) have been reported. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Experimental annotation of the human genome using microarray technology.

    PubMed

    Shoemaker, D D; Schadt, E E; Armour, C D; He, Y D; Garrett-Engele, P; McDonagh, P D; Loerch, P M; Leonardson, A; Lum, P Y; Cavet, G; Wu, L F; Altschuler, S J; Edwards, S; King, J; Tsang, J S; Schimmack, G; Schelter, J M; Koch, J; Ziman, M; Marton, M J; Li, B; Cundiff, P; Ward, T; Castle, J; Krolewski, M; Meyer, M R; Mao, M; Burchard, J; Kidd, M J; Dai, H; Phillips, J W; Linsley, P S; Stoughton, R; Scherer, S; Boguski, M S

    2001-02-15

    The most important product of the sequencing of a genome is a complete, accurate catalogue of genes and their products, primarily messenger RNA transcripts and their cognate proteins. Such a catalogue cannot be constructed by computational annotation alone; it requires experimental validation on a genome scale. Using 'exon' and 'tiling' arrays fabricated by ink-jet oligonucleotide synthesis, we devised an experimental approach to validate and refine computational gene predictions and define full-length transcripts on the basis of co-regulated expression of their exons. These methods can provide more accurate gene numbers and allow the detection of mRNA splice variants and identification of the tissue- and disease-specific conditions under which genes are expressed. We apply our technique to chromosome 22q under 69 experimental condition pairs, and to the entire human genome under two experimental conditions. We discuss implications for more comprehensive, consistent and reliable genome annotation, more efficient, full-length complementary DNA cloning strategies and application to complex diseases.

  5. A time-accurate high-resolution TVD scheme for solving the Navier-Stokes equations

    NASA Technical Reports Server (NTRS)

    Kim, Hyun Dae; Liu, Nan-Suey

    1992-01-01

    A total variation diminishing (TVD) scheme has been developed and incorporated into an existing time-accurate high-resolution Navier-Stokes code. The accuracy and the robustness of the resulting solution procedure have been assessed by performing many calculations in four different areas: shock tube flows, regular shock reflection, supersonic boundary layer, and shock boundary layer interactions. These numerical results compare well with corresponding exact solutions or experimental data.

  6. Simulation and experimental study of rheological properties of CeO2-water nanofluid

    NASA Astrophysics Data System (ADS)

    Loya, Adil; Stair, Jacqueline L.; Ren, Guogang

    2015-10-01

    Metal oxide nanoparticles offer great merits over controlling rheological, thermal, chemical and physical properties of solutions. The effectiveness of a nanoparticle to modify the properties of a fluid depends on its diffusive properties with respect to the fluid. In this study, rheological properties of aqueous fluids (i.e. water) were enhanced with the addition of CeO2 nanoparticles. This study was characterized by the outcomes of simulation and experimental results of nanofluids. The movement of nanoparticles in the fluidic media was simulated by a large-scale molecular thermal dynamic program (i.e. LAMMPS). The COMPASS force field was employed with smoothed particle hydrodynamic potential (SPH) and discrete particle dynamics potential (DPD). However, this study develops the understanding of how the rheological properties are affected due to the addition of nanoparticles in a fluid and the way DPD and SPH can be used for accurately estimating the rheological properties with Brownian effect. The rheological results of the simulation were confirmed by the convergence of the stress autocorrelation function, whereas experimental properties were measured using a rheometer. These rheological values of simulation were obtained and agreed within 5 % of the experimental values; they were identified and treated with a number of iterations and experimental tests. The results of the experiment and simulation show that 10 % CeO2 nanoparticles dispersion in water has a viscosity of 2.0-3.3 mPas.

  7. On the accurate analysis of vibroacoustics in head insert gradient coils.

    PubMed

    Winkler, Simone A; Alejski, Andrew; Wade, Trevor; McKenzie, Charles A; Rutt, Brian K

    2017-10-01

    To accurately analyze vibroacoustics in MR head gradient coils. A detailed theoretical model for gradient coil vibroacoustics, including the first description and modeling of Lorentz damping, is introduced and implemented in a multiphysics software package. Numerical finite-element method simulations were used to establish a highly accurate vibroacoustic model in head gradient coils in detail, including the newly introduced Lorentz damping effect. Vibroacoustic coupling was examined through an additional modal analysis. Thorough experimental studies were used to validate simulations. Average experimental sound pressure levels (SPLs) and accelerations over the 0-3000 Hz frequency range were 97.6 dB, 98.7 dB, and 95.4 dB, as well as 20.6 g, 8.7 g, and 15.6 g for the X-, Y-, and Z-gradients, respectively. A reasonable agreement between simulations and measurements was achieved. Vibroacoustic coupling showed a coupled resonance at 2300 Hz for the Z-gradient that is responsible for a sharp peak and the highest SPL value in the acoustic spectrum. We have developed and used more realistic multiphysics simulation methods to gain novel insights into the underlying concepts for vibroacoustics in head gradient coils, which will permit improved analyses of existing gradient coils and novel SPL reduction strategies for future gradient coil designs. Magn Reson Med 78:1635-1645, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

  8. Accurate forced-choice recognition without awareness of memory retrieval.

    PubMed

    Voss, Joel L; Baym, Carol L; Paller, Ken A

    2008-06-01

    Recognition confidence and the explicit awareness of memory retrieval commonly accompany accurate responding in recognition tests. Memory performance in recognition tests is widely assumed to measure explicit memory, but the generality of this assumption is questionable. Indeed, whether recognition in nonhumans is always supported by explicit memory is highly controversial. Here we identified circumstances wherein highly accurate recognition was unaccompanied by hallmark features of explicit memory. When memory for kaleidoscopes was tested using a two-alternative forced-choice recognition test with similar foils, recognition was enhanced by an attentional manipulation at encoding known to degrade explicit memory. Moreover, explicit recognition was most accurate when the awareness of retrieval was absent. These dissociations between accuracy and phenomenological features of explicit memory are consistent with the notion that correct responding resulted from experience-dependent enhancements of perceptual fluency with specific stimuli--the putative mechanism for perceptual priming effects in implicit memory tests. This mechanism may contribute to recognition performance in a variety of frequently-employed testing circumstances. Our results thus argue for a novel view of recognition, in that analyses of its neurocognitive foundations must take into account the potential for both (1) recognition mechanisms allied with implicit memory and (2) recognition mechanisms allied with explicit memory.

  9. A tungsten-rhenium interatomic potential for point defect studies

    DOE PAGES

    Setyawan, Wahyu; Gao, Ning; Kurtz, Richard J.

    2018-05-28

    A tungsten-rhenium (W-Re) classical interatomic potential is developed within the embedded atom method (EAM) interaction framework. A force-matching method is employed to fit the potential to ab initio forces, energies, and stresses. Simulated annealing is combined with the conjugate gradient technique to search for an optimum potential from over 1000 initial trial sets. The potential is designed for studying point defects in W-Re systems. It gives good predictions of the formation energies of Re defects in W and the binding energies of W self-interstitial clusters with Re. The potential is further evaluated for describing the formation energy of structures inmore » the σ and χ intermetallic phases. The predicted convex-hulls of formation energy are in excellent agreement with ab initio data. In pure Re, the potential can reproduce the formation energies of vacancy and self-interstitial defects sufficiently accurately, and gives the correct ground state self-interstitial configuration. Furthermore, by including liquid structures in the fit, the potential yields a Re melting temperature (3130 K) that is close to the experimental value (3459 K).« less

  10. A tungsten-rhenium interatomic potential for point defect studies

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Setyawan, Wahyu; Gao, Ning; Kurtz, Richard J.

    A tungsten-rhenium (W-Re) classical interatomic potential is developed within the embedded atom method (EAM) interaction framework. A force-matching method is employed to fit the potential to ab initio forces, energies, and stresses. Simulated annealing is combined with the conjugate gradient technique to search for an optimum potential from over 1000 initial trial sets. The potential is designed for studying point defects in W-Re systems. It gives good predictions of the formation energies of Re defects in W and the binding energies of W self-interstitial clusters with Re. The potential is further evaluated for describing the formation energy of structures inmore » the σ and χ intermetallic phases. The predicted convex-hulls of formation energy are in excellent agreement with ab initio data. In pure Re, the potential can reproduce the formation energies of vacancy and self-interstitial defects sufficiently accurately, and gives the correct ground state self-interstitial configuration. Furthermore, by including liquid structures in the fit, the potential yields a Re melting temperature (3130 K) that is close to the experimental value (3459 K).« less

  11. Accurate analytical modeling of junctionless DG-MOSFET by green's function approach

    NASA Astrophysics Data System (ADS)

    Nandi, Ashutosh; Pandey, Nilesh

    2017-11-01

    An accurate analytical model of Junctionless double gate MOSFET (JL-DG-MOSFET) in the subthreshold regime of operation is developed in this work using green's function approach. The approach considers 2-D mixed boundary conditions and multi-zone techniques to provide an exact analytical solution to 2-D Poisson's equation. The Fourier coefficients are calculated correctly to derive the potential equations that are further used to model the channel current and subthreshold slope of the device. The threshold voltage roll-off is computed from parallel shifts of Ids-Vgs curves between the long channel and short-channel devices. It is observed that the green's function approach of solving 2-D Poisson's equation in both oxide and silicon region can accurately predict channel potential, subthreshold current (Isub), threshold voltage (Vt) roll-off and subthreshold slope (SS) of both long & short channel devices designed with different doping concentrations and higher as well as lower tsi/tox ratio. All the analytical model results are verified through comparisons with TCAD Sentaurus simulation results. It is observed that the model matches quite well with TCAD device simulations.

  12. MnNiO3 revisited with modern theoretical and experimental methods

    NASA Astrophysics Data System (ADS)

    Dzubak, Allison L.; Mitra, Chandrima; Chance, Michael; Kuhn, Stephen; Jellison, Gerald E.; Sefat, Athena S.; Krogel, Jaron T.; Reboredo, Fernando A.

    2017-11-01

    MnNiO3 is a strongly correlated transition metal oxide that has recently been investigated theoretically for its potential application as an oxygen-evolution photocatalyst. However, there is no experimental report on critical quantities such as the band gap or bulk modulus. Recent theoretical predictions with standard functionals such as LDA+U and HSE show large discrepancies in the band gaps (about 1.23 eV), depending on the nature of the functional used. Hence there is clearly a need for an accurate quantitative prediction of the band gap to gauge its utility as a photocatalyst. In this work, we present a diffusion quantum Monte Carlo study of the bulk properties of MnNiO3 and revisit the synthesis and experimental properties of the compound. We predict quasiparticle band gaps of 2.0(5) eV and 3.8(6) eV for the majority and minority spin channels, respectively, and an equilibrium volume of 92.8 Å3, which compares well to the experimental value of 94.4 Å3. A bulk modulus of 217 GPa is predicted for MnNiO3. We rationalize the difficulty for the formation of ordered ilmenite-type structure with specific sites for Ni and Mn to be potentially due to the formation of antisite defects that form during synthesis, which ultimately affects the physical properties of MnNiO3.

  13. Exchange-Hole Dipole Dispersion Model for Accurate Energy Ranking in Molecular Crystal Structure Prediction.

    PubMed

    Whittleton, Sarah R; Otero-de-la-Roza, A; Johnson, Erin R

    2017-02-14

    Accurate energy ranking is a key facet to the problem of first-principles crystal-structure prediction (CSP) of molecular crystals. This work presents a systematic assessment of B86bPBE-XDM, a semilocal density functional combined with the exchange-hole dipole moment (XDM) dispersion model, for energy ranking using 14 compounds from the first five CSP blind tests. Specifically, the set of crystals studied comprises 11 rigid, planar compounds and 3 co-crystals. The experimental structure was correctly identified as the lowest in lattice energy for 12 of the 14 total crystals. One of the exceptions is 4-hydroxythiophene-2-carbonitrile, for which the experimental structure was correctly identified once a quasi-harmonic estimate of the vibrational free-energy contribution was included, evidencing the occasional importance of thermal corrections for accurate energy ranking. The other exception is an organic salt, where charge-transfer error (also called delocalization error) is expected to cause the base density functional to be unreliable. Provided the choice of base density functional is appropriate and an estimate of temperature effects is used, XDM-corrected density-functional theory is highly reliable for the energetic ranking of competing crystal structures.

  14. NNLOPS accurate associated HW production

    NASA Astrophysics Data System (ADS)

    Astill, William; Bizon, Wojciech; Re, Emanuele; Zanderighi, Giulia

    2016-06-01

    We present a next-to-next-to-leading order accurate description of associated HW production consistently matched to a parton shower. The method is based on reweighting events obtained with the HW plus one jet NLO accurate calculation implemented in POWHEG, extended with the MiNLO procedure, to reproduce NNLO accurate Born distributions. Since the Born kinematics is more complex than the cases treated before, we use a parametrization of the Collins-Soper angles to reduce the number of variables required for the reweighting. We present phenomenological results at 13 TeV, with cuts suggested by the Higgs Cross section Working Group.

  15. Experimental models for aging and their potential for novel drug discovery.

    PubMed

    Folch, Jaume; Busquets, Oriol; Sánchez-López, Miren EttchetoElena; Pallàs, Mercè; Beas-Zarate, Carlos; Marin, Miguel; Casadesus, Gemma; Olloquequi, Jordi; Auladell, Carme; Camins, Antoni

    2017-07-07

    The development of antiaging drugs is an interesting area of scientific research. In order to evaluate the beneficial effects of new potential drugs, it is necessary to gather the specific knowledge on the adequate preclinical models that are available. This review focuses on invertebrate and vertebrate preclinical models used to evaluate the efficacy of antiaging compounds, with the objective to extend lifespan and health span. Dietary restriction (DR), a common experimental process to extend lifespan in all organisms, is also discussed. Besides, classical antiaging drugs such as resveratrol, rapamycin and metformin, denominated DR mimetics, are reviewed. The main therapeutic targets of these drugs include sirtuins, IGF-1, and mTOR, all of them being modulated by DR. The National Institute on Aging (NIA) developed the Interventions Testing Program (ITP). At the preclinical level, the ITP uses genetically heterogeneous mice model (HET), which is probably the most suitable rodent model to study potential drugs preventing aging-related diseases. The accelerated-senescence mouse P8 is also an interesting rodent model for the research in the field of aging. Notwithstanding, non-human primates are still necessary prior to clinical trials, since they allow an easier extrapolation to humans due to their anatomical and physiological similarities. In this review, the different models and approaches for antiaging studies were evaluated. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  16. Solution of steady and unsteady transonic-vortex flows using Euler and full-potential equations

    NASA Technical Reports Server (NTRS)

    Kandil, Osama A.; Chuang, Andrew H.; Hu, Hong

    1989-01-01

    Two methods are presented for inviscid transonic flows: unsteady Euler equations in a rotating frame of reference for transonic-vortex flows and integral solution of full-potential equation with and without embedded Euler domains for transonic airfoil flows. The computational results covered: steady and unsteady conical vortex flows; 3-D steady transonic vortex flow; and transonic airfoil flows. The results are in good agreement with other computational results and experimental data. The rotating frame of reference solution is potentially efficient as compared with the space fixed reference formulation with dynamic gridding. The integral equation solution with embedded Euler domain is computationally efficient and as accurate as the Euler equations.

  17. Accurate Arabic Script Language/Dialect Classification

    DTIC Science & Technology

    2014-01-01

    Army Research Laboratory Accurate Arabic Script Language/Dialect Classification by Stephen C. Tratz ARL-TR-6761 January 2014 Approved for public...1197 ARL-TR-6761 January 2014 Accurate Arabic Script Language/Dialect Classification Stephen C. Tratz Computational and Information Sciences...Include area code) Standard Form 298 (Rev. 8/98) Prescribed by ANSI Std. Z39.18 January 2014 Final Accurate Arabic Script Language/Dialect Classification

  18. Simple Mathematical Models Do Not Accurately Predict Early SIV Dynamics

    PubMed Central

    Noecker, Cecilia; Schaefer, Krista; Zaccheo, Kelly; Yang, Yiding; Day, Judy; Ganusov, Vitaly V.

    2015-01-01

    Upon infection of a new host, human immunodeficiency virus (HIV) replicates in the mucosal tissues and is generally undetectable in circulation for 1–2 weeks post-infection. Several interventions against HIV including vaccines and antiretroviral prophylaxis target virus replication at this earliest stage of infection. Mathematical models have been used to understand how HIV spreads from mucosal tissues systemically and what impact vaccination and/or antiretroviral prophylaxis has on viral eradication. Because predictions of such models have been rarely compared to experimental data, it remains unclear which processes included in these models are critical for predicting early HIV dynamics. Here we modified the “standard” mathematical model of HIV infection to include two populations of infected cells: cells that are actively producing the virus and cells that are transitioning into virus production mode. We evaluated the effects of several poorly known parameters on infection outcomes in this model and compared model predictions to experimental data on infection of non-human primates with variable doses of simian immunodifficiency virus (SIV). First, we found that the mode of virus production by infected cells (budding vs. bursting) has a minimal impact on the early virus dynamics for a wide range of model parameters, as long as the parameters are constrained to provide the observed rate of SIV load increase in the blood of infected animals. Interestingly and in contrast with previous results, we found that the bursting mode of virus production generally results in a higher probability of viral extinction than the budding mode of virus production. Second, this mathematical model was not able to accurately describe the change in experimentally determined probability of host infection with increasing viral doses. Third and finally, the model was also unable to accurately explain the decline in the time to virus detection with increasing viral dose. These results

  19. An accurate automated technique for quasi-optics measurement of the microwave diagnostics for fusion plasma

    NASA Astrophysics Data System (ADS)

    Hu, Jianqiang; Liu, Ahdi; Zhou, Chu; Zhang, Xiaohui; Wang, Mingyuan; Zhang, Jin; Feng, Xi; Li, Hong; Xie, Jinlin; Liu, Wandong; Yu, Changxuan

    2017-08-01

    A new integrated technique for fast and accurate measurement of the quasi-optics, especially for the microwave/millimeter wave diagnostic systems of fusion plasma, has been developed. Using the LabVIEW-based comprehensive scanning system, we can realize not only automatic but also fast and accurate measurement, which will help to eliminate the effects of temperature drift and standing wave/multi-reflection. With the Matlab-based asymmetric two-dimensional Gaussian fitting method, all the desired parameters of the microwave beam can be obtained. This technique can be used in the design and testing of microwave diagnostic systems such as reflectometers and the electron cyclotron emission imaging diagnostic systems of the Experimental Advanced Superconducting Tokamak.

  20. Tools for Accurate and Efficient Analysis of Complex Evolutionary Mechanisms in Microbial Genomes. Final Report

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Nakhleh, Luay

    I proposed to develop computationally efficient tools for accurate detection and reconstruction of microbes' complex evolutionary mechanisms, thus enabling rapid and accurate annotation, analysis and understanding of their genomes. To achieve this goal, I proposed to address three aspects. (1) Mathematical modeling. A major challenge facing the accurate detection of HGT is that of distinguishing between these two events on the one hand and other events that have similar "effects." I proposed to develop a novel mathematical approach for distinguishing among these events. Further, I proposed to develop a set of novel optimization criteria for the evolutionary analysis of microbialmore » genomes in the presence of these complex evolutionary events. (2) Algorithm design. In this aspect of the project, I proposed to develop an array of e cient and accurate algorithms for analyzing microbial genomes based on the formulated optimization criteria. Further, I proposed to test the viability of the criteria and the accuracy of the algorithms in an experimental setting using both synthetic as well as biological data. (3) Software development. I proposed the nal outcome to be a suite of software tools which implements the mathematical models as well as the algorithms developed.« less

  1. Experimental Energy Levels and Partition Function of the 12C2 Molecule

    NASA Astrophysics Data System (ADS)

    Furtenbacher, Tibor; Szabó, István; Császár, Attila G.; Bernath, Peter F.; Yurchenko, Sergei N.; Tennyson, Jonathan

    2016-06-01

    The carbon dimer, the 12C2 molecule, is ubiquitous in astronomical environments. Experimental-quality rovibronic energy levels are reported for 12C2, based on rovibronic transitions measured for and among its singlet, triplet, and quintet electronic states, reported in 42 publications. The determination utilizes the Measured Active Rotational-Vibrational Energy Levels (MARVEL) technique. The 23,343 transitions measured experimentally and validated within this study determine 5699 rovibronic energy levels, 1325, 4309, and 65 levels for the singlet, triplet, and quintet states investigated, respectively. The MARVEL analysis provides rovibronic energies for six singlet, six triplet, and two quintet electronic states. For example, the lowest measurable energy level of the {{a}}{}3{{{\\Pi }}}{{u}} state, corresponding to the J = 2 total angular momentum quantum number and the F 1 spin-multiplet component, is 603.817(5) cm-1. This well-determined energy difference should facilitate observations of singlet-triplet intercombination lines, which are thought to occur in the interstellar medium and comets. The large number of highly accurate and clearly labeled transitions that can be derived by combining MARVEL energy levels with computed temperature-dependent intensities should help a number of astrophysical observations as well as corresponding laboratory measurements. The experimental rovibronic energy levels, augmented, where needed, with ab initio variational ones based on empirically adjusted and spin-orbit coupled potential energy curves obtained using the Duo code, are used to obtain a highly accurate partition function, and related thermodynamic data, for 12C2 up to 4000 K.

  2. Accurate mass measurements and their appropriate use for reliable analyte identification.

    PubMed

    Godfrey, A Ruth; Brenton, A Gareth

    2012-09-01

    Accurate mass instrumentation is becoming increasingly available to non-expert users. This data can be mis-used, particularly for analyte identification. Current best practice in assigning potential elemental formula for reliable analyte identification has been described with modern informatic approaches to analyte elucidation, including chemometric characterisation, data processing and searching using facilities such as the Chemical Abstracts Service (CAS) Registry and Chemspider.

  3. Ab Initio Calculation of Accurate Vibrational Frequencies for Molecules of Interest in Atmospheric Chemistry

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

    1996-01-01

    Due to advances in quantum mechanical methods over the last few years, it is now possible to determine ab initio potential energy surfaces in which fundamental vibrational frequencies are accurate to within +/- 8 cm(sup -1) on average, and molecular bond distances are accurate to within +/- 0.001-0.003 A, depending on the nature of the bond. That is, the potential energy surfaces have not been scaled or empirically adjusted in any way, showing that theoretical methods have progressed to the point of being useful in analyzing spectra that are not from a tightly controlled laboratory environment, such as rovibrational spectra from the interstellar medium. Some recent examples demonstrating this accuracy win be presented and discussed. These include the HNO, CH4, C2H4, and ClCN molecules. The HNO molecule is interesting due to the very large H-N anharmonicity, while ClCN has a very large Fermi resonance. The ab initio studies for the CH4 and C2H4 molecules present the first accurate full quartic force fields of any kind (i.e., whether theoretical or empirical) for a five-atom and six-atom system, respectively.

  4. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate... indispensable in examinations conducted within the Department of Veterans Affairs. Muscle atrophy must also be...

  5. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate... indispensable in examinations conducted within the Department of Veterans Affairs. Muscle atrophy must also be...

  6. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate... indispensable in examinations conducted within the Department of Veterans Affairs. Muscle atrophy must also be...

  7. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate... indispensable in examinations conducted within the Department of Veterans Affairs. Muscle atrophy must also be...

  8. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate... indispensable in examinations conducted within the Department of Veterans Affairs. Muscle atrophy must also be...

  9. COSMOS: accurate detection of somatic structural variations through asymmetric comparison between tumor and normal samples.

    PubMed

    Yamagata, Koichi; Yamanishi, Ayako; Kokubu, Chikara; Takeda, Junji; Sese, Jun

    2016-05-05

    An important challenge in cancer genomics is precise detection of structural variations (SVs) by high-throughput short-read sequencing, which is hampered by the high false discovery rates of existing analysis tools. Here, we propose an accurate SV detection method named COSMOS, which compares the statistics of the mapped read pairs in tumor samples with isogenic normal control samples in a distinct asymmetric manner. COSMOS also prioritizes the candidate SVs using strand-specific read-depth information. Performance tests on modeled tumor genomes revealed that COSMOS outperformed existing methods in terms of F-measure. We also applied COSMOS to an experimental mouse cell-based model, in which SVs were induced by genome engineering and gamma-ray irradiation, followed by polymerase chain reaction-based confirmation. The precision of COSMOS was 84.5%, while the next best existing method was 70.4%. Moreover, the sensitivity of COSMOS was the highest, indicating that COSMOS has great potential for cancer genome analysis. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  10. 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…

  11. Accurate Evaluation Method of Molecular Binding Affinity from Fluctuation Frequency

    NASA Astrophysics Data System (ADS)

    Hoshino, Tyuji; Iwamoto, Koji; Ode, Hirotaka; Ohdomari, Iwao

    2008-05-01

    Exact estimation of the molecular binding affinity is significantly important for drug discovery. The energy calculation is a direct method to compute the strength of the interaction between two molecules. This energetic approach is, however, not accurate enough to evaluate a slight difference in binding affinity when distinguishing a prospective substance from dozens of candidates for medicine. Hence more accurate estimation of drug efficacy in a computer is currently demanded. Previously we proposed a concept of estimating molecular binding affinity, focusing on the fluctuation at an interface between two molecules. The aim of this paper is to demonstrate the compatibility between the proposed computational technique and experimental measurements, through several examples for computer simulations of an association of human immunodeficiency virus type-1 (HIV-1) protease and its inhibitor (an example for a drug-enzyme binding), a complexation of an antigen and its antibody (an example for a protein-protein binding), and a combination of estrogen receptor and its ligand chemicals (an example for a ligand-receptor binding). The proposed affinity estimation has proven to be a promising technique in the advanced stage of the discovery and the design of drugs.

  12. Accurate pressure gradient calculations in hydrostatic atmospheric models

    NASA Technical Reports Server (NTRS)

    Carroll, John J.; Mendez-Nunez, Luis R.; Tanrikulu, Saffet

    1987-01-01

    A method for the accurate calculation of the horizontal pressure gradient acceleration in hydrostatic atmospheric models is presented which is especially useful in situations where the isothermal surfaces are not parallel to the vertical coordinate surfaces. The present method is shown to be exact if the potential temperature lapse rate is constant between the vertical pressure integration limits. The technique is applied to both the integration of the hydrostatic equation and the computation of the slope correction term in the horizontal pressure gradient. A fixed vertical grid and a dynamic grid defined by the significant levels in the vertical temperature distribution are employed.

  13. Examining ERP correlates of recognition memory: Evidence of accurate source recognition without recollection

    PubMed Central

    Addante, Richard, J.; Ranganath, Charan; Yonelinas, Andrew, P.

    2012-01-01

    Recollection is typically associated with high recognition confidence and accurate source memory. However, subjects sometimes make accurate source memory judgments even for items that are not confidently recognized, and it is not known whether these responses are based on recollection or some other memory process. In the current study, we measured event related potentials (ERPs) while subjects made item and source memory confidence judgments in order to determine whether recollection supported accurate source recognition responses for items that were not confidently recognized. In line with previous studies, we found that recognition memory was associated with two ERP effects: an early on-setting FN400 effect, and a later parietal old-new effect [Late Positive Component (LPC)], which have been associated with familiarity and recollection, respectively. The FN400 increased gradually with item recognition confidence, whereas the LPC was only observed for highly confident recognition responses. The LPC was also related to source accuracy, but only for items that had received a high confidence item recognition response; accurate source judgments to items that were less confidently recognized did not exhibit the typical ERP correlate of recollection or familiarity, but rather showed a late, broadly distributed negative ERP difference. The results indicate that accurate source judgments of episodic context can occur even when recollection fails. PMID:22548808

  14. Xenon Defects in Uranium Dioxide From First Principles and Interatomic Potentials

    NASA Astrophysics Data System (ADS)

    Thompson, Alexander

    In this thesis, we examine the defect energetics and migration energies of xenon atoms in uranium dioxide (UO2) from first principles and interatomic potentials. We also parameterize new, accurate interatomic potentials for xenon and uranium dioxide. To achieve accurate energetics and provide a foundation for subsequent calculations, we address difficulties in finding consistent energetics within Hubbard U corrected density functional theory (DFT+U). We propose a method of slowly ramping the U parameter in order to guide the calculation into low energy orbital occupations. We find that this method is successful for a variety of materials. We then examine the defect energetics of several noble gas atoms in UO2 for several different defect sites. We show that the energy to incorporate large noble gas atoms into interstitial sites is so large that it is energetically favorable for a Schottky defect cluster to be created to relieve the strain. We find that, thermodynamically, xenon will rarely ever be in the interstitial site of UO2. To study larger defects associated with the migration of xenon in UO 2, we turn to interatomic potentials. We benchmark several previously published potentials against DFT+U defect energetics and migration barriers. Using a combination of molecular dynamics and nudged elastic band calculations, we find a new, low energy migration pathway for xenon in UO2. We create a new potential for xenon that yields accurate defect energetics. We fit this new potential with a method we call Iterative Potential Refinement that parameterizes potentials to first principles data via a genetic algorithm. The potential finds accurate energetics for defects with relatively low amounts of strain (xenon in defect clusters). It is important to find accurate energetics for these sorts of low-strain defects because they essentially represent small xenon bubbles. Finally, we parameterize a new UO2 potential that simultaneously yields accurate vibrational properties

  15. Accurate Prediction of Contact Numbers for Multi-Spanning Helical Membrane Proteins

    PubMed Central

    Li, Bian; Mendenhall, Jeffrey; Nguyen, Elizabeth Dong; Weiner, Brian E.; Fischer, Axel W.; Meiler, Jens

    2017-01-01

    Prediction of the three-dimensional (3D) structures of proteins by computational methods is acknowledged as an unsolved problem. Accurate prediction of important structural characteristics such as contact number is expected to accelerate the otherwise slow progress being made in the prediction of 3D structure of proteins. Here, we present a dropout neural network-based method, TMH-Expo, for predicting the contact number of transmembrane helix (TMH) residues from sequence. Neuronal dropout is a strategy where certain neurons of the network are excluded from back-propagation to prevent co-adaptation of hidden-layer neurons. By using neuronal dropout, overfitting was significantly reduced and performance was noticeably improved. For multi-spanning helical membrane proteins, TMH-Expo achieved a remarkable Pearson correlation coefficient of 0.69 between predicted and experimental values and a mean absolute error of only 1.68. In addition, among those membrane protein–membrane protein interface residues, 76.8% were correctly predicted. Mapping of predicted contact numbers onto structures indicates that contact numbers predicted by TMH-Expo reflect the exposure patterns of TMHs and reveal membrane protein–membrane protein interfaces, reinforcing the potential of predicted contact numbers to be used as restraints for 3D structure prediction and protein–protein docking. TMH-Expo can be accessed via a Web server at www.meilerlab.org. PMID:26804342

  16. Accurate modeling of defects in graphene transport calculations

    NASA Astrophysics Data System (ADS)

    Linhart, Lukas; Burgdörfer, Joachim; Libisch, Florian

    2018-01-01

    We present an approach for embedding defect structures modeled by density functional theory into large-scale tight-binding simulations. We extract local tight-binding parameters for the vicinity of the defect site using Wannier functions. In the transition region between the bulk lattice and the defect the tight-binding parameters are continuously adjusted to approach the bulk limit far away from the defect. This embedding approach allows for an accurate high-level treatment of the defect orbitals using as many as ten nearest neighbors while keeping a small number of nearest neighbors in the bulk to render the overall computational cost reasonable. As an example of our approach, we consider an extended graphene lattice decorated with Stone-Wales defects, flower defects, double vacancies, or silicon substitutes. We predict distinct scattering patterns mirroring the defect symmetries and magnitude that should be experimentally accessible.

  17. Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots.

    PubMed

    Hajdin, Christine E; Bellaousov, Stanislav; Huggins, Wayne; Leonard, Christopher W; Mathews, David H; Weeks, Kevin M

    2013-04-02

    A pseudoknot forms in an RNA when nucleotides in a loop pair with a region outside the helices that close the loop. Pseudoknots occur relatively rarely in RNA but are highly overrepresented in functionally critical motifs in large catalytic RNAs, in riboswitches, and in regulatory elements of viruses. Pseudoknots are usually excluded from RNA structure prediction algorithms. When included, these pairings are difficult to model accurately, especially in large RNAs, because allowing this structure dramatically increases the number of possible incorrect folds and because it is difficult to search the fold space for an optimal structure. We have developed a concise secondary structure modeling approach that combines SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) experimental chemical probing information and a simple, but robust, energy model for the entropic cost of single pseudoknot formation. Structures are predicted with iterative refinement, using a dynamic programming algorithm. This melded experimental and thermodynamic energy function predicted the secondary structures and the pseudoknots for a set of 21 challenging RNAs of known structure ranging in size from 34 to 530 nt. On average, 93% of known base pairs were predicted, and all pseudoknots in well-folded RNAs were identified.

  18. A modified Embedded-Atom Method interatomic potential for uranium-silicide

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Beeler, Benjamin; Baskes, Michael; Andersson, David

    Uranium-silicide (U-Si) fuels are being pursued as a possible accident tolerant fuel (ATF). This uranium alloy fuel bene ts from higher thermal conductivity and higher ssile density compared to uranium dioxide (UO 2). In order to perform engineering scale nuclear fuel performance simulations, the material properties of the fuel must be known. Currently, the experimental data available for U-Si fuels is rather limited. Thus, multiscale modeling e orts are underway to address this gap in knowledge. In this study, a semi-empirical modi ed Embedded-Atom Method (MEAM) potential is presented for the description of the U-Si system. The potential is ttedmore » to the formation energy, defect energies and structural properties of U 3Si 2. The primary phase of interest (U 3Si 2) is accurately described over a wide temperature range and displays good behavior under irradiation and with free surfaces. The potential can also describe a variety of U-Si phases across the composition spectrum.« less

  19. A modified Embedded-Atom Method interatomic potential for uranium-silicide

    DOE PAGES

    Beeler, Benjamin; Baskes, Michael; Andersson, David; ...

    2017-08-18

    Uranium-silicide (U-Si) fuels are being pursued as a possible accident tolerant fuel (ATF). This uranium alloy fuel bene ts from higher thermal conductivity and higher ssile density compared to uranium dioxide (UO 2). In order to perform engineering scale nuclear fuel performance simulations, the material properties of the fuel must be known. Currently, the experimental data available for U-Si fuels is rather limited. Thus, multiscale modeling e orts are underway to address this gap in knowledge. In this study, a semi-empirical modi ed Embedded-Atom Method (MEAM) potential is presented for the description of the U-Si system. The potential is ttedmore » to the formation energy, defect energies and structural properties of U 3Si 2. The primary phase of interest (U 3Si 2) is accurately described over a wide temperature range and displays good behavior under irradiation and with free surfaces. The potential can also describe a variety of U-Si phases across the composition spectrum.« less

  20. A modified Embedded-Atom Method interatomic potential for uranium-silicide

    NASA Astrophysics Data System (ADS)

    Beeler, Benjamin; Baskes, Michael; Andersson, David; Cooper, Michael W. D.; Zhang, Yongfeng

    2017-11-01

    Uranium-silicide (U-Si) fuels are being pursued as a possible accident tolerant fuel (ATF). This uranium alloy fuel benefits from higher thermal conductivity and higher fissile density compared to uranium dioxide (UO2). In order to perform engineering scale nuclear fuel performance simulations, the material properties of the fuel must be known. Currently, the experimental data available for U-Si fuels is rather limited. Thus, multiscale modeling efforts are underway to address this gap in knowledge. In this study, a semi-empirical modified Embedded-Atom Method (MEAM) potential is presented for the description of the U-Si system. The potential is fitted to the formation energy, defect energies and structural properties of U3Si2. The primary phase of interest (U3Si2) is accurately described over a wide temperature range and displays good behavior under irradiation and with free surfaces. The potential can also describe a variety of U-Si phases across the composition spectrum.

  1. Accurate determination of the charge transfer efficiency of photoanodes for solar water splitting.

    PubMed

    Klotz, Dino; Grave, Daniel A; Rothschild, Avner

    2017-08-09

    The oxygen evolution reaction (OER) at the surface of semiconductor photoanodes is critical for photoelectrochemical water splitting. This reaction involves photo-generated holes that oxidize water via charge transfer at the photoanode/electrolyte interface. However, a certain fraction of the holes that reach the surface recombine with electrons from the conduction band, giving rise to the surface recombination loss. The charge transfer efficiency, η t , defined as the ratio between the flux of holes that contribute to the water oxidation reaction and the total flux of holes that reach the surface, is an important parameter that helps to distinguish between bulk and surface recombination losses. However, accurate determination of η t by conventional voltammetry measurements is complicated because only the total current is measured and it is difficult to discern between different contributions to the current. Chopped light measurement (CLM) and hole scavenger measurement (HSM) techniques are widely employed to determine η t , but they often lead to errors resulting from instrumental as well as fundamental limitations. Intensity modulated photocurrent spectroscopy (IMPS) is better suited for accurate determination of η t because it provides direct information on both the total photocurrent and the surface recombination current. However, careful analysis of IMPS measurements at different light intensities is required to account for nonlinear effects. This work compares the η t values obtained by these methods using heteroepitaxial thin-film hematite photoanodes as a case study. We show that a wide spread of η t values is obtained by different analysis methods, and even within the same method different values may be obtained depending on instrumental and experimental conditions such as the light source and light intensity. Statistical analysis of the results obtained for our model hematite photoanode show good correlation between different methods for

  2. Accurate Binding Free Energy Predictions in Fragment Optimization.

    PubMed

    Steinbrecher, Thomas B; Dahlgren, Markus; Cappel, Daniel; Lin, Teng; Wang, Lingle; Krilov, Goran; Abel, Robert; Friesner, Richard; Sherman, Woody

    2015-11-23

    Predicting protein-ligand binding free energies is a central aim of computational structure-based drug design (SBDD)--improved accuracy in binding free energy predictions could significantly reduce costs and accelerate project timelines in lead discovery and optimization. The recent development and validation of advanced free energy calculation methods represents a major step toward this goal. Accurately predicting the relative binding free energy changes of modifications to ligands is especially valuable in the field of fragment-based drug design, since fragment screens tend to deliver initial hits of low binding affinity that require multiple rounds of synthesis to gain the requisite potency for a project. In this study, we show that a free energy perturbation protocol, FEP+, which was previously validated on drug-like lead compounds, is suitable for the calculation of relative binding strengths of fragment-sized compounds as well. We study several pharmaceutically relevant targets with a total of more than 90 fragments and find that the FEP+ methodology, which uses explicit solvent molecular dynamics and physics-based scoring with no parameters adjusted, can accurately predict relative fragment binding affinities. The calculations afford R(2)-values on average greater than 0.5 compared to experimental data and RMS errors of ca. 1.1 kcal/mol overall, demonstrating significant improvements over the docking and MM-GBSA methods tested in this work and indicating that FEP+ has the requisite predictive power to impact fragment-based affinity optimization projects.

  3. Expression patterns of histone deacetylases in experimental stroke and potential targets for neuroprotection.

    PubMed

    Chen, Yan-Ting; Zang, Xue-Feng; Pan, Jie; Zhu, Xiao-Lei; Chen, Fei; Chen, Zhi-Bin; Xu, Yun

    2012-09-01

    1. Histone deacetylase (HDAC) inhibitors exert neuroprotection in both cellular and animal models of ischaemic stroke. However, which HDAC isoform (or isoforms) mediates this beneficial effect has not yet been determined. 2. In the present study, gene levels of the HDAC isoforms were determined in the mouse cortex using reverse transcription-polymerase chain reaction (RT-PCR), whereas changes in the expression of individual zinc-dependent HDAC family members were evaluated by western blotting, 3, 12, 24 and 48 h after cerebral ischaemia induced by transient middle cerebral artery occlusion in male Kunming mice. 3. The HDAC isoforms HDAC1-11 were all expressed in the mouse cortex and differentially affected by cerebral ischaemia. Notably, there was a substantial increase in HDAC3, HDAC6 and HDAC11 expression during the early phases of experimental stroke, indicating their contribution to stroke pathogenesis. Furthermore, induction of HDAC3 and HDAC6 in cortical neurons by ischaemic stroke was confirmed in vivo and in vitro using double-labelled immunostaining and RT-PCR, respectively. Therefore, small hairpin (sh) RNAs were used to selectively knock down HDAC3 or HDAC6. This knockdown appreciably promoted the survival of cortical neurons subjected to oxygen and glucose deprivation. 4. The findings of the present study demonstrate the expression patterns of HDAC isoforms during experimental ischaemic stroke. Furthermore, HDAC3 and HDAC6 were identified as potential mediators in the neurotoxicity of ischaemic stroke, suggesting that specific therapeutic approaches may be considered according to HDAC subtype. © 2012 The Authors Clinical and Experimental Pharmacology and Physiology © 2012 Wiley Publishing Asia Pty Ltd.

  4. Stochastic estimation of human shoulder impedance with robots: an experimental design.

    PubMed

    Park, Kyungbin; Chang, Pyung Hun

    2011-01-01

    Previous studies assumed the shoulder as a hinge joint during human arm impedance measurement. This is obviously a vast simplification since the shoulder is a complex of several joints with multiple degrees of freedom. In the present work, a practical methodology for more general and realistic estimation of human shoulder impedance is proposed and validated with a spring array. It includes a gravity compensation scheme, which is developed and used for the experiments with a spatial three degrees of freedom PUMA-type robot. The experimental results were accurate and reliable, and thus it has shown a strong potential of the proposed methodology in the estimation of human shoulder impedance. © 2011 IEEE

  5. Accurate and general treatment of electrostatic interaction in Hamiltonian adaptive resolution simulations

    NASA Astrophysics Data System (ADS)

    Heidari, M.; Cortes-Huerto, R.; Donadio, D.; Potestio, R.

    2016-10-01

    In adaptive resolution simulations the same system is concurrently modeled with different resolution in different subdomains of the simulation box, thereby enabling an accurate description in a small but relevant region, while the rest is treated with a computationally parsimonious model. In this framework, electrostatic interaction, whose accurate treatment is a crucial aspect in the realistic modeling of soft matter and biological systems, represents a particularly acute problem due to the intrinsic long-range nature of Coulomb potential. In the present work we propose and validate the usage of a short-range modification of Coulomb potential, the Damped shifted force (DSF) model, in the context of the Hamiltonian adaptive resolution simulation (H-AdResS) scheme. This approach, which is here validated on bulk water, ensures a reliable reproduction of the structural and dynamical properties of the liquid, and enables a seamless embedding in the H-AdResS framework. The resulting dual-resolution setup is implemented in the LAMMPS simulation package, and its customized version employed in the present work is made publicly available.

  6. An efficient and accurate 3D displacements tracking strategy for digital volume correlation

    NASA Astrophysics Data System (ADS)

    Pan, Bing; Wang, Bo; Wu, Dafang; Lubineau, Gilles

    2014-07-01

    Owing to its inherent computational complexity, practical implementation of digital volume correlation (DVC) for internal displacement and strain mapping faces important challenges in improving its computational efficiency. In this work, an efficient and accurate 3D displacement tracking strategy is proposed for fast DVC calculation. The efficiency advantage is achieved by using three improvements. First, to eliminate the need of updating Hessian matrix in each iteration, an efficient 3D inverse compositional Gauss-Newton (3D IC-GN) algorithm is introduced to replace existing forward additive algorithms for accurate sub-voxel displacement registration. Second, to ensure the 3D IC-GN algorithm that converges accurately and rapidly and avoid time-consuming integer-voxel displacement searching, a generalized reliability-guided displacement tracking strategy is designed to transfer accurate and complete initial guess of deformation for each calculation point from its computed neighbors. Third, to avoid the repeated computation of sub-voxel intensity interpolation coefficients, an interpolation coefficient lookup table is established for tricubic interpolation. The computational complexity of the proposed fast DVC and the existing typical DVC algorithms are first analyzed quantitatively according to necessary arithmetic operations. Then, numerical tests are performed to verify the performance of the fast DVC algorithm in terms of measurement accuracy and computational efficiency. The experimental results indicate that, compared with the existing DVC algorithm, the presented fast DVC algorithm produces similar precision and slightly higher accuracy at a substantially reduced computational cost.

  7. MnNiO 3 revisited with modern theoretical and experimental methods

    DOE PAGES

    Dzubak, Allison L.; Mitra, Chandrima; Chance, Michael; ...

    2017-11-03

    MnNiO 3 is a strongly correlated transition metal oxide that has recently been investigated theoretically for its potential application as an oxygen-evolution photocatalyst. However, there is no experimental report on critical quantities such as the band gap or bulk modulus. Recent theoretical predictions with standard functionals such as LDA+U and HSE show large discrepancies in the band gaps (about 1.23 eV), depending on the nature of the functional used. Hence there is clearly a need for an accurate quantitative prediction of the band gap to gauge its utility as a photocatalyst. In this work, we present a diffusion quantum Montemore » Carlo study of the bulk properties of MnNiO 3 and revisit the synthesis and experimental properties of the compound. We predict quasiparticle band gaps of 2.0(5) eV and 3.8(6) eV for the majority and minority spin channels, respectively, and an equilibrium volume of 92.8 Å 3, which compares well to the experimental value of 94.4 Å 3. A bulk modulus of 217 GPa is predicted for MnNiO 3. As a result, we rationalize the difficulty for the formation of ordered ilmenite-type structure with specific sites for Ni and Mn to be potentially due to the formation of antisite defects that form during synthesis, which ultimately affects the physical properties of MnNiO 3.« less

  8. MnNiO 3 revisited with modern theoretical and experimental methods

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Dzubak, Allison L.; Mitra, Chandrima; Chance, Michael

    MnNiO 3 is a strongly correlated transition metal oxide that has recently been investigated theoretically for its potential application as an oxygen-evolution photocatalyst. However, there is no experimental report on critical quantities such as the band gap or bulk modulus. Recent theoretical predictions with standard functionals such as LDA+U and HSE show large discrepancies in the band gaps (about 1.23 eV), depending on the nature of the functional used. Hence there is clearly a need for an accurate quantitative prediction of the band gap to gauge its utility as a photocatalyst. In this work, we present a diffusion quantum Montemore » Carlo study of the bulk properties of MnNiO 3 and revisit the synthesis and experimental properties of the compound. We predict quasiparticle band gaps of 2.0(5) eV and 3.8(6) eV for the majority and minority spin channels, respectively, and an equilibrium volume of 92.8 Å 3, which compares well to the experimental value of 94.4 Å 3. A bulk modulus of 217 GPa is predicted for MnNiO 3. As a result, we rationalize the difficulty for the formation of ordered ilmenite-type structure with specific sites for Ni and Mn to be potentially due to the formation of antisite defects that form during synthesis, which ultimately affects the physical properties of MnNiO 3.« less

  9. Accurate mode characterization of two-mode optical fibers by in-fiber acousto-optics.

    PubMed

    Alcusa-Sáez, E; Díez, A; Andrés, M V

    2016-03-07

    Acousto-optic interaction in optical fibers is exploited for the accurate and broadband characterization of two-mode optical fibers. Coupling between LP 01 and LP 1m modes is produced in a broadband wavelength range. Difference in effective indices, group indices, and chromatic dispersions between the guided modes, are obtained from experimental measurements. Additionally, we show that the technique is suitable to investigate the fine modes structure of LP modes, and some other intriguing features related with modes' cut-off.

  10. The determination of accurate dipole polarizabilities alpha and gamma for the noble gases

    NASA Technical Reports Server (NTRS)

    Rice, Julia E.; Taylor, Peter R.; Lee, Timothy J.; Almloef, Jan

    1989-01-01

    The static dipole polarizabilities alpha and gamma for the noble gases helium through xenon were determined using large flexible one-particle basis sets in conjunction with high-level treatments of electron correlation. The electron correlation methods include single and double excitation coupled-cluster theory (CCSD), an extension of CCSD that includes a perturbational estimate of connected triple excitations, CCSD(T), and second order perturbation theory (MP2). The computed alpha and gamma values are estimated to be accurate to within a few percent. Agreement with experimental data for the static hyperpolarizability gamma is good for neon and xenon, but for argon and krypton the differences are larger than the combined theoretical and experimental uncertainties. Based on our calculations, we suggest that the experimental value of gamma for argon is too low; adjusting this value would bring the experimental value of gamma for krypton into better agreement with our computed result. The MP2 values for the polarizabilities of neon, argon, krypton and zenon are in reasonabe agreement with the CCSD and CCSD(T) values, suggesting that this less expensive method may be useful in studies of polarizabilities for larger systems.

  11. Bayesian parameter estimation of a k-ε model for accurate jet-in-crossflow simulations

    DOE PAGES

    Ray, Jaideep; Lefantzi, Sophia; Arunajatesan, Srinivasan; ...

    2016-05-31

    Reynolds-averaged Navier–Stokes models are not very accurate for high-Reynolds-number compressible jet-in-crossflow interactions. The inaccuracy arises from the use of inappropriate model parameters and model-form errors in the Reynolds-averaged Navier–Stokes model. In this study, the hypothesis is pursued that Reynolds-averaged Navier–Stokes predictions can be significantly improved by using parameters inferred from experimental measurements of a supersonic jet interacting with a transonic crossflow.

  12. Experimental Investigation of Gas/Slag/Matte/Tridymite Equilibria in the Cu-Fe-O-S-Si System in Controlled Gas Atmospheres: Experimental Results at 1473 K (1200 °C) and P(SO2) = 0.25 atm

    NASA Astrophysics Data System (ADS)

    Fallah-Mehrjardi, Ata; Hidayat, Taufiq; Hayes, Peter C.; Jak, Evgueni

    2017-12-01

    Experimental studies were undertaken to determine the gas/slag/matte/tridymite equilibria in the Cu-Fe-O-S-Si system at 1473 K (1200 °C), P(SO2) = 0.25 atm, and a range of P(O2)'s. The experimental methodology involved high-temperature equilibration using a substrate support technique in controlled gas atmospheres (CO/CO2/SO2/Ar), rapid quenching of equilibrium phases, followed by direct measurement of the chemical compositions of the phases with Electron Probe X-ray Microanalysis (EPMA). The experimental data for slag and matte were presented as a function of copper concentration in matte (matte grade). The data provided are essential for the evaluation of the effect of oxygen potential under controlled atmosphere on the matte grade, liquidus composition of slag and chemically dissolved copper in slag. The new data provide important accurate and reliable quantitative foundation for improvement of the thermodynamic databases for copper-containing systems.

  13. Empirical temperature-dependent intermolecular potentials determined by data mining from crystal data

    NASA Astrophysics Data System (ADS)

    Hofmann, D. W. M.; Kuleshova, L. N.

    2018-05-01

    Modern force fields are accurate enough to describe thermal effects in molecular crystals. Here, we have extended our earlier approach to discrete force fields for various temperatures to a force field with a continuous function. For the parametrisation of the force field, we used data mining on experimental structures with the temperature as an additional descriptor. The obtained force field can be used to minimise energy at a finite temperature and for molecular dynamics with zero-K potentials. The applicability of the method has been demonstrated for the prediction of crystal density, temperature density gradients and transition temperature.

  14. Research on the Rapid and Accurate Positioning and Orientation Approach for Land Missile-Launching Vehicle

    PubMed Central

    Li, Kui; Wang, Lei; Lv, Yanhong; Gao, Pengyu; Song, Tianxiao

    2015-01-01

    Getting a land vehicle’s accurate position, azimuth and attitude rapidly is significant for vehicle based weapons’ combat effectiveness. In this paper, a new approach to acquire vehicle’s accurate position and orientation is proposed. It uses biaxial optical detection platform (BODP) to aim at and lock in no less than three pre-set cooperative targets, whose accurate positions are measured beforehand. Then, it calculates the vehicle’s accurate position, azimuth and attitudes by the rough position and orientation provided by vehicle based navigation systems and no less than three couples of azimuth and pitch angles measured by BODP. The proposed approach does not depend on Global Navigation Satellite System (GNSS), thus it is autonomous and difficult to interfere. Meanwhile, it only needs a rough position and orientation as algorithm’s iterative initial value, consequently, it does not have high performance requirement for Inertial Navigation System (INS), odometer and other vehicle based navigation systems, even in high precise applications. This paper described the system’s working procedure, presented theoretical deviation of the algorithm, and then verified its effectiveness through simulation and vehicle experiments. The simulation and experimental results indicate that the proposed approach can achieve positioning and orientation accuracy of 0.2 m and 20″ respectively in less than 3 min. PMID:26492249

  15. Research on the rapid and accurate positioning and orientation approach for land missile-launching vehicle.

    PubMed

    Li, Kui; Wang, Lei; Lv, Yanhong; Gao, Pengyu; Song, Tianxiao

    2015-10-20

    Getting a land vehicle's accurate position, azimuth and attitude rapidly is significant for vehicle based weapons' combat effectiveness. In this paper, a new approach to acquire vehicle's accurate position and orientation is proposed. It uses biaxial optical detection platform (BODP) to aim at and lock in no less than three pre-set cooperative targets, whose accurate positions are measured beforehand. Then, it calculates the vehicle's accurate position, azimuth and attitudes by the rough position and orientation provided by vehicle based navigation systems and no less than three couples of azimuth and pitch angles measured by BODP. The proposed approach does not depend on Global Navigation Satellite System (GNSS), thus it is autonomous and difficult to interfere. Meanwhile, it only needs a rough position and orientation as algorithm's iterative initial value, consequently, it does not have high performance requirement for Inertial Navigation System (INS), odometer and other vehicle based navigation systems, even in high precise applications. This paper described the system's working procedure, presented theoretical deviation of the algorithm, and then verified its effectiveness through simulation and vehicle experiments. The simulation and experimental results indicate that the proposed approach can achieve positioning and orientation accuracy of 0.2 m and 20″ respectively in less than 3 min.

  16. Experimental validation of the Helmoltz equation for the surface potential of Langmuir monolayers

    NASA Astrophysics Data System (ADS)

    El Abed, Abdel I.

    2009-10-01

    We show in this paper that monolayers of the nonhydrophilic F8H18 semifluorinated n -alkane constitute when spread on the hydrophobic top of an alamethicin Langmuir monolayer, a very good experimental system in order to check the validity of Helmoltz equation. This system allows for a good agreement between measured and calculated surface potentials of unionized Langmuir monolayers. We show also that the relative dielectric constant of the F8H18 monolayer does not vary upon compression of the monolayer, the measured 2.9 value is in a very good agreement with literature data. We attribute this behavior to the self-aggregation of F8H18 molecules in nanosized circular domains whose size remains constant upon compression as shown by atomic force microscopy.

  17. Computational identification of structural factors affecting the mutagenic potential of aromatic amines: study design and experimental validation.

    PubMed

    Slavov, Svetoslav H; Stoyanova-Slavova, Iva; Mattes, William; Beger, Richard D; Brüschweiler, Beat J

    2018-07-01

    A grid-based, alignment-independent 3D-SDAR (three-dimensional spectral data-activity relationship) approach based on simulated 13 C and 15 N NMR chemical shifts augmented with through-space interatomic distances was used to model the mutagenicity of 554 primary and 419 secondary aromatic amines. A robust modeling strategy supported by extensive validation including randomized training/hold-out test set pairs, validation sets, "blind" external test sets as well as experimental validation was applied to avoid over-parameterization and build Organization for Economic Cooperation and Development (OECD 2004) compliant models. Based on an experimental validation set of 23 chemicals tested in a two-strain Salmonella typhimurium Ames assay, 3D-SDAR was able to achieve performance comparable to 5-strain (Ames) predictions by Lhasa Limited's Derek and Sarah Nexus for the same set. Furthermore, mapping of the most frequently occurring bins on the primary and secondary aromatic amine structures allowed the identification of molecular features that were associated either positively or negatively with mutagenicity. Prominent structural features found to enhance the mutagenic potential included: nitrobenzene moieties, conjugated π-systems, nitrothiophene groups, and aromatic hydroxylamine moieties. 3D-SDAR was also able to capture "true" negative contributions that are particularly difficult to detect through alternative methods. These include sulphonamide, acetamide, and other functional groups, which not only lack contributions to the overall mutagenic potential, but are known to actively lower it, if present in the chemical structures of what otherwise would be potential mutagens.

  18. An experimental evaluation of potential scavenger effects on snake road mortality detections

    USGS Publications Warehouse

    Hubbard, Kaylan A.; Chalfoun, Anna D.

    2012-01-01

    As road networks expand and collisions between vehicles and wildlife become more common, accurately quantifying mortality rates for the taxa that are most impacted will be critical. Snakes are especially vulnerable to collisions with vehicles because of their physiology and behavior. Reptile road mortality is typically quantified using driving or walking surveys; however, scavengers can rapidly remove carcasses from the road and cause underestimation of mortality. Our objective was to determine the effect that scavengers might have had on our ability to accurately detect reptile road mortality during over 150 h and 4,000 km of driving surveys through arid shrublands in southwest Wyoming, which resulted in only two observations of mortality. We developed unique simulated snake carcasses out of Burbot (Lota lota), a locally invasive fish species, and examined removal rates across three different road types at three study sites. Carcass size was not a significant predictor of time of removal, and carcass removal was comparable during the daytime and nighttime hours. However, removal of simulated carcasses was higher on paved roads than unpaved or two-track roads at all study sites, with an average of 75% of the carcasses missing within 60 h compared to 34% and 31%, respectively. Scavengers may therefore negatively impact the ability of researchers to accurately detect herpetofaunal road mortality, especially for paved roads where road mortality is likely the most prevalent.

  19. Indexed variation graphs for efficient and accurate resistome profiling.

    PubMed

    Rowe, Will P M; Winn, Martyn D

    2018-05-14

    Antimicrobial resistance remains a major threat to global health. Profiling the collective antimicrobial resistance genes within a metagenome (the "resistome") facilitates greater understanding of antimicrobial resistance gene diversity and dynamics. In turn, this can allow for gene surveillance, individualised treatment of bacterial infections and more sustainable use of antimicrobials. However, resistome profiling can be complicated by high similarity between reference genes, as well as the sheer volume of sequencing data and the complexity of analysis workflows. We have developed an efficient and accurate method for resistome profiling that addresses these complications and improves upon currently available tools. Our method combines a variation graph representation of gene sets with an LSH Forest indexing scheme to allow for fast classification of metagenomic sequence reads using similarity-search queries. Subsequent hierarchical local alignment of classified reads against graph traversals enables accurate reconstruction of full-length gene sequences using a scoring scheme. We provide our implementation, GROOT, and show it to be both faster and more accurate than a current reference-dependent tool for resistome profiling. GROOT runs on a laptop and can process a typical 2 gigabyte metagenome in 2 minutes using a single CPU. Our method is not restricted to resistome profiling and has the potential to improve current metagenomic workflows. GROOT is written in Go and is available at https://github.com/will-rowe/groot (MIT license). will.rowe@stfc.ac.uk. Supplementary data are available at Bioinformatics online.

  20. Curing potential of experimental resin composites with systematically varying amount of bioactive glass: Degree of conversion, light transmittance and depth of cure.

    PubMed

    Par, Matej; Spanovic, Nika; Bjelovucic, Ruza; Skenderovic, Hrvoje; Gamulin, Ozren; Tarle, Zrinka

    2018-06-17

    The aim of this work was to investigate the curing potential of an experimental resin composite series with the systematically varying amount of bioactive glass 45S5 by evaluating the degree of conversion, light transmittance and depth of cure. Resin composites based on a Bis-GMA/TEGDMA resin with a total filler load of 70 wt% and a variable amount of bioactive glass (0-40 wt%) were prepared. The photoinitiator system was camphorquinone and ethyl-4-(dimethylamino) benzoate. The degree of conversion and light transmittance were measured by Raman spectroscopy and UV-vis spectroscopy, respectively. The depth of cure was evaluated according to the classical ISO 4049 test. The initial introduction of bioactive glass into the experimental series diminished the light transmittance while the further increase in the bioactive glass amount up to 40 wt% caused minor variations with no clear trend. The curing potential of the experimental composites was similar to or better than that of commercial resin composites. However, unsilanized bioactive glass fillers demonstrated the tendency to diminish both the maximum attainable conversion and the curing efficiency at depth. Experimental composite materials containing bioactive glass showed a clinically acceptable degree of conversion and depth of cure. The degree of conversion and depth of cure were diminished by bioactive glass fillers in a dose-dependent manner, although light transmittance was similar among all of the experimental composites containing 5-40 wt% of bioactive glass. Reduced curing potential caused by the bioactive glass has possible consequences on mechanical properties and biocompatibility. Copyright © 2018 Elsevier Ltd. All rights reserved.

  1. Dynamic sensing model for accurate delectability of environmental phenomena using event wireless sensor network

    NASA Astrophysics Data System (ADS)

    Missif, Lial Raja; Kadhum, Mohammad M.

    2017-09-01

    Wireless Sensor Network (WSN) has been widely used for monitoring where sensors are deployed to operate independently to sense abnormal phenomena. Most of the proposed environmental monitoring systems are designed based on a predetermined sensing range which does not reflect the sensor reliability, event characteristics, and the environment conditions. Measuring of the capability of a sensor node to accurately detect an event within a sensing field is of great important for monitoring applications. This paper presents an efficient mechanism for even detection based on probabilistic sensing model. Different models have been presented theoretically in this paper to examine their adaptability and applicability to the real environment applications. The numerical results of the experimental evaluation have showed that the probabilistic sensing model provides accurate observation and delectability of an event, and it can be utilized for different environment scenarios.

  2. A method to accurately estimate the muscular torques of human wearing exoskeletons by torque sensors.

    PubMed

    Hwang, Beomsoo; Jeon, Doyoung

    2015-04-09

    In exoskeletal robots, the quantification of the user's muscular effort is important to recognize the user's motion intentions and evaluate motor abilities. In this paper, we attempt to estimate users' muscular efforts accurately using joint torque sensor which contains the measurements of dynamic effect of human body such as the inertial, Coriolis, and gravitational torques as well as torque by active muscular effort. It is important to extract the dynamic effects of the user's limb accurately from the measured torque. The user's limb dynamics are formulated and a convenient method of identifying user-specific parameters is suggested for estimating the user's muscular torque in robotic exoskeletons. Experiments were carried out on a wheelchair-integrated lower limb exoskeleton, EXOwheel, which was equipped with torque sensors in the hip and knee joints. The proposed methods were evaluated by 10 healthy participants during body weight-supported gait training. The experimental results show that the torque sensors are to estimate the muscular torque accurately in cases of relaxed and activated muscle conditions.

  3. A Method to Accurately Estimate the Muscular Torques of Human Wearing Exoskeletons by Torque Sensors

    PubMed Central

    Hwang, Beomsoo; Jeon, Doyoung

    2015-01-01

    In exoskeletal robots, the quantification of the user’s muscular effort is important to recognize the user’s motion intentions and evaluate motor abilities. In this paper, we attempt to estimate users’ muscular efforts accurately using joint torque sensor which contains the measurements of dynamic effect of human body such as the inertial, Coriolis, and gravitational torques as well as torque by active muscular effort. It is important to extract the dynamic effects of the user’s limb accurately from the measured torque. The user’s limb dynamics are formulated and a convenient method of identifying user-specific parameters is suggested for estimating the user’s muscular torque in robotic exoskeletons. Experiments were carried out on a wheelchair-integrated lower limb exoskeleton, EXOwheel, which was equipped with torque sensors in the hip and knee joints. The proposed methods were evaluated by 10 healthy participants during body weight-supported gait training. The experimental results show that the torque sensors are to estimate the muscular torque accurately in cases of relaxed and activated muscle conditions. PMID:25860074

  4. Identification of antipsychotic drug fluspirilene as a potential p53-MDM2 inhibitor: a combined computational and experimental study

    NASA Astrophysics Data System (ADS)

    Patil, Sachin P.; Pacitti, Michael F.; Gilroy, Kevin S.; Ruggiero, John C.; Griffin, Jonathan D.; Butera, Joseph J.; Notarfrancesco, Joseph M.; Tran, Shawn; Stoddart, John W.

    2015-02-01

    The inhibition of tumor suppressor p53 protein due to its direct interaction with oncogenic murine double minute 2 (MDM2) protein, plays a central role in almost 50 % of all human tumor cells. Therefore, pharmacological inhibition of the p53-binding pocket on MDM2, leading to p53 activation, presents an important therapeutic target against these cancers expressing wild-type p53. In this context, the present study utilized an integrated virtual and experimental screening approach to screen a database of approved drugs for potential p53-MDM2 interaction inhibitors. Specifically, using an ensemble rigid-receptor docking approach with four MDM2 protein crystal structures, six drug molecules were identified as possible p53-MDM2 inhibitors. These drug molecules were then subjected to further molecular modeling investigation through flexible-receptor docking followed by Prime/MM-GBSA binding energy analysis. These studies identified fluspirilene, an approved antipsychotic drug, as a top hit with MDM2 binding mode and energy similar to that of a native MDM2 crystal ligand. The molecular dynamics simulations suggested stable binding of fluspirilene to the p53-binding pocket on MDM2 protein. The experimental testing of fluspirilene showed significant growth inhibition of human colon tumor cells in a p53-dependent manner. Fluspirilene also inhibited growth of several other human tumor cell lines in the NCI60 cell line panel. Taken together, these computational and experimental data suggest a potentially novel role of fluspirilene in inhibiting the p53-MDM2 interaction. It is noteworthy here that fluspirilene has a long history of safe human use, thus presenting immediate clinical potential as a cancer therapeutic. Furthermore, fluspirilene could also serve as a structurally-novel lead molecule for the development of more potent, small-molecule p53-MDM2 inhibitors against several types of cancer. Importantly, the combined computational and experimental screening protocol

  5. Time-Accurate Simulations and Acoustic Analysis of Slat Free-Shear Layer

    NASA Technical Reports Server (NTRS)

    Khorrami, Mehdi R.; Singer, Bart A.; Berkman, Mert E.

    2001-01-01

    A detailed computational aeroacoustic analysis of a high-lift flow field is performed. Time-accurate Reynolds Averaged Navier-Stokes (RANS) computations simulate the free shear layer that originates from the slat cusp. Both unforced and forced cases are studied. Preliminary results show that the shear layer is a good amplifier of disturbances in the low to mid-frequency range. The Ffowcs-Williams and Hawkings equation is solved to determine the acoustic field using the unsteady flow data from the RANS calculations. The noise radiated from the excited shear layer has a spectral shape qualitatively similar to that obtained from measurements in a corresponding experimental study of the high-lift system.

  6. Multiple Component Event-Related Potential (mcERP) Estimation

    NASA Technical Reports Server (NTRS)

    Knuth, K. H.; Clanton, S. T.; Shah, A. S.; Truccolo, W. A.; Ding, M.; Bressler, S. L.; Trejo, L. J.; Schroeder, C. E.; Clancy, Daniel (Technical Monitor)

    2002-01-01

    We show how model-based estimation of the neural sources responsible for transient neuroelectric signals can be improved by the analysis of single trial data. Previously, we showed that a multiple component event-related potential (mcERP) algorithm can extract the responses of individual sources from recordings of a mixture of multiple, possibly interacting, neural ensembles. McERP also estimated single-trial amplitudes and onset latencies, thus allowing more accurate estimation of ongoing neural activity during an experimental trial. The mcERP algorithm is related to informax independent component analysis (ICA); however, the underlying signal model is more physiologically realistic in that a component is modeled as a stereotypic waveshape varying both in amplitude and onset latency from trial to trial. The result is a model that reflects quantities of interest to the neuroscientist. Here we demonstrate that the mcERP algorithm provides more accurate results than more traditional methods such as factor analysis and the more recent ICA. Whereas factor analysis assumes the sources are orthogonal and ICA assumes the sources are statistically independent, the mcERP algorithm makes no such assumptions thus allowing investigators to examine interactions among components by estimating the properties of single-trial responses.

  7. Avoiding fractional electrons in subsystem DFT based ab-initio molecular dynamics yields accurate models for liquid water and solvated OH radical.

    PubMed

    Genova, Alessandro; Ceresoli, Davide; Pavanello, Michele

    2016-06-21

    In this work we achieve three milestones: (1) we present a subsystem DFT method capable of running ab-initio molecular dynamics simulations accurately and efficiently. (2) In order to rid the simulations of inter-molecular self-interaction error, we exploit the ability of semilocal frozen density embedding formulation of subsystem DFT to represent the total electron density as a sum of localized subsystem electron densities that are constrained to integrate to a preset, constant number of electrons; the success of the method relies on the fact that employed semilocal nonadditive kinetic energy functionals effectively cancel out errors in semilocal exchange-correlation potentials that are linked to static correlation effects and self-interaction. (3) We demonstrate this concept by simulating liquid water and solvated OH(•) radical. While the bulk of our simulations have been performed on a periodic box containing 64 independent water molecules for 52 ps, we also simulated a box containing 256 water molecules for 22 ps. The results show that, provided one employs an accurate nonadditive kinetic energy functional, the dynamics of liquid water and OH(•) radical are in semiquantitative agreement with experimental results or higher-level electronic structure calculations. Our assessments are based upon comparisons of radial and angular distribution functions as well as the diffusion coefficient of the liquid.

  8. Learning accurate and concise naïve Bayes classifiers from attribute value taxonomies and data

    PubMed Central

    Kang, D.-K.; Silvescu, A.; Honavar, V.

    2009-01-01

    In many application domains, there is a need for learning algorithms that can effectively exploit attribute value taxonomies (AVT)—hierarchical groupings of attribute values—to learn compact, comprehensible and accurate classifiers from data—including data that are partially specified. This paper describes AVT-NBL, a natural generalization of the naïve Bayes learner (NBL), for learning classifiers from AVT and data. Our experimental results show that AVT-NBL is able to generate classifiers that are substantially more compact and more accurate than those produced by NBL on a broad range of data sets with different percentages of partially specified values. We also show that AVT-NBL is more efficient in its use of training data: AVT-NBL produces classifiers that outperform those produced by NBL using substantially fewer training examples. PMID:20351793

  9. A More Accurate and Efficient Technique Developed for Using Computational Methods to Obtain Helical Traveling-Wave Tube Interaction Impedance

    NASA Technical Reports Server (NTRS)

    Kory, Carol L.

    1999-01-01

    The phenomenal growth of commercial communications has created a great demand for traveling-wave tube (TWT) amplifiers. Although the helix slow-wave circuit remains the mainstay of the TWT industry because of its exceptionally wide bandwidth, until recently it has been impossible to accurately analyze a helical TWT using its exact dimensions because of the complexity of its geometrical structure. For the first time, an accurate three-dimensional helical model was developed that allows accurate prediction of TWT cold-test characteristics including operating frequency, interaction impedance, and attenuation. This computational model, which was developed at the NASA Lewis Research Center, allows TWT designers to obtain a more accurate value of interaction impedance than is possible using experimental methods. Obtaining helical slow-wave circuit interaction impedance is an important part of the design process for a TWT because it is related to the gain and efficiency of the tube. This impedance cannot be measured directly; thus, conventional methods involve perturbing a helical circuit with a cylindrical dielectric rod placed on the central axis of the circuit and obtaining the difference in resonant frequency between the perturbed and unperturbed circuits. A mathematical relationship has been derived between this frequency difference and the interaction impedance (ref. 1). However, because of the complex configuration of the helical circuit, deriving this relationship involves several approximations. In addition, this experimental procedure is time-consuming and expensive, but until recently it was widely accepted as the most accurate means of determining interaction impedance. The advent of an accurate three-dimensional helical circuit model (ref. 2) made it possible for Lewis researchers to fully investigate standard approximations made in deriving the relationship between measured perturbation data and interaction impedance. The most prominent approximations made

  10. Accurate coarse-grained models for mixtures of colloids and linear polymers under good-solvent conditions

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    D’Adamo, Giuseppe, E-mail: giuseppe.dadamo@sissa.it; Pelissetto, Andrea, E-mail: andrea.pelissetto@roma1.infn.it; Pierleoni, Carlo, E-mail: carlo.pierleoni@aquila.infn.it

    2014-12-28

    A coarse-graining strategy, previously developed for polymer solutions, is extended here to mixtures of linear polymers and hard-sphere colloids. In this approach, groups of monomers are mapped onto a single pseudoatom (a blob) and the effective blob-blob interactions are obtained by requiring the model to reproduce some large-scale structural properties in the zero-density limit. We show that an accurate parametrization of the polymer-colloid interactions is obtained by simply introducing pair potentials between blobs and colloids. For the coarse-grained (CG) model in which polymers are modelled as four-blob chains (tetramers), the pair potentials are determined by means of the iterative Boltzmannmore » inversion scheme, taking full-monomer (FM) pair correlation functions at zero-density as targets. For a larger number n of blobs, pair potentials are determined by using a simple transferability assumption based on the polymer self-similarity. We validate the model by comparing its predictions with full-monomer results for the interfacial properties of polymer solutions in the presence of a single colloid and for thermodynamic and structural properties in the homogeneous phase at finite polymer and colloid density. The tetramer model is quite accurate for q ≲ 1 (q=R{sup ^}{sub g}/R{sub c}, where R{sup ^}{sub g} is the zero-density polymer radius of gyration and R{sub c} is the colloid radius) and reasonably good also for q = 2. For q = 2, an accurate coarse-grained description is obtained by using the n = 10 blob model. We also compare our results with those obtained by using single-blob models with state-dependent potentials.« less

  11. A Multiscale Red Blood Cell Model with Accurate Mechanics, Rheology, and Dynamics

    PubMed Central

    Fedosov, Dmitry A.; Caswell, Bruce; Karniadakis, George Em

    2010-01-01

    Abstract Red blood cells (RBCs) have highly deformable viscoelastic membranes exhibiting complex rheological response and rich hydrodynamic behavior governed by special elastic and bending properties and by the external/internal fluid and membrane viscosities. We present a multiscale RBC model that is able to predict RBC mechanics, rheology, and dynamics in agreement with experiments. Based on an analytic theory, the modeled membrane properties can be uniquely related to the experimentally established RBC macroscopic properties without any adjustment of parameters. The RBC linear and nonlinear elastic deformations match those obtained in optical-tweezers experiments. The rheological properties of the membrane are compared with those obtained in optical magnetic twisting cytometry, membrane thermal fluctuations, and creep followed by cell recovery. The dynamics of RBCs in shear and Poiseuille flows is tested against experiments and theoretical predictions, and the applicability of the latter is discussed. Our findings clearly indicate that a purely elastic model for the membrane cannot accurately represent the RBC's rheological properties and its dynamics, and therefore accurate modeling of a viscoelastic membrane is necessary. PMID:20483330

  12. Accurate van der Waals force field for gas adsorption in porous materials.

    PubMed

    Sun, Lei; Yang, Li; Zhang, Ya-Dong; Shi, Qi; Lu, Rui-Feng; Deng, Wei-Qiao

    2017-09-05

    An accurate van der Waals force field (VDW FF) was derived from highly precise quantum mechanical (QM) calculations. Small molecular clusters were used to explore van der Waals interactions between gas molecules and porous materials. The parameters of the accurate van der Waals force field were determined by QM calculations. To validate the force field, the prediction results from the VDW FF were compared with standard FFs, such as UFF, Dreiding, Pcff, and Compass. The results from the VDW FF were in excellent agreement with the experimental measurements. This force field can be applied to the prediction of the gas density (H 2 , CO 2 , C 2 H 4 , CH 4 , N 2 , O 2 ) and adsorption performance inside porous materials, such as covalent organic frameworks (COFs), zeolites and metal organic frameworks (MOFs), consisting of H, B, N, C, O, S, Si, Al, Zn, Mg, Ni, and Co. This work provides a solid basis for studying gas adsorption in porous materials. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  13. Lamb mode selection for accurate wall loss estimation via guided wave tomography

    NASA Astrophysics Data System (ADS)

    Huthwaite, P.; Ribichini, R.; Lowe, M. J. S.; Cawley, P.

    2014-02-01

    Guided wave tomography offers a method to accurately quantify wall thickness losses in pipes and vessels caused by corrosion. This is achieved using ultrasonic waves transmitted over distances of approximately 1-2m, which are measured by an array of transducers and then used to reconstruct a map of wall thickness throughout the inspected region. To achieve accurate estimations of remnant wall thickness, it is vital that a suitable Lamb mode is chosen. This paper presents a detailed evaluation of the fundamental modes, S0 and A0, which are of primary interest in guided wave tomography thickness estimates since the higher order modes do not exist at all thicknesses, to compare their performance using both numerical and experimental data while considering a range of challenging phenomena. The sensitivity of A0 to thickness variations was shown to be superior to S0, however, the attenuation from A0 when a liquid loading was present was much higher than S0. A0 was less sensitive to the presence of coatings on the surface of than S0.

  14. A fast and accurate frequency estimation algorithm for sinusoidal signal with harmonic components

    NASA Astrophysics Data System (ADS)

    Hu, Jinghua; Pan, Mengchun; Zeng, Zhidun; Hu, Jiafei; Chen, Dixiang; Tian, Wugang; Zhao, Jianqiang; Du, Qingfa

    2016-10-01

    Frequency estimation is a fundamental problem in many applications, such as traditional vibration measurement, power system supervision, and microelectromechanical system sensors control. In this paper, a fast and accurate frequency estimation algorithm is proposed to deal with low efficiency problem in traditional methods. The proposed algorithm consists of coarse and fine frequency estimation steps, and we demonstrate that it is more efficient than conventional searching methods to achieve coarse frequency estimation (location peak of FFT amplitude) by applying modified zero-crossing technique. Thus, the proposed estimation algorithm requires less hardware and software sources and can achieve even higher efficiency when the experimental data increase. Experimental results with modulated magnetic signal show that the root mean square error of frequency estimation is below 0.032 Hz with the proposed algorithm, which has lower computational complexity and better global performance than conventional frequency estimation methods.

  15. Cellular GFP Toxicity and Immunogenicity: Potential Confounders in in Vivo Cell Tracking Experiments.

    PubMed

    Ansari, Amir Mehdi; Ahmed, A Karim; Matsangos, Aerielle E; Lay, Frank; Born, Louis J; Marti, Guy; Harmon, John W; Sun, Zhaoli

    2016-10-01

    Green Fluorescent protein (GFP), used as a cellular tag, provides researchers with a valuable method of measuring gene expression and cell tracking. However, there is evidence to suggest that the immunogenicity and cytotoxicity of GFP potentially confounds the interpretation of in vivo experimental data. Studies have shown that GFP expression can deteriorate over time as GFP tagged cells are prone to death. Therefore, the cells that were originally marked with GFP do not survive and cannot be accurately traced over time. This review will present current evidence for the immunogenicity and cytotoxicity of GFP in in vivo studies by characterizing these responses.

  16. Absolute Standard Hydrogen Electrode Potential Measured by Reduction of Aqueous Nanodrops in the Gas Phase

    PubMed Central

    Donald, William A.; Leib, Ryan D.; O'Brien, Jeremy T.; Bush, Matthew F.; Williams, Evan R.

    2008-01-01

    In solution, half-cell potentials are measured relative to those of other half cells, thereby establishing a ladder of thermochemical values that are referenced to the standard hydrogen electrode (SHE), which is arbitrarily assigned a value of exactly 0 V. Although there has been considerable interest in, and efforts toward, establishing an absolute electrochemical half-cell potential in solution, there is no general consensus regarding the best approach to obtain this value. Here, ion-electron recombination energies resulting from electron capture by gas-phase nanodrops containing individual [M(NH3)6]3+, M = Ru, Co, Os, Cr, and Ir, and Cu2+ ions are obtained from the number of water molecules that are lost from the reduced precursors. These experimental data combined with nanodrop solvation energies estimated from Born theory and solution-phase entropies estimated from limited experimental data provide absolute reduction energies for these redox couples in bulk aqueous solution. A key advantage of this approach is that solvent effects well past two solvent shells, that are difficult to model accurately, are included in these experimental measurements. By evaluating these data relative to known solution-phase reduction potentials, an absolute value for the SHE of 4.2 ± 0.4 V versus a free electron is obtained. Although not achieved here, the uncertainty of this method could potentially be reduced to below 0.1 V, making this an attractive method for establishing an absolute electrochemical scale that bridges solution and gas-phase redox chemistry. PMID:18288835

  17. Obtaining Accurate Probabilities Using Classifier Calibration

    ERIC Educational Resources Information Center

    Pakdaman Naeini, Mahdi

    2016-01-01

    Learning probabilistic classification and prediction models that generate accurate probabilities is essential in many prediction and decision-making tasks in machine learning and data mining. One way to achieve this goal is to post-process the output of classification models to obtain more accurate probabilities. These post-processing methods are…

  18. Accurate monoenergetic electron parameters of laser wakefield in a bubble model

    NASA Astrophysics Data System (ADS)

    Raheli, A.; Rahmatallahpur, S. H.

    2012-11-01

    A reliable analytical expression for the potential of plasma waves with phase velocities near the speed of light is derived. The presented spheroid cavity model is more consistent than the previous spherical and ellipsoidal model and it explains the mono-energetic electron trajectory more accurately, especially at the relativistic region. As a result, the quasi-mono-energetic electrons output beam interacting with the laser plasma can be more appropriately described with this model.

  19. Approaching system equilibrium with accurate or not accurate feedback information in a two-route system

    NASA Astrophysics Data System (ADS)

    Zhao, Xiao-mei; Xie, Dong-fan; Li, Qi

    2015-02-01

    With the development of intelligent transport system, advanced information feedback strategies have been developed to reduce traffic congestion and enhance the capacity. However, previous strategies provide accurate information to travelers and our simulation results show that accurate information brings negative effects, especially in delay case. Because travelers prefer to the best condition route with accurate information, and delayed information cannot reflect current traffic condition but past. Then travelers make wrong routing decisions, causing the decrease of the capacity and the increase of oscillations and the system deviating from the equilibrium. To avoid the negative effect, bounded rationality is taken into account by introducing a boundedly rational threshold BR. When difference between two routes is less than the BR, routes have equal probability to be chosen. The bounded rationality is helpful to improve the efficiency in terms of capacity, oscillation and the gap deviating from the system equilibrium.

  20. Accurately Mapping M31's Microlensing Population

    NASA Astrophysics Data System (ADS)

    Crotts, Arlin

    2004-07-01

    We propose to augment an existing microlensing survey of M31 with source identifications provided by a modest amount of ACS {and WFPC2 parallel} observations to yield an accurate measurement of the masses responsible for microlensing in M31, and presumably much of its dark matter. The main benefit of these data is the determination of the physical {or "einstein"} timescale of each microlensing event, rather than an effective {"FWHM"} timescale, allowing masses to be determined more than twice as accurately as without HST data. The einstein timescale is the ratio of the lensing cross-sectional radius and relative velocities. Velocities are known from kinematics, and the cross-section is directly proportional to the {unknown} lensing mass. We cannot easily measure these quantities without knowing the amplification, hence the baseline magnitude, which requires the resolution of HST to find the source star. This makes a crucial difference because M31 lens m ass determinations can be more accurate than those towards the Magellanic Clouds through our Galaxy's halo {for the same number of microlensing events} due to the better constrained geometry in the M31 microlensing situation. Furthermore, our larger survey, just completed, should yield at least 100 M31 microlensing events, more than any Magellanic survey. A small amount of ACS+WFPC2 imaging will deliver the potential of this large database {about 350 nights}. For the whole survey {and a delta-function mass distribution} the mass error should approach only about 15%, or about 6% error in slope for a power-law distribution. These results will better allow us to pinpoint the lens halo fraction, and the shape of the halo lens spatial distribution, and allow generalization/comparison of the nature of halo dark matter in spiral galaxies. In addition, we will be able to establish the baseline magnitude for about 50, 000 variable stars, as well as measure an unprecedentedly deta iled color-magnitude diagram and luminosity

  1. Methods of experimentation with models and utilization of results

    NASA Technical Reports Server (NTRS)

    Robert,

    1924-01-01

    The present report treats the subject of testing small models in a wind tunnel and of the methods employed for rendering the results constant, accurate and comparable with one another. Detailed experimental results are given.

  2. Integrated circuits for accurate linear analogue electric signal processing

    NASA Astrophysics Data System (ADS)

    Huijsing, J. H.

    1981-11-01

    The main lines in the design of integrated circuits for accurate analog linear electric signal processing in a frequency range including DC are investigated. A categorization of universal active electronic devices is presented on the basis of the connections of one of the terminals of the input and output ports to the common ground potential. The means for quantifying the attributes of four types of universal active electronic devices are included. The design of integrated operational voltage amplifiers (OVA) is discussed. Several important applications in the field of general instrumentation are numerically evaluated, and the design of operatinal floating amplifiers is presented.

  3. Large-scale extraction of accurate drug-disease treatment pairs from biomedical literature for drug repurposing

    PubMed Central

    2013-01-01

    Background A large-scale, highly accurate, machine-understandable drug-disease treatment relationship knowledge base is important for computational approaches to drug repurposing. The large body of published biomedical research articles and clinical case reports available on MEDLINE is a rich source of FDA-approved drug-disease indication as well as drug-repurposing knowledge that is crucial for applying FDA-approved drugs for new diseases. However, much of this information is buried in free text and not captured in any existing databases. The goal of this study is to extract a large number of accurate drug-disease treatment pairs from published literature. Results In this study, we developed a simple but highly accurate pattern-learning approach to extract treatment-specific drug-disease pairs from 20 million biomedical abstracts available on MEDLINE. We extracted a total of 34,305 unique drug-disease treatment pairs, the majority of which are not included in existing structured databases. Our algorithm achieved a precision of 0.904 and a recall of 0.131 in extracting all pairs, and a precision of 0.904 and a recall of 0.842 in extracting frequent pairs. In addition, we have shown that the extracted pairs strongly correlate with both drug target genes and therapeutic classes, therefore may have high potential in drug discovery. Conclusions We demonstrated that our simple pattern-learning relationship extraction algorithm is able to accurately extract many drug-disease pairs from the free text of biomedical literature that are not captured in structured databases. The large-scale, accurate, machine-understandable drug-disease treatment knowledge base that is resultant of our study, in combination with pairs from structured databases, will have high potential in computational drug repurposing tasks. PMID:23742147

  4. Use of an inertial navigation system for accurate track recovery and coastal oceanographic measurements

    NASA Technical Reports Server (NTRS)

    Oliver, B. M.; Gower, J. F. R.

    1977-01-01

    A data acquisition system using a Litton LTN-51 inertial navigation unit (INU) was tested and used for aircraft track recovery and for location and tracking from the air of targets at sea. The characteristic position drift of the INU is compensated for by sighting landmarks of accurately known position at discrete time intervals using a visual sighting system in the transparent nose of the Beechcraft 18 aircraft used. For an aircraft altitude of about 300 m, theoretical and experimental tests indicate that calculated aircraft and/or target positions obtained from the interpolated INU drift curve will be accurate to within 10 m for landmarks spaced approximately every 15 minutes in time. For applications in coastal oceanography, such as surface current mapping by tracking artificial targets, the system allows a broad area to be covered without use of high altitude photography and its attendant needs for large targets and clear weather.

  5. Design, Fabrication, and Testing of Emissive Probes to Determine the Plasma Potential of the Plumes of Various Electric Thrusters

    NASA Technical Reports Server (NTRS)

    Chen, Erinna M.

    2005-01-01

    A significant problem in the use of electric thrusters in spacecraft is the formation of low-energy ions in the thruster plume. Low-energy ions are formed in the plume via random collisions between high-velocity ions ejected from the thruster and slow-moving neutral atoms of propellant effusing from the engine. The sputtering of spacecraft materials due to interactions with low-energy ions may result in erosion or contamination of the spacecraft. The trajectory of these ions is determined primarily by the plasma potential of the plume. Thus, accurate characterization of the plasma potential is essential to predicting low-energy ion contamination. Emissive probes were utilized to determine the plasma potential. When the ion and electron currents to the probe are balanced, the potential of such probes float to the plasma potential. Two emissive probes were fabricated; one utilizing a DC power supply, another utilizing a rectified AC power source. Labview programs were written to coordinate and automate probe motion in the thruster plume. Employing handshaking interaction, these motion programs were synchronized to various data acquisition programs to ensure precision and accuracy of the measurements. Comparing these experimental values to values from theoretical models will allow for a more accurate prediction of low-energy ion interaction.

  6. An Accurate ab initio Quartic Force Field and Vibrational Frequencies for CH4 and Isotopomers

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Martin, Jan M. L.; Taylor, Peter R.

    1995-01-01

    A very accurate ab initio quartic force field for CH4 and its isotopomers is presented. The quartic force field was determined with the singles and doubles coupled-cluster procedure that includes a quasiperturbative estimate of the effects of connected triple excitations, CCSD(T), using the correlation consistent polarized valence triple zeta, cc-pVTZ, basis set. Improved quadratic force constants were evaluated with the correlation consistent polarized valence quadruple zeta, cc-pVQZ, basis set. Fundamental vibrational frequencies are determined using second-order perturbation theory anharmonic analyses. All fundamentals of CH4 and isotopomers for which accurate experimental values exist and for which there is not a large Fermi resonance, are predicted to within +/- 6 cm(exp -1). It is thus concluded that our predictions for the harmonic frequencies and the anharmonic constants are the most accurate estimates available. It is also shown that using cubic and quartic force constants determined with the correlation consistent polarized double zeta, cc-pVDZ, basis set in conjunction with the cc-pVQZ quadratic force constants and equilibrium geometry leads to accurate predictions for the fundamental vibrational frequencies of methane, suggesting that this approach may be a viable alternative for larger molecules. Using CCSD(T), core correlation is found to reduce the CH4 r(e), by 0.0015 A. Our best estimate for r, is 1.0862 +/- 0.0005 A.

  7. State-of-the-art ab initio potential energy curve for the krypton atom pair and thermophysical properties of dilute krypton gas.

    PubMed

    Jäger, Benjamin; Hellmann, Robert; Bich, Eckard; Vogel, Eckhard

    2016-03-21

    A new reference krypton-krypton interatomic potential energy curve was developed by means of quantum-chemical ab initio calculations for 36 interatomic separations. Highly accurate values for the interaction energies at the complete basis set limit were obtained using the coupled-cluster method with single, double, and perturbative triple excitations as well as t-aug-cc-pV5Z and t-aug-cc-pV6Z basis sets including mid-bond functions, with the 6Z basis set being newly constructed for this study. Higher orders of coupled-cluster terms were considered in a successive scheme up to full quadruple excitations. Core-core and core-valence correlation effects were included. Furthermore, relativistic effects were studied not only at a scalar relativistic level using second-order direct perturbation theory, but also utilizing full four-component and Gaunt-effect computations. An analytical pair potential function was fitted to the interaction energies, which is characterized by a depth of 200.88 K with an estimated standard uncertainty of 0.51 K. Thermophysical properties of low-density krypton were calculated for temperatures up to 5000 K. Second and third virial coefficients were obtained from statistical thermodynamics. Viscosity and thermal conductivity as well as the self-diffusion coefficient were computed using the kinetic theory of gases. The theoretical results are compared with experimental data and with results for other pair potential functions from the literature, especially with those calculated from the recently developed ab initio potential of Waldrop et al. [J. Chem. Phys. 142, 204307 (2015)]. Highly accurate experimental viscosity data indicate that both the present ab initio pair potential and the one of Waldrop et al. can be regarded as reference potentials, even though the quantum-chemical methods and basis sets differ. However, the uncertainties of the present potential and of the derived properties are estimated to be considerably lower.

  8. A convenient and accurate parallel Input/Output USB device for E-Prime.

    PubMed

    Canto, Rosario; Bufalari, Ilaria; D'Ausilio, Alessandro

    2011-03-01

    Psychological and neurophysiological experiments require the accurate control of timing and synchrony for Input/Output signals. For instance, a typical Event-Related Potential (ERP) study requires an extremely accurate synchronization of stimulus delivery with recordings. This is typically done via computer software such as E-Prime, and fast communications are typically assured by the Parallel Port (PP). However, the PP is an old and disappearing technology that, for example, is no longer available on portable computers. Here we propose a convenient USB device enabling parallel I/O capabilities. We tested this device against the PP on both a desktop and a laptop machine in different stress tests. Our data demonstrate the accuracy of our system, which suggests that it may be a good substitute for the PP with E-Prime.

  9. Maximizing potential impact of experimental research into cognitive processes in health psychology: A systematic approach to material development.

    PubMed

    Hughes, Alicia M; Gordon, Rola; Chalder, Trudie; Hirsch, Colette R; Moss-Morris, Rona

    2016-11-01

    There is an abundance of research into cognitive processing biases in clinical psychology including the potential for applying cognitive bias modification techniques to assess the causal role of biases in maintaining anxiety and depression. Within the health psychology field, there is burgeoning interest in applying these experimental methods to assess potential cognitive biases in relation to physical health conditions and health-related behaviours. Experimental research in these areas could inform theoretical development by enabling measurement of implicit cognitive processes that may underlie unhelpful illness beliefs and help drive health-related behaviours. However, to date, there has been no systematic approach to adapting existing experimental paradigms for use within physical health research. Many studies fail to report how materials were developed for the population of interest or have used untested materials developed ad hoc. The lack of protocol for developing stimuli specificity has contributed to large heterogeneity in methodologies and findings. In this article, we emphasize the need for standardized methods for stimuli development and replication in experimental work, particularly as it extends beyond its original anxiety and depression scope to other physical conditions. We briefly describe the paradigms commonly used to assess cognitive biases in attention and interpretation and then describe the steps involved in comprehensive/robust stimuli development for attention and interpretation paradigms using illustrative examples from two conditions: chronic fatigue syndrome and breast cancer. This article highlights the value of preforming rigorous stimuli development and provides tools to aid researchers engage in this process. We believe this work is worthwhile to establish a body of high-quality and replicable experimental research within the health psychology literature. Statement of contribution What is already known on this subject? Cognitive

  10. Retrospective estimation of the electric and magnetic field exposure conditions in in vitro experimental reports reveal considerable potential for uncertainty.

    PubMed

    Portelli, Lucas A; Falldorf, Karsten; Thuróczy, György; Cuppen, Jan

    2018-04-01

    Experiments on cell cultures exposed to extremely low frequency (ELF, 3-300 Hz) magnetic fields are often subject to multiple sources of uncertainty associated with specific electric and magnetic field exposure conditions. Here we systemically quantify these uncertainties based on exposure conditions described in a group of bioelectromagnetic experimental reports for a representative sampling of the existing literature. The resulting uncertainties, stemming from insufficient, ambiguous, or erroneous description, design, implementation, or validation of the experimental methods and systems, were often substantial enough to potentially make any successful reproduction of the original experimental conditions difficult or impossible. Without making any assumption about the true biological relevance of ELF electric and magnetic fields, these findings suggest another contributing factor which may add to the overall variability and irreproducibility traditionally associated with experimental results of in vitro exposures to low-level ELF magnetic fields. Bioelectromagnetics. 39:231-243, 2018. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  11. Facilitating the selection and creation of accurate interatomic potentials with robust tools and characterization

    NASA Astrophysics Data System (ADS)

    Trautt, Zachary T.; Tavazza, Francesca; Becker, Chandler A.

    2015-10-01

    The Materials Genome Initiative seeks to significantly decrease the cost and time of development and integration of new materials. Within the domain of atomistic simulations, several roadblocks stand in the way of reaching this goal. While the NIST Interatomic Potentials Repository hosts numerous interatomic potentials (force fields), researchers cannot immediately determine the best choice(s) for their use case. Researchers developing new potentials, specifically those in restricted environments, lack a comprehensive portfolio of efficient tools capable of calculating and archiving the properties of their potentials. This paper elucidates one solution to these problems, which uses Python-based scripts that are suitable for rapid property evaluation and human knowledge transfer. Calculation results are visible on the repository website, which reduces the time required to select an interatomic potential for a specific use case. Furthermore, property evaluation scripts are being integrated with modern platforms to improve discoverability and access of materials property data. To demonstrate these scripts and features, we will discuss the automation of stacking fault energy calculations and their application to additional elements. While the calculation methodology was developed previously, we are using it here as a case study in simulation automation and property calculations. We demonstrate how the use of Python scripts allows for rapid calculation in a more easily managed way where the calculations can be modified, and the results presented in user-friendly and concise ways. Additionally, the methods can be incorporated into other efforts, such as openKIM.

  12. Serial fusion of Eulerian and Lagrangian approaches for accurate heart-rate estimation using face videos.

    PubMed

    Gupta, Puneet; Bhowmick, Brojeshwar; Pal, Arpan

    2017-07-01

    Camera-equipped devices are ubiquitous and proliferating in the day-to-day life. Accurate heart rate (HR) estimation from the face videos acquired from the low cost cameras in a non-contact manner, can be used in many real-world scenarios and hence, require rigorous exploration. This paper has presented an accurate and near real-time HR estimation system using these face videos. It is based on the phenomenon that the color and motion variations in the face video are closely related to the heart beat. The variations also contain the noise due to facial expressions, respiration, eye blinking and environmental factors which are handled by the proposed system. Neither Eulerian nor Lagrangian temporal signals can provide accurate HR in all the cases. The cases where Eulerian temporal signals perform spuriously are determined using a novel poorness measure and then both the Eulerian and Lagrangian temporal signals are employed for better HR estimation. Such a fusion is referred as serial fusion. Experimental results reveal that the error introduced in the proposed algorithm is 1.8±3.6 which is significantly lower than the existing well known systems.

  13. Aqueous solubility, effects of salts on aqueous solubility, and partitioning behavior of hexafluorobenzene: experimental results and COSMO-RS predictions.

    PubMed

    Schröder, Bernd; Freire, Mara G; Varanda, Fatima R; Marrucho, Isabel M; Santos, Luís M N B F; Coutinho, João A P

    2011-07-01

    The aqueous solubility of hexafluorobenzene has been determined, at 298.15K, using a shake-flask method with a spectrophotometric quantification technique. Furthermore, the solubility of hexafluorobenzene in saline aqueous solutions, at distinct salt concentrations, has been measured. Both salting-in and salting-out effects were observed and found to be dependent on the nature of the cationic/anionic composition of the salt. COSMO-RS, the Conductor-like Screening Model for Real Solvents, has been used to predict the corresponding aqueous solubilities at conditions similar to those used experimentally. The prediction results showed that the COSMO-RS approach is suitable for the prediction of salting-in/-out effects. The salting-in/-out phenomena have been rationalized with the support of COSMO-RS σ-profiles. The prediction potential of COSMO-RS regarding aqueous solubilities and octanol-water partition coefficients has been compared with typically used QSPR-based methods. Up to now, the absence of accurate solubility data for hexafluorobenzene hampered the calculation of the respective partition coefficients. Combining available accurate vapor pressure data with the experimentally determined water solubility, a novel air-water partition coefficient has been derived. Copyright © 2011 Elsevier Ltd. All rights reserved.

  14. A flexible and accurate digital volume correlation method applicable to high-resolution volumetric images

    NASA Astrophysics Data System (ADS)

    Pan, Bing; Wang, Bo

    2017-10-01

    Digital volume correlation (DVC) is a powerful technique for quantifying interior deformation within solid opaque materials and biological tissues. In the last two decades, great efforts have been made to improve the accuracy and efficiency of the DVC algorithm. However, there is still a lack of a flexible, robust and accurate version that can be efficiently implemented in personal computers with limited RAM. This paper proposes an advanced DVC method that can realize accurate full-field internal deformation measurement applicable to high-resolution volume images with up to billions of voxels. Specifically, a novel layer-wise reliability-guided displacement tracking strategy combined with dynamic data management is presented to guide the DVC computation from slice to slice. The displacements at specified calculation points in each layer are computed using the advanced 3D inverse-compositional Gauss-Newton algorithm with the complete initial guess of the deformation vector accurately predicted from the computed calculation points. Since only limited slices of interest in the reference and deformed volume images rather than the whole volume images are required, the DVC calculation can thus be efficiently implemented on personal computers. The flexibility, accuracy and efficiency of the presented DVC approach are demonstrated by analyzing computer-simulated and experimentally obtained high-resolution volume images.

  15. An accurate density functional theory for the vapor-liquid interface of associating chain molecules based on the statistical associating fluid theory for potentials of variable range

    NASA Astrophysics Data System (ADS)

    Gloor, Guy J.; Jackson, George; Blas, Felipe J.; del Río, Elvira Martín; de Miguel, Enrique

    2004-12-01

    A Helmholtz free energy density functional is developed to describe the vapor-liquid interface of associating chain molecules. The functional is based on the statistical associating fluid theory with attractive potentials of variable range (SAFT-VR) for the homogenous fluid [A. Gil-Villegas, A. Galindo, P. J. Whitehead, S. J. Mills, G. Jackson, and A. N. Burgess, J. Chem. Phys. 106, 4168 (1997)]. A standard perturbative density functional theory (DFT) is constructed by partitioning the free energy density into a reference term (which incorporates all of the short-range interactions, and is treated locally) and an attractive perturbation (which incorporates the long-range dispersion interactions). In our previous work [F. J. Blas, E. Martín del Río, E. de Miguel, and G. Jackson, Mol. Phys. 99, 1851 (2001); G. J. Gloor, F. J. Blas, E. Martín del Río, E. de Miguel, and G. Jackson, Fluid Phase Equil. 194, 521 (2002)] we used a mean-field version of the theory (SAFT-HS) in which the pair correlations were neglected in the attractive term. This provides only a qualitative description of the vapor-liquid interface, due to the inadequate mean-field treatment of the vapor-liquid equilibria. Two different approaches are used to include the correlations in the attractive term: in the first, the free energy of the homogeneous fluid is partitioned such that the effect of correlations are incorporated in the local reference term; in the second, a density averaged correlation function is incorporated into the perturbative term in a similar way to that proposed by Toxvaerd [S. Toxvaerd, J. Chem. Phys. 64, 2863 (1976)]. The latter is found to provide the most accurate description of the vapor-liquid surface tension on comparison with new simulation data for a square-well fluid of variable range. The SAFT-VR DFT is used to examine the effect of molecular chain length and association on the surface tension. Different association schemes (dimerization, straight and branched chain

  16. Accurate prediction of protein-protein interactions by integrating potential evolutionary information embedded in PSSM profile and discriminative vector machine classifier.

    PubMed

    Li, Zheng-Wei; You, Zhu-Hong; Chen, Xing; Li, Li-Ping; Huang, De-Shuang; Yan, Gui-Ying; Nie, Ru; Huang, Yu-An

    2017-04-04

    Identification of protein-protein interactions (PPIs) is of critical importance for deciphering the underlying mechanisms of almost all biological processes of cell and providing great insight into the study of human disease. Although much effort has been devoted to identifying PPIs from various organisms, existing high-throughput biological techniques are time-consuming, expensive, and have high false positive and negative results. Thus it is highly urgent to develop in silico methods to predict PPIs efficiently and accurately in this post genomic era. In this article, we report a novel computational model combining our newly developed discriminative vector machine classifier (DVM) and an improved Weber local descriptor (IWLD) for the prediction of PPIs. Two components, differential excitation and orientation, are exploited to build evolutionary features for each protein sequence. The main characteristics of the proposed method lies in introducing an effective feature descriptor IWLD which can capture highly discriminative evolutionary information from position-specific scoring matrixes (PSSM) of protein data, and employing the powerful and robust DVM classifier. When applying the proposed method to Yeast and H. pylori data sets, we obtained excellent prediction accuracies as high as 96.52% and 91.80%, respectively, which are significantly better than the previous methods. Extensive experiments were then performed for predicting cross-species PPIs and the predictive results were also pretty promising. To further validate the performance of the proposed method, we compared it with the state-of-the-art support vector machine (SVM) classifier on Human data set. The experimental results obtained indicate that our method is highly effective for PPIs prediction and can be taken as a supplementary tool for future proteomics research.

  17. Accurate Mobile Urban Mapping via Digital Map-Based SLAM †

    PubMed Central

    Roh, Hyunchul; Jeong, Jinyong; Cho, Younggun; Kim, Ayoung

    2016-01-01

    This paper presents accurate urban map generation using digital map-based Simultaneous Localization and Mapping (SLAM). Throughout this work, our main objective is generating a 3D and lane map aiming for sub-meter accuracy. In conventional mapping approaches, achieving extremely high accuracy was performed by either (i) exploiting costly airborne sensors or (ii) surveying with a static mapping system in a stationary platform. Mobile scanning systems recently have gathered popularity but are mostly limited by the availability of the Global Positioning System (GPS). We focus on the fact that the availability of GPS and urban structures are both sporadic but complementary. By modeling both GPS and digital map data as measurements and integrating them with other sensor measurements, we leverage SLAM for an accurate mobile mapping system. Our proposed algorithm generates an efficient graph SLAM and achieves a framework running in real-time and targeting sub-meter accuracy with a mobile platform. Integrated with the SLAM framework, we implement a motion-adaptive model for the Inverse Perspective Mapping (IPM). Using motion estimation derived from SLAM, the experimental results show that the proposed approaches provide stable bird’s-eye view images, even with significant motion during the drive. Our real-time map generation framework is validated via a long-distance urban test and evaluated at randomly sampled points using Real-Time Kinematic (RTK)-GPS. PMID:27548175

  18. [Accurate 3D free-form registration between fan-beam CT and cone-beam CT].

    PubMed

    Liang, Yueqiang; Xu, Hongbing; Li, Baosheng; Li, Hongsheng; Yang, Fujun

    2012-06-01

    Because the X-ray scatters, the CT numbers in cone-beam CT cannot exactly correspond to the electron densities. This, therefore, results in registration error when the intensity-based registration algorithm is used to register planning fan-beam CT and cone-beam CT. In order to reduce the registration error, we have developed an accurate gradient-based registration algorithm. The gradient-based deformable registration problem is described as a minimization of energy functional. Through the calculus of variations and Gauss-Seidel finite difference method, we derived the iterative formula of the deformable registration. The algorithm was implemented by GPU through OpenCL framework, with which the registration time was greatly reduced. Our experimental results showed that the proposed gradient-based registration algorithm could register more accurately the clinical cone-beam CT and fan-beam CT images compared with the intensity-based algorithm. The GPU-accelerated algorithm meets the real-time requirement in the online adaptive radiotherapy.

  19. Simulated Screens of DNA Encoded Libraries: The Potential Influence of Chemical Synthesis Fidelity on Interpretation of Structure-Activity Relationships.

    PubMed

    Satz, Alexander L

    2016-07-11

    Simulated screening of DNA encoded libraries indicates that the presence of truncated byproducts complicates the relationship between library member enrichment and equilibrium association constant (these truncates result from incomplete chemical reactions during library synthesis). Further, simulations indicate that some patterns observed in reported experimental data may result from the presence of truncated byproducts in the library mixture and not structure-activity relationships. Potential experimental methods of minimizing the presence of truncates are assessed via simulation; the relationship between enrichment and equilibrium association constant for libraries of differing purities is investigated. Data aggregation techniques are demonstrated that allow for more accurate analysis of screening results, in particular when the screened library contains significant quantities of truncates.

  20. Refined method for predicting electrochemical windows of ionic liquids and experimental validation studies.

    PubMed

    Zhang, Yong; Shi, Chaojun; Brennecke, Joan F; Maginn, Edward J

    2014-06-12

    A combined classical molecular dynamics (MD) and ab initio MD (AIMD) method was developed for the calculation of electrochemical windows (ECWs) of ionic liquids. In the method, the liquid phase of ionic liquid is explicitly sampled using classical MD. The electrochemical window, estimated by the energy difference between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO), is calculated at the density functional theory (DFT) level based on snapshots obtained from classical MD trajectories. The snapshots were relaxed using AIMD and quenched to their local energy minima, which assures that the HOMO/LUMO calculations are based on stable configurations on the same potential energy surface. The new procedure was applied to a group of ionic liquids for which the ECWs were also experimentally measured in a self-consistent manner. It was found that the predicted ECWs not only agree with the experimental trend very well but also the values are quantitatively accurate. The proposed method provides an efficient way to compare ECWs of ionic liquids in the same context, which has been difficult in experiments or simulation due to the fact that ECW values sensitively depend on experimental setup and conditions.

  1. First-principles energy band calculation of Ruddlesden–Popper compound Sr{sub 3}Sn{sub 2}O{sub 7} using modified Becke–Johnson exchange potential

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kamimura, Sunao, E-mail: kamimura-sunao@che.kyutech.ac.jp; National Institute of Advanced Industrial Science and Technology; Department of Molecular and Material Sciences, Interdisciplinary Graduate School of Engineering Science, Kyushu University, 6-1 Kasuga Kouen, Kasuga, Fukuoka 816-8580 Japan

    The electronic structure of Sr{sub 3}Sn{sub 2}O{sub 7} is evaluated by the scalar-relativistic full potential linearized augmented plane wave (FLAPW+lo) method using the modified Becke–Johnson potential (Tran–Blaha potential) combined with the local density approximation correlation (MBJ–LDA). The fundamental gap between the valence band (VB) and conduction band (CB) is estimated to be 3.96 eV, which is close to the experimental value. Sn 5s states and Sr 4d states are predominant in the lower and upper CB, respectively. On the other hand, the lower VB is mainly composed of Sn 5s, 5p, and O 2p states, while the upper VB mainlymore » consists of O 2p states. These features of the DOS are well reflected by the optical transition between the upper VB and lower CB, as seen in the energy dependence of the dielectric function. Furthermore, the absorption coefficient estimated from the MBJ–LDA is similar to the experimental result. - Graphical abstract: Calculated energy band structure along the symmetry lines of the first BZ of Sr{sub 3}Sn{sub 2}O{sub 7} crystal obtained using the MBJ potential. - Highlights: • Electronic structure of Sr{sub 3}Sn{sub 2}O{sub 7} is calculated on the basis of MBJ–LDA method for the first time. • Band gap of Sr{sub 3}Sn{sub 2}O{sub 7} is determined accurately on the basis of MBJ–LDA method. • The experimental absorption spectrum of Sr{sub 3}Sn{sub 2}O{sub 7} produced by MBJ–LDA is more accurate than that obtained by GGA method.« less

  2. A fast and accurate dihedral interpolation loop subdivision scheme

    NASA Astrophysics Data System (ADS)

    Shi, Zhuo; An, Yalei; Wang, Zhongshuai; Yu, Ke; Zhong, Si; Lan, Rushi; Luo, Xiaonan

    2018-04-01

    In this paper, we propose a fast and accurate dihedral interpolation Loop subdivision scheme for subdivision surfaces based on triangular meshes. In order to solve the problem of surface shrinkage, we keep the limit condition unchanged, which is important. Extraordinary vertices are handled using modified Butterfly rules. Subdivision schemes are computationally costly as the number of faces grows exponentially at higher levels of subdivision. To address this problem, our approach is to use local surface information to adaptively refine the model. This is achieved simply by changing the threshold value of the dihedral angle parameter, i.e., the angle between the normals of a triangular face and its adjacent faces. We then demonstrate the effectiveness of the proposed method for various 3D graphic triangular meshes, and extensive experimental results show that it can match or exceed the expected results at lower computational cost.

  3. Accurate determination of complex materials coefficients of piezoelectric resonators.

    PubMed

    Du, Xiao-Hong; Wang, Qing-Ming; Uchino, Kenji

    2003-03-01

    This paper presents a method of accurately determining the complex piezoelectric and elastic coefficients of piezoelectric ceramic resonators from the measurement of the normalized electric admittance, Y, which is electric admittance Y of piezoelectric resonator normalized by the angular frequency omega. The coefficients are derived from the measurements near three special frequency points that correspond to the maximum and the minimum normalized susceptance (B) and the maximum normalized conductance (G). The complex elastic coefficient is determined from the frequencies at these points, and the real and imaginary parts of the piezoelectric coefficient are related to the derivative of the susceptance with respect to the frequency and the asymmetry of the conductance, respectively, near the maximum conductance point. The measurements for some lead zirconate titanate (PZT) based ceramics are used as examples to demonstrate the calculation and experimental procedures and the comparisons with the standard methods.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

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

    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, andmore » 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.« less

  5. Benchmarking quantum mechanical calculations with experimental NMR chemical shifts of 2-HADNT

    NASA Astrophysics Data System (ADS)

    Liu, Yuemin; Junk, Thomas; Liu, Yucheng; Tzeng, Nianfeng; Perkins, Richard

    2015-04-01

    In this study, both GIAO-DFT and GIAO-MP2 calculations of nuclear magnetic resonance (NMR) spectra were benchmarked with experimental chemical shifts. The experimental chemical shifts were determined experimentally for carbon-13 (C-13) of seven carbon atoms for the TNT degradation product 2-hydroxylamino-4,6-dinitrotoluene (2-HADNT). Quantum mechanics GIAO calculations were implemented using Becke-3-Lee-Yang-Parr (B3LYP) and other six hybrid DFT methods (Becke-1-Lee-Yang-Parr (B1LYP), Becke-half-and-half-Lee-Yang-Parr (BH and HLYP), Cohen-Handy-3-Lee-Yang-Parr (O3LYP), Coulomb-attenuating-B3LYP (CAM-B3LYP), modified-Perdew-Wang-91-Lee-Yang-Parr (mPW1LYP), and Xu-3-Lee-Yang-Parr (X3LYP)) which use the same correlation functional LYP. Calculation results showed that the GIAO-MP2 method gives the most accurate chemical shift values, and O3LYP method provides the best prediction of chemical shifts among the B3LYP and other five DFT methods. Three types of atomic partial charges, Mulliken (MK), electrostatic potential (ESP), and natural bond orbital (NBO), were also calculated using MP2/aug-cc-pVDZ method. A reasonable correlation was discovered between NBO partial charges and experimental chemical shifts of carbon-13 (C-13).

  6. Characterization of the basal angiosperm Aristolochia fimbriata: a potential experimental system for genetic studies

    PubMed Central

    2013-01-01

    Background Previous studies in basal angiosperms have provided insight into the diversity within the angiosperm lineage and helped to polarize analyses of flowering plant evolution. However, there is still not an experimental system for genetic studies among basal angiosperms to facilitate comparative studies and functional investigation. It would be desirable to identify a basal angiosperm experimental system that possesses many of the features found in existing plant model systems (e.g., Arabidopsis and Oryza). Results We have considered all basal angiosperm families for general characteristics important for experimental systems, including availability to the scientific community, growth habit, and membership in a large basal angiosperm group that displays a wide spectrum of phenotypic diversity. Most basal angiosperms are woody or aquatic, thus are not well-suited for large scale cultivation, and were excluded. We further investigated members of Aristolochiaceae for ease of culture, life cycle, genome size, and chromosome number. We demonstrated self-compatibility for Aristolochia elegans and A. fimbriata, and transformation with a GFP reporter construct for Saruma henryi and A. fimbriata. Furthermore, A. fimbriata was easily cultivated with a life cycle of just three months, could be regenerated in a tissue culture system, and had one of the smallest genomes among basal angiosperms. An extensive multi-tissue EST dataset was produced for A. fimbriata that includes over 3.8 million 454 sequence reads. Conclusions Aristolochia fimbriata has numerous features that facilitate genetic studies and is suggested as a potential model system for use with a wide variety of technologies. Emerging genetic and genomic tools for A. fimbriata and closely related species can aid the investigation of floral biology, developmental genetics, biochemical pathways important in plant-insect interactions as well as human health, and various other features present in early angiosperms

  7. Reference Genes for Accurate Transcript Normalization in Citrus Genotypes under Different Experimental Conditions

    PubMed Central

    Mafra, Valéria; Kubo, Karen S.; Alves-Ferreira, Marcio; Ribeiro-Alves, Marcelo; Stuart, Rodrigo M.; Boava, Leonardo P.; Rodrigues, Carolina M.; Machado, Marcos A.

    2012-01-01

    Real-time reverse transcription PCR (RT-qPCR) has emerged as an accurate and widely used technique for expression profiling of selected genes. However, obtaining reliable measurements depends on the selection of appropriate reference genes for gene expression normalization. The aim of this work was to assess the expression stability of 15 candidate genes to determine which set of reference genes is best suited for transcript normalization in citrus in different tissues and organs and leaves challenged with five pathogens (Alternaria alternata, Phytophthora parasitica, Xylella fastidiosa and Candidatus Liberibacter asiaticus). We tested traditional genes used for transcript normalization in citrus and orthologs of Arabidopsis thaliana genes described as superior reference genes based on transcriptome data. geNorm and NormFinder algorithms were used to find the best reference genes to normalize all samples and conditions tested. Additionally, each biotic stress was individually analyzed by geNorm. In general, FBOX (encoding a member of the F-box family) and GAPC2 (GAPDH) was the most stable candidate gene set assessed under the different conditions and subsets tested, while CYP (cyclophilin), TUB (tubulin) and CtP (cathepsin) were the least stably expressed genes found. Validation of the best suitable reference genes for normalizing the expression level of the WRKY70 transcription factor in leaves infected with Candidatus Liberibacter asiaticus showed that arbitrary use of reference genes without previous testing could lead to misinterpretation of data. Our results revealed FBOX, SAND (a SAND family protein), GAPC2 and UPL7 (ubiquitin protein ligase 7) to be superior reference genes, and we recommend their use in studies of gene expression in citrus species and relatives. This work constitutes the first systematic analysis for the selection of superior reference genes for transcript normalization in different citrus organs and under biotic stress. PMID:22347455

  8. A multiscale red blood cell model with accurate mechanics, rheology, and dynamics.

    PubMed

    Fedosov, Dmitry A; Caswell, Bruce; Karniadakis, George Em

    2010-05-19

    Red blood cells (RBCs) have highly deformable viscoelastic membranes exhibiting complex rheological response and rich hydrodynamic behavior governed by special elastic and bending properties and by the external/internal fluid and membrane viscosities. We present a multiscale RBC model that is able to predict RBC mechanics, rheology, and dynamics in agreement with experiments. Based on an analytic theory, the modeled membrane properties can be uniquely related to the experimentally established RBC macroscopic properties without any adjustment of parameters. The RBC linear and nonlinear elastic deformations match those obtained in optical-tweezers experiments. The rheological properties of the membrane are compared with those obtained in optical magnetic twisting cytometry, membrane thermal fluctuations, and creep followed by cell recovery. The dynamics of RBCs in shear and Poiseuille flows is tested against experiments and theoretical predictions, and the applicability of the latter is discussed. Our findings clearly indicate that a purely elastic model for the membrane cannot accurately represent the RBC's rheological properties and its dynamics, and therefore accurate modeling of a viscoelastic membrane is necessary. Copyright 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  9. MICCA: a complete and accurate software for taxonomic profiling of metagenomic data.

    PubMed

    Albanese, Davide; Fontana, Paolo; De Filippo, Carlotta; Cavalieri, Duccio; Donati, Claudio

    2015-05-19

    The introduction of high throughput sequencing technologies has triggered an increase of the number of studies in which the microbiota of environmental and human samples is characterized through the sequencing of selected marker genes. While experimental protocols have undergone a process of standardization that makes them accessible to a large community of scientist, standard and robust data analysis pipelines are still lacking. Here we introduce MICCA, a software pipeline for the processing of amplicon metagenomic datasets that efficiently combines quality filtering, clustering of Operational Taxonomic Units (OTUs), taxonomy assignment and phylogenetic tree inference. MICCA provides accurate results reaching a good compromise among modularity and usability. Moreover, we introduce a de-novo clustering algorithm specifically designed for the inference of Operational Taxonomic Units (OTUs). Tests on real and synthetic datasets shows that thanks to the optimized reads filtering process and to the new clustering algorithm, MICCA provides estimates of the number of OTUs and of other common ecological indices that are more accurate and robust than currently available pipelines. Analysis of public metagenomic datasets shows that the higher consistency of results improves our understanding of the structure of environmental and human associated microbial communities. MICCA is an open source project.

  10. Fast and accurate: high-speed metrological large-range AFM for surface and nanometrology

    NASA Astrophysics Data System (ADS)

    Dai, Gaoliang; Koenders, Ludger; Fluegge, Jens; Hemmleb, Matthias

    2018-05-01

    Low measurement speed remains a major shortcoming of the scanning probe microscopic technique. It not only leads to a low measurement throughput, but a significant measurement drift over the long measurement time needed (up to hours or even days). To overcome this challenge, PTB, the national metrology institute of Germany, has developed a high-speed metrological large-range atomic force microscope (HS Met. LR-AFM) capable of measuring speeds up to 1 mm s‑1. This paper has introduced the design concept in detail. After modelling scanning probe microscopic measurements, our results suggest that the signal spectrum of the surface to be measured is the spatial spectrum of the surface scaled by the scanning speed. The higher the scanning speed , the broader the spectrum to be measured. To realise an accurate HS Met. LR-AFM, our solution is to combine different stages/sensors synchronously in measurements, which provide a much larger spectrum area for high-speed measurement capability. Two application examples have been demonstrated. The first is a new concept called reference areal surface metrology. Using the developed HS Met. LR-AFM, surfaces are measured accurately and traceably at a speed of 500 µm s‑1 and the results are applied as a reference 3D data map of the surfaces. By correlating the reference 3D data sets and 3D data sets of tools under calibration, which are measured at the same surface, it has the potential to comprehensively characterise the tools, for instance, the spectrum properties of the tools. The investigation results of two commercial confocal microscopes are demonstrated, indicating very promising results. The second example is the calibration of a kind of 3D nano standard, which has spatially distributed landmarks, i.e. special unique features defined by 3D-coordinates. Experimental investigations confirmed that the calibration accuracy is maintained at a measurement speed of 100 µm s‑1, which improves the calibration efficiency by a

  11. AtomDB: Expanding an Accessible and Accurate Atomic Database for X-ray Astronomy

    NASA Astrophysics Data System (ADS)

    Smith, Randall

    Since its inception in 2001, the AtomDB has become the standard repository of accurate and accessible atomic data for the X-ray astrophysics community, including laboratory astrophysicists, observers, and modelers. Modern calculations of collisional excitation rates now exist - and are in AtomDB - for all abundant ions in a hot plasma. AtomDB has expanded beyond providing just a collisional model, and now also contains photoionization data from XSTAR as well as a charge exchange model, amongst others. However, building and maintaining an accurate and complete database that can fully exploit the diagnostic potential of high-resolution X-ray spectra requires further work. The Hitomi results, sadly limited as they were, demonstrated the urgent need for the best possible wavelength and rate data, not merely for the strongest lines but for the diagnostic features that may have 1% or less of the flux of the strong lines. In particular, incorporation of weak but powerfully diagnostic satellite lines will be crucial to understanding the spectra expected from upcoming deep observations with Chandra and XMM-Newton, as well as the XARM and Athena satellites. Beyond incorporating this new data, a number of groups, both experimental and theoretical, have begun to produce data with errors and/or sensitivity estimates. We plan to use this to create statistically meaningful spectral errors on collisional plasmas, providing practical uncertainties together with model spectra. We propose to continue to (1) engage the X-ray astrophysics community regarding their issues and needs, notably by a critical comparison with other related databases and tools, (2) enhance AtomDB to incorporate a large number of satellite lines as well as updated wavelengths with error estimates, (3) continue to update the AtomDB with the latest calculations and laboratory measurements, in particular velocity-dependent charge exchange rates, and (4) enhance existing tools, and create new ones as needed to

  12. How to validate similarity in linear transform models of event-related potentials between experimental conditions?

    PubMed

    Cong, Fengyu; Lin, Qiu-Hua; Astikainen, Piia; Ristaniemi, Tapani

    2014-10-30

    It is well-known that data of event-related potentials (ERPs) conform to the linear transform model (LTM). For group-level ERP data processing using principal/independent component analysis (PCA/ICA), ERP data of different experimental conditions and different participants are often concatenated. It is theoretically assumed that different experimental conditions and different participants possess the same LTM. However, how to validate the assumption has been seldom reported in terms of signal processing methods. When ICA decomposition is globally optimized for ERP data of one stimulus, we gain the ratio between two coefficients mapping a source in brain to two points along the scalp. Based on such a ratio, we defined a relative mapping coefficient (RMC). If RMCs between two conditions for an ERP are not significantly different in practice, mapping coefficients of this ERP between the two conditions are statistically identical. We examined whether the same LTM of ERP data could be applied for two different stimulus types of fearful and happy facial expressions. They were used in an ignore oddball paradigm in adult human participants. We found no significant difference in LTMs (based on ICASSO) of N170 responses to the fearful and the happy faces in terms of RMCs of N170. We found no methods for straightforward comparison. The proposed RMC in light of ICA decomposition is an effective approach for validating the similarity of LTMs of ERPs between experimental conditions. This is very fundamental to apply group-level PCA/ICA to process ERP data. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. Accurate prediction of X-ray pulse properties from a free-electron laser using machine learning

    DOE PAGES

    Sanchez-Gonzalez, A.; Micaelli, P.; Olivier, C.; ...

    2017-06-05

    Free-electron lasers providing ultra-short high-brightness pulses of X-ray radiation have great potential for a wide impact on science, and are a critical element for unravelling the structural dynamics of matter. To fully harness this potential, we must accurately know the X-ray properties: intensity, spectrum and temporal profile. Owing to the inherent fluctuations in free-electron lasers, this mandates a full characterization of the properties for each and every pulse. While diagnostics of these properties exist, they are often invasive and many cannot operate at a high-repetition rate. Here, we present a technique for circumventing this limitation. Employing a machine learning strategy,more » we can accurately predict X-ray properties for every shot using only parameters that are easily recorded at high-repetition rate, by training a model on a small set of fully diagnosed pulses. Lastly, this opens the door to fully realizing the promise of next-generation high-repetition rate X-ray lasers.« less

  14. Accurate prediction of X-ray pulse properties from a free-electron laser using machine learning

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sanchez-Gonzalez, A.; Micaelli, P.; Olivier, C.

    Free-electron lasers providing ultra-short high-brightness pulses of X-ray radiation have great potential for a wide impact on science, and are a critical element for unravelling the structural dynamics of matter. To fully harness this potential, we must accurately know the X-ray properties: intensity, spectrum and temporal profile. Owing to the inherent fluctuations in free-electron lasers, this mandates a full characterization of the properties for each and every pulse. While diagnostics of these properties exist, they are often invasive and many cannot operate at a high-repetition rate. Here, we present a technique for circumventing this limitation. Employing a machine learning strategy,more » we can accurately predict X-ray properties for every shot using only parameters that are easily recorded at high-repetition rate, by training a model on a small set of fully diagnosed pulses. Lastly, this opens the door to fully realizing the promise of next-generation high-repetition rate X-ray lasers.« less

  15. Accuracy of Protein Embedding Potentials: An Analysis in Terms of Electrostatic Potentials.

    PubMed

    Olsen, Jógvan Magnus Haugaard; List, Nanna Holmgaard; Kristensen, Kasper; Kongsted, Jacob

    2015-04-14

    Quantum-mechanical embedding methods have in recent years gained significant interest and may now be applied to predict a wide range of molecular properties calculated at different levels of theory. To reach a high level of accuracy in embedding methods, both the electronic structure model of the active region and the embedding potential need to be of sufficiently high quality. In fact, failures in quantum mechanics/molecular mechanics (QM/MM)-based embedding methods have often been associated with the QM/MM methodology itself; however, in many cases the reason for such failures is due to the use of an inaccurate embedding potential. In this paper, we investigate in detail the quality of the electronic component of embedding potentials designed for calculations on protein biostructures. We show that very accurate explicitly polarizable embedding potentials may be efficiently designed using fragmentation strategies combined with single-fragment ab initio calculations. In fact, due to the self-interaction error in Kohn-Sham density functional theory (KS-DFT), use of large full-structure quantum-mechanical calculations based on conventional (hybrid) functionals leads to less accurate embedding potentials than fragment-based approaches. We also find that standard protein force fields yield poor embedding potentials, and it is therefore not advisable to use such force fields in general QM/MM-type calculations of molecular properties other than energies and structures.

  16. Biomarker Surrogates Do Not Accurately Predict Sputum Eosinophils and Neutrophils in Asthma

    PubMed Central

    Hastie, Annette T.; Moore, Wendy C.; Li, Huashi; Rector, Brian M.; Ortega, Victor E.; Pascual, Rodolfo M.; Peters, Stephen P.; Meyers, Deborah A.; Bleecker, Eugene R.

    2013-01-01

    Background Sputum eosinophils (Eos) are a strong predictor of airway inflammation, exacerbations, and aid asthma management, whereas sputum neutrophils (Neu) indicate a different severe asthma phenotype, potentially less responsive to TH2-targeted therapy. Variables such as blood Eos, total IgE, fractional exhaled nitric oxide (FeNO) or FEV1% predicted, may predict airway Eos, while age, FEV1%predicted, or blood Neu may predict sputum Neu. Availability and ease of measurement are useful characteristics, but accuracy in predicting airway Eos and Neu, individually or combined, is not established. Objectives To determine whether blood Eos, FeNO, and IgE accurately predict sputum eosinophils, and age, FEV1% predicted, and blood Neu accurately predict sputum neutrophils (Neu). Methods Subjects in the Wake Forest Severe Asthma Research Program (N=328) were characterized by blood and sputum cells, healthcare utilization, lung function, FeNO, and IgE. Multiple analytical techniques were utilized. Results Despite significant association with sputum Eos, blood Eos, FeNO and total IgE did not accurately predict sputum Eos, and combinations of these variables failed to improve prediction. Age, FEV1%predicted and blood Neu were similarly unsatisfactory for prediction of sputum Neu. Factor analysis and stepwise selection found FeNO, IgE and FEV1% predicted, but not blood Eos, correctly predicted 69% of sputum Eosaccurately assigned only 41% of samples. Conclusion Despite statistically significant associations FeNO, IgE, blood Eos and Neu, FEV1%predicted, and age are poor surrogates, separately and combined, for accurately predicting sputum eosinophils and neutrophils. PMID:23706399

  17. Accurate Energy Consumption Modeling of IEEE 802.15.4e TSCH Using Dual-BandOpenMote Hardware.

    PubMed

    Daneels, Glenn; Municio, Esteban; Van de Velde, Bruno; Ergeerts, Glenn; Weyn, Maarten; Latré, Steven; Famaey, Jeroen

    2018-02-02

    The Time-Slotted Channel Hopping (TSCH) mode of the IEEE 802.15.4e amendment aims to improve reliability and energy efficiency in industrial and other challenging Internet-of-Things (IoT) environments. This paper presents an accurate and up-to-date energy consumption model for devices using this IEEE 802.15.4e TSCH mode. The model identifies all network-related CPU and radio state changes, thus providing a precise representation of the device behavior and an accurate prediction of its energy consumption. Moreover, energy measurements were performed with a dual-band OpenMote device, running the OpenWSN firmware. This allows the model to be used for devices using 2.4 GHz, as well as 868 MHz. Using these measurements, several network simulations were conducted to observe the TSCH energy consumption effects in end-to-end communication for both frequency bands. Experimental verification of the model shows that it accurately models the consumption for all possible packet sizes and that the calculated consumption on average differs less than 3% from the measured consumption. This deviation includes measurement inaccuracies and the variations of the guard time. As such, the proposed model is very suitable for accurate energy consumption modeling of TSCH networks.

  18. Accurate Energy Consumption Modeling of IEEE 802.15.4e TSCH Using Dual-BandOpenMote Hardware

    PubMed Central

    Municio, Esteban; Van de Velde, Bruno; Latré, Steven

    2018-01-01

    The Time-Slotted Channel Hopping (TSCH) mode of the IEEE 802.15.4e amendment aims to improve reliability and energy efficiency in industrial and other challenging Internet-of-Things (IoT) environments. This paper presents an accurate and up-to-date energy consumption model for devices using this IEEE 802.15.4e TSCH mode. The model identifies all network-related CPU and radio state changes, thus providing a precise representation of the device behavior and an accurate prediction of its energy consumption. Moreover, energy measurements were performed with a dual-band OpenMote device, running the OpenWSN firmware. This allows the model to be used for devices using 2.4 GHz, as well as 868 MHz. Using these measurements, several network simulations were conducted to observe the TSCH energy consumption effects in end-to-end communication for both frequency bands. Experimental verification of the model shows that it accurately models the consumption for all possible packet sizes and that the calculated consumption on average differs less than 3% from the measured consumption. This deviation includes measurement inaccuracies and the variations of the guard time. As such, the proposed model is very suitable for accurate energy consumption modeling of TSCH networks. PMID:29393900

  19. Experimental investigation of a transonic potential flow around a symmetric airfoil

    NASA Technical Reports Server (NTRS)

    Hiller, W. J.; Meier, G. E. A.

    1981-01-01

    Experimental flow investigations on smooth airfoils were done using numerical solutions for transonic airfoil streaming with shockless supersonic range. The experimental flow reproduced essential sections of the theoretically computed frictionless solution. Agreement is better in the expansion part of the of the flow than in the compression part. The flow was nearly stationary in the entire velocity range investigated.

  20. Avoiding fractional electrons in subsystem DFT based ab-initio molecular dynamics yields accurate models for liquid water and solvated OH radical

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Genova, Alessandro, E-mail: alessandro.genova@rutgers.edu; Pavanello, Michele, E-mail: m.pavanello@rutgers.edu; Ceresoli, Davide, E-mail: davide.ceresoli@cnr.it

    2016-06-21

    In this work we achieve three milestones: (1) we present a subsystem DFT method capable of running ab-initio molecular dynamics simulations accurately and efficiently. (2) In order to rid the simulations of inter-molecular self-interaction error, we exploit the ability of semilocal frozen density embedding formulation of subsystem DFT to represent the total electron density as a sum of localized subsystem electron densities that are constrained to integrate to a preset, constant number of electrons; the success of the method relies on the fact that employed semilocal nonadditive kinetic energy functionals effectively cancel out errors in semilocal exchange–correlation potentials that aremore » linked to static correlation effects and self-interaction. (3) We demonstrate this concept by simulating liquid water and solvated OH{sup •} radical. While the bulk of our simulations have been performed on a periodic box containing 64 independent water molecules for 52 ps, we also simulated a box containing 256 water molecules for 22 ps. The results show that, provided one employs an accurate nonadditive kinetic energy functional, the dynamics of liquid water and OH{sup •} radical are in semiquantitative agreement with experimental results or higher-level electronic structure calculations. Our assessments are based upon comparisons of radial and angular distribution functions as well as the diffusion coefficient of the liquid.« less

  1. Measurement of the membrane potential in small cells using patch clamp methods

    PubMed Central

    Wilson, James R; Clark, Robert B; Banderali, Umberto

    2011-01-01

    The resting membrane potential, Em, of mammalian cells is a fundamental physiological parameter. Even small changes in Em can modulate excitability, contractility and rates of cell migration. At present accurate, reproducible measurements of Em and determination of its ionic basis remain significant challenges when patch clamp methods are applied to small cells. In this study, a mathematical model has been developed which incorporates many of the main biophysical principles which govern recordings of the resting potential of “small cells”. Such a prototypical cell (approx. capacitance, 6 pF; input resistance 5 GΩ) is representative of neonatal cardiac myocytes, and other cells in the cardiovascular system (endothelium, fibroblasts) and small cells in other tissues, e.g., bone (osteoclasts) articular joints (chondrocytes) and the pancreas (β cells). Two common experimental conditions have been examined: (1) when the background K+ conductance is linear; and (2) when this K+ conductance is highly nonlinear and shows pronounced inward rectification. In the case of a linear K+ conductance, the presence of a “leakage” current through the seal resistance between the cell membrane and the patch pipette always depolarizes Em. Our calculations confirm that accurate characterization of Em is possible when the seal resistance is at least five times larger than the input resistance of the targeted cell. Measurement of Em under conditions in which the main background current includes a markedly nonlinear K+ conductance (due to inward rectification) yields complex and somewhat counter-intuitive findings. In fact, there are at least two possible stable values of resting membrane potential for a cell when the nonlinear, inwardly rectifying K+ conductance interacts with the seal current. This type of bistable behavior has been reported in a variety of small mammalian cells, including those from the heart, endothelium, smooth muscle and bone. Our theoretical treatment of

  2. Modeling of capacitor charging dynamics in an energy harvesting system considering accurate electromechanical coupling effects

    NASA Astrophysics Data System (ADS)

    Bagheri, Shahriar; Wu, Nan; Filizadeh, Shaahin

    2018-06-01

    This paper presents an iterative numerical method that accurately models an energy harvesting system charging a capacitor with piezoelectric patches. The constitutive relations of piezoelectric materials connected with an external charging circuit with a diode bridge and capacitors lead to the electromechanical coupling effect and the difficulty of deriving accurate transient mechanical response, as well as the charging progress. The proposed model is built upon the Euler-Bernoulli beam theory and takes into account the electromechanical coupling effects as well as the dynamic process of charging an external storage capacitor. The model is validated through experimental tests on a cantilever beam coated with piezoelectric patches. Several parametric studies are performed and the functionality of the model is verified. The efficiency of power harvesting system can be predicted and tuned considering variations in different design parameters. Such a model can be utilized to design robust and optimal energy harvesting system.

  3. Numerical simulations for quantitative analysis of electrostatic interaction between atomic force microscopy probe and an embedded electrode within a thin dielectric: meshing optimization, sensitivity to potential distribution and impact of cantilever contribution

    NASA Astrophysics Data System (ADS)

    Azib, M.; Baudoin, F.; Binaud, N.; Villeneuve-Faure, C.; Bugarin, F.; Segonds, S.; Teyssedre, G.

    2018-04-01

    Recent experimental results demonstrated that an electrostatic force distance curve (EFDC) can be used for space charge probing in thin dielectric layers. A main advantage of the method is claimed to be its sensitivity to charge localization, which, however, needs to be substantiated by numerical simulations. In this paper, we have developed a model which permits us to compute an EFDC accurately by using the most sophisticated and accurate geometry for the atomic force microscopy probe. To avoid simplifications and in order to reproduce experimental conditions, the EFDC has been simulated for a system constituted of a polarized electrode embedded in a thin dielectric layer (SiN x ). The individual contributions of forces on the tip and on the cantilever have been analyzed separately to account for possible artefacts. The EFDC sensitivity to potential distribution is studied through the change in electrode shape, namely the width and the depth. Finally, the numerical results have been compared with experimental data.

  4. Gender-specific effects of early nutritional restriction on adult obesity risk: evidence from quasi-experimental studies.

    PubMed

    Robinson, Whitney R

    2012-12-01

    In countries undergoing nutrition transition and historically poor minority groups in wealthy countries, obesity tends to be more common in women than men. A potential contributor to this female excess of obesity is a mismatch between perinatal nutritional restriction and a later calorie-rich environment. Several epidemiologic and quasi-experimental studies support a gender-differential effect of early nutritional deprivation on adult obesity. The quasi-experimental studies are of particular interest because results of quasi-experimental studies are typically less vulnerable to confounding bias than observational studies. Four quasi-experimental studies-exploiting 20th century famines that occurred in Europe, Africa, and Asia-provide evidence that perinatal nutritional restriction followed by relative caloric abundance may increase adult obesity risk to a greater extent in women than men. If the findings are accurate and generalizable to contemporary food environments, they suggest that the female offspring of poor, or otherwise nutritionally restricted, women in rapidly developing and wealthy countries may be at particularly high risk of adult obesity. Research into gender-specific effects of early life nutritional deprivation and its interactions with later environmental exposures may provide insight into global gender differences in obesity prevalence.

  5. Assessing potential abiotic and biotic complications of crayfish-induced gravel transport in experimental streams

    NASA Astrophysics Data System (ADS)

    Statzner, Bernhard; Peltret, Odile

    2006-03-01

    Biogeomorphology adds the element "biological dynamics" (of populations or communities) to chemical and physical geomorphic factors and thus complicates the framework of geomorphic processes. Such biological complications of the animal-induced transport of solids in streams should be particularly important in crayfish, as crayfish affect this transport through their overall activity and intraspecific aggression levels, which could be modified by shelter availability or the establishment of dominance hierarchies among individuals not knowing each other. Using experimental streams, we tested these hypotheses by measuring how shelter availability or residential crayfish group invasion by unknown individuals affected the impact of the crayfish Orconectes limosus on the (i) transport of gravel at baseflow (during 12 experimental days); (ii) sediment surface characteristics (after 12 days); and (iii) critical shear stress causing incipient gravel motion during simulated floods (after 12 days). The two potentially important factors shelter availability or residential group invasion negligibly affected the crayfish impact on gravel sediments, suggesting that habitat unfamiliarity (a third potentially important factor affecting crayfish activity) should increase the crayfish-induced sediment transport. Because habitat unfamiliarity is associated with sporadic long-distance migrations of a few crayfish individuals, this third factor should play a minor role in real streams, where crayfish biomass should be a key factor in relations with crayfish effects on sediments. Therefore, we combined the results of this study with those of previous crayfish experiments to assess how crayfish biomass could serve in modelling the gravel transport. Crayfish biomass explained 47% of the variability in the baseflow gravel transport and, in combination with the coefficient of variation of the bed elevation and algal cover, 72% of the variability in the critical gravel shear stress. These

  6. Experimental studies of MOS inversion and accumulation layers: Quantum mechanical effects and mobility

    NASA Astrophysics Data System (ADS)

    Chindalore, Gowrishankar L.

    The development of fast, multi-functional, and energy efficient integrated circuits, is made possible by aggressively scaling the gate lengths of the MOS devices into the sub-quarter micron regime. However, with the increasing cost of fabrication, there is a strong need for the development of reliable and accurate device simulation capabilities. The development of the theoretical models for simulators is guided by extensive experimental data, which enable an experimental verification of the models, and lead to a better understanding of the underlying physics. This dissertation presents the methodology and the results for one such experimental effort, where two important physical effects in the inversion layer and the accumulation layer of a MOS device, namely, the quantum mechanical (QM) effects and the carrier mobility are investigated. Accordingly, this dissertation has been divided into two parts, with the first part discussing the increase in the threshold voltage and the accumulation electrical oxide thickness due to QM effects. The second part discusses the methodology and the experimental results for the extraction of the majority carrier mobilities in the accumulation layers of a MOSFET. The continued scaling of the MOS gate length requires decreased gate oxide thickness (tox) and increased channel doping (NB) in order to improve device performance while suppressing the short- channel effects. The combination of the two result in large enough transverse electric fields to cause significant quantization of the carriers in the potential well at the Si/SiO2 interface. Hence, compared to the classical calculations (where the QM effects are ignored), the QM effects are found to lead to an increase in the experimental threshold voltage by approximately 100mV, and an overestimation of the physical oxide thickness by approximately 3-4A, in MOSFET devices with a gate oxide thickness and the doping level anticipated for technologies with sub-quarter micron gate

  7. Can numerical simulations accurately predict hydrodynamic instabilities in liquid films?

    NASA Astrophysics Data System (ADS)

    Denner, Fabian; Charogiannis, Alexandros; Pradas, Marc; van Wachem, Berend G. M.; Markides, Christos N.; Kalliadasis, Serafim

    2014-11-01

    Understanding the dynamics of hydrodynamic instabilities in liquid film flows is an active field of research in fluid dynamics and non-linear science in general. Numerical simulations offer a powerful tool to study hydrodynamic instabilities in film flows and can provide deep insights into the underlying physical phenomena. However, the direct comparison of numerical results and experimental results is often hampered by several reasons. For instance, in numerical simulations the interface representation is problematic and the governing equations and boundary conditions may be oversimplified, whereas in experiments it is often difficult to extract accurate information on the fluid and its behavior, e.g. determine the fluid properties when the liquid contains particles for PIV measurements. In this contribution we present the latest results of our on-going, extensive study on hydrodynamic instabilities in liquid film flows, which includes direct numerical simulations, low-dimensional modelling as well as experiments. The major focus is on wave regimes, wave height and wave celerity as a function of Reynolds number and forcing frequency of a falling liquid film. Specific attention is paid to the differences in numerical and experimental results and the reasons for these differences. The authors are grateful to the EPSRC for their financial support (Grant EP/K008595/1).

  8. Profitable capitation requires accurate costing.

    PubMed

    West, D A; Hicks, L L; Balas, E A; West, T D

    1996-01-01

    In the name of costing accuracy, nurses are asked to track inventory use on per treatment basis when more significant costs, such as general overhead and nursing salaries, are usually allocated to patients or treatments on an average cost basis. Accurate treatment costing and financial viability require analysis of all resources actually consumed in treatment delivery, including nursing services and inventory. More precise costing information enables more profitable decisions as is demonstrated by comparing the ratio-of-cost-to-treatment method (aggregate costing) with alternative activity-based costing methods (ABC). Nurses must participate in this costing process to assure that capitation bids are based upon accurate costs rather than simple averages.

  9. Theoretical study on the dissociation energies, ionization potentials and electron affinities of three perfluoroalkyl iodides

    NASA Astrophysics Data System (ADS)

    Cheng, Li; Shen, Zuochun; Lu, Jianye; Gao, Huide; Lü, Zhiwei

    2005-11-01

    Dissociation energies, ionization potentials and electron affinities of three perfluoroalkyl iodides, CF 3I, C 2F 5I, and i-C 3F 7I are calculated accurately with B3LYP, MP n ( n = 2-4), QCISD, QCISD(T), CCSD, and CCSD(T) methods. Calculations are performed by using large-core correlation-consistent pseudopotential basis set (SDB-aug-cc-pVTZ) for iodine atom. In all energy calculations, the zero point vibration energy is corrected. And the basis set superposition error is corrected by counterpoise method in the calculation of dissociation energy. Theoretical results are compared with the experimental values.

  10. The CC/DFT Route towards Accurate Structures and Spectroscopic Features for Observed and Elusive Conformers of Flexible Molecules: Pyruvic Acid as Case Study

    PubMed Central

    Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Cimino, Paola; Penocchio, Emanuele; Puzzarini, Cristina

    2018-01-01

    The structures, relative stabilities as well as the rotational and vibrational spectra of the three low-energy conformers of Pyruvic acid (PA) have been characterized using a state-of-the-art quantum-mechanical approach designed for flexible molecules. By making use of the available experimental rotational constants for several isotopologues of the most stable PA conformer, Tc-PA, the semi-experimental equilibrium structure has been derived. The latter provides a reference for the pure theoretical determination of the equilibrium geometries for all conformers, thus confirming for these structures an accuracy of 0.001 Å and 0.1 deg. for bond lengths and angles, respectively. Highly accurate relative energies of all conformers (Tc-, Tt- and Ct-PA) and of the transition states connecting them are provided along with the thermodynamic properties at low and high temperatures, thus leading to conformational enthalpies accurate to 1 kJ mol−1. Concerning microwave spectroscopy, rotational constants accurate to about 20 MHz are provided for the Tt- and Ct-PA conformers, together with the computed centrifugal-distortion constants and dipole moments required to simulate their rotational spectra. For Ct-PA, vibrational frequencies in the mid-infrared region accurate to 10 cm−1 are reported along with theoretical estimates for the transitions in the near-infrared range, and the corresponding infrared spectrum including fundamental transitions, overtones and combination bands has been simulated. In addition to the new data described above, theoretical results for the Tc- and Tt-PA conformers are compared with all available experimental data to further confirm the accuracy of the hybrid coupled-cluster/density functional theory (CC/DFT) protocol applied in the present study. Finally, we discuss in detail the accuracy of computational models fully based on double-hybrid DFT functionals (mainly at the B2PLYP/aug-cc-pVTZ level) that avoid the use of very expensive CC

  11. A new surface-potential-based compact model for the MoS2 field effect transistors in active matrix display applications

    NASA Astrophysics Data System (ADS)

    Cao, Jingchen; Peng, Songang; Liu, Wei; Wu, Quantan; Li, Ling; Geng, Di; Yang, Guanhua; Ji, Zhouyu; Lu, Nianduan; Liu, Ming

    2018-02-01

    We present a continuous surface-potential-based compact model for molybdenum disulfide (MoS2) field effect transistors based on the multiple trapping release theory and the variable-range hopping theory. We also built contact resistance and velocity saturation models based on the analytical surface potential. This model is verified with experimental data and is able to accurately predict the temperature dependent behavior of the MoS2 field effect transistor. Our compact model is coded in Verilog-A, which can be implemented in a computer-aided design environment. Finally, we carried out an active matrix display simulation, which suggested that the proposed model can be successfully applied to circuit design.

  12. An experimental study of potential residential and commercial applications of small-scale hybrid power systems

    NASA Astrophysics Data System (ADS)

    Acosta, Michael Anthony

    The research presented in this thesis provides an understanding of small-scale hybrid power systems. Experiments were conducted to identify potential applications of renewable energy in residential and commercial applications in the Rio Grande Valley of Texas. Solar and wind energy converted into electric energy was stored in batteries and inverted to power common household and commercial appliances. Several small to medium size hybrid power systems were setup and utilized to conduct numerous tests to study renewable energy prospects and feasibility for various applications. The experimental results obtained indicate that carefully constructed solar power systems can provide people living in isolated communities with sufficient energy to consistently meet their basic power needs.

  13. Efficient experimental design for uncertainty reduction in gene regulatory networks.

    PubMed

    Dehghannasiri, Roozbeh; Yoon, Byung-Jun; Dougherty, Edward R

    2015-01-01

    An accurate understanding of interactions among genes plays a major role in developing therapeutic intervention methods. Gene regulatory networks often contain a significant amount of uncertainty. The process of prioritizing biological experiments to reduce the uncertainty of gene regulatory networks is called experimental design. Under such a strategy, the experiments with high priority are suggested to be conducted first. The authors have already proposed an optimal experimental design method based upon the objective for modeling gene regulatory networks, such as deriving therapeutic interventions. The experimental design method utilizes the concept of mean objective cost of uncertainty (MOCU). MOCU quantifies the expected increase of cost resulting from uncertainty. The optimal experiment to be conducted first is the one which leads to the minimum expected remaining MOCU subsequent to the experiment. In the process, one must find the optimal intervention for every gene regulatory network compatible with the prior knowledge, which can be prohibitively expensive when the size of the network is large. In this paper, we propose a computationally efficient experimental design method. This method incorporates a network reduction scheme by introducing a novel cost function that takes into account the disruption in the ranking of potential experiments. We then estimate the approximate expected remaining MOCU at a lower computational cost using the reduced networks. Simulation results based on synthetic and real gene regulatory networks show that the proposed approximate method has close performance to that of the optimal method but at lower computational cost. The proposed approximate method also outperforms the random selection policy significantly. A MATLAB software implementing the proposed experimental design method is available at http://gsp.tamu.edu/Publications/supplementary/roozbeh15a/.

  14. MM-ISMSA: An Ultrafast and Accurate Scoring Function for Protein-Protein Docking.

    PubMed

    Klett, Javier; Núñez-Salgado, Alfonso; Dos Santos, Helena G; Cortés-Cabrera, Álvaro; Perona, Almudena; Gil-Redondo, Rubén; Abia, David; Gago, Federico; Morreale, Antonio

    2012-09-11

    An ultrafast and accurate scoring function for protein-protein docking is presented. It includes (1) a molecular mechanics (MM) part based on a 12-6 Lennard-Jones potential; (2) an electrostatic component based on an implicit solvent model (ISM) with individual desolvation penalties for each partner in the protein-protein complex plus a hydrogen bonding term; and (3) a surface area (SA) contribution to account for the loss of water contacts upon protein-protein complex formation. The accuracy and performance of the scoring function, termed MM-ISMSA, have been assessed by (1) comparing the total binding energies, the electrostatic term, and its components (charge-charge and individual desolvation energies), as well as the per residue contributions, to results obtained with well-established methods such as APBSA or MM-PB(GB)SA for a set of 1242 decoy protein-protein complexes and (2) testing its ability to recognize the docking solution closest to the experimental structure as that providing the most favorable total binding energy. For this purpose, a test set consisting of 15 protein-protein complexes with known 3D structure mixed with 10 decoys for each complex was used. The correlation between the values afforded by MM-ISMSA and those from the other methods is quite remarkable (r(2) ∼ 0.9), and only 0.2-5.0 s (depending on the number of residues) are spent on a single calculation including an all vs all pairwise energy decomposition. On the other hand, MM-ISMSA correctly identifies the best docking solution as that closest to the experimental structure in 80% of the cases. Finally, MM-ISMSA can process molecular dynamics trajectories and reports the results as averaged values with their standard deviations. MM-ISMSA has been implemented as a plugin to the widely used molecular graphics program PyMOL, although it can also be executed in command-line mode. MM-ISMSA is distributed free of charge to nonprofit organizations.

  15. Progress in calculating the potential energy surface of H3+.

    PubMed

    Adamowicz, Ludwik; Pavanello, Michele

    2012-11-13

    The most accurate electronic structure calculations are performed using wave function expansions in terms of basis functions explicitly dependent on the inter-electron distances. In our recent work, we use such basis functions to calculate a highly accurate potential energy surface (PES) for the H(3)(+) ion. The functions are explicitly correlated Gaussians, which include inter-electron distances in the exponent. Key to obtaining the high accuracy in the calculations has been the use of the analytical energy gradient determined with respect to the Gaussian exponential parameters in the minimization of the Rayleigh-Ritz variational energy functional. The effective elimination of linear dependences between the basis functions and the automatic adjustment of the positions of the Gaussian centres to the changing molecular geometry of the system are the keys to the success of the computational procedure. After adiabatic and relativistic corrections are added to the PES and with an effective accounting of the non-adiabatic effects in the calculation of the rotational/vibrational states, the experimental H(3)(+) rovibrational spectrum is reproduced at the 0.1 cm(-1) accuracy level up to 16,600 cm(-1) above the ground state.

  16. An accurate metric for the spacetime around rotating neutron stars

    NASA Astrophysics Data System (ADS)

    Pappas, George

    2017-04-01

    The problem of having an accurate description of the spacetime around rotating neutron stars is of great astrophysical interest. For astrophysical applications, one needs to have a metric that captures all the properties of the spacetime around a rotating neutron star. Furthermore, an accurate appropriately parametrized metric, I.e. a metric that is given in terms of parameters that are directly related to the physical structure of the neutron star, could be used to solve the inverse problem, which is to infer the properties of the structure of a neutron star from astrophysical observations. In this work, we present such an approximate stationary and axisymmetric metric for the exterior of rotating neutron stars, which is constructed using the Ernst formalism and is parametrized by the relativistic multipole moments of the central object. This metric is given in terms of an expansion on the Weyl-Papapetrou coordinates with the multipole moments as free parameters and is shown to be extremely accurate in capturing the physical properties of a neutron star spacetime as they are calculated numerically in general relativity. Because the metric is given in terms of an expansion, the expressions are much simpler and easier to implement, in contrast to previous approaches. For the parametrization of the metric in general relativity, the recently discovered universal 3-hair relations are used to produce a three-parameter metric. Finally, a straightforward extension of this metric is given for scalar-tensor theories with a massless scalar field, which also admit a formulation in terms of an Ernst potential.

  17. Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Dunn, Nicholas J. H.; Noid, W. G., E-mail: wnoid@chem.psu.edu

    2015-12-28

    The present work investigates the capability of bottom-up coarse-graining (CG) methods for accurately modeling both structural and thermodynamic properties of all-atom (AA) models for molecular liquids. In particular, we consider 1, 2, and 3-site CG models for heptane, as well as 1 and 3-site CG models for toluene. For each model, we employ the multiscale coarse-graining method to determine interaction potentials that optimally approximate the configuration dependence of the many-body potential of mean force (PMF). We employ a previously developed “pressure-matching” variational principle to determine a volume-dependent contribution to the potential, U{sub V}(V), that approximates the volume-dependence of the PMF.more » We demonstrate that the resulting CG models describe AA density fluctuations with qualitative, but not quantitative, accuracy. Accordingly, we develop a self-consistent approach for further optimizing U{sub V}, such that the CG models accurately reproduce the equilibrium density, compressibility, and average pressure of the AA models, although the CG models still significantly underestimate the atomic pressure fluctuations. Additionally, by comparing this array of models that accurately describe the structure and thermodynamic pressure of heptane and toluene at a range of different resolutions, we investigate the impact of bottom-up coarse-graining upon thermodynamic properties. In particular, we demonstrate that U{sub V} accounts for the reduced cohesion in the CG models. Finally, we observe that bottom-up coarse-graining introduces subtle correlations between the resolution, the cohesive energy density, and the “simplicity” of the model.« less

  18. Accurate computation of gravitational field of a tesseroid

    NASA Astrophysics Data System (ADS)

    Fukushima, Toshio

    2018-02-01

    We developed an accurate method to compute the gravitational field of a tesseroid. The method numerically integrates a surface integral representation of the gravitational potential of the tesseroid by conditionally splitting its line integration intervals and by using the double exponential quadrature rule. Then, it evaluates the gravitational acceleration vector and the gravity gradient tensor by numerically differentiating the numerically integrated potential. The numerical differentiation is conducted by appropriately switching the central and the single-sided second-order difference formulas with a suitable choice of the test argument displacement. If necessary, the new method is extended to the case of a general tesseroid with the variable density profile, the variable surface height functions, and/or the variable intervals in longitude or in latitude. The new method is capable of computing the gravitational field of the tesseroid independently on the location of the evaluation point, namely whether outside, near the surface of, on the surface of, or inside the tesseroid. The achievable precision is 14-15 digits for the potential, 9-11 digits for the acceleration vector, and 6-8 digits for the gradient tensor in the double precision environment. The correct digits are roughly doubled if employing the quadruple precision computation. The new method provides a reliable procedure to compute the topographic gravitational field, especially that near, on, and below the surface. Also, it could potentially serve as a sure reference to complement and elaborate the existing approaches using the Gauss-Legendre quadrature or other standard methods of numerical integration.

  19. Integrated experimental and modeling assessment of potential effects of gas leakages on groundwater composition

    NASA Astrophysics Data System (ADS)

    Berta, Marton; Dethlefsen, Frank; Ebert, Markus; Schäfer, Dirk

    2017-04-01

    Storing renewably produced energy is one of the major challenges for the energy systems of the upcoming decades. Power-to-gas technologies coupled to geological storage of compressed air, methane, and hydrogen offer a comparatively safe and cost-efficient way for large-scale energy storage. However, the stored gases can potentially escape from their geological reservoir and may thus affect protected natural goods such as groundwater. The geochemical reactions responsible for these composition changes are usually investigated separately in experiments and numerical models. Here we present the outcomes of an integrated experimental and modeling approach through the example of a compressed air leakage scenario. A main consequence of the presence of oxygen to be assessed in an aquifer is pyrite oxidation, well known from acid mine drainage sites. However, in contrast to acid mine drainage sites exhibiting unsaturated sediments and fed by meteoric low-carbonate water, aquifers such as in Northern Germany contain a considerable amount of solid and dissolved inorganic carbon species potentially buffering pH changes. High pressure flow-through column experiments representing an intrusion of compressed air into an aquifer were carried out to quantify pyrite oxidation kinetics and to incorporate the observations into a descriptive reaction model. Surface passivation was found to decrease the reactivity of pyrite by more than 90% after a few months of experimental run time. We propose that the carbonate buffer system enables the precipitation of a passivating mineral layer on the pyrite surface reducing the overall reaction rate significantly. Consequently, an established rate law from the literature was extended by a reactive surface passivation term[1]. This improved reaction rate equation was incorporated into a 3D numerical model using OpenGeoSys with parameters representing similarly typical aquifer conditions the experiments had characterized. These boundaries include

  20. Experimental evaluation of radiosity for room sound-field prediction.

    PubMed

    Hodgson, Murray; Nosal, Eva-Marie

    2006-08-01

    An acoustical radiosity model was evaluated for how it performs in predicting real room sound fields. This was done by comparing radiosity predictions with experimental results for three existing rooms--a squash court, a classroom, and an office. Radiosity predictions were also compared with those by ray tracing--a "reference" prediction model--for both specular and diffuse surface reflection. Comparisons were made for detailed and discretized echograms, sound-decay curves, sound-propagation curves, and the variations with frequency of four room-acoustical parameters--EDT, RT, D50, and C80. In general, radiosity and diffuse ray tracing gave very similar predictions. Predictions by specular ray tracing were often very different. Radiosity agreed well with experiment in some cases, less well in others. Definitive conclusions regarding the accuracy with which the rooms were modeled, or the accuracy of the radiosity approach, were difficult to draw. The results suggest that radiosity predicts room sound fields with some accuracy, at least as well as diffuse ray tracing and, in general, better than specular ray tracing. The predictions of detailed echograms are less accurate, those of derived room-acoustical parameters more accurate. The results underline the need to develop experimental methods for accurately characterizing the absorptive and reflective characteristics of room surfaces, possible including phase.

  1. Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations.

    PubMed

    Martínez-Romero, Marcos; O'Connor, Martin J; Shankar, Ravi D; Panahiazar, Maryam; Willrett, Debra; Egyedi, Attila L; Gevaert, Olivier; Graybeal, John; Musen, Mark A

    2017-01-01

    In biomedicine, high-quality metadata are crucial for finding experimental datasets, for understanding how experiments were performed, and for reproducing those experiments. Despite the recent focus on metadata, the quality of metadata available in public repositories continues to be extremely poor. A key difficulty is that the typical metadata acquisition process is time-consuming and error prone, with weak or nonexistent support for linking metadata to ontologies. There is a pressing need for methods and tools to speed up the metadata acquisition process and to increase the quality of metadata that are entered. In this paper, we describe a methodology and set of associated tools that we developed to address this challenge. A core component of this approach is a value recommendation framework that uses analysis of previously entered metadata and ontology-based metadata specifications to help users rapidly and accurately enter their metadata. We performed an initial evaluation of this approach using metadata from a public metadata repository.

  2. Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations

    PubMed Central

    Martínez-Romero, Marcos; O’Connor, Martin J.; Shankar, Ravi D.; Panahiazar, Maryam; Willrett, Debra; Egyedi, Attila L.; Gevaert, Olivier; Graybeal, John; Musen, Mark A.

    2017-01-01

    In biomedicine, high-quality metadata are crucial for finding experimental datasets, for understanding how experiments were performed, and for reproducing those experiments. Despite the recent focus on metadata, the quality of metadata available in public repositories continues to be extremely poor. A key difficulty is that the typical metadata acquisition process is time-consuming and error prone, with weak or nonexistent support for linking metadata to ontologies. There is a pressing need for methods and tools to speed up the metadata acquisition process and to increase the quality of metadata that are entered. In this paper, we describe a methodology and set of associated tools that we developed to address this challenge. A core component of this approach is a value recommendation framework that uses analysis of previously entered metadata and ontology-based metadata specifications to help users rapidly and accurately enter their metadata. We performed an initial evaluation of this approach using metadata from a public metadata repository. PMID:29854196

  3. Iterative feature refinement for accurate undersampled MR image reconstruction

    NASA Astrophysics Data System (ADS)

    Wang, Shanshan; Liu, Jianbo; Liu, Qiegen; Ying, Leslie; Liu, Xin; Zheng, Hairong; Liang, Dong

    2016-05-01

    Accelerating MR scan is of great significance for clinical, research and advanced applications, and one main effort to achieve this is the utilization of compressed sensing (CS) theory. Nevertheless, the existing CSMRI approaches still have limitations such as fine structure loss or high computational complexity. This paper proposes a novel iterative feature refinement (IFR) module for accurate MR image reconstruction from undersampled K-space data. Integrating IFR with CSMRI which is equipped with fixed transforms, we develop an IFR-CS method to restore meaningful structures and details that are originally discarded without introducing too much additional complexity. Specifically, the proposed IFR-CS is realized with three iterative steps, namely sparsity-promoting denoising, feature refinement and Tikhonov regularization. Experimental results on both simulated and in vivo MR datasets have shown that the proposed module has a strong capability to capture image details, and that IFR-CS is comparable and even superior to other state-of-the-art reconstruction approaches.

  4. Numerical algorithm comparison for the accurate and efficient computation of high-incidence vortical flow

    NASA Technical Reports Server (NTRS)

    Chaderjian, Neal M.

    1991-01-01

    Computations from two Navier-Stokes codes, NSS and F3D, are presented for a tangent-ogive-cylinder body at high angle of attack. Features of this steady flow include a pair of primary vortices on the leeward side of the body as well as secondary vortices. The topological and physical plausibility of this vortical structure is discussed. The accuracy of these codes are assessed by comparison of the numerical solutions with experimental data. The effects of turbulence model, numerical dissipation, and grid refinement are presented. The overall efficiency of these codes are also assessed by examining their convergence rates, computational time per time step, and maximum allowable time step for time-accurate computations. Overall, the numerical results from both codes compared equally well with experimental data, however, the NSS code was found to be significantly more efficient than the F3D code.

  5. Skin microbiome surveys are strongly influenced by experimental design

    PubMed Central

    Meisel, Jacquelyn S.; Hannigan, Geoffrey D.; Tyldsley, Amanda S.; SanMiguel, Adam J.; Hodkinson, Brendan P.; Zheng, Qi; Grice, Elizabeth A.

    2016-01-01

    Culture-independent studies to characterize skin microbiota are increasingly common, due in part to affordable and accessible sequencing and analysis platforms. Compared to culture-based techniques, DNA sequencing of the bacterial 16S ribosomal RNA (rRNA) gene or whole metagenome shotgun (WMS) sequencing provide more precise microbial community characterizations. Most widely used protocols were developed to characterize microbiota of other habitats (i.e. gastrointestinal), and have not been systematically compared for their utility in skin microbiome surveys. Here we establish a resource for the cutaneous research community to guide experimental design in characterizing skin microbiota. We compare two widely sequenced regions of the 16S rRNA gene to WMS sequencing for recapitulating skin microbiome community composition, diversity, and genetic functional enrichment. We show that WMS sequencing most accurately recapitulates microbial communities, but sequencing of hypervariable regions 1-3 of the 16S rRNA gene provides highly similar results. Sequencing of hypervariable region 4 poorly captures skin commensal microbiota, especially Propionibacterium. WMS sequencing, which is resource- and cost-intensive, provides evidence of a community’s functional potential; however, metagenome predictions based on 16S rRNA sequence tags closely approximate WMS genetic functional profiles. This work highlights the importance of experimental design for downstream results in skin microbiome surveys. PMID:26829039

  6. LCC-Demons: a robust and accurate symmetric diffeomorphic registration algorithm.

    PubMed

    Lorenzi, M; Ayache, N; Frisoni, G B; Pennec, X

    2013-11-01

    Non-linear registration is a key instrument for computational anatomy to study the morphology of organs and tissues. However, in order to be an effective instrument for the clinical practice, registration algorithms must be computationally efficient, accurate and most importantly robust to the multiple biases affecting medical images. In this work we propose a fast and robust registration framework based on the log-Demons diffeomorphic registration algorithm. The transformation is parameterized by stationary velocity fields (SVFs), and the similarity metric implements a symmetric local correlation coefficient (LCC). Moreover, we show how the SVF setting provides a stable and consistent numerical scheme for the computation of the Jacobian determinant and the flux of the deformation across the boundaries of a given region. Thus, it provides a robust evaluation of spatial changes. We tested the LCC-Demons in the inter-subject registration setting, by comparing with state-of-the-art registration algorithms on public available datasets, and in the intra-subject longitudinal registration problem, for the statistically powered measurements of the longitudinal atrophy in Alzheimer's disease. Experimental results show that LCC-Demons is a generic, flexible, efficient and robust algorithm for the accurate non-linear registration of images, which can find several applications in the field of medical imaging. Without any additional optimization, it solves equally well intra & inter-subject registration problems, and compares favorably to state-of-the-art methods. Copyright © 2013 Elsevier Inc. All rights reserved.

  7. Multiple-frequency continuous wave ultrasonic system for accurate distance measurement

    NASA Astrophysics Data System (ADS)

    Huang, C. F.; Young, M. S.; Li, Y. C.

    1999-02-01

    A highly accurate multiple-frequency continuous wave ultrasonic range-measuring system for use in air is described. The proposed system uses a method heretofore applied to radio frequency distance measurement but not to air-based ultrasonic systems. The method presented here is based upon the comparative phase shifts generated by three continuous ultrasonic waves of different but closely spaced frequencies. In the test embodiment to confirm concept feasibility, two low cost 40 kHz ultrasonic transducers are set face to face and used to transmit and receive ultrasound. Individual frequencies are transmitted serially, each generating its own phase shift. For any given frequency, the transmitter/receiver distance modulates the phase shift between the transmitted and received signals. Comparison of the phase shifts allows a highly accurate evaluation of target distance. A single-chip microcomputer-based multiple-frequency continuous wave generator and phase detector was designed to record and compute the phase shift information and the resulting distance, which is then sent to either a LCD or a PC. The PC is necessary only for calibration of the system, which can be run independently after calibration. Experiments were conducted to test the performance of the whole system. Experimentally, ranging accuracy was found to be within ±0.05 mm, with a range of over 1.5 m. The main advantages of this ultrasonic range measurement system are high resolution, low cost, narrow bandwidth requirements, and ease of implementation.

  8. Recent advances in thermal desorption-gas chromatography-mass spectrometery method to eliminate the matrix effect between air and water samples: application to the accurate determination of Henry's law constant.

    PubMed

    Kim, Yong-Hyun; Kim, Ki-Hyun

    2014-05-16

    Accurate values for the Henry's law constants are essential to describe the environmental dynamics of a solute, but substantial errors are recognized in many reported data due to practical difficulties in measuring solubility and/or vapor pressure. Despite such awareness, validation of experimental approaches has scarcely been made. An experimental approach based on thermal desorption-gas chromatography-mass spectrometery (TD-GC-MS) method was developed to concurrently allow the accurate determination of target compounds from the headspace and aqueous samples in closed equilibrated system. The analysis of six aromatics and eight non-aromatic oxygenates was then carried out in a static headspace mode. An estimation of the potential bias and mass balance (i.e., sum of mass measured individually from gas and liquid phases vs. the mass initially added to the system) demonstrates compound-specific phase dependency so that the best results are obtained by aqueous (less soluble aromatics) and headspace analysis (more soluble non-aromatics). Accordingly, we were able to point to the possible sources of biases in previous studies and provide the best estimates for the Henry's constants (Matm(-1)): benzene (0.17), toluene (0.15), p-xylene (0.13), m-xylene (0.13), o-xylene (0.19), styrene (0.27); propionaldehyde (9.26), butyraldehyde (6.19), isovaleraldehyde (2.14), n-valeraldehyde (3.98), methyl ethyl ketone (10.5), methyl isobutyl ketone (3.93), n-butyl acetate (2.41), and isobutyl alcohol (22.2). Copyright © 2014 Elsevier B.V. All rights reserved.

  9. Near transferable phenomenological n-body potentials for noble metals

    NASA Astrophysics Data System (ADS)

    Pontikis, Vassilis; Baldinozzi, Gianguido; Luneville, Laurence; Simeone, David

    2017-09-01

    We present a semi-empirical model of cohesion in noble metals with suitable parameters reproducing a selected set of experimental properties of perfect and defective lattices in noble metals. It consists of two short-range, n-body terms accounting respectively for attractive and repulsive interactions, the former deriving from the second moment approximation of the tight-binding scheme and the latter from the gas approximation of the kinetic energy of electrons. The stability of the face centred cubic versus the hexagonal compact stacking is obtained via a long-range, pairwise function of customary use with ionic pseudo-potentials. Lattice dynamics, molecular statics, molecular dynamics and nudged elastic band calculations show that, unlike previous potentials, this cohesion model reproduces and predicts quite accurately thermodynamic properties in noble metals. In particular, computed surface energies, largely underestimated by existing empirical cohesion models, compare favourably with measured values, whereas predicted unstable stacking-fault energy profiles fit almost perfectly ab initio evaluations from the literature. All together the results suggest that this semi-empirical model is nearly transferable.

  10. Near transferable phenomenological n-body potentials for noble metals.

    PubMed

    Pontikis, Vassilis; Baldinozzi, Gianguido; Luneville, Laurence; Simeone, David

    2017-09-06

    We present a semi-empirical model of cohesion in noble metals with suitable parameters reproducing a selected set of experimental properties of perfect and defective lattices in noble metals. It consists of two short-range, n-body terms accounting respectively for attractive and repulsive interactions, the former deriving from the second moment approximation of the tight-binding scheme and the latter from the gas approximation of the kinetic energy of electrons. The stability of the face centred cubic versus the hexagonal compact stacking is obtained via a long-range, pairwise function of customary use with ionic pseudo-potentials. Lattice dynamics, molecular statics, molecular dynamics and nudged elastic band calculations show that, unlike previous potentials, this cohesion model reproduces and predicts quite accurately thermodynamic properties in noble metals. In particular, computed surface energies, largely underestimated by existing empirical cohesion models, compare favourably with measured values, whereas predicted unstable stacking-fault energy profiles fit almost perfectly ab initio evaluations from the literature. All together the results suggest that this semi-empirical model is nearly transferable.

  11. Characterizing the ozone formation potential of agricultural sources in California's San Joaquin Valley: A computational and experimental approach

    NASA Astrophysics Data System (ADS)

    Howard, Cody Jerome

    The global pattern of expanding urban centers and increasing agricultural intensity is leading to more frequent interactions between air pollution emissions from urban and agricultural sources. The confluence of these emissions that traditionally have been separated by hundreds of kilometers is creating new air quality challenges in numerous regions across the United States. An area of particular interest is California's San Joaquin Valley (SJV), which has an agricultural output higher than many countries, a rapidly expanding human population, and ozone concentrations that are already higher than many dense urban areas. New regulations in the SJV restrict emissions of reactive organic gases (ROG) from animal sources in an attempt to meet Federal and State ozone standards designed to protect human health. A transportable "smog" chamber was developed and tested to directly measure the ozone formation potential of a variety of agricultural emissions in representative urban and rural atmospheres. After validation of the experimental procedure, four animal types were examined: beef cattle, dairy cattle, swine, and poultry, as well as six commonly used animal feeds: cereal silage (wheat grain and oat grain), alfalfa silage, corn silage, high moisture ground corn, almond shells, almond hulls, and total mixed ration. The emitted ROG composition was also measured so that the theoretical incremental reactivity could be calculated for a variety of atmospheres and directly compared with the measured ozone formation potential (OFP) under the experimental conditions. A computational model was created based on a modified form of the Caltech Atmospheric Chemistry Mechanism and validated against experimental results. After validation, the computational model was used to predict OFP across a range of NOx and ROG concentrations. The ROG OFP measurements combined with adjusted agricultural ROG emissions inventory estimates were used to predict the actual ozone production in the SJV

  12. A Robust Adaptive Autonomous Approach to Optimal Experimental Design

    NASA Astrophysics Data System (ADS)

    Gu, Hairong

    Experimentation is the fundamental tool of scientific inquiries to understand the laws governing the nature and human behaviors. Many complex real-world experimental scenarios, particularly in quest of prediction accuracy, often encounter difficulties to conduct experiments using an existing experimental procedure for the following two reasons. First, the existing experimental procedures require a parametric model to serve as the proxy of the latent data structure or data-generating mechanism at the beginning of an experiment. However, for those experimental scenarios of concern, a sound model is often unavailable before an experiment. Second, those experimental scenarios usually contain a large number of design variables, which potentially leads to a lengthy and costly data collection cycle. Incompetently, the existing experimental procedures are unable to optimize large-scale experiments so as to minimize the experimental length and cost. Facing the two challenges in those experimental scenarios, the aim of the present study is to develop a new experimental procedure that allows an experiment to be conducted without the assumption of a parametric model while still achieving satisfactory prediction, and performs optimization of experimental designs to improve the efficiency of an experiment. The new experimental procedure developed in the present study is named robust adaptive autonomous system (RAAS). RAAS is a procedure for sequential experiments composed of multiple experimental trials, which performs function estimation, variable selection, reverse prediction and design optimization on each trial. Directly addressing the challenges in those experimental scenarios of concern, function estimation and variable selection are performed by data-driven modeling methods to generate a predictive model from data collected during the course of an experiment, thus exempting the requirement of a parametric model at the beginning of an experiment; design optimization is

  13. Fractional viscoelasticity in fractal and non-fractal media: Theory, experimental validation, and uncertainty analysis

    NASA Astrophysics Data System (ADS)

    Mashayekhi, Somayeh; Miles, Paul; Hussaini, M. Yousuff; Oates, William S.

    2018-02-01

    In this paper, fractional and non-fractional viscoelastic models for elastomeric materials are derived and analyzed in comparison to experimental results. The viscoelastic models are derived by expanding thermodynamic balance equations for both fractal and non-fractal media. The order of the fractional time derivative is shown to strongly affect the accuracy of the viscoelastic constitutive predictions. Model validation uses experimental data describing viscoelasticity of the dielectric elastomer Very High Bond (VHB) 4910. Since these materials are known for their broad applications in smart structures, it is important to characterize and accurately predict their behavior across a large range of time scales. Whereas integer order viscoelastic models can yield reasonable agreement with data, the model parameters often lack robustness in prediction at different deformation rates. Alternatively, fractional order models of viscoelasticity provide an alternative framework to more accurately quantify complex rate-dependent behavior. Prior research that has considered fractional order viscoelasticity lacks experimental validation and contains limited links between viscoelastic theory and fractional order derivatives. To address these issues, we use fractional order operators to experimentally validate fractional and non-fractional viscoelastic models in elastomeric solids using Bayesian uncertainty quantification. The fractional order model is found to be advantageous as predictions are significantly more accurate than integer order viscoelastic models for deformation rates spanning four orders of magnitude.

  14. Animal models of protein allergenicity: potential benefits, pitfalls and challenges.

    PubMed

    Dearman, R J; Kimber, I

    2009-04-01

    Food allergy is an important health issue. With an increasing interest in novel foods derived from transgenic crop plants, there is a growing need for the development of approaches suitable for the characterization of the allergenic potential of proteins. There are methods available currently (such as homology searches and serological testing) that are very effective at identifying proteins that are likely to cross-react with known allergens. However, animal models may play a role in the identification of truly novel proteins, such as bacterial or fungal proteins, that have not been experienced previously in the diet. We consider here the potential benefits, pitfalls and challenges of the selection of various animal models, including the mouse, the rat, the dog and the neonatal swine. The advantages and disadvantages of various experimental end-points are discussed, including the measurement of specific IgE by ELISA, Western blotting or functional tests such as the passive cutaneous anaphylaxis assay, and the assessment of challenge-induced clinical symptoms in previously sensitized animals. The experimental variables of route of exposure to test proteins and the incorporation of adjuvant to increase the sensitivity of the responses are considered also. It is important to emphasize that currently none of these approaches has been validated for the purposes of hazard identification in the context of a safety assessment. However, the available evidence suggests that the judicious use of an accurate and robust animal model could provide important additional data that would contribute significantly to the assessment of the potential allergenicity of novel proteins.

  15. Evaluation of factors affecting accurate measurements of atmospheric CO2 and CH4 by wavelength-scanned cavity ring-down spectroscopy

    NASA Astrophysics Data System (ADS)

    Nara, H.; Tanimoto, H.; Tohjima, Y.; Mukai, H.; Nojiri, Y.; Katsumata, K.; Rella, C.

    2012-07-01

    We examined potential interferences from water vapor and atmospheric background gases (N2, O2, and Ar), and biases by isotopologues of target species, on accurate measurement of atmospheric CO2 and CH4 by means of wavelength-scanned cavity ring-down spectroscopy (WS-CRDS). Variations in the composition of the background gas substantially impacted the CO2 and CH4 measurements: the measured amounts of CO2 and CH4 decreased with increasing N2 mole fraction, but increased with increasing O2 and Ar, suggesting that the pressure-broadening effects (PBEs) increased as Ar < O2 < N2. Using these experimental results, we inferred PBEs for the measurement of synthetic standard gases. The PBEs were negligible (up to 0.05 ppm for CO2 and 0.01 ppb for CH4) for gas standards balanced with purified air, although the PBEs were substantial (up to 0.87 ppm for CO2 and 1.4 ppb for CH4) for standards balanced with synthetic air. For isotopic biases on CO2 measurements, we compared experimental results and theoretical calculations, which showed excellent agreement within their uncertainty. We derived empirical correction functions for water vapor for three WS-CRDS instruments (Picarro EnviroSense 3000i, G-1301, and G-2301). Although the transferability of the functions was not clear, no significant difference was found in the water vapor correction values among these instruments within the typical analytical precision at sufficiently low water concentrations (< 0.3%V for CO2 and < 0.4%V for CH4). For accurate measurements of CO2 and CH4 in ambient air, we concluded that WS-CRDS measurements should be performed under complete dehumidification of air samples, or moderate dehumidification followed by application of a water vapor correction function, along with calibration by natural air-based standard gases or purified air-balanced synthetic standard gases with isotopic correction.

  16. Molecular acidity: An accurate description with information-theoretic approach in density functional reactivity theory.

    PubMed

    Cao, Xiaofang; Rong, Chunying; Zhong, Aiguo; Lu, Tian; Liu, Shubin

    2018-01-15

    Molecular acidity is one of the important physiochemical properties of a molecular system, yet its accurate calculation and prediction are still an unresolved problem in the literature. In this work, we propose to make use of the quantities from the information-theoretic (IT) approach in density functional reactivity theory and provide an accurate description of molecular acidity from a completely new perspective. To illustrate our point, five different categories of acidic series, singly and doubly substituted benzoic acids, singly substituted benzenesulfinic acids, benzeneseleninic acids, phenols, and alkyl carboxylic acids, have been thoroughly examined. We show that using IT quantities such as Shannon entropy, Fisher information, Ghosh-Berkowitz-Parr entropy, information gain, Onicescu information energy, and relative Rényi entropy, one is able to simultaneously predict experimental pKa values of these different categories of compounds. Because of the universality of the quantities employed in this work, which are all density dependent, our approach should be general and be applicable to other systems as well. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  17. Highly accurate potential energy surface, dipole moment surface, rovibrational energy levels, and infrared line list for {sup 32}S{sup 16}O{sub 2} up to 8000 cm{sup −1}

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Huang, Xinchuan, E-mail: Xinchuan.Huang-1@nasa.gov, E-mail: Timothy.J.Lee@nasa.gov; Schwenke, David W., E-mail: David.W.Schwenke@nasa.gov; Lee, Timothy J., E-mail: Xinchuan.Huang-1@nasa.gov, E-mail: Timothy.J.Lee@nasa.gov

    2014-03-21

    A purely ab initio potential energy surface (PES) was refined with selected {sup 32}S{sup 16}O{sub 2} HITRAN data. Compared to HITRAN, the root-mean-squares error (σ{sub RMS}) for all J = 0–80 rovibrational energy levels computed on the refined PES (denoted Ames-1) is 0.013 cm{sup −1}. Combined with a CCSD(T)/aug-cc-pV(Q+d)Z dipole moment surface (DMS), an infrared (IR) line list (denoted Ames-296K) has been computed at 296 K and covers up to 8000 cm{sup −1}. Compared to the HITRAN and CDMS databases, the intensity agreement for most vibrational bands is better than 85%–90%. Our predictions for {sup 34}S{sup 16}O{sub 2} band origins,more » higher energy {sup 32}S{sup 16}O{sub 2} band origins and missing {sup 32}S{sup 16}O{sub 2} IR bands have been verified by most recent experiments and available HITRAN data. We conclude that the Ames-1 PES is able to predict {sup 32/34}S{sup 16}O{sub 2} band origins below 5500 cm{sup −1} with 0.01–0.03 cm{sup −1} uncertainties, and the Ames-296K line list provides continuous, reliable and accurate IR simulations. The K{sub a}-dependence of both line position and line intensity errors is discussed. The line list will greatly facilitate SO{sub 2} IR spectral experimental analysis, as well as elimination of SO{sub 2} lines in high-resolution astronomical observations.« less

  18. Full-dimensional quantum calculations of ground-state tunneling splitting of malonaldehyde using an accurate ab initio potential energy surface

    NASA Astrophysics Data System (ADS)

    Wang, Yimin; Braams, Bastiaan J.; Bowman, Joel M.; Carter, Stuart; Tew, David P.

    2008-06-01

    Quantum calculations of the ground vibrational state tunneling splitting of H-atom and D-atom transfer in malonaldehyde are performed on a full-dimensional ab initio potential energy surface (PES). The PES is a fit to 11 147 near basis-set-limit frozen-core CCSD(T) electronic energies. This surface properly describes the invariance of the potential with respect to all permutations of identical atoms. The saddle-point barrier for the H-atom transfer on the PES is 4.1 kcal/mol, in excellent agreement with the reported ab initio value. Model one-dimensional and ``exact'' full-dimensional calculations of the splitting for H- and D-atom transfer are done using this PES. The tunneling splittings in full dimensionality are calculated using the unbiased ``fixed-node'' diffusion Monte Carlo (DMC) method in Cartesian and saddle-point normal coordinates. The ground-state tunneling splitting is found to be 21.6 cm-1 in Cartesian coordinates and 22.6 cm-1 in normal coordinates, with an uncertainty of 2-3 cm-1. This splitting is also calculated based on a model which makes use of the exact single-well zero-point energy (ZPE) obtained with the MULTIMODE code and DMC ZPE and this calculation gives a tunneling splitting of 21-22 cm-1. The corresponding computed splittings for the D-atom transfer are 3.0, 3.1, and 2-3 cm-1. These calculated tunneling splittings agree with each other to within less than the standard uncertainties obtained with the DMC method used, which are between 2 and 3 cm-1, and agree well with the experimental values of 21.6 and 2.9 cm-1 for the H and D transfer, respectively.

  19. Full-dimensional quantum calculations of ground-state tunneling splitting of malonaldehyde using an accurate ab initio potential energy surface.

    PubMed

    Wang, Yimin; Braams, Bastiaan J; Bowman, Joel M; Carter, Stuart; Tew, David P

    2008-06-14

    Quantum calculations of the ground vibrational state tunneling splitting of H-atom and D-atom transfer in malonaldehyde are performed on a full-dimensional ab initio potential energy surface (PES). The PES is a fit to 11 147 near basis-set-limit frozen-core CCSD(T) electronic energies. This surface properly describes the invariance of the potential with respect to all permutations of identical atoms. The saddle-point barrier for the H-atom transfer on the PES is 4.1 kcalmol, in excellent agreement with the reported ab initio value. Model one-dimensional and "exact" full-dimensional calculations of the splitting for H- and D-atom transfer are done using this PES. The tunneling splittings in full dimensionality are calculated using the unbiased "fixed-node" diffusion Monte Carlo (DMC) method in Cartesian and saddle-point normal coordinates. The ground-state tunneling splitting is found to be 21.6 cm(-1) in Cartesian coordinates and 22.6 cm(-1) in normal coordinates, with an uncertainty of 2-3 cm(-1). This splitting is also calculated based on a model which makes use of the exact single-well zero-point energy (ZPE) obtained with the MULTIMODE code and DMC ZPE and this calculation gives a tunneling splitting of 21-22 cm(-1). The corresponding computed splittings for the D-atom transfer are 3.0, 3.1, and 2-3 cm(-1). These calculated tunneling splittings agree with each other to within less than the standard uncertainties obtained with the DMC method used, which are between 2 and 3 cm(-1), and agree well with the experimental values of 21.6 and 2.9 cm(-1) for the H and D transfer, respectively.

  20. 77 FR 3800 - Accurate NDE & Inspection, LLC; Confirmatory Order

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-25

    ... In the Matter of Accurate NDE & Docket: 150-00017, General Inspection, LLC Broussard, Louisiana... an attempt to resolve issues associated with this matter. In response, on August 9, 2011, Accurate NDE requested ADR to resolve this matter with the NRC. On September 28, 2011, the NRC and Accurate NDE...

  1. Accurate determination of Brillouin frequency based on cross recurrence plot analysis in Brillouin distributed fiber sensor

    NASA Astrophysics Data System (ADS)

    Haneef, Shahna M.; Srijith, K.; Venkitesh, D.; Srinivasan, B.

    2017-04-01

    We propose and demonstrate the use of cross recurrence plot analysis (CRPA) to accurately determine the Brillouin shift due to strain and temperature in a Brillouin distributed fiber sensor. This signal processing technique, which is implemented in Brillouin sensors for the first time relies on apriori data i.e, the lineshape of the Brillouin gain spectrum and its similarity with the spectral features measured at different locations along the fiber. Analytical and experimental investigation of the proposed scheme is presented in this paper.

  2. Accurate Characterization of Benign and Cancerous Breast Tissues: Aspecific Patient Studies using Piezoresistive Microcantilevers

    PubMed Central

    PANDYA, HARDIK J.; ROY, RAJARSHI; CHEN, WENJIN; CHEKMAREVA, MARINA A.; FORAN, DAVID J.; DESAI, JAYDEV P.

    2014-01-01

    Breast cancer is the largest detected cancer amongst women in the US. In this work, our team reports on the development of piezoresistive microcantilevers (PMCs) to investigate their potential use in the accurate detection and characterization of benign and diseased breast tissues by performing indentations on the micro-scale tissue specimens. The PMCs used in these experiments have been fabricated using laboratory-made silicon-on-insulator (SOI) substrate, which significantly reduces the fabrication costs. The PMCs are 260 μm long, 35 μm wide and 2 μm thick with resistivity of order 1.316 X 10−3 Ω-cm obtained by using boron diffusion technique. For indenting the tissue, we utilized 8 μm thick cylindrical SU-8 tip. The PMC was calibrated against a known AFM probe. Breast tissue cores from seven different specimens were indented using PMC to identify benign and cancerous tissue cores. Furthermore, field emission scanning electron microscopy (FE-SEM) of benign and cancerous specimens showed marked differences in the tissue morphology, which further validates our observed experimental data with the PMCs. While these patient aspecific feasibility studies clearly demonstrate the ability to discriminate between benign and cancerous breast tissues, further investigation is necessary to perform automated mechano-phenotyping (classification) of breast cancer: from onset to disease progression. PMID:25128621

  3. Accurate position estimation methods based on electrical impedance tomography measurements

    NASA Astrophysics Data System (ADS)

    Vergara, Samuel; Sbarbaro, Daniel; Johansen, T. A.

    2017-08-01

    Electrical impedance tomography (EIT) is a technology that estimates the electrical properties of a body or a cross section. Its main advantages are its non-invasiveness, low cost and operation free of radiation. The estimation of the conductivity field leads to low resolution images compared with other technologies, and high computational cost. However, in many applications the target information lies in a low intrinsic dimensionality of the conductivity field. The estimation of this low-dimensional information is addressed in this work. It proposes optimization-based and data-driven approaches for estimating this low-dimensional information. The accuracy of the results obtained with these approaches depends on modelling and experimental conditions. Optimization approaches are sensitive to model discretization, type of cost function and searching algorithms. Data-driven methods are sensitive to the assumed model structure and the data set used for parameter estimation. The system configuration and experimental conditions, such as number of electrodes and signal-to-noise ratio (SNR), also have an impact on the results. In order to illustrate the effects of all these factors, the position estimation of a circular anomaly is addressed. Optimization methods based on weighted error cost functions and derivate-free optimization algorithms provided the best results. Data-driven approaches based on linear models provided, in this case, good estimates, but the use of nonlinear models enhanced the estimation accuracy. The results obtained by optimization-based algorithms were less sensitive to experimental conditions, such as number of electrodes and SNR, than data-driven approaches. Position estimation mean squared errors for simulation and experimental conditions were more than twice for the optimization-based approaches compared with the data-driven ones. The experimental position estimation mean squared error of the data-driven models using a 16-electrode setup was less

  4. A simple and accurate rule-based modeling framework for simulation of autocrine/paracrine stimulation of glioblastoma cell motility and proliferation by L1CAM in 2-D culture.

    PubMed

    Caccavale, Justin; Fiumara, David; Stapf, Michael; Sweitzer, Liedeke; Anderson, Hannah J; Gorky, Jonathan; Dhurjati, Prasad; Galileo, Deni S

    2017-12-11

    Glioblastoma multiforme (GBM) is a devastating brain cancer for which there is no known cure. Its malignancy is due to rapid cell division along with high motility and invasiveness of cells into the brain tissue. Simple 2-dimensional laboratory assays (e.g., a scratch assay) commonly are used to measure the effects of various experimental perturbations, such as treatment with chemical inhibitors. Several mathematical models have been developed to aid the understanding of the motile behavior and proliferation of GBM cells. However, many are mathematically complicated, look at multiple interdependent phenomena, and/or use modeling software not freely available to the research community. These attributes make the adoption of models and simulations of even simple 2-dimensional cell behavior an uncommon practice by cancer cell biologists. Herein, we developed an accurate, yet simple, rule-based modeling framework to describe the in vitro behavior of GBM cells that are stimulated by the L1CAM protein using freely available NetLogo software. In our model L1CAM is released by cells to act through two cell surface receptors and a point of signaling convergence to increase cell motility and proliferation. A simple graphical interface is provided so that changes can be made easily to several parameters controlling cell behavior, and behavior of the cells is viewed both pictorially and with dedicated graphs. We fully describe the hierarchical rule-based modeling framework, show simulation results under several settings, describe the accuracy compared to experimental data, and discuss the potential usefulness for predicting future experimental outcomes and for use as a teaching tool for cell biology students. It is concluded that this simple modeling framework and its simulations accurately reflect much of the GBM cell motility behavior observed experimentally in vitro in the laboratory. Our framework can be modified easily to suit the needs of investigators interested in other

  5. Analytical approximation of the InGaZnO thin-film transistors surface potential

    NASA Astrophysics Data System (ADS)

    Colalongo, Luigi

    2016-10-01

    Surface-potential-based mathematical models are among the most accurate and physically based compact models of thin-film transistors, and in turn of indium gallium zinc oxide TFTs, available today. However, the need of iterative computations of the surface potential limits their computational efficiency and diffusion in CAD applications. The existing closed-form approximations of the surface potential are based on regional approximations and empirical smoothing functions that could result not accurate enough in particular to model transconductances and transcapacitances. In this work we present an extremely accurate (in the range of nV) and computationally efficient non-iterative approximation of the surface potential that can serve as a basis for advanced surface-potential-based indium gallium zinc oxide TFTs models.

  6. MICCA: a complete and accurate software for taxonomic profiling of metagenomic data

    PubMed Central

    Albanese, Davide; Fontana, Paolo; De Filippo, Carlotta; Cavalieri, Duccio; Donati, Claudio

    2015-01-01

    The introduction of high throughput sequencing technologies has triggered an increase of the number of studies in which the microbiota of environmental and human samples is characterized through the sequencing of selected marker genes. While experimental protocols have undergone a process of standardization that makes them accessible to a large community of scientist, standard and robust data analysis pipelines are still lacking. Here we introduce MICCA, a software pipeline for the processing of amplicon metagenomic datasets that efficiently combines quality filtering, clustering of Operational Taxonomic Units (OTUs), taxonomy assignment and phylogenetic tree inference. MICCA provides accurate results reaching a good compromise among modularity and usability. Moreover, we introduce a de-novo clustering algorithm specifically designed for the inference of Operational Taxonomic Units (OTUs). Tests on real and synthetic datasets shows that thanks to the optimized reads filtering process and to the new clustering algorithm, MICCA provides estimates of the number of OTUs and of other common ecological indices that are more accurate and robust than currently available pipelines. Analysis of public metagenomic datasets shows that the higher consistency of results improves our understanding of the structure of environmental and human associated microbial communities. MICCA is an open source project. PMID:25988396

  7. State-of-the-art ab initio potential energy curve for the krypton atom pair and thermophysical properties of dilute krypton gas

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Jäger, Benjamin, E-mail: benjamin.jaeger@uni-rostock.de; Hellmann, Robert, E-mail: robert.hellmann@uni-rostock.de; Bich, Eckard

    2016-03-21

    A new reference krypton-krypton interatomic potential energy curve was developed by means of quantum-chemical ab initio calculations for 36 interatomic separations. Highly accurate values for the interaction energies at the complete basis set limit were obtained using the coupled-cluster method with single, double, and perturbative triple excitations as well as t-aug-cc-pV5Z and t-aug-cc-pV6Z basis sets including mid-bond functions, with the 6Z basis set being newly constructed for this study. Higher orders of coupled-cluster terms were considered in a successive scheme up to full quadruple excitations. Core-core and core-valence correlation effects were included. Furthermore, relativistic effects were studied not only atmore » a scalar relativistic level using second-order direct perturbation theory, but also utilizing full four-component and Gaunt-effect computations. An analytical pair potential function was fitted to the interaction energies, which is characterized by a depth of 200.88 K with an estimated standard uncertainty of 0.51 K. Thermophysical properties of low-density krypton were calculated for temperatures up to 5000 K. Second and third virial coefficients were obtained from statistical thermodynamics. Viscosity and thermal conductivity as well as the self-diffusion coefficient were computed using the kinetic theory of gases. The theoretical results are compared with experimental data and with results for other pair potential functions from the literature, especially with those calculated from the recently developed ab initio potential of Waldrop et al. [J. Chem. Phys. 142, 204307 (2015)]. Highly accurate experimental viscosity data indicate that both the present ab initio pair potential and the one of Waldrop et al. can be regarded as reference potentials, even though the quantum-chemical methods and basis sets differ. However, the uncertainties of the present potential and of the derived properties are estimated to be considerably lower.« less

  8. Detecting circular RNAs: bioinformatic and experimental challenges

    PubMed Central

    Szabo, Linda; Salzman, Julia

    2017-01-01

    The pervasive expression of circular RNAs (circRNAs) is a recently discovered feature of gene expression in highly diverged eukaryotes. Numerous algorithms that are used to detect genome-wide circRNA expression from RNA sequencing (RNA-seq) data have been developed in the past few years, but there is little overlap in their predictions and no clear gold-standard method to assess the accuracy of these algorithms. We review sources of experimental and bioinformatic biases that complicate the accurate discovery of circRNAs and discuss statistical approaches to address these biases. We conclude with a discussion of the current experimental progress on the topic. PMID:27739534

  9. Molecular Simulation of the Free Energy for the Accurate Determination of Phase Transition Properties of Molecular Solids

    NASA Astrophysics Data System (ADS)

    Sellers, Michael; Lisal, Martin; Brennan, John

    2015-06-01

    Investigating the ability of a molecular model to accurately represent a real material is crucial to model development and use. When the model simulates materials in extreme conditions, one such property worth evaluating is the phase transition point. However, phase transitions are often overlooked or approximated because of difficulty or inaccuracy when simulating them. Techniques such as super-heating or super-squeezing a material to induce a phase change suffer from inherent timescale limitations leading to ``over-driving,'' and dual-phase simulations require many long-time runs to seek out what frequently results in an inexact location of phase-coexistence. We present a compilation of methods for the determination of solid-solid and solid-liquid phase transition points through the accurate calculation of the chemical potential. The methods are applied to the Smith-Bharadwaj atomistic potential's representation of cyclotrimethylene trinitramine (RDX) to accurately determine its melting point (Tm) and the alpha to gamma solid phase transition pressure. We also determine Tm for a coarse-grain model of RDX, and compare its value to experiment and atomistic counterpart. All methods are employed via the LAMMPS simulator, resulting in 60-70 simulations that total 30-50 ns. Approved for public release. Distribution is unlimited.

  10. Nonisentropic unsteady three dimensional small disturbance potential theory

    NASA Technical Reports Server (NTRS)

    Gibbons, M. D.; Whitlow, W., Jr.; Williams, M. H.

    1986-01-01

    Modifications that allow for more accurate modeling of flow fields when strong shocks are present were made into three dimensional transonic small disturbance (TSD) potential theory. The Engquist-Osher type-dependent differencing was incorporated into the solution algorithm. The modified theory was implemented in the XTRAN3S computer code. Steady flows over a rectangular wing with a constant NACA 0012 airfoil section and an aspect ratio of 12 were calculated for freestream Mach numbers (M) of 0.82, 0.84, and 0.86. The obtained results are compared using the modified and unmodified TSD theories and the results from a three dimensional Euler code are presented. Nonunique solutions in three dimensions are shown to appear for the rectangular wing as aspect ratio increases. Steady and unsteady results are shown for the RAE tailplane model at M = 0.90. Calculations using unmodified theory, modified theory and experimental data are compared.

  11. Non-equilibrium steady-state distributions of colloids in a tilted periodic potential

    NASA Astrophysics Data System (ADS)

    Ma, Xiaoguang; Lai, Pik-Yin; Ackerson, Bruce; Tong, Penger

    A two-layer colloidal system is constructed to study the effects of the external force F on the non-equilibrium steady-state (NESS) dynamics of the diffusing particles over a tilted periodic potential, in which detailed balance is broken due to the presence of a steady particle flux. The periodic potential is provided by the bottom layer colloidal spheres forming a fixed crystalline pattern on a glass substrate. The corrugated surface of the bottom colloidal crystal provides a gravitational potential field for the top layer diffusing particles. By tilting the sample with respect to gravity, a tangential component F is applied to the diffusing particles. The measured NESS probability density function Pss (x , y) of the particles is found to deviate from the equilibrium distribution depending on the driving or distance from equilibrium. The experimental results are compared with the exact solution of the 1D Smoluchowski equation and the numerical results of the 2D Smoluchowski equation. Moreover, from the obtained exact 1D solution, we develop an analytical method to accurately extract the 1D potential U0 (x) from the measured Pss (x) . Work supported in part by the Research Grants Council of Hong Kong SAR.

  12. Accurate object tracking system by integrating texture and depth cues

    NASA Astrophysics Data System (ADS)

    Chen, Ju-Chin; Lin, Yu-Hang

    2016-03-01

    A robust object tracking system that is invariant to object appearance variations and background clutter is proposed. Multiple instance learning with a boosting algorithm is applied to select discriminant texture information between the object and background data. Additionally, depth information, which is important to distinguish the object from a complicated background, is integrated. We propose two depth-based models that can compensate texture information to cope with both appearance variants and background clutter. Moreover, in order to reduce the risk of drifting problem increased for the textureless depth templates, an update mechanism is proposed to select more precise tracking results to avoid incorrect model updates. In the experiments, the robustness of the proposed system is evaluated and quantitative results are provided for performance analysis. Experimental results show that the proposed system can provide the best success rate and has more accurate tracking results than other well-known algorithms.

  13. Estimating the Effective Permittivity for Reconstructing Accurate Microwave-Radar Images.

    PubMed

    Lavoie, Benjamin R; Okoniewski, Michal; Fear, Elise C

    2016-01-01

    We present preliminary results from a method for estimating the optimal effective permittivity for reconstructing microwave-radar images. Using knowledge of how microwave-radar images are formed, we identify characteristics that are typical of good images, and define a fitness function to measure the relative image quality. We build a polynomial interpolant of the fitness function in order to identify the most likely permittivity values of the tissue. To make the estimation process more efficient, the polynomial interpolant is constructed using a locally and dimensionally adaptive sampling method that is a novel combination of stochastic collocation and polynomial chaos. Examples, using a series of simulated, experimental and patient data collected using the Tissue Sensing Adaptive Radar system, which is under development at the University of Calgary, are presented. These examples show how, using our method, accurate images can be reconstructed starting with only a broad estimate of the permittivity range.

  14. Accurate oscillator strengths for interstellar ultraviolet lines of Cl I

    NASA Technical Reports Server (NTRS)

    Schectman, R. M.; Federman, S. R.; Beideck, D. J.; Ellis, D. J.

    1993-01-01

    Analyses on the abundance of interstellar chlorine rely on accurate oscillator strengths for ultraviolet transitions. Beam-foil spectroscopy was used to obtain f-values for the astrophysically important lines of Cl I at 1088, 1097, and 1347 A. In addition, the line at 1363 A was studied. Our f-values for 1088, 1097 A represent the first laboratory measurements for these lines; the values are f(1088)=0.081 +/- 0.007 (1 sigma) and f(1097) = 0.0088 +/- 0.0013 (1 sigma). These results resolve the issue regarding the relative strengths for 1088, 1097 A in favor of those suggested by astronomical measurements. For the other lines, our results of f(1347) = 0.153 +/- 0.011 (1 sigma) and f(1363) = 0.055 +/- 0.004 (1 sigma) are the most precisely measured values available. The f-values are somewhat greater than previous experimental and theoretical determinations.

  15. Is Cancer Information Exchanged on Social Media Scientifically Accurate?

    PubMed

    Gage-Bouchard, Elizabeth A; LaValley, Susan; Warunek, Molli; Beaupin, Lynda Kwon; Mollica, Michelle

    2017-07-19

    Cancer patients and their caregivers are increasingly using social media as a platform to share cancer experiences, connect with support, and exchange cancer-related information. Yet, little is known about the nature and scientific accuracy of cancer-related information exchanged on social media. We conducted a content analysis of 12 months of data from 18 publically available Facebook Pages hosted by parents of children with acute lymphoblastic leukemia (N = 15,852 posts) and extracted all exchanges of medically-oriented cancer information. We systematically coded for themes in the nature of cancer-related information exchanged on personal Facebook Pages and two oncology experts independently evaluated the scientific accuracy of each post. Of the 15,852 total posts, 171 posts contained medically-oriented cancer information. The most frequent type of cancer information exchanged was information related to treatment protocols and health services use (35%) followed by information related to side effects and late effects (26%), medication (16%), medical caregiving strategies (13%), alternative and complementary therapies (8%), and other (2%). Overall, 67% of all cancer information exchanged was deemed medically/scientifically accurate, 19% was not medically/scientifically accurate, and 14% described unproven treatment modalities. These findings highlight the potential utility of social media as a cancer-related resource, but also indicate that providers should focus on recommending reliable, evidence-based sources to patients and caregivers.

  16. Quasi-experimental study designs series-paper 9: collecting data from quasi-experimental studies.

    PubMed

    Aloe, Ariel M; Becker, Betsy Jane; Duvendack, Maren; Valentine, Jeffrey C; Shemilt, Ian; Waddington, Hugh

    2017-09-01

    To identify variables that must be coded when synthesizing primary studies that use quasi-experimental designs. All quasi-experimental (QE) designs. When designing a systematic review of QE studies, potential sources of heterogeneity-both theory-based and methodological-must be identified. We outline key components of inclusion criteria for syntheses of quasi-experimental studies. We provide recommendations for coding content-relevant and methodological variables and outlined the distinction between bivariate effect sizes and partial (i.e., adjusted) effect sizes. Designs used and controls used are viewed as of greatest importance. Potential sources of bias and confounding are also addressed. Careful consideration must be given to inclusion criteria and the coding of theoretical and methodological variables during the design phase of a synthesis of quasi-experimental studies. The success of the meta-regression analysis relies on the data available to the meta-analyst. Omission of critical moderator variables (i.e., effect modifiers) will undermine the conclusions of a meta-analysis. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. Efficient experimental design for uncertainty reduction in gene regulatory networks

    PubMed Central

    2015-01-01

    Background An accurate understanding of interactions among genes plays a major role in developing therapeutic intervention methods. Gene regulatory networks often contain a significant amount of uncertainty. The process of prioritizing biological experiments to reduce the uncertainty of gene regulatory networks is called experimental design. Under such a strategy, the experiments with high priority are suggested to be conducted first. Results The authors have already proposed an optimal experimental design method based upon the objective for modeling gene regulatory networks, such as deriving therapeutic interventions. The experimental design method utilizes the concept of mean objective cost of uncertainty (MOCU). MOCU quantifies the expected increase of cost resulting from uncertainty. The optimal experiment to be conducted first is the one which leads to the minimum expected remaining MOCU subsequent to the experiment. In the process, one must find the optimal intervention for every gene regulatory network compatible with the prior knowledge, which can be prohibitively expensive when the size of the network is large. In this paper, we propose a computationally efficient experimental design method. This method incorporates a network reduction scheme by introducing a novel cost function that takes into account the disruption in the ranking of potential experiments. We then estimate the approximate expected remaining MOCU at a lower computational cost using the reduced networks. Conclusions Simulation results based on synthetic and real gene regulatory networks show that the proposed approximate method has close performance to that of the optimal method but at lower computational cost. The proposed approximate method also outperforms the random selection policy significantly. A MATLAB software implementing the proposed experimental design method is available at http://gsp.tamu.edu/Publications/supplementary/roozbeh15a/. PMID:26423515

  18. Metabolite signal identification in accurate mass metabolomics data with MZedDB, an interactive m/z annotation tool utilising predicted ionisation behaviour 'rules'

    PubMed Central

    Draper, John; Enot, David P; Parker, David; Beckmann, Manfred; Snowdon, Stuart; Lin, Wanchang; Zubair, Hassan

    2009-01-01

    Background Metabolomics experiments using Mass Spectrometry (MS) technology measure the mass to charge ratio (m/z) and intensity of ionised molecules in crude extracts of complex biological samples to generate high dimensional metabolite 'fingerprint' or metabolite 'profile' data. High resolution MS instruments perform routinely with a mass accuracy of < 5 ppm (parts per million) thus providing potentially a direct method for signal putative annotation using databases containing metabolite mass information. Most database interfaces support only simple queries with the default assumption that molecules either gain or lose a single proton when ionised. In reality the annotation process is confounded by the fact that many ionisation products will be not only molecular isotopes but also salt/solvent adducts and neutral loss fragments of original metabolites. This report describes an annotation strategy that will allow searching based on all potential ionisation products predicted to form during electrospray ionisation (ESI). Results Metabolite 'structures' harvested from publicly accessible databases were converted into a common format to generate a comprehensive archive in MZedDB. 'Rules' were derived from chemical information that allowed MZedDB to generate a list of adducts and neutral loss fragments putatively able to form for each structure and calculate, on the fly, the exact molecular weight of every potential ionisation product to provide targets for annotation searches based on accurate mass. We demonstrate that data matrices representing populations of ionisation products generated from different biological matrices contain a large proportion (sometimes > 50%) of molecular isotopes, salt adducts and neutral loss fragments. Correlation analysis of ESI-MS data features confirmed the predicted relationships of m/z signals. An integrated isotope enumerator in MZedDB allowed verification of exact isotopic pattern distributions to corroborate experimental data

  19. Resonances for Symmetric Two-Barrier Potentials

    ERIC Educational Resources Information Center

    Fernandez, Francisco M.

    2011-01-01

    We describe a method for the accurate calculation of bound-state and resonance energies for one-dimensional potentials. We calculate the shape resonances for symmetric two-barrier potentials and compare them with those coming from the Siegert approximation, the complex scaling method and the box-stabilization method. A comparison of the…

  20. Rheology and Seismic Potential of Experimentally-Deformed Natural Serpentinites

    NASA Astrophysics Data System (ADS)

    Gasc, J.; Hilairet, N.; Wang, Y.; Yu, T.; Ferrand, T. P.; Schubnel, A.

    2016-12-01

    The origin of intermediate-depth earthquakes, which occur at depths of 60-300 km along subducting slabs, remains somehow enigmatic. In the pressure and temperature conditions involved, rocks should indeed deform in a ductile fashion. One, or more, mechanism is therefore responsible for mechanical instabilities. Dehydration embrittlement, due to serpentine breakdown, was long considered a good candidate. However, in recent years, experimental studies have challenged this theory, by showing that deformation and faulting of serpentinites, related to dehydration, occurs in a stable and aseismic way (Chernak and Hirth, 2011; Gasc et al., 2011). In order to assess the seismic potential of serpentinites, high pressure deformation experiments were carried out on natural samples, during which micro-seismicity was monitored by recording Acoustic Emissions (AE's). Deformation was performed at pressures of 3-5 GPa, using a Deformation-DIA device, and over a wide range of temperatures, both within and outside antigorite's stability field. The results show that, below 400 C, serpentinite deformation involves aseismic semi-brittle mechanisms, even in cases where strain localization is observed. At high temperature (i.e., above 600 C), despite conditions propitious to dehydration embrittlement (i.e., with fast strain rates and reaction kinetics), joint deformation and dehydration leads to ductile shear, without generation of AE's. On the other hand, a brittle temperature window, centered at ca. 500 C, is evidenced. In this latter case, AE's are consistently collected upon deformation and faulting with extremely sharp strain localization is observed. This brittle field may therefore be a source of seismicity in subducting slabs at mantle pressures. However, analysis of the acoustic signal shows that it is relatively orders of magnitude weaker than its real-earth counterparts, which suggests that other mechanisms are responsible for larger intermediate-depth earthquakes. In fact

  1. An accurate fatigue damage model for welded joints subjected to variable amplitude loading

    NASA Astrophysics Data System (ADS)

    Aeran, A.; Siriwardane, S. C.; Mikkelsen, O.; Langen, I.

    2017-12-01

    Researchers in the past have proposed several fatigue damage models to overcome the shortcomings of the commonly used Miner’s rule. However, requirements of material parameters or S-N curve modifications restricts their practical applications. Also, application of most of these models under variable amplitude loading conditions have not been found. To overcome these restrictions, a new fatigue damage model is proposed in this paper. The proposed model can be applied by practicing engineers using only the S-N curve given in the standard codes of practice. The model is verified with experimentally derived damage evolution curves for C 45 and 16 Mn and gives better agreement compared to previous models. The model predicted fatigue lives are also in better correlation with experimental results compared to previous models as shown in earlier published work by the authors. The proposed model is applied to welded joints subjected to variable amplitude loadings in this paper. The model given around 8% shorter fatigue lives compared to Eurocode given Miner’s rule. This shows the importance of applying accurate fatigue damage models for welded joints.

  2. Accurate band-to-band registration of AOTF imaging spectrometer using motion detection technology

    NASA Astrophysics Data System (ADS)

    Zhou, Pengwei; Zhao, Huijie; Jin, Shangzhong; Li, Ningchuan

    2016-05-01

    This paper concerns the problem of platform vibration induced band-to-band misregistration with acousto-optic imaging spectrometer in spaceborne application. Registrating images of different bands formed at different time or different position is difficult, especially for hyperspectral images form acousto-optic tunable filter (AOTF) imaging spectrometer. In this study, a motion detection method is presented using the polychromatic undiffracted beam of AOTF. The factors affecting motion detect accuracy are analyzed theoretically, and calculations show that optical distortion is an easily overlooked factor to achieve accurate band-to-band registration. Hence, a reflective dual-path optical system has been proposed for the first time, with reduction of distortion and chromatic aberration, indicating the potential of higher registration accuracy. Consequently, a spectra restoration experiment using additional motion detect channel is presented for the first time, which shows the accurate spectral image registration capability of this technique.

  3. A Combined Experimental and Computational Study on Selected Physical Properties of Aminosilicones

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Perry, RJ; Genovese, SE; Farnum, RL

    2014-01-29

    A number of physical properties of aminosilicones have been determined experimentally and predicted computationally. It was found that COSMO-RS predicted the densities of the materials under study to within about 4% of the experimentally determined values. Vapor pressure measurements were performed, and all of the aminosilicones of interest were found to be significantly less volatile than the benchmark MEA material. COSMO-RS was reasonably accurate for predicting the vapor pressures for aminosilicones that were thermally stable. The heat capacities of all aminosilicones tested were between 2.0 and 2.3 J/(g.degrees C); again substantially lower than a benchmark 30% aqueous MEA solution. Surfacemore » energies for the aminosilicones were found to be 23.3-28.3 dyne/cm and were accurately predicted using the parachor method.« less

  4. Fast and accurate reference-free alignment of subtomograms.

    PubMed

    Chen, Yuxiang; Pfeffer, Stefan; Hrabe, Thomas; Schuller, Jan Michael; Förster, Friedrich

    2013-06-01

    In cryoelectron tomography alignment and averaging of subtomograms, each dnepicting the same macromolecule, improves the resolution compared to the individual subtomogram. Major challenges of subtomogram alignment are noise enhancement due to overfitting, the bias of an initial reference in the iterative alignment process, and the computational cost of processing increasingly large amounts of data. Here, we propose an efficient and accurate alignment algorithm via a generalized convolution theorem, which allows computation of a constrained correlation function using spherical harmonics. This formulation increases computational speed of rotational matching dramatically compared to rotation search in Cartesian space without sacrificing accuracy in contrast to other spherical harmonic based approaches. Using this sampling method, a reference-free alignment procedure is proposed to tackle reference bias and overfitting, which also includes contrast transfer function correction by Wiener filtering. Application of the method to simulated data allowed us to obtain resolutions near the ground truth. For two experimental datasets, ribosomes from yeast lysate and purified 20S proteasomes, we achieved reconstructions of approximately 20Å and 16Å, respectively. The software is ready-to-use and made public to the community. Copyright © 2013 Elsevier Inc. All rights reserved.

  5. Sequential experimental design based generalised ANOVA

    NASA Astrophysics Data System (ADS)

    Chakraborty, Souvik; Chowdhury, Rajib

    2016-07-01

    Over the last decade, surrogate modelling technique has gained wide popularity in the field of uncertainty quantification, optimization, model exploration and sensitivity analysis. This approach relies on experimental design to generate training points and regression/interpolation for generating the surrogate. In this work, it is argued that conventional experimental design may render a surrogate model inefficient. In order to address this issue, this paper presents a novel distribution adaptive sequential experimental design (DA-SED). The proposed DA-SED has been coupled with a variant of generalised analysis of variance (G-ANOVA), developed by representing the component function using the generalised polynomial chaos expansion. Moreover, generalised analytical expressions for calculating the first two statistical moments of the response, which are utilized in predicting the probability of failure, have also been developed. The proposed approach has been utilized in predicting probability of failure of three structural mechanics problems. It is observed that the proposed approach yields accurate and computationally efficient estimate of the failure probability.

  6. An X-band waveguide measurement technique for the accurate characterization of materials with low dielectric loss permittivity

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Allen, Kenneth W., E-mail: kenneth.allen@gtri.gatech.edu; Scott, Mark M.; Reid, David R.

    In this work, we present a new X-band waveguide (WR90) measurement method that permits the broadband characterization of the complex permittivity for low dielectric loss tangent material specimens with improved accuracy. An electrically long polypropylene specimen that partially fills the cross-section is inserted into the waveguide and the transmitted scattering parameter (S{sub 21}) is measured. The extraction method relies on computational electromagnetic simulations, coupled with a genetic algorithm, to match the experimental S{sub 21} measurement. The sensitivity of the technique to sample length was explored by simulating specimen lengths from 2.54 to 15.24 cm, in 2.54 cm increments. Analysis ofmore » our simulated data predicts the technique will have the sensitivity to measure loss tangent values on the order of 10{sup −3} for materials such as polymers with relatively low real permittivity values. The ability to accurately characterize low-loss dielectric material specimens of polypropylene is demonstrated experimentally. The method was validated by excellent agreement with a free-space focused-beam system measurement of a polypropylene sheet. This technique provides the material measurement community with the ability to accurately extract material properties of low-loss material specimen over the entire X-band range. This technique could easily be extended to other frequency bands.« less

  7. An accurate and efficient method for evaluating the kernel of the integral equation relating pressure to normalwash in unsteady potential flow

    NASA Technical Reports Server (NTRS)

    Desmarais, R. N.

    1982-01-01

    This paper describes an accurate economical method for generating approximations to the kernel of the integral equation relating unsteady pressure to normalwash in nonplanar flow. The method is capable of generating approximations of arbitrary accuracy. It is based on approximating the algebraic part of the non elementary integrals in the kernel by exponential approximations and then integrating termwise. The exponent spacing in the approximation is a geometric sequence. The coefficients and exponent multiplier of the exponential approximation are computed by least squares so the method is completely automated. Exponential approximates generated in this manner are two orders of magnitude more accurate than the exponential approximation that is currently most often used for this purpose. Coefficients for 8, 12, 24, and 72 term approximations are tabulated in the report. Also, since the method is automated, it can be used to generate approximations to attain any desired trade-off between accuracy and computing cost.

  8. Integrated experimental and theoretical approach for the structural characterization of Hg2+ aqueous solutions

    NASA Astrophysics Data System (ADS)

    D'Angelo, Paola; Migliorati, Valentina; Mancini, Giordano; Barone, Vincenzo; Chillemi, Giovanni

    2008-02-01

    The structural and dynamic properties of the solvated Hg2+ ion in aqueous solution have been investigated by a combined experimental-theoretical approach employing x-ray absorption spectroscopy and molecular dynamics (MD) simulations. This method allows one to perform a quantitative analysis of the x-ray absorption near-edge structure (XANES) spectra of ionic solutions using a proper description of the thermal and structural fluctuations. XANES spectra have been computed starting from the MD trajectory, without carrying out any minimization in the structural parameter space. The XANES experimental data are accurately reproduced by a first-shell heptacoordinated cluster only if the second hydration shell is included in the calculations. These results confirm at the same time the existence of a sevenfold first hydration shell for the Hg2+ ion in aqueous solution and the reliability of the potentials used in the MD simulations. The combination of MD and XANES is found to be very helpful to get important new insights into the quantitative estimation of structural properties of disordered systems.

  9. s -wave scattering length of a Gaussian potential

    NASA Astrophysics Data System (ADS)

    Jeszenszki, Peter; Cherny, Alexander Yu.; Brand, Joachim

    2018-04-01

    We provide accurate expressions for the s -wave scattering length for a Gaussian potential well in one, two, and three spatial dimensions. The Gaussian potential is widely used as a pseudopotential in the theoretical description of ultracold-atomic gases, where the s -wave scattering length is a physically relevant parameter. We first describe a numerical procedure to compute the value of the s -wave scattering length from the parameters of the Gaussian, but find that its accuracy is limited in the vicinity of singularities that result from the formation of new bound states. We then derive simple analytical expressions that capture the correct asymptotic behavior of the s -wave scattering length near the bound states. Expressions that are increasingly accurate in wide parameter regimes are found by a hierarchy of approximations that capture an increasing number of bound states. The small number of numerical coefficients that enter these expressions is determined from accurate numerical calculations. The approximate formulas combine the advantages of the numerical and approximate expressions, yielding an accurate and simple description from the weakly to the strongly interacting limit.

  10. Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions

    PubMed Central

    2016-01-01

    Almost 50 years have passed from the first computer simulations of water, and a large number of molecular models have been proposed since then to elucidate the unique behavior of water across different phases. In this article, we review the recent progress in the development of analytical potential energy functions that aim at correctly representing many-body effects. Starting from the many-body expansion of the interaction energy, specific focus is on different classes of potential energy functions built upon a hierarchy of approximations and on their ability to accurately reproduce reference data obtained from state-of-the-art electronic structure calculations and experimental measurements. We show that most recent potential energy functions, which include explicit short-range representations of two-body and three-body effects along with a physically correct description of many-body effects at all distances, predict the properties of water from the gas to the condensed phase with unprecedented accuracy, thus opening the door to the long-sought “universal model” capable of describing the behavior of water under different conditions and in different environments. PMID:27186804

  11. CALCULATED MOLECULAR STRUCTURES AND POTENTIAL ENERGY FUNCTIONS OF PAHS WITH METHYL CROWDING IN THE BAY REGION AND THEIR METABOLITES: COMPARISON TO EXPERIMENTAL STRUCTURES

    EPA Science Inventory

    Calculated molecular structures and potential energy functions ofP AHs with methyl crowding in the bay region and their metabolites: Comparison to experimental structures

    PAHs with methyl group substitution near a bay region represent a class of chemicals associated with ...

  12. CALCULATED MOLECULAR STRUCTURES AND POTENTIAL ENERGY FUNCTIONS OF PAHS WITH METHYL CROWDING IN THE BAY REGION AND THEIR METABOLITES: COMPARISON TO EXPERIMENTAL STRUCTURES

    EPA Science Inventory

    Abstract Title: Calculated molecular structures and potential energy functions of P AHs with methyl crowding in the bay region and their metabolites: Comparison to experimental structures.

    Abstract:
    PAHs with methyl group substitution near a bay region represent a cl...

  13. Highly accurate surface maps from profilometer measurements

    NASA Astrophysics Data System (ADS)

    Medicus, Kate M.; Nelson, Jessica D.; Mandina, Mike P.

    2013-04-01

    Many aspheres and free-form optical surfaces are measured using a single line trace profilometer which is limiting because accurate 3D corrections are not possible with the single trace. We show a method to produce an accurate fully 2.5D surface height map when measuring a surface with a profilometer using only 6 traces and without expensive hardware. The 6 traces are taken at varying angular positions of the lens, rotating the part between each trace. The output height map contains low form error only, the first 36 Zernikes. The accuracy of the height map is ±10% of the actual Zernike values and within ±3% of the actual peak to valley number. The calculated Zernike values are affected by errors in the angular positioning, by the centering of the lens, and to a small effect, choices made in the processing algorithm. We have found that the angular positioning of the part should be better than 1?, which is achievable with typical hardware. The centering of the lens is essential to achieving accurate measurements. The part must be centered to within 0.5% of the diameter to achieve accurate results. This value is achievable with care, with an indicator, but the part must be edged to a clean diameter.

  14. A facile electrode preparation method for accurate electrochemical measurements of double-side-coated electrode from commercial Li-ion batteries

    NASA Astrophysics Data System (ADS)

    Zhou, Ge; Wang, Qiyu; Wang, Shuo; Ling, Shigang; Zheng, Jieyun; Yu, Xiqian; Li, Hong

    2018-04-01

    The post mortem electrochemical analysis, including charge-discharge and electrochemical impedance spectroscopy (EIS) measurements, are critical steps for revealing the failure mechanisms of commercial lithium-ion batteries (LIBs). These post measurements usually require the reassembling of coin-cell with electrode which is often double-side-coated in commercial LIBs. It is difficult to use such double-side-coated electrode to perform accurate electrochemical measurements because the back side of the electrode is coated with active materials, rather than single-side-coated electrode that is often used in coin-cell measurements. In this study, we report a facile tape-covering sample preparation method, which can effectively suppress the influence of back side of the double-side-coated electrodes on capacity and EIS measurements in coin-cells. By tape-covering the unwanted side, the areal capacity of the desired investigated side of the electrode has been accurately measured with an experimental error of about 0.5% at various current densities, and accurate EIS measurements and analysis have been conducted as well.

  15. Accurate transport properties for H–CO and H–CO{sub 2}

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Dagdigian, Paul J., E-mail: pjdagdigian@jhu.edu

    2015-08-07

    Transport properties for collisions of hydrogen atoms with CO and CO{sub 2} have been computed by means of quantum scattering calculations. The carbon oxides are important species in hydrocarbon combustion. The following potential energy surfaces (PES’s) for the interaction of the molecule fixed in its equilibrium geometry were employed: for H–CO, the PES was taken from the work of Song et al. [J. Phys. Chem. A 117, 7571 (2013)], while the PES for H–CO{sub 2} was computed in this study by a restricted coupled cluster method that included single, double, and (perturbatively) triple excitations. The computed transport properties were foundmore » to be significantly different from those computed by the conventional approach that employs isotropic Lennard-Jones (12-6) potentials. The effect of using the presently computed accurate transport properties in 1-dimensional combustion simulations of methane-air flames was investigated.« less

  16. Statically screened ion potential and Bohm potential in a quantum plasma

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Moldabekov, Zhandos; Institute for Experimental and Theoretical Physics, Al-Farabi Kazakh National University, 71 Al-Farabi Str., 050040 Almaty; Schoof, Tim

    2015-10-15

    The effective potential Φ of a classical ion in a weakly correlated quantum plasma in thermodynamic equilibrium at finite temperature is well described by the random phase approximation screened Coulomb potential. Additionally, collision effects can be included via a relaxation time ansatz (Mermin dielectric function). These potentials are used to study the quality of various statically screened potentials that were recently proposed by Shukla and Eliasson (SE) [Phys. Rev. Lett. 108, 165007 (2012)], Akbari-Moghanjoughi (AM) [Phys. Plasmas 22, 022103 (2015)], and Stanton and Murillo (SM) [Phys. Rev. E 91, 033104 (2015)] starting from quantum hydrodynamic (QHD) theory. Our analysis revealsmore » that the SE potential is qualitatively different from the full potential, whereas the SM potential (at any temperature) and the AM potential (at zero temperature) are significantly more accurate. This confirms the correctness of the recently derived [Michta et al., Contrib. Plasma Phys. 55, 437 (2015)] pre-factor 1/9 in front of the Bohm term of QHD for fermions.« less

  17. Novel serologic biomarkers provide accurate estimates of recent Plasmodium falciparum exposure for individuals and communities

    PubMed Central

    Helb, Danica A.; Tetteh, Kevin K. A.; Felgner, Philip L.; Skinner, Jeff; Hubbard, Alan; Arinaitwe, Emmanuel; Mayanja-Kizza, Harriet; Ssewanyana, Isaac; Kamya, Moses R.; Beeson, James G.; Tappero, Jordan; Smith, David L.; Crompton, Peter D.; Rosenthal, Philip J.; Dorsey, Grant; Drakeley, Christopher J.; Greenhouse, Bryan

    2015-01-01

    Tools to reliably measure Plasmodium falciparum (Pf) exposure in individuals and communities are needed to guide and evaluate malaria control interventions. Serologic assays can potentially produce precise exposure estimates at low cost; however, current approaches based on responses to a few characterized antigens are not designed to estimate exposure in individuals. Pf-specific antibody responses differ by antigen, suggesting that selection of antigens with defined kinetic profiles will improve estimates of Pf exposure. To identify novel serologic biomarkers of malaria exposure, we evaluated responses to 856 Pf antigens by protein microarray in 186 Ugandan children, for whom detailed Pf exposure data were available. Using data-adaptive statistical methods, we identified combinations of antibody responses that maximized information on an individual’s recent exposure. Responses to three novel Pf antigens accurately classified whether an individual had been infected within the last 30, 90, or 365 d (cross-validated area under the curve = 0.86–0.93), whereas responses to six antigens accurately estimated an individual’s malaria incidence in the prior year. Cross-validated incidence predictions for individuals in different communities provided accurate stratification of exposure between populations and suggest that precise estimates of community exposure can be obtained from sampling a small subset of that community. In addition, serologic incidence predictions from cross-sectional samples characterized heterogeneity within a community similarly to 1 y of continuous passive surveillance. Development of simple ELISA-based assays derived from the successful selection strategy outlined here offers the potential to generate rich epidemiologic surveillance data that will be widely accessible to malaria control programs. PMID:26216993

  18. Novel serologic biomarkers provide accurate estimates of recent Plasmodium falciparum exposure for individuals and communities.

    PubMed

    Helb, Danica A; Tetteh, Kevin K A; Felgner, Philip L; Skinner, Jeff; Hubbard, Alan; Arinaitwe, Emmanuel; Mayanja-Kizza, Harriet; Ssewanyana, Isaac; Kamya, Moses R; Beeson, James G; Tappero, Jordan; Smith, David L; Crompton, Peter D; Rosenthal, Philip J; Dorsey, Grant; Drakeley, Christopher J; Greenhouse, Bryan

    2015-08-11

    Tools to reliably measure Plasmodium falciparum (Pf) exposure in individuals and communities are needed to guide and evaluate malaria control interventions. Serologic assays can potentially produce precise exposure estimates at low cost; however, current approaches based on responses to a few characterized antigens are not designed to estimate exposure in individuals. Pf-specific antibody responses differ by antigen, suggesting that selection of antigens with defined kinetic profiles will improve estimates of Pf exposure. To identify novel serologic biomarkers of malaria exposure, we evaluated responses to 856 Pf antigens by protein microarray in 186 Ugandan children, for whom detailed Pf exposure data were available. Using data-adaptive statistical methods, we identified combinations of antibody responses that maximized information on an individual's recent exposure. Responses to three novel Pf antigens accurately classified whether an individual had been infected within the last 30, 90, or 365 d (cross-validated area under the curve = 0.86-0.93), whereas responses to six antigens accurately estimated an individual's malaria incidence in the prior year. Cross-validated incidence predictions for individuals in different communities provided accurate stratification of exposure between populations and suggest that precise estimates of community exposure can be obtained from sampling a small subset of that community. In addition, serologic incidence predictions from cross-sectional samples characterized heterogeneity within a community similarly to 1 y of continuous passive surveillance. Development of simple ELISA-based assays derived from the successful selection strategy outlined here offers the potential to generate rich epidemiologic surveillance data that will be widely accessible to malaria control programs.

  19. A model-updating procedure to stimulate piezoelectric transducers accurately.

    PubMed

    Piranda, B; Ballandras, S; Steichen, W; Hecart, B

    2001-09-01

    The use of numerical calculations based on finite element methods (FEM) has yielded significant improvements in the simulation and design of piezoelectric transducers piezoelectric transducer utilized in acoustic imaging. However, the ultimate precision of such models is directly controlled by the accuracy of material characterization. The present work is dedicated to the development of a model-updating technique adapted to the problem of piezoelectric transducer. The updating process is applied using the experimental admittance of a given structure for which a finite element analysis is performed. The mathematical developments are reported and then applied to update the entries of a FEM of a two-layer structure (a PbZrTi-PZT-ridge glued on a backing) for which measurements were available. The efficiency of the proposed approach is demonstrated, yielding the definition of a new set of constants well adapted to predict the structure response accurately. Improvement of the proposed approach, consisting of the updating of material coefficients not only on the admittance but also on the impedance data, is finally discussed.

  20. Concurrent and Accurate Short Read Mapping on Multicore Processors.

    PubMed

    Martínez, Héctor; Tárraga, Joaquín; Medina, Ignacio; Barrachina, Sergio; Castillo, Maribel; Dopazo, Joaquín; Quintana-Ortí, Enrique S

    2015-01-01

    We introduce a parallel aligner with a work-flow organization for fast and accurate mapping of RNA sequences on servers equipped with multicore processors. Our software, HPG Aligner SA (HPG Aligner SA is an open-source application. The software is available at http://www.opencb.org, exploits a suffix array to rapidly map a large fraction of the RNA fragments (reads), as well as leverages the accuracy of the Smith-Waterman algorithm to deal with conflictive reads. The aligner is enhanced with a careful strategy to detect splice junctions based on an adaptive division of RNA reads into small segments (or seeds), which are then mapped onto a number of candidate alignment locations, providing crucial information for the successful alignment of the complete reads. The experimental results on a platform with Intel multicore technology report the parallel performance of HPG Aligner SA, on RNA reads of 100-400 nucleotides, which excels in execution time/sensitivity to state-of-the-art aligners such as TopHat 2+Bowtie 2, MapSplice, and STAR.

  1. Highly accurate symplectic element based on two variational principles

    NASA Astrophysics Data System (ADS)

    Qing, Guanghui; Tian, Jia

    2018-02-01

    For the stability requirement of numerical resultants, the mathematical theory of classical mixed methods are relatively complex. However, generalized mixed methods are automatically stable, and their building process is simple and straightforward. In this paper, based on the seminal idea of the generalized mixed methods, a simple, stable, and highly accurate 8-node noncompatible symplectic element (NCSE8) was developed by the combination of the modified Hellinger-Reissner mixed variational principle and the minimum energy principle. To ensure the accuracy of in-plane stress results, a simultaneous equation approach was also suggested. Numerical experimentation shows that the accuracy of stress results of NCSE8 are nearly the same as that of displacement methods, and they are in good agreement with the exact solutions when the mesh is relatively fine. NCSE8 has advantages of the clearing concept, easy calculation by a finite element computer program, higher accuracy and wide applicability for various linear elasticity compressible and nearly incompressible material problems. It is possible that NCSE8 becomes even more advantageous for the fracture problems due to its better accuracy of stresses.

  2. Accurate paleointensities - the multi-method approach

    NASA Astrophysics Data System (ADS)

    de Groot, Lennart

    2016-04-01

    The accuracy of models describing rapid changes in the geomagnetic field over the past millennia critically depends on the availability of reliable paleointensity estimates. Over the past decade methods to derive paleointensities from lavas (the only recorder of the geomagnetic field that is available all over the globe and through geologic times) have seen significant improvements and various alternative techniques were proposed. The 'classical' Thellier-style approach was optimized and selection criteria were defined in the 'Standard Paleointensity Definitions' (Paterson et al, 2014). The Multispecimen approach was validated and the importance of additional tests and criteria to assess Multispecimen results must be emphasized. Recently, a non-heating, relative paleointensity technique was proposed -the pseudo-Thellier protocol- which shows great potential in both accuracy and efficiency, but currently lacks a solid theoretical underpinning. Here I present work using all three of the aforementioned paleointensity methods on suites of young lavas taken from the volcanic islands of Hawaii, La Palma, Gran Canaria, Tenerife, and Terceira. Many of the sampled cooling units are <100 years old, the actual field strength at the time of cooling is therefore reasonably well known. Rather intuitively, flows that produce coherent results from two or more different paleointensity methods yield the most accurate estimates of the paleofield. Furthermore, the results for some flows pass the selection criteria for one method, but fail in other techniques. Scrutinizing and combing all acceptable results yielded reliable paleointensity estimates for 60-70% of all sampled cooling units - an exceptionally high success rate. This 'multi-method paleointensity approach' therefore has high potential to provide the much-needed paleointensities to improve geomagnetic field models for the Holocene.

  3. Experimental Study of the NaK 3 1Π State

    NASA Astrophysics Data System (ADS)

    Laub, E.; Mazsa, I.; Webb, S. C.; La Civita, J.; Prodan, I.; Jabbour, Z. J.; Namiotka, R. K.; Huennekens, J.

    1999-02-01

    We report the results of an optical-optical double resonance experiment to determine the NaK 31Π state potential energy curve. In the first step, a narrow band cw dye laser (PUMP) is tuned to line center of a particular 2(A)1Σ+(v‧,J‧) ← 1(X)1Σ+(v",J") transition, and its frequency is then fixed. A second narrowband tunable cw Ti:Sapphirelaser (PROBE) is then scanned, while 31Π → 1(X)1Σ+violet fluorescence is monitored. The Doppler-free signals accurately map the 31Π(v,J) ro-vibrational energy levels. These energy levels are then fit to a Dunham expansion to provide a set of molecular constants. The Dunham constants, in turn, are used to construct an RKR potential curve. Resolved 31Π(v,J) → 1(X)1Σ+(v",J") fluorescence scans are also recorded with both PUMP and PROBE laser frequencies fixed. Comparison between observed and calculated Franck-Condon factors is used to determine the absolute vibrational numbering of the 31Π state levels and to determine the variation of the 31Π → 1(X)1Σ+transitiondipole moment with internuclear separation. The recent theoretical calculation of the NaK 31Π state potential reported by Magnier and Millié (1996,Phys. Rev. A54, 204) is in excellent agreement with the present experimental RKR curve.

  4. An Accurate Projector Calibration Method Based on Polynomial Distortion Representation

    PubMed Central

    Liu, Miao; Sun, Changku; Huang, Shujun; Zhang, Zonghua

    2015-01-01

    In structure light measurement systems or 3D printing systems, the errors caused by optical distortion of a digital projector always affect the precision performance and cannot be ignored. Existing methods to calibrate the projection distortion rely on calibration plate and photogrammetry, so the calibration performance is largely affected by the quality of the plate and the imaging system. This paper proposes a new projector calibration approach that makes use of photodiodes to directly detect the light emitted from a digital projector. By analyzing the output sequence of the photoelectric module, the pixel coordinates can be accurately obtained by the curve fitting method. A polynomial distortion representation is employed to reduce the residuals of the traditional distortion representation model. Experimental results and performance evaluation show that the proposed calibration method is able to avoid most of the disadvantages in traditional methods and achieves a higher accuracy. This proposed method is also practically applicable to evaluate the geometric optical performance of other optical projection system. PMID:26492247

  5. Experimental and theoretical kinetics for the H2O+ + H2/D2 → H3O+/H2DO+ + H/D reactions: observation of the rotational effect in the temperature dependence.

    PubMed

    Ard, Shaun G; Li, Anyang; Martinez, Oscar; Shuman, Nicholas S; Viggiano, Albert A; Guo, Hua

    2014-12-11

    Thermal rate coefficients for the title reactions computed using a quasi-classical trajectory method on an accurate global potential energy surface fitted to ∼81,000 high-level ab initio points are compared with experimental values measured between 100 and 600 K using a variable temperature selected ion flow tube instrument. Excellent agreement is found across the entire temperature range, showing a subtle, but unusual temperature dependence of the rate coefficients. For both reactions the temperature dependence has a maximum around 350 K, which is a result of H2O(+) rotations increasing the reactivity, while kinetic energy is decreasing the reactivity. A strong isotope effect is found, although the calculations slightly overestimate the kinetic isotope effect. The good experiment-theory agreement not only validates the accuracy of the potential energy surface but also provides more accurate kinetic data over a large temperature range.

  6. Branch and bound algorithm for accurate estimation of analytical isotropic bidirectional reflectance distribution function models.

    PubMed

    Yu, Chanki; Lee, Sang Wook

    2016-05-20

    We present a reliable and accurate global optimization framework for estimating parameters of isotropic analytical bidirectional reflectance distribution function (BRDF) models. This approach is based on a branch and bound strategy with linear programming and interval analysis. Conventional local optimization is often very inefficient for BRDF estimation since its fitting quality is highly dependent on initial guesses due to the nonlinearity of analytical BRDF models. The algorithm presented in this paper employs L1-norm error minimization to estimate BRDF parameters in a globally optimal way and interval arithmetic to derive our feasibility problem and lower bounding function. Our method is developed for the Cook-Torrance model but with several normal distribution functions such as the Beckmann, Berry, and GGX functions. Experiments have been carried out to validate the presented method using 100 isotropic materials from the MERL BRDF database, and our experimental results demonstrate that the L1-norm minimization provides a more accurate and reliable solution than the L2-norm minimization.

  7. All-dimensional H2-CO potential: Validation with fully quantum second virial coefficients.

    PubMed

    Garberoglio, Giovanni; Jankowski, Piotr; Szalewicz, Krzysztof; Harvey, Allan H

    2017-02-07

    We use a new high-accuracy all-dimensional potential to compute the cross second virial coefficient B 12 (T) between molecular hydrogen and carbon monoxide. The path-integral method is used to fully account for quantum effects. Values are calculated from 10 K to 2000 K and the uncertainty of the potential is propagated into uncertainties of B 12 . Our calculated B 12 (T) are in excellent agreement with most of the limited experimental data available, but cover a much wider range of temperatures and have lower uncertainties. Similar to recently reported findings from scattering calculations, we find that the reduced-dimensionality potential obtained by averaging over the rovibrational motion of the monomers gives results that are a good approximation to those obtained when flexibility is fully taken into account. Also, the four-dimensional approximation with monomers taken at their vibrationally averaged bond lengths works well. This finding is important, since full-dimensional potentials are difficult to develop even for triatomic monomers and are not currently possible to obtain for larger molecules. Likewise, most types of accurate quantum mechanical calculations, e.g., spectral or scattering, are severely limited in the number of dimensions that can be handled.

  8. Leaf water potentials measured with a pressure chamber.

    PubMed

    Boyer, J S

    1967-01-01

    Leaf water potentials were estimated from the sum of the balancing pressure measured with a pressure chamber and the osmotic potential of the xylem sap in leafy shoots or leaves. When leaf water potentials in yew, rhododendron, and sunflower were compared with those measured with a thermocouple psychrometer known to indicate accurate values of leaf water potential, determinations were within +/- 2 bars of the psychrometer measurements with sunflower and yew. In rhododendron. water potentials measured with the pressure chamber plus xylem sap were 2.5 bars less negative to 4 bars more negative than psychrometer measurements.The discrepancies in the rhododendron measurements could be attributed, at least in part, to the filling of tissues other than xylem with xylem sap during measurements with the pressure chamber. It was concluded that, although stem characteristics may affect the measurements, pressure chamber determinations were sufficiently close to psychrometer measurements that the pressure chamber may be used for relative measurements of leaf water potentials, especially in sunflower and yew. For accurate determinations of leaf water potential, however, pressure chamber measurements must be calibrated with a thermocouple psychrometer.

  9. Ab initio ground and excited state potential energy surfaces for NO-Kr complex and dynamics of Kr solids with NO impurity

    NASA Astrophysics Data System (ADS)

    Castro-Palacios, Juan Carlos; Rubayo-Soneira, Jesús; Ishii, Keisaku; Yamashita, Koichi

    2007-04-01

    The intermolecular potentials for the NO(XΠ2)-Kr and NO(AΣ+2)-Kr systems have been calculated using highly accurate ab initio calculations. The spin-restricted coupled cluster method for the ground 1A'2 state [NO(XΠ2)-Kr ] and the multireference singles and doubles configuration interaction method for the excited 2A'2 state [NO(AΣ+2)-Kr], respectively, were used. The potential energy surfaces (PESs) show two linear wells and one that is almost in the perpendicular position. An analytical representation of the PESs has been constructed for the triatomic systems and used to carry out molecular dynamics (MD) simulations of the NO-doped krypton matrix response after excitation of NO. MD results are shown comparatively for three sets of potentials: (1) anisotropic ab initio potentials [NO molecule direction fixed during the dynamics and considered as a point (its center of mass)], (2) isotropic ab initio potentials (isotropic part in a Legendre polynomial expansion of the PESs), and (3) fitted Kr-NO potentials to the spectroscopic data. An important finding of this work is that the anisotropic and isotropic ab initio potentials calculated for the Kr-NO triatomic system are not suitable for describing the dynamics of structural relaxation upon Rydberg excitation of a NO impurity in the crystal. However, the isotropic ab initio potential in the ground state almost overlaps the published experimental potential, being almost independent of the angle asymmetry. This fact is also manifested in the radial distribution function around NO. However, in the case of the excited state the isotropic ab initio potential differs from the fitted potentials, which indicates that the Kr-NO interaction in the matrix is quite different because of the presence of the surrounding Kr atoms acting on the NO molecule. MD simulations for isotropic potentials reasonably reproduce the experimental observables for the femtosecond response and the bubble size but do not match spectroscopic

  10. DFT study on the standard electrode potentials of imidazole, tetrathiafulvalene, and tetrathiafulvalene-imidazole.

    PubMed

    Tugsuz, Tugba

    2010-12-30

    Extensive DFT calculations on the standard electrode potentials of imidazole (Im), tetrathiafulvalene (TTF), and 2-, 4-, and 5-TTF-Im were carried out. Geometries and Gibbs free energies of H-bonded dimer, anion, protonated cation, and neutral structures of Im, mono- and dication, and neutral structures of TTF in gas and acetonitrile solvent were computed by using 10 hybrid density functionals (B3LYP, TPSSH, PBEH1PBE, M06, M062X, X3LYP, BMK, B1B95, M05, M052X) combined with the TZVP basis set. CPCM and SMD solvation models were applied to predict the Gibbs free energies of molecules in acetonitrile solvent. Frequency calculations were carried out for all structures, and none of them has been found to exhibit any imaginary frequency. Finally, the BMK hybrid functional was selected for computation of the standard electrode potential of TTF-Im, because it gives the most accurate values in both Im and TTF, differing by 0.05 V from the experimental ones. Moreover, frequencies from the BMK functional are reasonably close to the experimental ones. The standard electrode potentials of 2-, 4-, and 5-TTF-Im predicted for two-electron oxidation are 0.946, 0.870, and 0.839 V in CPCM and 0.927, 0.866, and 0.824 V in SMD. For one-electron oxidation these are 0.491, 0.421, and 0.400 V in CPCM and 0.476, 0.377, and 0.360 V in SMD, respectively.

  11. Potential surface for the collinear collision of Ne and H/sub 2//sup +/. [eendoergicity, surface parametrization

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hayes, E.F.; Siu, A.K.Q.; Chapman, F.M. Jr.

    1976-09-01

    A potential energy surface for the Ne--H/sub 2//sup +/ reaction has been obtained in the LCAO--MO--SCF approximation. Analysis of the surface indicates that the reaction Ne+H/sub 2//sup +/..-->..NeH/sup +/+H should proceed with an endoergicity of 12 kcal/mole, in agreement with the experimental results of Chupka and Russell. Several procedures for parameterizing a diatomics-in-molecules (DIM) representation of the NeH/sub 2//sup +/ surface are considered. The results show that an accurate representation of the SCF surface can be obtained from the DIM model using a minimum of diatomic and triatomic data. (AIP)

  12. How to obtain accurate resist simulations in very low-k1 era?

    NASA Astrophysics Data System (ADS)

    Chiou, Tsann-Bim; Park, Chan-Ha; Choi, Jae-Seung; Min, Young-Hong; Hansen, Steve; Tseng, Shih-En; Chen, Alek C.; Yim, Donggyu

    2006-03-01

    A procedure for calibrating a resist model iteratively adjusts appropriate parameters until the simulations of the model match the experimental data. The tunable parameters may include the shape of the illuminator, the geometry and transmittance/phase of the mask, light source and scanner-related parameters that affect imaging quality, resist process control and most importantly the physical/chemical factors in the resist model. The resist model can be accurately calibrated by measuring critical dimensions (CD) of a focus-exposure matrix (FEM) and the technique has been demonstrated to be very successful in predicting lithographic performance. However, resist model calibration is more challenging in the low k1 (<0.3) regime because numerous uncertainties, such as mask and resist CD metrology errors, are becoming too large to be ignored. This study demonstrates a resist model calibration procedure for a 0.29 k1 process using a 6% halftone mask containing 2D brickwall patterns. The influence of different scanning electron microscopes (SEM) and their wafer metrology signal analysis algorithms on the accuracy of the resist model is evaluated. As an example of the metrology issue of the resist pattern, the treatment of a sidewall angle is demonstrated for the resist line ends where the contrast is relatively low. Additionally, the mask optical proximity correction (OPC) and corner rounding are considered in the calibration procedure that is based on captured SEM images. Accordingly, the average root-mean-square (RMS) error, which is the difference between simulated and experimental CDs, can be improved by considering the metrological issues. Moreover, a weighting method and a measured CD tolerance are proposed to handle the different CD variations of the various edge points of the wafer resist pattern. After the weighting method is implemented and the CD selection criteria applied, the RMS error can be further suppressed. Therefore, the resist CD and process window can

  13. Skin Microbiome Surveys Are Strongly Influenced by Experimental Design.

    PubMed

    Meisel, Jacquelyn S; Hannigan, Geoffrey D; Tyldsley, Amanda S; SanMiguel, Adam J; Hodkinson, Brendan P; Zheng, Qi; Grice, Elizabeth A

    2016-05-01

    Culture-independent studies to characterize skin microbiota are increasingly common, due in part to affordable and accessible sequencing and analysis platforms. Compared to culture-based techniques, DNA sequencing of the bacterial 16S ribosomal RNA (rRNA) gene or whole metagenome shotgun (WMS) sequencing provides more precise microbial community characterizations. Most widely used protocols were developed to characterize microbiota of other habitats (i.e., gastrointestinal) and have not been systematically compared for their utility in skin microbiome surveys. Here we establish a resource for the cutaneous research community to guide experimental design in characterizing skin microbiota. We compare two widely sequenced regions of the 16S rRNA gene to WMS sequencing for recapitulating skin microbiome community composition, diversity, and genetic functional enrichment. We show that WMS sequencing most accurately recapitulates microbial communities, but sequencing of hypervariable regions 1-3 of the 16S rRNA gene provides highly similar results. Sequencing of hypervariable region 4 poorly captures skin commensal microbiota, especially Propionibacterium. WMS sequencing, which is resource and cost intensive, provides evidence of a community's functional potential; however, metagenome predictions based on 16S rRNA sequence tags closely approximate WMS genetic functional profiles. This study highlights the importance of experimental design for downstream results in skin microbiome surveys. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  14. Carbene footprinting accurately maps binding sites in protein-ligand and protein-protein interactions

    NASA Astrophysics Data System (ADS)

    Manzi, Lucio; Barrow, Andrew S.; Scott, Daniel; Layfield, Robert; Wright, Timothy G.; Moses, John E.; Oldham, Neil J.

    2016-11-01

    Specific interactions between proteins and their binding partners are fundamental to life processes. The ability to detect protein complexes, and map their sites of binding, is crucial to understanding basic biology at the molecular level. Methods that employ sensitive analytical techniques such as mass spectrometry have the potential to provide valuable insights with very little material and on short time scales. Here we present a differential protein footprinting technique employing an efficient photo-activated probe for use with mass spectrometry. Using this methodology the location of a carbohydrate substrate was accurately mapped to the binding cleft of lysozyme, and in a more complex example, the interactions between a 100 kDa, multi-domain deubiquitinating enzyme, USP5 and a diubiquitin substrate were located to different functional domains. The much improved properties of this probe make carbene footprinting a viable method for rapid and accurate identification of protein binding sites utilizing benign, near-UV photoactivation.

  15. Broad screening of illicit ingredients in cosmetics using ultra-high-performance liquid chromatography-hybrid quadrupole-Orbitrap mass spectrometry with customized accurate-mass database and mass spectral library.

    PubMed

    Meng, Xianshuang; Bai, Hua; Guo, Teng; Niu, Zengyuan; Ma, Qiang

    2017-12-15

    Comprehensive identification and quantitation of 100 multi-class regulated ingredients in cosmetics was achieved using ultra-high-performance liquid chromatography (UHPLC) coupled with hybrid quadrupole-Orbitrap high-resolution mass spectrometry (Q-Orbitrap HRMS). A simple, efficient, and inexpensive sample pretreatment protocol was developed using ultrasound-assisted extraction (UAE), followed by dispersive solid-phase extraction (dSPE). The cosmetic samples were analyzed by UHPLC-Q-Orbitrap HRMS under synchronous full-scan MS and data-dependent MS/MS (full-scan MS 1 /dd-MS 2 ) acquisition mode. The mass resolution was set to 70,000 FWHM (full width at half maximum) for full-scan MS 1 and 17,500 FWHM for dd-MS 2 stage with the experimentally measured mass deviations of less than 2ppm (parts per million) for quasi-molecular ions and 5ppm for characteristic fragment ions for each individual analyte. An accurate-mass database and a mass spectral library were built in house for searching the 100 target compounds. Broad screening was conducted by comparing the experimentally measured exact mass of precursor and fragment ions, retention time, isotopic pattern, and ionic ratio with the accurate-mass database and by matching the acquired MS/MS spectra against the mass spectral library. The developed methodology was evaluated and validated in terms of limits of detection (LODs), limits of quantitation (LOQs), linearity, stability, accuracy, and matrix effect. The UHPLC-Q-Orbitrap HRMS approach was applied for the analysis of 100 target illicit ingredients in 123 genuine cosmetic samples, and exhibited great potential for high-throughput, sensitive, and reliable screening of multi-class illicit compounds in cosmetics. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Accurate Measurement of the Optical Constants for Organic and Organophosphorous Liquid Layers and Drops

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Myers, Tanya L.; Tonkyn, Russell G.; Danby, Tyler O.

    We present accurate measurements for the determination of the optical constants for a series of organic liquids, including organophosphorous compounds. Bulk liquids are rarely encountered in the environment, but more commonly are present as droplets of liquids or thin layers on various substrates. Providing reference spectra to account for the plethora of morphological conditions that may be encountered under different scenarios is a challenge. An alternative approach is to provide the complex optical constants, n and k, which can be used to model the optical phenomena in media and at interfaces, minimizing the need for a vast number of laboratorymore » measurements. In this work, we present improved protocols for measuring the optical constants for a series of liquids that span the range from 7800 to 400 cm-1. The broad spectral range means that one needs to account for both the strong and weak spectral features that are encountered, all of which can be useful for detection, depending on the scenario. To span this dynamic range, both long and short cells are required for accurate measurements. The protocols are presented along with experimental and modeling results for thin layers of silicone oil on aluminum.« less

  17. Kinetic approach to degradation mechanisms in polymer solar cells and their accurate lifetime predictions

    NASA Astrophysics Data System (ADS)

    Arshad, Muhammad Azeem; Maaroufi, AbdelKrim

    2018-07-01

    A beginning has been made in the present study regarding the accurate lifetime predictions of polymer solar cells. Certain reservations about the conventionally employed temperature accelerated lifetime measurements test for its unworthiness of predicting reliable lifetimes of polymer solar cells are brought into light. Critical issues concerning the accelerated lifetime testing include, assuming reaction mechanism instead of determining it, and relying solely on the temperature acceleration of a single property of material. An advanced approach comprising a set of theoretical models to estimate the accurate lifetimes of polymer solar cells is therefore suggested in order to suitably alternate the accelerated lifetime testing. This approach takes into account systematic kinetic modeling of various possible polymer degradation mechanisms under natural weathering conditions. The proposed kinetic approach is substantiated by its applications on experimental aging data-sets of polymer solar materials/solar cells including, P3HT polymer film, bulk heterojunction (MDMO-PPV:PCBM) and dye-sensitized solar cells. Based on the suggested approach, an efficacious lifetime determination formula for polymer solar cells is derived and tested on dye-sensitized solar cells. Some important merits of the proposed method are also pointed out and its prospective applications are discussed.

  18. Robust and accurate decoding of motoneuron behavior and prediction of the resulting force output.

    PubMed

    Thompson, Christopher K; Negro, Francesco; Johnson, Michael D; Holmes, Matthew R; McPherson, Laura Miller; Powers, Randall K; Farina, Dario; Heckman, Charles J

    2018-05-03

    The spinal alpha motoneuron is the only cell in the human CNS whose discharge can be routinely recorded in humans. We have reengineered motor unit collection and decomposition approaches, originally developed in humans, to measure the neural drive to muscle and estimate muscle force generation in the decerebrate cat model. Experimental, computational, and predictive approaches are used to demonstrate the validity of this approach across a wide range of modes to activate the motor pool. The utility of this approach is shown through the ability to track individual motor units across trials, allowing for better predictions of muscle force than the electromyography signal, and providing insights in to the stereotypical discharge characteristics in response to synaptic activation of the motor pool. This approach now allows for a direct link between the intracellular data of single motoneurons, the discharge properties of motoneuron populations, and muscle force generation in the same preparation. The discharge of a spinal alpha motoneuron and the resulting contraction of its muscle fibers represents the functional quantum of the motor system. Recent advances in the recording and decomposition of the electromyographic signal allows for the identification of several tens of concurrently active motor units. These detailed population data provide the potential to achieve deep insights into the synaptic organization of motor commands. Yet most of our understanding of the synaptic input to motoneurons is derived from intracellular recordings in animal preparations. Thus, it is necessary to extend the new electrode and decomposition methods to recording of motor unit populations in these same preparations. To achieve this goal, we use high-density electrode arrays and decomposition techniques, analogous to those developed for humans, to record and decompose the activity of tens of concurrently active motor units in a hindlimb muscle in the decerebrate cat. Our results showed

  19. Rapid experimental measurements of physicochemical properties to inform models and testing.

    PubMed

    Nicolas, Chantel I; Mansouri, Kamel; Phillips, Katherine A; Grulke, Christopher M; Richard, Ann M; Williams, Antony J; Rabinowitz, James; Isaacs, Kristin K; Yau, Alice; Wambaugh, John F

    2018-05-02

    The structures and physicochemical properties of chemicals are important for determining their potential toxicological effects, toxicokinetics, and route(s) of exposure. These data are needed to prioritize the risk for thousands of environmental chemicals, but experimental values are often lacking. In an attempt to efficiently fill data gaps in physicochemical property information, we generated new data for 200 structurally diverse compounds, which were rigorously selected from the USEPA ToxCast chemical library, and whose structures are available within the Distributed Structure-Searchable Toxicity Database (DSSTox). This pilot study evaluated rapid experimental methods to determine five physicochemical properties, including the log of the octanol:water partition coefficient (known as log(K ow ) or logP), vapor pressure, water solubility, Henry's law constant, and the acid dissociation constant (pKa). For most compounds, experiments were successful for at least one property; log(K ow ) yielded the largest return (176 values). It was determined that 77 ToxPrint structural features were enriched in chemicals with at least one measurement failure, indicating which features may have played a role in rapid method failures. To gauge consistency with traditional measurement methods, the new measurements were compared with previous measurements (where available). Since quantitative structure-activity/property relationship (QSAR/QSPR) models are used to fill gaps in physicochemical property information, 5 suites of QSPRs were evaluated for their predictive ability and chemical coverage or applicability domain of new experimental measurements. The ability to have accurate measurements of these properties will facilitate better exposure predictions in two ways: 1) direct input of these experimental measurements into exposure models; and 2) construction of QSPRs with a wider applicability domain, as their predicted physicochemical values can be used to parameterize exposure

  20. EXPERIMENTAL INVESTIGATIONS OF FINE PARTICLE CHARGING BY UNIPOLAR IONS: A REVIEW

    EPA Science Inventory

    The paper gives results of a study relating experimental data to many theories that have been offered in attempts to describe accurately the rate of charge accumulation of fine particles in a unipolar field. The data are reviewed and compiled, and additional particle charging exp...

  1. Optimizing Within-Subject Experimental Designs for jICA of Multi-Channel ERP and fMRI

    PubMed Central

    Mangalathu-Arumana, Jain; Liebenthal, Einat; Beardsley, Scott A.

    2018-01-01

    Joint independent component analysis (jICA) can be applied within subject for fusion of multi-channel event-related potentials (ERP) and functional magnetic resonance imaging (fMRI), to measure brain function at high spatiotemporal resolution (Mangalathu-Arumana et al., 2012). However, the impact of experimental design choices on jICA performance has not been systematically studied. Here, the sensitivity of jICA for recovering neural sources in individual data was evaluated as a function of imaging SNR, number of independent representations of the ERP/fMRI data, relationship between instantiations of the joint ERP/fMRI activity (linear, non-linear, uncoupled), and type of sources (varying parametrically and non-parametrically across representations of the data), using computer simulations. Neural sources were simulated with spatiotemporal and noise attributes derived from experimental data. The best performance, maximizing both cross-modal data fusion and the separation of brain sources, occurred with a moderate number of representations of the ERP/fMRI data (10–30), as in a mixed block/event related experimental design. Importantly, the type of relationship between instantiations of the ERP/fMRI activity, whether linear, non-linear or uncoupled, did not in itself impact jICA performance, and was accurately recovered in the common profiles (i.e., mixing coefficients). Thus, jICA provides an unbiased way to characterize the relationship between ERP and fMRI activity across brain regions, in individual data, rendering it potentially useful for characterizing pathological conditions in which neurovascular coupling is adversely affected. PMID:29410611

  2. [Experimental orthopedic surgery: the practical aspects and management].

    PubMed

    Di Denia, P; Caligiuri, G; Guzzardella, G A; Fini, M; Giardino, R

    1996-01-01

    The funds to grant for a scientific research project are more and more interesting public and private administrations. A quantitative analysis of experimental research prices in all its phases is mandatory for an optimization process. The aim of this paper is to define practical and economical aspects of the experimental 'in vivo' models designed for the validation of biomaterials, with particular respect to the managerial bookkeeping of consumer goods, based on the experience of our Institute. Some tables were realized in order to quantify the resources needed to perform experimental 'in vivo' models. These tables represent a reliable tool for a continuous monitoring of managerial costs for the current year and for an accurate budget planning for the future years considering the experimental projects in progress and the planned researches. A business organization of public research facilities may lead to an optimization of costs and an easier national and international funds achievement increasing, also, the partnership with private appointers.

  3. Validation of an Accurate Three-Dimensional Helical Slow-Wave Circuit Model

    NASA Technical Reports Server (NTRS)

    Kory, Carol L.

    1997-01-01

    The helical slow-wave circuit embodies a helical coil of rectangular tape supported in a metal barrel by dielectric support rods. Although the helix slow-wave circuit remains the mainstay of the traveling-wave tube (TWT) industry because of its exceptionally wide bandwidth, a full helical circuit, without significant dimensional approximations, has not been successfully modeled until now. Numerous attempts have been made to analyze the helical slow-wave circuit so that the performance could be accurately predicted without actually building it, but because of its complex geometry, many geometrical approximations became necessary rendering the previous models inaccurate. In the course of this research it has been demonstrated that using the simulation code, MAFIA, the helical structure can be modeled with actual tape width and thickness, dielectric support rod geometry and materials. To demonstrate the accuracy of the MAFIA model, the cold-test parameters including dispersion, on-axis interaction impedance and attenuation have been calculated for several helical TWT slow-wave circuits with a variety of support rod geometries including rectangular and T-shaped rods, as well as various support rod materials including isotropic, anisotropic and partially metal coated dielectrics. Compared with experimentally measured results, the agreement is excellent. With the accuracy of the MAFIA helical model validated, the code was used to investigate several conventional geometric approximations in an attempt to obtain the most computationally efficient model. Several simplifications were made to a standard model including replacing the helical tape with filaments, and replacing rectangular support rods with shapes conforming to the cylindrical coordinate system with effective permittivity. The approximate models are compared with the standard model in terms of cold-test characteristics and computational time. The model was also used to determine the sensitivity of various

  4. Accurate physical laws can permit new standard units: The two laws F→=ma→ and the proportionality of weight to mass

    NASA Astrophysics Data System (ADS)

    Saslow, Wayne M.

    2014-04-01

    Three common approaches to F→=ma→ are: (1) as an exactly true definition of force F→ in terms of measured inertial mass m and measured acceleration a→; (2) as an exactly true axiom relating measured values of a→, F→ and m; and (3) as an imperfect but accurately true physical law relating measured a→ to measured F→, with m an experimentally determined, matter-dependent constant, in the spirit of the resistance R in Ohm's law. In the third case, the natural units are those of a→ and F→, where a→ is normally specified using distance and time as standard units, and F→ from a spring scale as a standard unit; thus mass units are derived from force, distance, and time units such as newtons, meters, and seconds. The present work develops the third approach when one includes a second physical law (again, imperfect but accurate)—that balance-scale weight W is proportional to m—and the fact that balance-scale measurements of relative weight are more accurate than those of absolute force. When distance and time also are more accurately measurable than absolute force, this second physical law permits a shift to standards of mass, distance, and time units, such as kilograms, meters, and seconds, with the unit of force—the newton—a derived unit. However, were force and distance more accurately measurable than time (e.g., time measured with an hourglass), this second physical law would permit a shift to standards of force, mass, and distance units such as newtons, kilograms, and meters, with the unit of time—the second—a derived unit. Therefore, the choice of the most accurate standard units depends both on what is most accurately measurable and on the accuracy of physical law.

  5. Experimental Demonstration of Frequency Regulation by Commercial Buildings – Part II: Results and Performance Evaluation

    DOE PAGES

    Vrettos, Evangelos; Kara, Emre Can; MacDonald, Jason; ...

    2016-11-15

    This paper is the second part of a two-part series presenting the results from an experimental demonstration of frequency regulation in a commercial building test facility. We developed relevant building models and designed a hierarchical controller for reserve scheduling, building climate control and frequency regulation in Part I. In Part II, we introduce the communication architecture and experiment settings, and present extensive experimental results under frequency regulation. More specifically, we compute the day-ahead reserve capacity of the test facility under different assumptions and conditions. Furthermore, we demonstrate the ability of model predictive control to satisfy comfort constraints under frequency regulation,more » and show that fan speed control can track the fast-moving RegD signal of the Pennsylvania, Jersey, and Maryland Power Market (PJM) very accurately. In addition, we discuss potential effects of frequency regulation on building operation (e.g., increase in energy consumption, oscillations in supply air temperature, and effect on chiller cycling), and provide suggestions for real-world implementation projects. Our results show that hierarchical control is appropriate for frequency regulation from commercial buildings.« less

  6. Application of iterative robust model-based optimal experimental design for the calibration of biocatalytic models.

    PubMed

    Van Daele, Timothy; Gernaey, Krist V; Ringborg, Rolf H; Börner, Tim; Heintz, Søren; Van Hauwermeiren, Daan; Grey, Carl; Krühne, Ulrich; Adlercreutz, Patrick; Nopens, Ingmar

    2017-09-01

    The aim of model calibration is to estimate unique parameter values from available experimental data, here applied to a biocatalytic process. The traditional approach of first gathering data followed by performing a model calibration is inefficient, since the information gathered during experimentation is not actively used to optimize the experimental design. By applying an iterative robust model-based optimal experimental design, the limited amount of data collected is used to design additional informative experiments. The algorithm is used here to calibrate the initial reaction rate of an ω-transaminase catalyzed reaction in a more accurate way. The parameter confidence region estimated from the Fisher Information Matrix is compared with the likelihood confidence region, which is not only more accurate but also a computationally more expensive method. As a result, an important deviation between both approaches is found, confirming that linearization methods should be applied with care for nonlinear models. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1278-1293, 2017. © 2017 American Institute of Chemical Engineers.

  7. In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation.

    PubMed

    Gray, Alan; Harlen, Oliver G; Harris, Sarah A; Khalid, Syma; Leung, Yuk Ming; Lonsdale, Richard; Mulholland, Adrian J; Pearson, Arwen R; Read, Daniel J; Richardson, Robin A

    2015-01-01

    Despite huge advances in the computational techniques available for simulating biomolecules at the quantum-mechanical, atomistic and coarse-grained levels, there is still a widespread perception amongst the experimental community that these calculations are highly specialist and are not generally applicable by researchers outside the theoretical community. In this article, the successes and limitations of biomolecular simulation and the further developments that are likely in the near future are discussed. A brief overview is also provided of the experimental biophysical methods that are commonly used to probe biomolecular structure and dynamics, and the accuracy of the information that can be obtained from each is compared with that from modelling. It is concluded that progress towards an accurate spatial and temporal model of biomacromolecules requires a combination of all of these biophysical techniques, both experimental and computational.

  8. Anti-glaucoma potential of Heliotropium indicum Linn in experimentally-induced glaucoma.

    PubMed

    Kyei, Samuel; Koffuor, George Asumeng; Ramkissoon, Paul; Owusu-Afriyie, Osei

    2015-01-01

    Heliotropium indicum is used as a traditional remedy for hypertension in Ghana. The aim of the study was to evaluate the anti-glaucoma potential of an aqueous whole plant extract of H. indicum to manage experimentally-induced glaucoma. The percentage change in intraocular pressure (IOP), after inducing acute glaucoma (15 mLkg(-1) of 5 % dextrose, i.v.), in New Zealand White rabbits pretreated with Heliotropium indicum aqueous extract (HIE) (30-300 mgkg(-1)), acetazolamide (5 mgkg(-1)), and normal saline (10 mLkg(-1)) per os were measured. IOPs were also monitored in chronic glaucoma in rabbits (induced by 1 % prednisolone acetate drops, 12 hourly for 21 days) after treatments with the same doses of HIE, acetazolamide, and normal saline for 2 weeks. The anti-oxidant property of the extract was assessed by assaying for glutathione levels in the aqueous humour. Glutamate concentration in the vitreous humour was also determined using ELISA technique. Histopathological assessment of the ciliary bodies was made. The extract significantly reduced intraocular pressure (p ≤ 0.05-0.001) in acute and chronic glaucoma, preserved glutathione levels and glutamate concentration (p ≤ 0.01-0.001). Histological assessment of the ciliary body showed a decrease in inflammatory infiltration in the extract and acetazolamide-treated group compared with the normal saline-treated group. The aqueous whole plant extract of Heliotropium indicum has ocular hypotensive, anti-oxidant and possible neuro-protective effects, which therefore underscore its plausible utility as an anti-glaucoma drug with further investigation.

  9. Accurate and noninvasive embryos screening during in vitro fertilization (IVF) assisted by Raman analysis of embryos culture medium Accurate and noninvasive embryos screening during IVF

    NASA Astrophysics Data System (ADS)

    Shen, A. G.; Peng, J.; Zhao, Q. H.; Su, L.; Wang, X. H.; Hu, J. M.; Yang, J.

    2012-04-01

    In combination with morphological evaluation tests, we employ Raman spectroscopy to select higher potential reproductive embryos during in vitro fertilization (IVF) based on chemical composition of embryos culture medium. In this study, 57 Raman spectra are acquired from both higher and lower quality embryos culture medium (ECM) from 10 patients which have been preliminarily confirmed by clinical assay. Data are fit by using a linear combination model of least squares method in which 12 basis spectra represent the chemical features of ECM. The final fitting coefficients provide insight into the chemical compositions of culture medium samples and are subsequently used as criterion to evaluate the quality of embryos. The relative fitting coefficients ratios of sodium pyruvate/albumin and phenylalanine/albumin seem act as key roles in the embryo screening, attaining 85.7% accuracy in comparison with clinical pregnancy. The good results demonstrate that Raman spectroscopy therefore is an important candidate for an accurate and noninvasive screening of higher quality embryos, which potentially decrease the time-consuming clinical trials during IVF.

  10. GlycoDeNovo - an Efficient Algorithm for Accurate de novo Glycan Topology Reconstruction from Tandem Mass Spectra

    NASA Astrophysics Data System (ADS)

    Hong, Pengyu; Sun, Hui; Sha, Long; Pu, Yi; Khatri, Kshitij; Yu, Xiang; Tang, Yang; Lin, Cheng

    2017-08-01

    A major challenge in glycomics is the characterization of complex glycan structures that are essential for understanding their diverse roles in many biological processes. We present a novel efficient computational approach, named GlycoDeNovo, for accurate elucidation of the glycan topologies from their tandem mass spectra. Given a spectrum, GlycoDeNovo first builds an interpretation-graph specifying how to interpret each peak using preceding interpreted peaks. It then reconstructs the topologies of peaks that contribute to interpreting the precursor ion. We theoretically prove that GlycoDeNovo is highly efficient. A major innovative feature added to GlycoDeNovo is a data-driven IonClassifier which can be used to effectively rank candidate topologies. IonClassifier is automatically learned from experimental spectra of known glycans to distinguish B- and C-type ions from all other ion types. Our results showed that GlycoDeNovo is robust and accurate for topology reconstruction of glycans from their tandem mass spectra. [Figure not available: see fulltext.

  11. Membrane Potential and Calcium Dynamics in Beta Cells from Mouse Pancreas Tissue Slices: Theory, Experimentation, and Analysis.

    PubMed

    Dolenšek, Jurij; Špelič, Denis; Klemen, Maša Skelin; Žalik, Borut; Gosak, Marko; Rupnik, Marjan Slak; Stožer, Andraž

    2015-10-28

    Beta cells in the pancreatic islets of Langerhans are precise biological sensors for glucose and play a central role in balancing the organism between catabolic and anabolic needs. A hallmark of the beta cell response to glucose are oscillatory changes of membrane potential that are tightly coupled with oscillatory changes in intracellular calcium concentration which, in turn, elicit oscillations of insulin secretion. Both membrane potential and calcium changes spread from one beta cell to the other in a wave-like manner. In order to assess the properties of the abovementioned responses to physiological and pathological stimuli, the main challenge remains how to effectively measure membrane potential and calcium changes at the same time with high spatial and temporal resolution, and also in as many cells as possible. To date, the most wide-spread approach has employed the electrophysiological patch-clamp method to monitor membrane potential changes. Inherently, this technique has many advantages, such as a direct contact with the cell and a high temporal resolution. However, it allows one to assess information from a single cell only. In some instances, this technique has been used in conjunction with CCD camera-based imaging, offering the opportunity to simultaneously monitor membrane potential and calcium changes, but not in the same cells and not with a reliable cellular or subcellular spatial resolution. Recently, a novel family of highly-sensitive membrane potential reporter dyes in combination with high temporal and spatial confocal calcium imaging allows for simultaneously detecting membrane potential and calcium changes in many cells at a time. Since the signals yielded from both types of reporter dyes are inherently noisy, we have developed complex methods of data denoising that permit for visualization and pixel-wise analysis of signals. Combining the experimental approach of high-resolution imaging with the advanced analysis of noisy data enables novel

  12. Experimental and Modeling Characterization of PETN Mobilization Mechanisms During Recrystallization at Ambient Conditions

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Burnham, A K; Gee, R; Maiti, A

    2005-11-03

    Experimental measurements suggest that pentaerythritoltetranitrate (PETN) undergoes changes at the molecular level that cause macroscopic changes in the overall PETN powder characteristics over time. These changes have been attributed to the high molecular mobility of PETN, but the underlying mechanism(s) responsible for this redistribution are still uncertain. Two basic approaches have been implemented in the past year to provide insight into the nature of these underlying mechanisms. The first approach is of an experimental nature, utilizing both AFM and evaporation measurements, which address both surface mobility and evaporation. These data include AFM measurements performed at LLNL and evaporation rate measurementsmore » performed at Texas Tech. These results are compared to earlier vapor pressure measurements performed at SNL, and estimates of recrystallization time frames are given. The second approach utilizes first-principle calculations and simulations that will be used to compare directly to those experimental quantities measured. We are developing an accurate intermolecular potential for PETN, which via kinetic Monte Carlo (KMC) simulations would mimic real crystallite shapes. Once the basic theory is in place for the growth of single crystallites, we will be in a position to investigate realistic grain coarsening phenomena in multi-crystallite simulations. This will also enable us to study how to control the morphological evolution, e.g., through thermal cycling, or through the action of custom additives and impurities.« less

  13. Predicting Transport of 3,5,6-Trichloro-2-Pyridinol Into Saliva Using a Combination Experimental and Computational Approach

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Smith, Jordan Ned; Carver, Zana A.; Weber, Thomas J.

    A combination experimental and computational approach was developed to predict chemical transport into saliva. A serous-acinar chemical transport assay was established to measure chemical transport with non-physiological (standard cell culture medium) and physiological (using surrogate plasma and saliva medium) conditions using 3,5,6-trichloro-2-pyridinol (TCPy) a metabolite of the pesticide chlorpyrifos. High levels of TCPy protein binding was observed in cell culture medium and rat plasma resulting in different TCPy transport behaviors in the two experimental conditions. In the non-physiological transport experiment, TCPy reached equilibrium at equivalent concentrations in apical and basolateral chambers. At higher TCPy doses, increased unbound TCPy was observed,more » and TCPy concentrations in apical and basolateral chambers reached equilibrium faster than lower doses, suggesting only unbound TCPy is able to cross the cellular monolayer. In the physiological experiment, TCPy transport was slower than non-physiological conditions, and equilibrium was achieved at different concentrations in apical and basolateral chambers at a comparable ratio (0.034) to what was previously measured in rats dosed with TCPy (saliva:blood ratio: 0.049). A cellular transport computational model was developed based on TCPy protein binding kinetics and accurately simulated all transport experiments using different permeability coefficients for the two experimental conditions (1.4 vs 0.4 cm/hr for non-physiological and physiological experiments, respectively). The computational model was integrated into a physiologically based pharmacokinetic (PBPK) model and accurately predicted TCPy concentrations in saliva of rats dosed with TCPy. Overall, this study demonstrates an approach to predict chemical transport in saliva potentially increasing the utility of salivary biomonitoring in the future.« less

  14. Accurate recognition and effective treatment of ventricular fibrillation by automated external defibrillators in adolescents.

    PubMed

    Atkins, D L; Hartley, L L; York, D K

    1998-03-01

    To evaluate the accuracy and efficacy of automated external defibrillators (AEDs) in patients <16 years old. AEDs are standard therapy in out-of-hospital resuscitation of adults and have led to higher success rates. Their use in children and adolescents has never been evaluated, despite recommendations from the American Heart Association that they be used in children >8 years of age. This was a retrospective cohort study of children <16 years old who underwent out-of-hospital cardiac resuscitation and on whom an AED was used during the resuscitation. The setting was rural and urban prehospital emergency medical systems. Patients were identified by review of a database of cardiac arrests maintained by a large surveillance program of these services. AEDs were used to assess cardiac rhythm in 18 patients with a mean age of 12.1 +/- 3.7 years. The cardiac rhythms were analyzed 67 times and included ventricular fibrillation (25), asystole/pulseless electrical activity (32), sinus bradycardia (6), and sinus tachycardia (4). The AEDs recognized all nonshockable rhythms accurately and advised no shock. Ventricular fibrillation was recognized accurately in 22 (88%) of 25 episodes and advised or administered a shock 22 times. Sensitivity and specificity for accurate rhythm analysis were 88% and 100%, respectively. One patient with a nonshockable rhythm survived, whereas 3 of 9 patients with ventricular fibrillation survived. These data furnish evidence that AEDs provide accurate rhythm detection and shock delivery to children and young adolescents. AED use is potentially as effective for children as it is for adults.

  15. Pelvic orientation for total hip arthroplasty in lateral decubitus: can it be accurately measured?

    PubMed

    Sykes, Alice M; Hill, Janet C; Orr, John F; Gill, Harinderjit S; Salazar, Jose J; Humphreys, Lee D; Beverland, David E

    2016-05-16

    During total hip arthroplasty (THA), accurately predicting acetabular cup orientation remains a key challenge, in great part because of uncertainty about pelvic orientation. This pilot study aimed to develop and validate a technique to measure pelvic orientation; establish its accuracy in the location of anatomical landmarks and subsequently; investigate if limb movement during a simulated surgical procedure alters pelvic orientation. The developed technique measured 3-D orientation of an isolated Sawbone pelvis, it was then implemented to measure pelvic orientation in lateral decubitus with post-THA patients (n = 20) using a motion capture system. Orientation of the isolated Sawbone pelvis was accurately measured, demonstrated by high correlations with angular data from a coordinate measurement machine; R-squared values close to 1 for all pelvic axes. When applied to volunteer subjects, largest movements occurred about the longitudinal pelvic axis; internal and external pelvic rotation. Rotations about the anteroposterior axis, which directly affect inclination angles, showed >75% of participants had movement within ±5° of neutral, 0°. The technique accurately measured orientation of the isolated bony pelvis. This was not the case in a simulated theatre environment. Soft tissue landmarks were difficult to palpate repeatedly. These findings have direct clinical relevance, landmark registration in lateral decubitus is a potential source of error, contributing here to large ranges in measured movement. Surgeons must be aware that present techniques using bony landmarks to reference pelvic orientation for cup implantation, both computer-based and mechanical, may not be sufficiently accurate.

  16. All-Dimensional H2–CO Potential: Validation with Fully Quantum Second Virial Coefficients

    PubMed Central

    Garberoglio, Giovanni; Jankowski, Piotr; Szalewicz, Krzysztof; Harvey, Allan H.

    2017-01-01

    We use a new high-accuracy all-dimensional potential to compute the cross second virial coefficient B12(T) between molecular hydrogen and carbon monoxide. The path-integral method is used to fully account for quantum effects. Values are calculated from 10 K to 2000 K and the uncertainty of the potential is propagated into uncertainties of B12. Our calculated B12(T) are in excellent agreement with most of the limited experimental data available, but cover a much wider range of temperatures and have lower uncertainties. Similar to recently reported findings from scattering calculations, we find that the reduced-dimensionality potential obtained by averaging over the rovibrational motion of the monomers gives results that are a good approximation to those obtained when flexibility is fully taken into account. Also, the four-dimensional approximation with monomers taken at their vibrationally averaged bond lengths works well. This finding is important, since full-dimensional potentials are difficult to develop even for triatomic monomers and are not currently possible to obtain for larger molecules. Likewise, most types of accurate quantum mechanical calculations, e.g., spectral or scattering, are severely limited in the number of dimensions that can be handled. PMID:28178790

  17. Precise and accurate assay of pregnenolone and five other neurosteroids in monkey brain tissue by LC-MS/MS.

    PubMed

    Dury, Alain Y; Ke, Yuyong; Labrie, Fernand

    2016-09-01

    A series of steroids present in the brain have been named "neurosteroids" following the possibility of their role in the central nervous system impairments such as anxiety disorders, depression, premenstrual dysphoric disorder (PMDD), addiction, or even neurodegenerative disorders such as Alzheimer's and Parkinson's diseases. Study of their potential role requires a sensitive and accurate assay of their concentration in the monkey brain, the closest model to the human. We have thus developed a robust, precise and accurate liquid chromatography-tandem mass spectrometry method for the assay of pregnenolone, pregnanolone, epipregnanolone, allopregnanolone, epiallopregnanolone, and androsterone in the cynomolgus monkey brain. The extraction method includes a thorough sample cleanup using protein precipitation and phospholipid removal, followed by hexane liquid-liquid extraction and a Girard T ketone-specific derivatization. This method opens the possibility of investigating the potential implication of these six steroids in the most suitable animal model for neurosteroid-related research. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. Accurate bond energies of hydrocarbons from complete basis set extrapolated multi-reference singles and doubles configuration interaction.

    PubMed

    Oyeyemi, Victor B; Pavone, Michele; Carter, Emily A

    2011-12-09

    Quantum chemistry has become one of the most reliable tools for characterizing the thermochemical underpinnings of reactions, such as bond dissociation energies (BDEs). The accurate prediction of these particular properties (BDEs) are challenging for ab initio methods based on perturbative corrections or coupled cluster expansions of the single-determinant Hartree-Fock wave function: the processes of bond breaking and forming are inherently multi-configurational and require an accurate description of non-dynamical electron correlation. To this end, we present a systematic ab initio approach for computing BDEs that is based on three components: 1) multi-reference single and double excitation configuration interaction (MRSDCI) for the electronic energies; 2) a two-parameter scheme for extrapolating MRSDCI energies to the complete basis set limit; and 3) DFT-B3LYP calculations of minimum-energy structures and vibrational frequencies to account for zero point energy and thermal corrections. We validated our methodology against a set of reliable experimental BDE values of CC and CH bonds of hydrocarbons. The goal of chemical accuracy is achieved, on average, without applying any empirical corrections to the MRSDCI electronic energies. We then use this composite scheme to make predictions of BDEs in a large number of hydrocarbon molecules for which there are no experimental data, so as to provide needed thermochemical estimates for fuel molecules. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Accurate collision-induced line-coupling parameters for the fundamental band of CO in He - Close coupling and coupled states scattering calculations

    NASA Technical Reports Server (NTRS)

    Green, Sheldon; Boissoles, J.; Boulet, C.

    1988-01-01

    The first accurate theoretical values for off-diagonal (i.e., line-coupling) pressure-broadening cross sections are presented. Calculations were done for CO perturbed by He at thermal collision energies using an accurate ab initio potential energy surface. Converged close coupling, i.e., numerically exact values, were obtained for coupling to the R(0) and R(2) lines. These were used to test the coupled states (CS) and infinite order sudden (IOS) approximate scattering methods. CS was found to be of quantitative accuracy (a few percent) and has been used to obtain coupling values for lines to R(10). IOS values are less accurate, but, owing to their simplicity, may nonetheless prove useful as has been recently demonstrated.

  20. Nanoparticle-mediated drug delivery to treat infections in the female reproductive tract: evaluation of experimental systems and the potential for mathematical modeling.

    PubMed

    Sims, Lee B; Frieboes, Hermann B; Steinbach-Rankins, Jill M

    2018-01-01

    A variety of drug-delivery platforms have been employed to deliver therapeutic agents across cervicovaginal mucus (CVM) and the vaginal mucosa, offering the capability to increase the longevity and retention of active agents to treat infections of the female reproductive tract (FRT). Nanoparticles (NPs) have been shown to improve retention, diffusion, and cell-specific targeting via specific surface modifications, relative to other delivery platforms. In particular, polymeric NPs represent a promising option that has shown improved distribution through the CVM. These NPs are typically fabricated from nontoxic, non-inflammatory, US Food and Drug Administration-approved polymers that improve biocompatibility. This review summarizes recent experimental studies that have evaluated NP transport in the FRT, and highlights research areas that more thoroughly and efficiently inform polymeric NP design, including mathematical modeling. An overview of the in vitro, ex vivo, and in vivo NP studies conducted to date - whereby transport parameters are determined, extrapolated, and validated - is presented first. The impact of different NP design features on transport through the FRT is summarized, and gaps that exist due to the limitations of iterative experimentation alone are identified. The potential of mathematical modeling to complement the characterization and evaluation of diffusion and transport of delivery vehicles and active agents through the CVM and mucosa is discussed. Lastly, potential advancements combining experimental and mathematical knowledge are suggested to inform next-generation NP designs, such that infections in the FRT may be more effectively treated.

  1. Non-degenerate two-photon absorption in silicon waveguides. Analytical and experimental study

    DOE PAGES

    Zhang, Yanbing; Husko, Chad; Lefrancois, Simon; ...

    2015-06-22

    We theoretically and experimentally investigate the nonlinear evolution of two optical pulses in a silicon waveguide. We provide an analytic solution for the weak probe wave undergoing non-degenerate two-photon absorption (TPA) from the strong pump. At larger pump intensities, we employ a numerical solution to study the interplay between TPA and photo-generated free carriers. We develop a simple and powerful approach to extract and separate out the distinct loss contributions of TPA and free-carrier absorption from readily available experimental data. Our analysis accounts accurately for experimental results in silicon photonic crystal waveguides.

  2. Accurate isotopic fission yields of electromagnetically induced fission of 238U measured in inverse kinematics at relativistic energies

    NASA Astrophysics Data System (ADS)

    Pellereau, E.; Taïeb, J.; Chatillon, A.; Alvarez-Pol, H.; Audouin, L.; Ayyad, Y.; Bélier, G.; Benlliure, J.; Boutoux, G.; Caamaño, M.; Casarejos, E.; Cortina-Gil, D.; Ebran, A.; Farget, F.; Fernández-Domínguez, B.; Gorbinet, T.; Grente, L.; Heinz, A.; Johansson, H.; Jurado, B.; Kelić-Heil, A.; Kurz, N.; Laurent, B.; Martin, J.-F.; Nociforo, C.; Paradela, C.; Pietri, S.; Rodríguez-Sánchez, J. L.; Schmidt, K.-H.; Simon, H.; Tassan-Got, L.; Vargas, J.; Voss, B.; Weick, H.

    2017-05-01

    SOFIA (Studies On Fission with Aladin) is a novel experimental program, dedicated to accurate measurements of fission-fragment isotopic yields. The setup allows us to fully identify, in nuclear charge and mass, both fission fragments in coincidence for the whole fission-fragment range. It was installed at the GSI facility (Darmstadt), to benefit from the relativistic heavy-ion beams available there, and thus to use inverse kinematics. This paper reports on fission yields obtained in electromagnetically induced fission of 238U.

  3. An Experimental and Theoretical Study of Nitrogen-Broadened Acetylene Lines

    NASA Technical Reports Server (NTRS)

    Thibault, Franck; Martinez, Raul Z.; Bermejo, Dionisio; Ivanov, Sergey V.; Buzykin, Oleg G.; Ma, Qiancheng

    2014-01-01

    We present experimental nitrogen-broadening coefficients derived from Voigt profiles of isotropic Raman Q-lines measured in the 2 band of acetylene (C2H2) at 150 K and 298 K, and compare them to theoretical values obtained through calculations that were carried out specifically for this work. Namely, full classical calculations based on Gordon's approach, two kinds of semi-classical calculations based on Robert Bonamy method as well as full quantum dynamical calculations were performed. All the computations employed exactly the same ab initio potential energy surface for the C2H2N2 system which is, to our knowledge, the most realistic, accurate and up-to-date one. The resulting calculated collisional half-widths are in good agreement with the experimental ones only for the full classical and quantum dynamical methods. In addition, we have performed similar calculations for IR absorption lines and compared the results to bibliographic values. Results obtained with the full classical method are again in good agreement with the available room temperature experimental data. The quantum dynamical close-coupling calculations are too time consuming to provide a complete set of values and therefore have been performed only for the R(0) line of C2H2. The broadening coefficient obtained for this line at 173 K and 297 K also compares quite well with the available experimental data. The traditional Robert Bonamy semi-classical formalism, however, strongly overestimates the values of half-width for both Qand R-lines. The refined semi-classical Robert Bonamy method, first proposed for the calculations of pressure broadening coefficients of isotropic Raman lines, is also used for IR lines. By using this improved model that takes into account effects from line coupling, the calculated semi-classical widths are significantly reduced and closer to the measured ones.

  4. JP-8 jet fuel exposure potentiates tumor development in two experimental model systems.

    PubMed

    Harris, D T; Sakiestewa, D; Titone, D; He, X; Hyde, J; Witten, M

    2007-11-01

    The US Air Force has implemented the widespread use of JP-8 jet fuel in its operations, although a thorough understanding of its potential effects upon exposed personnel is unclear. Previous work has reported that JP-8 exposure is immunosuppressive. Exposure of mice to JP-8 for 1 h/day resulted in immediate secretion of two immunosuppressive agents; namely, interleukin-10 (IL-10) and prostaglandin E2 (PGE2). Thus, it was of interest to determine if jet fuel exposure might promote tumor growth and metastasis. The syngeneic B16 tumor model was used for these studies. Animals were injected intravenously with tumor cells, and lung colonies were enumerated. Animals were also examined for metastatic spread of the tumor. Mice were either exposed to 1000 mg/m3 JP-8 (1 h/ day) for 7 days before tumor injection or were exposed to JP-8 at the time of tumor injection. All animals were killed 17 days after tumor injection. In the present study, JP8 exposure potentiated the growth and metastases of B16 tumors in an animal model. Exposure of mice to JP-8 for 1 h/day before tumor induction resulted in an approximately 8.7-fold increase in tumors, whereas those mice exposed to JP8 at the time of tumor induction had a 5.6-fold increase in tumor numbers. Thus, low concentration JP-8 jet fuel exposures have significant immune suppressive effects on the immune system that can result in increased tumor formation and metastases. We have now extended the observations to an experimental subcutaneous tumor model. JP8 exposure at the time of tumor induction in this model did not affect the growth of the tumor. However, JP8-exposed, tumor-bearing animals died at an accelerated rate as compared with air-exposed, tumor-bearing mice.

  5. The development of the experimental setup for measuring the cell membrane electrical potential by Sucrose-Gap Technique

    NASA Astrophysics Data System (ADS)

    Yuzhakov, AD; Nosarev, AV; Aleinik, AN

    2017-11-01

    This article describes the development of the experimental setup for measuring the cell membrane electrical potential by Double -Sucrose-Gap Technique. The double-gap isolation method allows the simultaneous measurement of electrical activity and tension output from contracting segments of muscle fibers. This technique has been widely used as a convenient tool for recording of the membrane activities from myelinated or unmyelinated nerves and muscle preparations. This device can be an effective way to provide undergraduate biomedical engineering students with invaluable experiences in neurophysiology. The installation design and its main characteristics are described. The advantages of the described device are the simplicity of the experiment, relatively low cost, the possibility of long-term experiment.

  6. Accuracy in streamflow measurements on the Fernow Experimental Forest

    Treesearch

    James W. Hornbeck

    1965-01-01

    Measurement of streamflow from small watersheds on the Fernow Experimental Forest at Parsons, West Virginia was begun in 1951. Stream-gaging stations are now being operated on 9 watersheds ranging from 29 to 96 acres in size; and 91 watershed-years of record have been collected. To determine how accurately streamflow is being measured at these stations, several of the...

  7. Clinical trials transparency and the Trial and Experimental Studies Transparency (TEST) act.

    PubMed

    Logvinov, Ilana

    2014-03-01

    Clinical trial research is the cornerstone for successful advancement of medicine that provides hope for millions of people in the future. Full transparency in clinical trials may allow independent investigators to evaluate study designs, perform additional analysis of data, and potentially eliminate duplicate studies. Current regulatory system and publishers rely on investigators and pharmaceutical industries for complete and accurate reporting of results from completed clinical trials. Legislation seems to be the only way to enforce mandatory disclosure of results. The Trial and Experimental Studies Transparency (TEST) Act of 2012 was introduced to the legislators in the United States to promote greater transparency in research industry. Public safety and advancement of science are the driving forces for the proposed policy change. The TEST Act may benefit the society and researchers; however, there are major concerns with participants' privacy and intellectual property protection. Copyright © 2014 Elsevier Inc. All rights reserved.

  8. Leaf Water Potentials Measured with a Pressure Chamber

    PubMed Central

    Boyer, J. S.

    1967-01-01

    Leaf water potentials were estimated from the sum of the balancing pressure measured with a pressure chamber and the osmotic potential of the xylem sap in leafy shoots or leaves. When leaf water potentials in yew, rhododendron, and sunflower were compared with those measured with a thermocouple psychrometer known to indicate accurate values of leaf water potential, determinations were within ± 2 bars of the psychrometer measurements with sunflower and yew. In rhododendron. water potentials measured with the pressure chamber plus xylem sap were 2.5 bars less negative to 4 bars more negative than psychrometer measurements. The discrepancies in the rhododendron measurements could be attributed, at least in part, to the filling of tissues other than xylem with xylem sap during measurements with the pressure chamber. It was concluded that, although stem characteristics may affect the measurements, pressure chamber determinations were sufficiently close to psychrometer measurements that the pressure chamber may be used for relative measurements of leaf water potentials, especially in sunflower and yew. For accurate determinations of leaf water potential, however, pressure chamber measurements must be calibrated with a thermocouple psychrometer. PMID:16656476

  9. Sequential experimental design based generalised ANOVA

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Chakraborty, Souvik, E-mail: csouvik41@gmail.com; Chowdhury, Rajib, E-mail: rajibfce@iitr.ac.in

    Over the last decade, surrogate modelling technique has gained wide popularity in the field of uncertainty quantification, optimization, model exploration and sensitivity analysis. This approach relies on experimental design to generate training points and regression/interpolation for generating the surrogate. In this work, it is argued that conventional experimental design may render a surrogate model inefficient. In order to address this issue, this paper presents a novel distribution adaptive sequential experimental design (DA-SED). The proposed DA-SED has been coupled with a variant of generalised analysis of variance (G-ANOVA), developed by representing the component function using the generalised polynomial chaos expansion. Moreover,more » generalised analytical expressions for calculating the first two statistical moments of the response, which are utilized in predicting the probability of failure, have also been developed. The proposed approach has been utilized in predicting probability of failure of three structural mechanics problems. It is observed that the proposed approach yields accurate and computationally efficient estimate of the failure probability.« less

  10. Multireference configuration interaction calculations of the first six ionization potentials of the uranium atom

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bross, David H.; Parmar, Payal; Peterson, Kirk A.

    The first 6 ionization potentials (IPs) of the uranium atom have been calculated using multireference configuration interaction (MRCI+Q) with extrapolations to the complete basis set (CBS) limit using new all-electron correlation consistent basis sets. The latter were carried out with the third-order Douglas-Kroll-Hess Hamiltonian. Correlation down through the 5s5p5d electrons have been taken into account, as well as contributions to the IPs due to the Lamb shift. Spin-orbit coupling contributions calculated at the 4-component Kramers restricted configuration interaction level, as well as the Gaunt term computed at the Dirac-Hartree-Fock level, were added to the best scalar relativistic results. As amore » result, the final ionization potentials are expected to be accurate to at least 5 kcal/mol (0.2 eV), and thus more reliable than the current experimental values of IP 3 through IP 6.« less

  11. Multireference configuration interaction calculations of the first six ionization potentials of the uranium atom

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bross, David H.; Parmar, Payal; Peterson, Kirk A., E-mail: kipeters@wsu.edu

    The first 6 ionization potentials (IPs) of the uranium atom have been calculated using multireference configuration interaction (MRCI+Q) with extrapolations to the complete basis set limit using new all-electron correlation consistent basis sets. The latter was carried out with the third-order Douglas-Kroll-Hess Hamiltonian. Correlation down through the 5s5p5d electrons has been taken into account, as well as contributions to the IPs due to the Lamb shift. Spin-orbit coupling contributions calculated at the 4-component Kramers restricted configuration interaction level, as well as the Gaunt term computed at the Dirac-Hartree-Fock level, were added to the best scalar relativistic results. The final ionizationmore » potentials are expected to be accurate to at least 5 kcal/mol (0.2 eV) and thus more reliable than the current experimental values of IP{sub 3} through IP{sub 6}.« less

  12. Experimental results for correlation-based wavefront sensing

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Poyneer, L A; Palmer, D W; LaFortune, K N

    2005-07-01

    Correlation wave-front sensing can improve Adaptive Optics (AO) system performance in two keys areas. For point-source-based AO systems, Correlation is more accurate, more robust to changing conditions and provides lower noise than a centroiding algorithm. Experimental results from the Lick AO system and the SSHCL laser AO system confirm this. For remote imaging, Correlation enables the use of extended objects for wave-front sensing. Results from short horizontal-path experiments will show algorithm properties and requirements.

  13. Experimental and numerical study of physiological responses in hot environments.

    PubMed

    Yang, Jie; Weng, Wenguo; Zhang, Baoting

    2014-10-01

    This paper proposed a multi-node human thermal model to predict human thermal responses in hot environments. The model was extended based on the Tanabe's work by considering the effects of high temperature on heat production, blood flow rate, and heat exchange coefficients. Five healthy men dressed in shorts were exposed in thermal neutral (29 °C) and high temperature (45 °C) environments. The rectal temperatures and skin temperatures of seven human body segments were continuously measured during the experiment. Validation of this model was conducted with experimental data. The results showed that the current model could accurately predict the skin and core temperatures in terms of the tendency and absolute values. In the human body segments expect calf and trunk, the temperature differences between the experimental data and the predicted results in high temperature environment were smaller than those in the thermally neutral environment conditions. The extended model was proved to be capable of predicting accurately human physiological responses in hot environments. Copyright © 2014 Elsevier Ltd. All rights reserved.

  14. Accurate dipole moment curve and non-adiabatic effects on the high resolution spectroscopic properties of the LiH molecule

    NASA Astrophysics Data System (ADS)

    Diniz, Leonardo G.; Kirnosov, Nikita; Alijah, Alexander; Mohallem, José R.; Adamowicz, Ludwik

    2016-04-01

    A very accurate dipole moment curve (DMC) for the ground X1Σ+ electronic state of the 7LiH molecule is reported. It is calculated with the use of all-particle explicitly correlated Gaussian functions with shifted centers. The DMC - the most accurate to our knowledge - and the corresponding highly accurate potential energy curve are used to calculate the transition energies, the transition dipole moments, and the Einstein coefficients for the rovibrational transitions with ΔJ = - 1 and Δv ⩽ 5 . The importance of the non-adiabatic effects in determining these properties is evaluated using the model of a vibrational R-dependent effective reduced mass in the rovibrational calculations introduced earlier (Diniz et al., 2015). The results of the present calculations are used to assess the quality of the two complete linelists of 7LiH available in the literature.

  15. High-temperature experimental and thermodynamic modelling research on the pyrometallurgical processing of copper

    NASA Astrophysics Data System (ADS)

    Hidayat, Taufiq; Shishin, Denis; Decterov, Sergei A.; Hayes, Peter C.; Jak, Evgueni

    2017-01-01

    Uncertainty in the metal price and competition between producers mean that the daily operation of a smelter needs to target high recovery of valuable elements at low operating cost. Options for the improvement of the plant operation can be examined and decision making can be informed based on accurate information from laboratory experimentation coupled with predictions using advanced thermodynamic models. Integrated high-temperature experimental and thermodynamic modelling research on phase equilibria and thermodynamics of copper-containing systems have been undertaken at the Pyrometallurgy Innovation Centre (PYROSEARCH). The experimental phase equilibria studies involve high-temperature equilibration, rapid quenching and direct measurement of phase compositions using electron probe X-ray microanalysis (EPMA). The thermodynamic modelling deals with the development of accurate thermodynamic database built through critical evaluation of experimental data, selection of solution models, and optimization of models parameters. The database covers the Al-Ca-Cu-Fe-Mg-O-S-Si chemical system. The gas, slag, matte, liquid and solid metal phases, spinel solid solution as well as numerous solid oxide and sulphide phases are included. The database works within the FactSage software environment. Examples of phase equilibria data and thermodynamic models of selected systems, as well as possible implementation of the research outcomes to selected copper making processes are presented.

  16. Communication: Rigorous quantum dynamics of O + O{sub 2} exchange reactions on an ab initio potential energy surface substantiate the negative temperature dependence of rate coefficients

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Li, Yaqin; Sun, Zhigang, E-mail: zsun@dicp.ac.cn, E-mail: dawesr@mst.edu, E-mail: hguo@unm.edu; Center for Advanced Chemical Physics, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026

    2014-08-28

    The kinetics and dynamics of several O + O{sub 2} isotope exchange reactions have been investigated on a recently determined accurate global O{sub 3} potential energy surface using a time-dependent wave packet method. The agreement between calculated and measured rate coefficients is significantly improved over previous work. More importantly, the experimentally observed negative temperature dependence of the rate coefficients is for the first time rigorously reproduced theoretically. This negative temperature dependence can be attributed to the absence in the new potential energy surface of a submerged “reef” structure, which was present in all previous potential energy surfaces. In addition, contributionsmore » of rotational excited states of the diatomic reactant further accentuate the negative temperature dependence.« less

  17. Towards First Principles-Based Prediction of Highly Accurate Electrochemical Pourbaix Diagrams

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zeng, Zhenhua; Chan, Maria K. Y.; Zhao, Zhi-Jian

    2015-08-13

    Electrochemical potential/pH (Pourbaix) diagrams underpin many aqueous electrochemical processes and are central to the identification of stable phases of metals for processes ranging from electrocatalysis to corrosion. Even though standard DFT calculations are potentially powerful tools for the prediction of such diagrams, inherent errors in the description of transition metal (hydroxy)oxides, together with neglect of van der Waals interactions, have limited the reliability of such predictions for even the simplest pure metal bulk compounds, and corresponding predictions for more complex alloy or surface structures are even more challenging. In the present work, through synergistic use of a Hubbard U correction,more » a state-of-the-art dispersion correction, and a water-based bulk reference state for the calculations, these errors are systematically corrected. The approach describes the weak binding that occurs between hydroxyl-containing functional groups in certain compounds in Pourbaix diagrams, corrects for self-interaction errors in transition metal compounds, and reduces residual errors on oxygen atoms by preserving a consistent oxidation state between the reference state, water, and the relevant bulk phases. The strong performance is illustrated on a series of bulk transition metal (Mn, Fe, Co and Ni) hydroxides, oxyhydroxides, binary, and ternary oxides, where the corresponding thermodynamics of redox and (de)hydration are described with standard errors of 0.04 eV per (reaction) formula unit. The approach further preserves accurate descriptions of the overall thermodynamics of electrochemically-relevant bulk reactions, such as water formation, which is an essential condition for facilitating accurate analysis of reaction energies for electrochemical processes on surfaces. The overall generality and transferability of the scheme suggests that it may find useful application in the construction of a broad array of electrochemical phase diagrams, including

  18. Time travel, Clock Puzzles and Their Experimental Tests

    NASA Astrophysics Data System (ADS)

    Ciufolini, Ignazio

    2013-09-01

    Is time travel possible? What is Einstein's theory of relativity mathematically predicting in that regard? Is time travel related to the so-called clock `paradoxes' of relativity and if so how? Is there any accurate experimental evidence of the phenomena regarding the different flow of time predicted by General Relativity and is there any possible application of the temporal phenomena predicted by relativity to our everyday life? Which temporal phenomena are predicted in the vicinities of a rotating body and of a mass-energy current, and do we have any experimental test of the occurrence of these phenomena near a rotating body? In this paper, we address and answer some of these questions.

  19. Accurate Sample Assignment in a Multiplexed, Ultrasensitive, High-Throughput Sequencing Assay for Minimal Residual Disease.

    PubMed

    Bartram, Jack; Mountjoy, Edward; Brooks, Tony; Hancock, Jeremy; Williamson, Helen; Wright, Gary; Moppett, John; Goulden, Nick; Hubank, Mike

    2016-07-01

    High-throughput sequencing (HTS) (next-generation sequencing) of the rearranged Ig and T-cell receptor genes promises to be less expensive and more sensitive than current methods of monitoring minimal residual disease (MRD) in patients with acute lymphoblastic leukemia. However, the adoption of new approaches by clinical laboratories requires careful evaluation of all potential sources of error and the development of strategies to ensure the highest accuracy. Timely and efficient clinical use of HTS platforms will depend on combining multiple samples (multiplexing) in each sequencing run. Here we examine the Ig heavy-chain gene HTS on the Illumina MiSeq platform for MRD. We identify errors associated with multiplexing that could potentially impact the accuracy of MRD analysis. We optimize a strategy that combines high-purity, sequence-optimized oligonucleotides, dual indexing, and an error-aware demultiplexing approach to minimize errors and maximize sensitivity. We present a probability-based, demultiplexing pipeline Error-Aware Demultiplexer that is suitable for all MiSeq strategies and accurately assigns samples to the correct identifier without excessive loss of data. Finally, using controls quantified by digital PCR, we show that HTS-MRD can accurately detect as few as 1 in 10(6) copies of specific leukemic MRD. Crown Copyright © 2016. Published by Elsevier Inc. All rights reserved.

  20. Generating Facial Expressions Using an Anatomically Accurate Biomechanical Model.

    PubMed

    Wu, Tim; Hung, Alice; Mithraratne, Kumar

    2014-11-01

    This paper presents a computational framework for modelling the biomechanics of human facial expressions. A detailed high-order (Cubic-Hermite) finite element model of the human head was constructed using anatomical data segmented from magnetic resonance images. The model includes a superficial soft-tissue continuum consisting of skin, the subcutaneous layer and the superficial Musculo-Aponeurotic system. Embedded within this continuum mesh, are 20 pairs of facial muscles which drive facial expressions. These muscles were treated as transversely-isotropic and their anatomical geometries and fibre orientations were accurately depicted. In order to capture the relative composition of muscles and fat, material heterogeneity was also introduced into the model. Complex contact interactions between the lips, eyelids, and between superficial soft tissue continuum and deep rigid skeletal bones were also computed. In addition, this paper investigates the impact of incorporating material heterogeneity and contact interactions, which are often neglected in similar studies. Four facial expressions were simulated using the developed model and the results were compared with surface data obtained from a 3D structured-light scanner. Predicted expressions showed good agreement with the experimental data.

  1. Constructing high-accuracy intermolecular potential energy surface with multi-dimension Morse/Long-Range model

    NASA Astrophysics Data System (ADS)

    Zhai, Yu; Li, Hui; Le Roy, Robert J.

    2018-04-01

    Spectroscopically accurate Potential Energy Surfaces (PESs) are fundamental for explaining and making predictions of the infrared and microwave spectra of van der Waals (vdW) complexes, and the model used for the potential energy function is critically important for providing accurate, robust and portable analytical PESs. The Morse/Long-Range (MLR) model has proved to be one of the most general, flexible and accurate one-dimensional (1D) model potentials, as it has physically meaningful parameters, is flexible, smooth and differentiable everywhere, to all orders and extrapolates sensibly at both long and short ranges. The Multi-Dimensional Morse/Long-Range (mdMLR) potential energy model described herein is based on that 1D MLR model, and has proved to be effective and accurate in the potentiology of various types of vdW complexes. In this paper, we review the current status of development of the mdMLR model and its application to vdW complexes. The future of the mdMLR model is also discussed. This review can serve as a tutorial for the construction of an mdMLR PES.

  2. Modeling an Excitable Biosynthetic Tissue with Inherent Variability for Paired Computational-Experimental Studies.

    PubMed

    Gokhale, Tanmay A; Kim, Jong M; Kirkton, Robert D; Bursac, Nenad; Henriquez, Craig S

    2017-01-01

    To understand how excitable tissues give rise to arrhythmias, it is crucially necessary to understand the electrical dynamics of cells in the context of their environment. Multicellular monolayer cultures have proven useful for investigating arrhythmias and other conduction anomalies, and because of their relatively simple structure, these constructs lend themselves to paired computational studies that often help elucidate mechanisms of the observed behavior. However, tissue cultures of cardiomyocyte monolayers currently require the use of neonatal cells with ionic properties that change rapidly during development and have thus been poorly characterized and modeled to date. Recently, Kirkton and Bursac demonstrated the ability to create biosynthetic excitable tissues from genetically engineered and immortalized HEK293 cells with well-characterized electrical properties and the ability to propagate action potentials. In this study, we developed and validated a computational model of these excitable HEK293 cells (called "Ex293" cells) using existing electrophysiological data and a genetic search algorithm. In order to reproduce not only the mean but also the variability of experimental observations, we examined what sources of variation were required in the computational model. Random cell-to-cell and inter-monolayer variation in both ionic conductances and tissue conductivity was necessary to explain the experimentally observed variability in action potential shape and macroscopic conduction, and the spatial organization of cell-to-cell conductance variation was found to not impact macroscopic behavior; the resulting model accurately reproduces both normal and drug-modified conduction behavior. The development of a computational Ex293 cell and tissue model provides a novel framework to perform paired computational-experimental studies to study normal and abnormal conduction in multidimensional excitable tissue, and the methodology of modeling variation can be

  3. Accurate spectroscopic characterization of oxirane: A valuable route to its identification in Titan's atmosphere and the assignment of unidentified infrared bands

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Puzzarini, Cristina; Biczysko, Malgorzata; Bloino, Julien

    2014-04-20

    In an effort to provide an accurate spectroscopic characterization of oxirane, state-of-the-art computational methods and approaches have been employed to determine highly accurate fundamental vibrational frequencies and rotational parameters. Available experimental data were used to assess the reliability of our computations, and an accuracy on average of 10 cm{sup –1} for fundamental transitions as well as overtones and combination bands has been pointed out. Moving to rotational spectroscopy, relative discrepancies of 0.1%, 2%-3%, and 3%-4% were observed for rotational, quartic, and sextic centrifugal-distortion constants, respectively. We are therefore confident that the highly accurate spectroscopic data provided herein can be usefulmore » for identification of oxirane in Titan's atmosphere and the assignment of unidentified infrared bands. Since oxirane was already observed in the interstellar medium and some astronomical objects are characterized by very high D/H ratios, we also considered the accurate determination of the spectroscopic parameters for the mono-deuterated species, oxirane-d1. For the latter, an empirical scaling procedure allowed us to improve our computed data and to provide predictions for rotational transitions with a relative accuracy of about 0.02% (i.e., an uncertainty of about 40 MHz for a transition lying at 200 GHz).« less

  4. A convenient and accurate wide-range parameter relationship between Buckingham and Morse potential energy functions

    NASA Astrophysics Data System (ADS)

    Lim, Teik-Cheng; Dawson, James Alexander

    2018-05-01

    This study explores the close-range, short-range and long-range relationships between the parameters of the Morse and Buckingham potential energy functions. The results show that the close-range and short-range relationships are valid for bond compression and for very small changes in bond length, respectively, while the long-range relationship is valid for bond stretching. A wide-range relationship is proposed to combine the comparative advantages of the close-range, short-range and long-range parameter relationships. The wide-range relationship is useful for replacing the close-range, short-range and long-range parameter relationships, thereby preventing the undesired effects of potential energy jumps resulting from functional switching between the close-range, short-range and long-range interaction energies.

  5. Validation of potential fishing zone forecast using experimental fishing method in Tolo Bay, Central Sulawesi Province

    NASA Astrophysics Data System (ADS)

    Rintaka, W. E.; Susilo, E.

    2018-04-01

    The national scale of Indonesian Potential Fishing Zone (PFZ) forecast system has been established since 2000. Recent times this system use Single Image Edge Detection algorithm to automatically identify thermal front from remote sensing images. Its generate two fishing ground/FG criteria: FG (high probability) and potential fishing ground/PFG (medium/low probability). To quantify the accuracy of this algorithm, an experimental fishing/EF was carried out in Tolo Bay, Central Sulawesi Province at September 2016 the late southeast monsoon period by using a pole and line fishing vessel. Four fishing activities (P1, P2, P3, and P4) were conducted during this study at a different location nearby the PFZ forecast position, two of them had good results. Based on distance measurement, these locations P1 and P4 were associated with PFZ forecast position. They were associated with PFG and FG criteria. The distance between EF to P1 and P4 were 9.7 and 6.69 nautical miles. The amount of catch for each location was 850 and 900 kg, respectively. The other locations P2 and P3 were also associated with PFG criteria, but there was no catch. We conclude that the number of the catch is influenced by the distance from PFZ forecast position and criteria.

  6. 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.

  7. Development of a Strontium Magneto-Optical Trap for Probing Casimir-Polder Potentials

    NASA Astrophysics Data System (ADS)

    Martin, Paul J.

    In recent years, cold atoms have been the centerpiece of many remarkably sensitive measurements, and much effort has been made to devise miniaturized quantum sensors and quantum information processing devices. At small distances, however, mechanical effects of the quantum vacuum begin to significantly impact the behavior of the cold-atom systems. A better understanding of how surface composition and geometry affect Casimir and Casimir-Polder potentials would benefit future engineering of small-scale devices. Unfortunately, theoretical solutions are limited and the number of experimental techniques that can accurately detect such short-range forces is relatively small. We believe the exemplary properties of atomic strontium--which have enabled unprecedented frequency metrology in optical lattice clocks--make it an ideal candidate for probing slight spectroscopic perturbations caused by vacuum fluctuations. To that end, we have constructed a magneto-optical trap for strontium to enable future study of atom-surface potentials, and the apparatus and proposed detection scheme are discussed herein. Of special note is a passively stable external-cavity diode laser we developed that is both affordable and competitive with high-end commercial options.

  8. Reward-prospect interacts with trial-by-trial preparation for potential distraction

    PubMed Central

    Marini, Francesco; van den Berg, Berry; Woldorff, Marty G.

    2015-01-01

    When attending for impending visual stimuli, cognitive systems prepare to identify relevant information while ignoring irrelevant, potentially distracting input. Recent work (Marini et al., 2013) showed that a supramodal distracter-filtering mechanism is invoked in blocked designs involving expectation of possible distracter stimuli, although this entails a cost (distraction-filtering cost) on speeded performance when distracters are expected but not presented. Here we used an arrow-flanker task to study whether an analogous cost, potentially reflecting the recruitment of a specific distraction-filtering mechanism, occurs dynamically when potential distraction is cued trial-to-trial (cued distracter-expectation cost). In order to promote the maximal utilization of cue information by participants, in some experimental conditions the cue also signaled the possibility of earning a monetary reward for fast and accurate performance. This design also allowed us to investigate the interplay between anticipation for distracters and anticipation of reward, which is known to engender attentional preparation. Only in reward contexts did participants show a cued distracter-expectation cost, which was larger with higher reward prospect and when anticipation for both distracters and reward were manipulated trial-to-trial. Thus, these results indicate that reward prospect interacts with the distracter expectation during trial-by-trial preparatory processes for potential distraction. These findings highlight how reward guides cue-driven attentional preparation. PMID:26180506

  9. Reward-prospect interacts with trial-by-trial preparation for potential distraction.

    PubMed

    Marini, Francesco; van den Berg, Berry; Woldorff, Marty G

    2015-02-01

    When attending for impending visual stimuli, cognitive systems prepare to identify relevant information while ignoring irrelevant, potentially distracting input. Recent work (Marini et al., 2013) showed that a supramodal distracter-filtering mechanism is invoked in blocked designs involving expectation of possible distracter stimuli, although this entails a cost ( distraction-filtering cost ) on speeded performance when distracters are expected but not presented. Here we used an arrow-flanker task to study whether an analogous cost, potentially reflecting the recruitment of a specific distraction-filtering mechanism, occurs dynamically when potential distraction is cued trial-to-trial ( cued distracter-expectation cost ). In order to promote the maximal utilization of cue information by participants, in some experimental conditions the cue also signaled the possibility of earning a monetary reward for fast and accurate performance. This design also allowed us to investigate the interplay between anticipation for distracters and anticipation of reward, which is known to engender attentional preparation. Only in reward contexts did participants show a cued distracter-expectation cost, which was larger with higher reward prospect and when anticipation for both distracters and reward were manipulated trial-to-trial. Thus, these results indicate that reward prospect interacts with the distracter expectation during trial-by-trial preparatory processes for potential distraction. These findings highlight how reward guides cue-driven attentional preparation.

  10. Accurate path integration in continuous attractor network models of grid cells.

    PubMed

    Burak, Yoram; Fiete, Ila R

    2009-02-01

    Grid cells in the rat entorhinal cortex display strikingly regular firing responses to the animal's position in 2-D space and have been hypothesized to form the neural substrate for dead-reckoning. However, errors accumulate rapidly when velocity inputs are integrated in existing models of grid cell activity. To produce grid-cell-like responses, these models would require frequent resets triggered by external sensory cues. Such inadequacies, shared by various models, cast doubt on the dead-reckoning potential of the grid cell system. Here we focus on the question of accurate path integration, specifically in continuous attractor models of grid cell activity. We show, in contrast to previous models, that continuous attractor models can generate regular triangular grid responses, based on inputs that encode only the rat's velocity and heading direction. We consider the role of the network boundary in the integration performance of the network and show that both periodic and aperiodic networks are capable of accurate path integration, despite important differences in their attractor manifolds. We quantify the rate at which errors in the velocity integration accumulate as a function of network size and intrinsic noise within the network. With a plausible range of parameters and the inclusion of spike variability, our model networks can accurately integrate velocity inputs over a maximum of approximately 10-100 meters and approximately 1-10 minutes. These findings form a proof-of-concept that continuous attractor dynamics may underlie velocity integration in the dorsolateral medial entorhinal cortex. The simulations also generate pertinent upper bounds on the accuracy of integration that may be achieved by continuous attractor dynamics in the grid cell network. We suggest experiments to test the continuous attractor model and differentiate it from models in which single cells establish their responses independently of each other.

  11. Experimental Study of the NaK 3(1)Pi State.

    PubMed

    Laub; Mazsa; Webb; La Civita J; Prodan; Jabbour; Namiotka; Huennekens

    1999-02-01

    We report the results of an optical-optical double resonance experiment to determine the NaK 3(1)Pi state potential energy curve. In the first step, a narrow band cw dye laser (PUMP) is tuned to line center of a particular 2(A)1Sigma+(v', J') <-- 1(X)1Sigma+(v", J") transition, and its frequency is then fixed. A second narrowband tunable cw Ti:Sapphirelaser (PROBE) is then scanned, while 3(1)Pi --> 1(X)1Sigma+ violet fluorescence is monitored. The Doppler-free signals accurately map the 3(1)Pi(v, J) ro-vibrational energy levels. These energy levels are then fit to a Dunham expansion to provide a set of molecular constants. The Dunham constants, in turn, are used to construct an RKR potential curve. Resolved 3(1)Pi(v, J) --> 1(X)1Sigma+(v", J") fluorescence scans are also recorded with both PUMP and PROBE laser frequencies fixed. Comparison between observed and calculated Franck-Condon factors is used to determine the absolute vibrational numbering of the 3(1)Pi state levels and to determine the variation of the 3(1)Pi --> 1(X)1Sigma+ transitiondipole moment with internuclear separation. The recent theoretical calculation of the NaK 3(1)Pi state potential reported by Magnier and Millié (1996, Phys. Rev. A 54, 204) is in excellent agreement with the present experimental RKR curve. Copyright 1999 Academic Press.

  12. Magnetic gaps in organic tri-radicals: From a simple model to accurate estimates.

    PubMed

    Barone, Vincenzo; Cacelli, Ivo; Ferretti, Alessandro; Prampolini, Giacomo

    2017-03-14

    The calculation of the energy gap between the magnetic states of organic poly-radicals still represents a challenging playground for quantum chemistry, and high-level techniques are required to obtain accurate estimates. On these grounds, the aim of the present study is twofold. From the one side, it shows that, thanks to recent algorithmic and technical improvements, we are able to compute reliable quantum mechanical results for the systems of current fundamental and technological interest. From the other side, proper parameterization of a simple Hubbard Hamiltonian allows for a sound rationalization of magnetic gaps in terms of basic physical effects, unraveling the role played by electron delocalization, Coulomb repulsion, and effective exchange in tuning the magnetic character of the ground state. As case studies, we have chosen three prototypical organic tri-radicals, namely, 1,3,5-trimethylenebenzene, 1,3,5-tridehydrobenzene, and 1,2,3-tridehydrobenzene, which differ either for geometric or electronic structure. After discussing the differences among the three species and their consequences on the magnetic properties in terms of the simple model mentioned above, accurate and reliable values for the energy gap between the lowest quartet and doublet states are computed by means of the so-called difference dedicated configuration interaction (DDCI) technique, and the final results are discussed and compared to both available experimental and computational estimates.

  13. [Behavior of late ventricular potentials in acute experimental myocardial ischemia].

    PubMed

    Duck, H J; Pankau, H; Köhler, H

    1985-06-01

    Locally retarded depolarizations of the ischaemic myocardium are regarded as frequent trigger mechanisms of dangerous ventricular arrhythmias. Up to now, however, there are scarcely systematic investigations concerning their concrete developmental conditions in man, since late potentials can be made evident only by means of expensive invasive methods or signal mediation techniques. Therefore, an animal model should be built, which is suitable for the control of new therapy conceptions with antiarrhythmic drugs. The investigations were performed on 22 pigs in whom under insufflation anaesthesia altogether 10 pressure, flow and contractility parameters as well as 6 epicardial ECG signals were continuously recorded. The episodes of ischaemia were caused by LAD occlusions of different duration and intensity. Typical late potentials could be registered in 5 animals who all had survived complete interruptions of the coronary blood flow of longer than 10 min. The mean duration of the late potentials was 20 +/- 9.2 ms, their amplitudes reached from 150 to 600 microV. Also with regard to time and cycle constancy, the delay of the late Q-potential and the morphology they corresponded to the homogeneous phenomenon, known from man. They always could be derived only from electrodes outside the immediate zone of ischaemia. Neither partial occlusions nor complete interruption of the coronary blood flow in intervals shorter than 10 minutes led to the development of a late potential. The animal model used altogether appears very suitable to investigate the medicamentous influencibility of arrhythmogenic areas of the myocardium under direct control of the dynamic behaviour of ventricular late potentials.

  14. Experimental validation of flexible robot arm modeling and control

    NASA Technical Reports Server (NTRS)

    Ulsoy, A. Galip

    1989-01-01

    Flexibility is important for high speed, high precision operation of lightweight manipulators. Accurate dynamic modeling of flexible robot arms is needed. Previous work has mostly been based on linear elasticity with prescribed rigid body motions (i.e., no effect of flexible motion on rigid body motion). Little or no experimental validation of dynamic models for flexible arms is available. Experimental results are also limited for flexible arm control. Researchers include the effects of prismatic as well as revolute joints. They investigate the effect of full coupling between the rigid and flexible motions, and of axial shortening, and consider the control of flexible arms using only additional sensors.

  15. Data Mining for Efficient and Accurate Large Scale Retrieval of Geophysical Parameters

    NASA Astrophysics Data System (ADS)

    Obradovic, Z.; Vucetic, S.; Peng, K.; Han, B.

    2004-12-01

    Our effort is devoted to developing data mining technology for improving efficiency and accuracy of the geophysical parameter retrievals by learning a mapping from observation attributes to the corresponding parameters within the framework of classification and regression. We will describe a method for efficient learning of neural network-based classification and regression models from high-volume data streams. The proposed procedure automatically learns a series of neural networks of different complexities on smaller data stream chunks and then properly combines them into an ensemble predictor through averaging. Based on the idea of progressive sampling the proposed approach starts with a very simple network trained on a very small chunk and then gradually increases the model complexity and the chunk size until the learning performance no longer improves. Our empirical study on aerosol retrievals from data obtained with the MISR instrument mounted at Terra satellite suggests that the proposed method is successful in learning complex concepts from large data streams with near-optimal computational effort. We will also report on a method that complements deterministic retrievals by constructing accurate predictive algorithms and applying them on appropriately selected subsets of observed data. The method is based on developing more accurate predictors aimed to catch global and local properties synthesized in a region. The procedure starts by learning the global properties of data sampled over the entire space, and continues by constructing specialized models on selected localized regions. The global and local models are integrated through an automated procedure that determines the optimal trade-off between the two components with the objective of minimizing the overall mean square errors over a specific region. Our experimental results on MISR data showed that the combined model can increase the retrieval accuracy significantly. The preliminary results on various

  16. A new ab initio potential energy surface for the Ne-H 2 interaction

    NASA Astrophysics Data System (ADS)

    Lique, François

    2009-03-01

    A new accurate three-dimensional potential energy surface for the Ne-H 2 system, which explicitly takes into account the r-dependence of the H 2 vibration, was determined from ab initio calculations. It was obtained with the single and double excitation coupled-cluster method with noniterative perturbational treatment of triple excitation [CCSD(T)]. Calculations was been performed using the augmented correlation-consistent polarized quintuple zeta basis set (aug-cc-pV5Z) for the three atoms. We checked the accuracy of the present ab initio calculations. We have determined, using the new Ne-H 2 potential energy surface, differential cross-sections for the rotational excitation of the H 2 and D 2 molecules in collision with Ne and we have compared them with experimental results of Faubel et al. [M. Faubel, F.A. Gianturco, F. Ragnetti, L.Y. Rusin, F. Sondermann, U. Tappe, J.P. Toennies, J. Chem. Phys. 101 (1994) 8800]. The overall agreement confirms that the new potential energy surface can be used for the simulation of molecular collisions and/or molecular spectroscopy of the van der Waals complex Ne-H 2.

  17. Accurate estimations of electromagnetic transitions of Sn IV for stellar and interstellar media

    NASA Astrophysics Data System (ADS)

    Biswas, Swapan; Das, Arghya; Bhowmik, Anal; Majumder, Sonjoy

    2018-04-01

    Here we report on accurate ab initio calculations to study astrophysically important electromagnetic transition parameters among different low-lying states of Sn IV. Our ab initio calculations are based on the sophisticated relativistic coupled-cluster theory, which almost exhausts many important electron correlations. To establish the accuracy of the calculations, we compare our results with the available experiments and estimates the transition amplitudes in length and velocity gauged forms. Most of these allowed and forbidden transition wavelengths lie in the infrared region, and they can be observed in the different cool stellar and interstellar media. For the improvement of uncertainty, we use experimental energies to the estimations of the above transition parameters. The presented data will be helpful to find the abundances of the ion in different astrophysical and laboratory plasma.

  18. Apparatus for accurate density measurements of fluids based on a magnetic suspension balance

    NASA Astrophysics Data System (ADS)

    Gong, Maoqiong; Li, Huiya; Guo, Hao; Dong, Xueqiang; Wu, J. F.

    2012-06-01

    A new apparatus for accurate pressure, density and temperature (p, ρ, T) measurements over wide ranges of (p, ρ, T) (90 K to 290 K; 0 MPa to 3 MPa; 0 kg/m3 to 2000 kg/m3) is described. This apparatus is based on a magnetic suspension balance which applies the Archimedes' buoyancy principle. In order to verify the new apparatus, comprehensive (p, ρ, T) measurements on pure nitrogen were carried out. The maximum relative standard uncertainty is 0.09% in density. The maximum standard uncertainty in temperature is 5 mK, and that in pressure is 250 Pa for 1.5 MPa and 390 Pa for 3MPa full scale range respectively. The experimental data were compared with selected literature data and good agreements were found.

  19. Accurate estimations of electromagnetic transitions of Sn IV for stellar and interstellar media

    NASA Astrophysics Data System (ADS)

    Biswas, Swapan; Das, Arghya; Bhowmik, Anal; Majumder, Sonjoy

    2018-07-01

    Here, we report on accurate ab initio calculations to study astrophysically important electromagnetic transition parameters among different low-lying states of Sn IV. Our ab initio calculations are based on the sophisticated relativistic coupled cluster theory, which almost exhausts many important electron correlations. To establish the accuracy of the calculations, we compare our results with the available experiments and estimate the transition amplitudes in length and velocity gauged forms. Most of these allowed and forbidden transition wavelengths lie in the infrared region, and they can be observed in the different cool stellar and interstellar media. For the improvement of uncertainty, we use experimental energies to the estimations of the above transition parameters. The presented data will be helpful to find the abundances of the ion in different astrophysical and laboratory plasma.

  20. Fast and accurate automated cell boundary determination for fluorescence microscopy

    NASA Astrophysics Data System (ADS)

    Arce, Stephen Hugo; Wu, Pei-Hsun; Tseng, Yiider

    2013-07-01

    Detailed measurement of cell phenotype information from digital fluorescence images has the potential to greatly advance biomedicine in various disciplines such as patient diagnostics or drug screening. Yet, the complexity of cell conformations presents a major barrier preventing effective determination of cell boundaries, and introduces measurement error that propagates throughout subsequent assessment of cellular parameters and statistical analysis. State-of-the-art image segmentation techniques that require user-interaction, prolonged computation time and specialized training cannot adequately provide the support for high content platforms, which often sacrifice resolution to foster the speedy collection of massive amounts of cellular data. This work introduces a strategy that allows us to rapidly obtain accurate cell boundaries from digital fluorescent images in an automated format. Hence, this new method has broad applicability to promote biotechnology.

  1. Non-invasive prenatal diagnosis of achondroplasia and thanatophoric dysplasia: next-generation sequencing allows for a safer, more accurate, and comprehensive approach

    PubMed Central

    Chitty, Lyn S; Mason, Sarah; Barrett, Angela N; McKay, Fiona; Lench, Nicholas; Daley, Rebecca; Jenkins, Lucy A

    2015-01-01

    Abstract Objective Accurate prenatal diagnosis of genetic conditions can be challenging and usually requires invasive testing. Here, we demonstrate the potential of next-generation sequencing (NGS) for the analysis of cell-free DNA in maternal blood to transform prenatal diagnosis of monogenic disorders. Methods Analysis of cell-free DNA using a PCR and restriction enzyme digest (PCR–RED) was compared with a novel NGS assay in pregnancies at risk of achondroplasia and thanatophoric dysplasia. Results PCR–RED was performed in 72 cases and was correct in 88.6%, inconclusive in 7% with one false negative. NGS was performed in 47 cases and was accurate in 96.2% with no inconclusives. Both approaches were used in 27 cases, with NGS giving the correct result in the two cases inconclusive with PCR–RED. Conclusion NGS provides an accurate, flexible approach to non-invasive prenatal diagnosis of de novo and paternally inherited mutations. It is more sensitive than PCR–RED and is ideal when screening a gene with multiple potential pathogenic mutations. These findings highlight the value of NGS in the development of non-invasive prenatal diagnosis for other monogenic disorders. © 2015 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd. What's already known about this topic? Non-invasive prenatal diagnosis (NIPD) using PCR-based methods has been reported for the detection or exclusion of individual paternally inherited or de novo alleles in maternal plasma. What does this study add? NIPD using next generation sequencing provides an accurate, more sensitive approach which can be used to detect multiple mutations in a single assay and so is ideal when screening a gene with multiple potential pathogenic mutations. Next generation sequencing thus provides a flexible approach to non-invasive prenatal diagnosis ideal for use in a busy service laboratory. PMID:25728633

  2. Experimental confirmation of long-memory correlations in star-wander data.

    PubMed

    Zunino, Luciano; Gulich, Damián; Funes, Gustavo; Ziad, Aziz

    2014-07-01

    In this Letter we have analyzed the temporal correlations of the angle-of-arrival fluctuations of stellar images. Experimentally measured data were carefully examined by implementing multifractal detrended fluctuation analysis. This algorithm is able to discriminate the presence of fractal and multifractal structures in recorded time sequences. We have confirmed that turbulence-degraded stellar wavefronts are compatible with a long-memory correlated monofractal process. This experimental result is quite significant for the accurate comprehension and modeling of the atmospheric turbulence effects on the stellar images. It can also be of great utility within the adaptive optics field.

  3. Non-invasive prenatal diagnosis of achondroplasia and thanatophoric dysplasia: next-generation sequencing allows for a safer, more accurate, and comprehensive approach.

    PubMed

    Chitty, Lyn S; Mason, Sarah; Barrett, Angela N; McKay, Fiona; Lench, Nicholas; Daley, Rebecca; Jenkins, Lucy A

    2015-07-01

    Accurate prenatal diagnosis of genetic conditions can be challenging and usually requires invasive testing. Here, we demonstrate the potential of next-generation sequencing (NGS) for the analysis of cell-free DNA in maternal blood to transform prenatal diagnosis of monogenic disorders. Analysis of cell-free DNA using a PCR and restriction enzyme digest (PCR-RED) was compared with a novel NGS assay in pregnancies at risk of achondroplasia and thanatophoric dysplasia. PCR-RED was performed in 72 cases and was correct in 88.6%, inconclusive in 7% with one false negative. NGS was performed in 47 cases and was accurate in 96.2% with no inconclusives. Both approaches were used in 27 cases, with NGS giving the correct result in the two cases inconclusive with PCR-RED. NGS provides an accurate, flexible approach to non-invasive prenatal diagnosis of de novo and paternally inherited mutations. It is more sensitive than PCR-RED and is ideal when screening a gene with multiple potential pathogenic mutations. These findings highlight the value of NGS in the development of non-invasive prenatal diagnosis for other monogenic disorders. © 2015 John Wiley & Sons, Ltd.

  4. Thermodynamic modeling and experimental validation of the Fe-Al-Ni-Cr-Mo alloy system

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Teng, Zhenke; Zhang, F; Miller, Michael K

    2012-01-01

    NiAl-type precipitate-strengthened ferritic steels have been known as potential materials for the steam turbine applications. In this study, thermodynamic descriptions of the B2-NiAl type nano-scaled precipitates and body-centered-cubic (BCC) Fe matrix phase for four alloys based on the Fe-Al-Ni-Cr-Mo system were developed as a function of the alloy composition at the aging temperature. The calculated phase structure, composition, and volume fraction were validated by the experimental investigations using synchrotron X-ray diffraction and atom probe tomography. With the ability to accurately predict the key microstructural features related to the mechanical properties in a given alloy system, the established thermodynamic model inmore » the current study may significantly accelerate the alloy design process of the NiAl-strengthened ferritic steels.« less

  5. Active machine learning-driven experimentation to determine compound effects on protein patterns.

    PubMed

    Naik, Armaghan W; Kangas, Joshua D; Sullivan, Devin P; Murphy, Robert F

    2016-02-03

    High throughput screening determines the effects of many conditions on a given biological target. Currently, to estimate the effects of those conditions on other targets requires either strong modeling assumptions (e.g. similarities among targets) or separate screens. Ideally, data-driven experimentation could be used to learn accurate models for many conditions and targets without doing all possible experiments. We have previously described an active machine learning algorithm that can iteratively choose small sets of experiments to learn models of multiple effects. We now show that, with no prior knowledge and with liquid handling robotics and automated microscopy under its control, this learner accurately learned the effects of 48 chemical compounds on the subcellular localization of 48 proteins while performing only 29% of all possible experiments. The results represent the first practical demonstration of the utility of active learning-driven biological experimentation in which the set of possible phenotypes is unknown in advance.

  6. Active machine learning-driven experimentation to determine compound effects on protein patterns

    PubMed Central

    Naik, Armaghan W; Kangas, Joshua D; Sullivan, Devin P; Murphy, Robert F

    2016-01-01

    High throughput screening determines the effects of many conditions on a given biological target. Currently, to estimate the effects of those conditions on other targets requires either strong modeling assumptions (e.g. similarities among targets) or separate screens. Ideally, data-driven experimentation could be used to learn accurate models for many conditions and targets without doing all possible experiments. We have previously described an active machine learning algorithm that can iteratively choose small sets of experiments to learn models of multiple effects. We now show that, with no prior knowledge and with liquid handling robotics and automated microscopy under its control, this learner accurately learned the effects of 48 chemical compounds on the subcellular localization of 48 proteins while performing only 29% of all possible experiments. The results represent the first practical demonstration of the utility of active learning-driven biological experimentation in which the set of possible phenotypes is unknown in advance. DOI: http://dx.doi.org/10.7554/eLife.10047.001 PMID:26840049

  7. Calibrating GPS With TWSTFT For Accurate Time Transfer

    DTIC Science & Technology

    2008-12-01

    40th Annual Precise Time and Time Interval (PTTI) Meeting 577 CALIBRATING GPS WITH TWSTFT FOR ACCURATE TIME TRANSFER Z. Jiang1 and...primary time transfer techniques are GPS and TWSTFT (Two-Way Satellite Time and Frequency Transfer, TW for short). 83% of UTC time links are...Calibrating GPS With TWSTFT For Accurate Time Transfer 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT

  8. An accurate method for evaluating the kernel of the integral equation relating lift to downwash in unsteady potential flow

    NASA Technical Reports Server (NTRS)

    Desmarais, R. N.

    1982-01-01

    The method is capable of generating approximations of arbitrary accuracy. It is based on approximating the algebraic part of the nonelementary integrals in the kernel by exponential functions and then integrating termwise. The exponent spacing in the approximation is a geometric sequence. The coefficients and exponent multiplier of the exponential approximation are computed by least squares so the method is completely automated. Exponential approximates generated in this manner are two orders of magnitude more accurate than the exponential approximation that is currently most often used for this purpose. The method can be used to generate approximations to attain any desired trade-off between accuracy and computing cost.

  9. Mental models accurately predict emotion transitions.

    PubMed

    Thornton, Mark A; Tamir, Diana I

    2017-06-06

    Successful social interactions depend on people's ability to predict others' future actions and emotions. People possess many mechanisms for perceiving others' current emotional states, but how might they use this information to predict others' future states? We hypothesized that people might capitalize on an overlooked aspect of affective experience: current emotions predict future emotions. By attending to regularities in emotion transitions, perceivers might develop accurate mental models of others' emotional dynamics. People could then use these mental models of emotion transitions to predict others' future emotions from currently observable emotions. To test this hypothesis, studies 1-3 used data from three extant experience-sampling datasets to establish the actual rates of emotional transitions. We then collected three parallel datasets in which participants rated the transition likelihoods between the same set of emotions. Participants' ratings of emotion transitions predicted others' experienced transitional likelihoods with high accuracy. Study 4 demonstrated that four conceptual dimensions of mental state representation-valence, social impact, rationality, and human mind-inform participants' mental models. Study 5 used 2 million emotion reports on the Experience Project to replicate both of these findings: again people reported accurate models of emotion transitions, and these models were informed by the same four conceptual dimensions. Importantly, neither these conceptual dimensions nor holistic similarity could fully explain participants' accuracy, suggesting that their mental models contain accurate information about emotion dynamics above and beyond what might be predicted by static emotion knowledge alone.

  10. Mental models accurately predict emotion transitions

    PubMed Central

    Thornton, Mark A.; Tamir, Diana I.

    2017-01-01

    Successful social interactions depend on people’s ability to predict others’ future actions and emotions. People possess many mechanisms for perceiving others’ current emotional states, but how might they use this information to predict others’ future states? We hypothesized that people might capitalize on an overlooked aspect of affective experience: current emotions predict future emotions. By attending to regularities in emotion transitions, perceivers might develop accurate mental models of others’ emotional dynamics. People could then use these mental models of emotion transitions to predict others’ future emotions from currently observable emotions. To test this hypothesis, studies 1–3 used data from three extant experience-sampling datasets to establish the actual rates of emotional transitions. We then collected three parallel datasets in which participants rated the transition likelihoods between the same set of emotions. Participants’ ratings of emotion transitions predicted others’ experienced transitional likelihoods with high accuracy. Study 4 demonstrated that four conceptual dimensions of mental state representation—valence, social impact, rationality, and human mind—inform participants’ mental models. Study 5 used 2 million emotion reports on the Experience Project to replicate both of these findings: again people reported accurate models of emotion transitions, and these models were informed by the same four conceptual dimensions. Importantly, neither these conceptual dimensions nor holistic similarity could fully explain participants’ accuracy, suggesting that their mental models contain accurate information about emotion dynamics above and beyond what might be predicted by static emotion knowledge alone. PMID:28533373

  11. Efficient and Adaptive Methods for Computing Accurate Potential Surfaces for Quantum Nuclear Effects: Applications to Hydrogen-Transfer Reactions.

    PubMed

    DeGregorio, Nicole; Iyengar, Srinivasan S

    2018-01-09

    We present two sampling measures to gauge critical regions of potential energy surfaces. These sampling measures employ (a) the instantaneous quantum wavepacket density, an approximation to the (b) potential surface, its (c) gradients, and (d) a Shannon information theory based expression that estimates the local entropy associated with the quantum wavepacket. These four criteria together enable a directed sampling of potential surfaces that appears to correctly describe the local oscillation frequencies, or the local Nyquist frequency, of a potential surface. The sampling functions are then utilized to derive a tessellation scheme that discretizes the multidimensional space to enable efficient sampling of potential surfaces. The sampled potential surface is then combined with four different interpolation procedures, namely, (a) local Hermite curve interpolation, (b) low-pass filtered Lagrange interpolation, (c) the monomial symmetrization approximation (MSA) developed by Bowman and co-workers, and (d) a modified Shepard algorithm. The sampling procedure and the fitting schemes are used to compute (a) potential surfaces in highly anharmonic hydrogen-bonded systems and (b) study hydrogen-transfer reactions in biogenic volatile organic compounds (isoprene) where the transferring hydrogen atom is found to demonstrate critical quantum nuclear effects. In the case of isoprene, the algorithm discussed here is used to derive multidimensional potential surfaces along a hydrogen-transfer reaction path to gauge the effect of quantum-nuclear degrees of freedom on the hydrogen-transfer process. Based on the decreased computational effort, facilitated by the optimal sampling of the potential surfaces through the use of sampling functions discussed here, and the accuracy of the associated potential surfaces, we believe the method will find great utility in the study of quantum nuclear dynamics problems, of which application to hydrogen-transfer reactions and hydrogen

  12. Students' views about the nature of experimental physics

    NASA Astrophysics Data System (ADS)

    Wilcox, Bethany R.; Lewandowski, H. J.

    2017-12-01

    The physics community explores and explains the physical world through a blend of theoretical and experimental studies. The future of physics as a discipline depends on training of students in both the theoretical and experimental aspects of the field. However, while student learning within lecture courses has been the subject of extensive research, lab courses remain relatively under-studied. In particular, there is little, if any, data available that address the effectiveness of physics lab courses at encouraging students to recognize the nature and importance of experimental physics within the discipline as a whole. To address this gap, we present the first large-scale, national study (Ninstitutions=75 and Nstudents=7167 ) of undergraduate physics lab courses through analysis of students' responses to a research-validated assessment designed to investigate students' beliefs about the nature of experimental physics. We find that students often enter and leave physics lab courses with ideas about experimental physics as practiced in their courses that are inconsistent with the views of practicing experimental physicists, and this trend holds at both the introductory and upper-division levels. Despite this inconsistency, we find that both introductory and upper-division students are able to accurately predict the expertlike response even in cases where their views about experimentation in their lab courses disagree. These finding have implications for the recruitment, retention, and adequate preparation of students in physics.

  13. Cumulative atomic multipole moments complement any atomic charge model to obtain more accurate electrostatic properties

    NASA Technical Reports Server (NTRS)

    Sokalski, W. A.; Shibata, M.; Ornstein, R. L.; Rein, R.

    1992-01-01

    The quality of several atomic charge models based on different definitions has been analyzed using cumulative atomic multipole moments (CAMM). This formalism can generate higher atomic moments starting from any atomic charges, while preserving the corresponding molecular moments. The atomic charge contribution to the higher molecular moments, as well as to the electrostatic potentials, has been examined for CO and HCN molecules at several different levels of theory. The results clearly show that the electrostatic potential obtained from CAMM expansion is convergent up to R-5 term for all atomic charge models used. This illustrates that higher atomic moments can be used to supplement any atomic charge model to obtain more accurate description of electrostatic properties.

  14. Experimental constrain of hydrogen production during early serpentinization stages

    NASA Astrophysics Data System (ADS)

    Clément, M.; Munoz, M.; Vidal, O.; Parra, T.

    2009-04-01

    Hydrothermal alteration of mantellic peridotites and ultramafic rocks along axial valleys of low spread oceanic ridges plays a key role in different fundamental domains like, 1) energetic gaz production (H2 and hydrocarbons) representing a potential source of energy for future generations, 2) formation of organic pre-biotic molecules in potential relation with the origin of life. Moreover, such complex volcanic-related alteration processes play fundamental role in economic geology, being widely associated to important polymetallic sulphides ore deposits. Recent researches proposed an initial hydrogen production due to the integration of ferric iron in Fe,Mg-serpentine. To better understand the early stages of hydrogen production, a series of natural peridotite rocks have been experimentally exposed to hydrothermal conditions, up to 300°C, 300 bars during different time scales. Experiments have been performed in using autoclaves with a sampling gas system. A systematic mineralogical characterization of the new products was carried out using classical spectroscopic tools. In particular, we focused on the iron behaviour using a redox and structural micro-XANES investigation. Redox information has been accurately derived from the pre-peak features previously calibrated from model compounds, while structural information about short and medium range order around iron has been extracted from the XANES region of the spectra, based both on experimental standards and ab-initio theoretical calculations. Two processes of oxidation emerged. Before two month experiment duration, serpentine displays a not negligible oxidation of ferrous iron in his structure (up to 60%), while after two months, iron oxides and hydroxides appear in the system. These results seem to correspond to natural observations. The iron coordination decreases linearly with time. It means that iron also integrates the serpentine tetrahedral sites. Moreover, high resolution µ-XAS maps on experimental samples

  15. Assessment of Experimental Uncertainty for a Floating Wind Semisubmersible under Hydrodynamic Loading: Preprint

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Robertson, Amy N; Wendt, Fabian F; Jonkman, Jason

    The objective of this paper is to assess the sources of experimental uncertainty in an offshore wind validation campaign focused on better understanding the nonlinear hydrodynamic response behavior of a floating semisubmersible. The test specimen and conditions were simplified compared to other floating wind test campaigns to reduce potential sources of uncertainties and better focus on the hydrodynamic load attributes. Repeat tests were used to understand the repeatability of the test conditions and to assess the level of random uncertainty in the measurements. Attention was also given to understanding bias in all components of the test. The end goal ofmore » this work is to set uncertainty bounds on the response metrics of interest, which will be used in future work to evaluate the success of modeling tools in accurately calculating hydrodynamic loads and the associated motion responses of the system.« less

  16. DNA barcode data accurately assign higher spider taxa

    PubMed Central

    Coddington, Jonathan A.; Agnarsson, Ingi; Cheng, Ren-Chung; Čandek, Klemen; Driskell, Amy; Frick, Holger; Gregorič, Matjaž; Kostanjšek, Rok; Kropf, Christian; Kweskin, Matthew; Lokovšek, Tjaša; Pipan, Miha; Vidergar, Nina

    2016-01-01

    The use of unique DNA sequences as a method for taxonomic identification is no longer fundamentally controversial, even though debate continues on the best markers, methods, and technology to use. Although both existing databanks such as GenBank and BOLD, as well as reference taxonomies, are imperfect, in best case scenarios “barcodes” (whether single or multiple, organelle or nuclear, loci) clearly are an increasingly fast and inexpensive method of identification, especially as compared to manual identification of unknowns by increasingly rare expert taxonomists. Because most species on Earth are undescribed, a complete reference database at the species level is impractical in the near term. The question therefore arises whether unidentified species can, using DNA barcodes, be accurately assigned to more inclusive groups such as genera and families—taxonomic ranks of putatively monophyletic groups for which the global inventory is more complete and stable. We used a carefully chosen test library of CO1 sequences from 49 families, 313 genera, and 816 species of spiders to assess the accuracy of genus and family-level assignment. We used BLAST queries of each sequence against the entire library and got the top ten hits. The percent sequence identity was reported from these hits (PIdent, range 75–100%). Accurate assignment of higher taxa (PIdent above which errors totaled less than 5%) occurred for genera at PIdent values >95 and families at PIdent values ≥ 91, suggesting these as heuristic thresholds for accurate generic and familial identifications in spiders. Accuracy of identification increases with numbers of species/genus and genera/family in the library; above five genera per family and fifteen species per genus all higher taxon assignments were correct. We propose that using percent sequence identity between conventional barcode sequences may be a feasible and reasonably accurate method to identify animals to family/genus. However, the quality of

  17. Development of anatomically and dielectrically accurate breast phantoms for microwave imaging applications

    NASA Astrophysics Data System (ADS)

    O'Halloran, M.; Lohfeld, S.; Ruvio, G.; Browne, J.; Krewer, F.; Ribeiro, C. O.; Inacio Pita, V. C.; Conceicao, R. C.; Jones, E.; Glavin, M.

    2014-05-01

    Breast cancer is one of the most common cancers in women. In the United States alone, it accounts for 31% of new cancer cases, and is second only to lung cancer as the leading cause of deaths in American women. More than 184,000 new cases of breast cancer are diagnosed each year resulting in approximately 41,000 deaths. Early detection and intervention is one of the most significant factors in improving the survival rates and quality of life experienced by breast cancer sufferers, since this is the time when treatment is most effective. One of the most promising breast imaging modalities is microwave imaging. The physical basis of active microwave imaging is the dielectric contrast between normal and malignant breast tissue that exists at microwave frequencies. The dielectric contrast is mainly due to the increased water content present in the cancerous tissue. Microwave imaging is non-ionizing, does not require breast compression, is less invasive than X-ray mammography, and is potentially low cost. While several prototype microwave breast imaging systems are currently in various stages of development, the design and fabrication of anatomically and dielectrically representative breast phantoms to evaluate these systems is often problematic. While some existing phantoms are composed of dielectrically representative materials, they rarely accurately represent the shape and size of a typical breast. Conversely, several phantoms have been developed to accurately model the shape of the human breast, but have inappropriate dielectric properties. This study will brie y review existing phantoms before describing the development of a more accurate and practical breast phantom for the evaluation of microwave breast imaging systems.

  18. Classical calculation of the equilibrium constants for true bound dimers using complete potential energy surface.

    PubMed

    Buryak, Ilya; Vigasin, Andrey A

    2015-12-21

    The present paper aims at deriving classical expressions which permit calculation of the equilibrium constant for weakly interacting molecular pairs using a complete multidimensional potential energy surface. The latter is often available nowadays as a result of the more and more sophisticated and accurate ab initio calculations. The water dimer formation is considered as an example. It is shown that even in case of a rather strongly bound dimer the suggested expression permits obtaining quite reliable estimate for the equilibrium constant. The reliability of our obtained water dimer equilibrium constant is briefly discussed by comparison with the available data based on experimental observations, quantum calculations, and the use of RRHO approximation, provided the latter is restricted to formation of true bound states only.

  19. Novel nonlinear knowledge-based mean force potentials based on machine learning.

    PubMed

    Dong, Qiwen; Zhou, Shuigeng

    2011-01-01

    The prediction of 3D structures of proteins from amino acid sequences is one of the most challenging problems in molecular biology. An essential task for solving this problem with coarse-grained models is to deduce effective interaction potentials. The development and evaluation of new energy functions is critical to accurately modeling the properties of biological macromolecules. Knowledge-based mean force potentials are derived from statistical analysis of proteins of known structures. Current knowledge-based potentials are almost in the form of weighted linear sum of interaction pairs. In this study, a class of novel nonlinear knowledge-based mean force potentials is presented. The potential parameters are obtained by nonlinear classifiers, instead of relative frequencies of interaction pairs against a reference state or linear classifiers. The support vector machine is used to derive the potential parameters on data sets that contain both native structures and decoy structures. Five knowledge-based mean force Boltzmann-based or linear potentials are introduced and their corresponding nonlinear potentials are implemented. They are the DIH potential (single-body residue-level Boltzmann-based potential), the DFIRE-SCM potential (two-body residue-level Boltzmann-based potential), the FS potential (two-body atom-level Boltzmann-based potential), the HR potential (two-body residue-level linear potential), and the T32S3 potential (two-body atom-level linear potential). Experiments are performed on well-established decoy sets, including the LKF data set, the CASP7 data set, and the Decoys “R”Us data set. The evaluation metrics include the energy Z score and the ability of each potential to discriminate native structures from a set of decoy structures. Experimental results show that all nonlinear potentials significantly outperform the corresponding Boltzmann-based or linear potentials, and the proposed discriminative framework is effective in developing knowledge

  20. Extracting Time-Accurate Acceleration Vectors From Nontrivial Accelerometer Arrangements.

    PubMed

    Franck, Jennifer A; Blume, Janet; Crisco, Joseph J; Franck, Christian

    2015-09-01

    Sports-related concussions are of significant concern in many impact sports, and their detection relies on accurate measurements of the head kinematics during impact. Among the most prevalent recording technologies are videography, and more recently, the use of single-axis accelerometers mounted in a helmet, such as the HIT system. Successful extraction of the linear and angular impact accelerations depends on an accurate analysis methodology governed by the equations of motion. Current algorithms are able to estimate the magnitude of acceleration and hit location, but make assumptions about the hit orientation and are often limited in the position and/or orientation of the accelerometers. The newly formulated algorithm presented in this manuscript accurately extracts the full linear and rotational acceleration vectors from a broad arrangement of six single-axis accelerometers directly from the governing set of kinematic equations. The new formulation linearizes the nonlinear centripetal acceleration term with a finite-difference approximation and provides a fast and accurate solution for all six components of acceleration over long time periods (>250 ms). The approximation of the nonlinear centripetal acceleration term provides an accurate computation of the rotational velocity as a function of time and allows for reconstruction of a multiple-impact signal. Furthermore, the algorithm determines the impact location and orientation and can distinguish between glancing, high rotational velocity impacts, or direct impacts through the center of mass. Results are shown for ten simulated impact locations on a headform geometry computed with three different accelerometer configurations in varying degrees of signal noise. Since the algorithm does not require simplifications of the actual impacted geometry, the impact vector, or a specific arrangement of accelerometer orientations, it can be easily applied to many impact investigations in which accurate kinematics need