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Sample records for accurate interaction potentials

  1. Accurate first principles model potentials for intermolecular interactions.

    PubMed

    Gordon, Mark S; Smith, Quentin A; Xu, Peng; Slipchenko, Lyudmila V

    2013-01-01

    The general effective fragment potential (EFP) method provides model potentials for any molecule that is derived from first principles, with no empirically fitted parameters. The EFP method has been interfaced with most currently used ab initio single-reference and multireference quantum mechanics (QM) methods, ranging from Hartree-Fock and coupled cluster theory to multireference perturbation theory. The most recent innovations in the EFP model have been to make the computationally expensive charge transfer term much more efficient and to interface the general EFP dispersion and exchange repulsion interactions with QM methods. Following a summary of the method and its implementation in generally available computer programs, these most recent new developments are discussed.

  2. Cation-π interactions: accurate intermolecular potential from symmetry-adapted perturbation theory.

    PubMed

    Ansorg, Kay; Tafipolsky, Maxim; Engels, Bernd

    2013-09-01

    Symmetry-adapted perturbation theory (SAPT) is used to decompose the total intermolecular interaction energy between the ammonium cation and a benzene molecule into four physically motivated individual contributions: electrostatics, exchange, dispersion, and induction. Based on this rigorous decomposition, it is shown unambiguously that both the electrostatic and the induction energy components contribute almost equally to the attractive forces stabilizing the dimer with a nonnegligible contribution coming from the dispersion term. A polarizable potential model for the interaction of ammonium cation with benzene is parametrized by fitting these four energy components separately using the functional forms of the AMOEBA force field augmented with the missing charge penetration energy term calculated as a sum over pairwise electrostatic energies between spherical atoms. It is shown that the proposed model is able to produce accurate intermolecular interaction energies as compared to ab initio results, thus avoiding error compensation to a large extent.

  3. Accurate and Efficient Calculation of van der Waals Interactions Within Density Functional Theory by Local Atomic Potential Approach

    SciTech Connect

    Sun, Y. Y.; Kim, Y. H.; Lee, K.; Zhang, S. B.

    2008-01-01

    Density functional theory (DFT) in the commonly used local density or generalized gradient approximation fails to describe van der Waals (vdW) interactions that are vital to organic, biological, and other molecular systems. Here, we propose a simple, efficient, yet accurate local atomic potential (LAP) approach, named DFT+LAP, for including vdW interactions in the framework of DFT. The LAPs for H, C, N, and O are generated by fitting the DFT+LAP potential energy curves of small molecule dimers to those obtained from coupled cluster calculations with single, double, and perturbatively treated triple excitations, CCSD(T). Excellent transferability of the LAPs is demonstrated by remarkable agreement with the JSCH-2005 benchmark database [P. Jurecka et al. Phys. Chem. Chem. Phys. 8, 1985 (2006)], which provides the interaction energies of CCSD(T) quality for 165 vdW and hydrogen-bonded complexes. For over 100 vdW dominant complexes in this database, our DFT+LAP calculations give a mean absolute deviation from the benchmark results less than 0.5 kcal/mol. The DFT+LAP approach involves no extra computational cost other than standard DFT calculations and no modification of existing DFT codes, which enables straightforward quantum simulations, such as ab initio molecular dynamics, on biomolecular systems, as well as on other organic systems.

  4. Small and efficient basis sets for the evaluation of accurate interaction energies: aromatic molecule-argon ground-state intermolecular potentials and rovibrational states.

    PubMed

    Cybulski, Hubert; Baranowska-Łączkowska, Angelika; Henriksen, Christian; Fernández, Berta

    2014-11-01

    By evaluating a representative set of CCSD(T) ground state interaction energies for van der Waals dimers formed by aromatic molecules and the argon atom, we test the performance of the polarized basis sets of Sadlej et al. (J. Comput. Chem. 2005, 26, 145; Collect. Czech. Chem. Commun. 1988, 53, 1995) and the augmented polarization-consistent bases of Jensen (J. Chem. Phys. 2002, 117, 9234) in providing accurate intermolecular potentials for the benzene-, naphthalene-, and anthracene-argon complexes. The basis sets are extended by addition of midbond functions. As reference we consider CCSD(T) results obtained with Dunning's bases. For the benzene complex a systematic basis set study resulted in the selection of the (Z)Pol-33211 and the aug-pc-1-33321 bases to obtain the intermolecular potential energy surface. The interaction energy values and the shape of the CCSD(T)/(Z)Pol-33211 calculated potential are very close to the best available CCSD(T)/aug-cc-pVTZ-33211 potential with the former basis set being considerably smaller. The corresponding differences for the CCSD(T)/aug-pc-1-33321 potential are larger. In the case of the naphthalene-argon complex, following a similar study, we selected the (Z)Pol-3322 and aug-pc-1-333221 bases. The potentials show four symmetric absolute minima with energies of -483.2 cm(-1) for the (Z)Pol-3322 and -486.7 cm(-1) for the aug-pc-1-333221 basis set. To further check the performance of the selected basis sets, we evaluate intermolecular bound states of the complexes. The differences between calculated vibrational levels using the CCSD(T)/(Z)Pol-33211 and CCSD(T)/aug-cc-pVTZ-33211 benzene-argon potentials are small and for the lowest energy levels do not exceed 0.70 cm(-1). Such differences are substantially larger for the CCSD(T)/aug-pc-1-33321 calculated potential. For naphthalene-argon, bound state calculations demonstrate that the (Z)Pol-3322 and aug-pc-1-333221 potentials are of similar quality. The results show that these

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

    SciTech Connect

    Li, Y.; Krieger, J.B. ); Norman, M.R. ); Iafrate, G.J. )

    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 is 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.

  6. An accurate potential energy curve for helium based on ab initio calculations

    NASA Astrophysics Data System (ADS)

    Janzen, A. R.; Aziz, R. A.

    1997-07-01

    Korona, Williams, Bukowski, Jeziorski, and Szalewicz [J. Chem. Phys. 106, 1 (1997)] constructed a completely ab initio potential for He2 by fitting their calculations using infinite order symmetry adapted perturbation theory at intermediate range, existing Green's function Monte Carlo calculations at short range and accurate dispersion coefficients at long range to a modified Tang-Toennies potential form. The potential with retardation added to the dipole-dipole dispersion is found to predict accurately a large set of microscopic and macroscopic experimental data. The potential with a significantly larger well depth than other recent potentials is judged to be the most accurate characterization of the helium interaction yet proposed.

  7. Accurate momentum transfer cross section for the attractive Yukawa potential

    SciTech Connect

    Khrapak, S. A.

    2014-04-15

    Accurate expression for the momentum transfer cross section for the attractive Yukawa potential is proposed. This simple analytic expression agrees with the numerical results better than to within ±2% in the regime relevant for ion-particle collisions in complex (dusty) plasmas.

  8. On the use of explicitly correlated treatment methods for the generation of accurate polyatomic -He/H2 interaction potential energy surfaces: The case of C3-He complex and generalization

    NASA Astrophysics Data System (ADS)

    Al Mogren, M. M.; Denis-Alpizar, O.; Abdallah, D. Ben; Stoecklin, T.; Halvick, P.; Senent, M.-L.; Hochlaf, M.

    2014-07-01

    Through the study of the C3({tilde X}1Σg+) + He(1S) astrophysical relevant system using standard (CCSD(T)) and explicitly correlated (CCSD(T)-F12) coupled cluster approaches, we show that the CCSD(T)-F12/aug-cc-pVTZ level represents a good compromise between accuracy and low computational cost for the generation of multi-dimensional potential energy surfaces (PESs) over both intra- and inter-monomer degrees of freedom. Indeed, the CCSD(T)-F12/aug-cc-pVTZ 2D-PES for linear C3 and the CCSD(T)-F12/aug-cc-pVTZ 4D-PES for bent C3 configurations gently approach those mapped at the CCSD(T)/aug-cc-pVXZ (X = T,Q) + bond functions level, whereas a strong reduction of computational effort is observed. After exact dynamical computations, the pattern of the rovibrational levels of the intermediate C3-He complex and the rotational and rovibrational (de-) excitation of C3 by He derived using both sets of PESs agree quite well. Since C3 shows a floppy character, the interaction PES is defined in four dimensions to obtain realistic collisional parameters. The C-C-C bending mode, which fundamental lies at 63 cm-1 and can be excited at very low temperatures is explicitly considered as independent coordinate. Our work suggests hence that CCSD(T)-F12/aug-cc-pVTZ methodology is the key method for the generation of accurate polyatomic - He/H2 multi-dimensional PESs.

  9. Accurate nuclear radii and binding energies from a chiral interaction

    SciTech Connect

    Ekstrom, Jan A.; Jansen, G. R.; Wendt, Kyle A.; Hagen, Gaute; Papenbrock, Thomas F.; Carlsson, Boris; Forssen, Christian; Hjorth-Jensen, M.; Navratil, Petr; Nazarewicz, Witold

    2015-05-01

    With the goal of developing predictive ab initio capability for light and medium-mass nuclei, two-nucleon and three-nucleon forces from chiral effective field theory are optimized simultaneously to low-energy nucleon-nucleon scattering data, as well as binding energies and radii of few-nucleon systems and selected isotopes of carbon and oxygen. Coupled-cluster calculations based on this interaction, named NNLOsat, yield accurate binding energies and radii of nuclei up to 40Ca, and are consistent with the empirical saturation point of symmetric nuclear matter. In addition, the low-lying collective Jπ=3- states in 16O and 40Ca are described accurately, while spectra for selected p- and sd-shell nuclei are in reasonable agreement with experiment.

  10. Accurate nuclear radii and binding energies from a chiral interaction

    DOE PAGES

    Ekstrom, Jan A.; Jansen, G. R.; Wendt, Kyle A.; Hagen, Gaute; Papenbrock, Thomas F.; Carlsson, Boris; Forssen, Christian; Hjorth-Jensen, M.; Navratil, Petr; Nazarewicz, Witold

    2015-05-01

    With the goal of developing predictive ab initio capability for light and medium-mass nuclei, two-nucleon and three-nucleon forces from chiral effective field theory are optimized simultaneously to low-energy nucleon-nucleon scattering data, as well as binding energies and radii of few-nucleon systems and selected isotopes of carbon and oxygen. Coupled-cluster calculations based on this interaction, named NNLOsat, yield accurate binding energies and radii of nuclei up to 40Ca, and are consistent with the empirical saturation point of symmetric nuclear matter. In addition, the low-lying collective Jπ=3- states in 16O and 40Ca are described accurately, while spectra for selected p- and sd-shellmore » nuclei are in reasonable agreement with experiment.« less

  11. Interactive Isogeometric Volume Visualization with Pixel-Accurate Geometry.

    PubMed

    Fuchs, Franz G; Hjelmervik, Jon M

    2016-02-01

    A recent development, called isogeometric analysis, provides a unified approach for design, analysis and optimization of functional products in industry. Traditional volume rendering methods for inspecting the results from the numerical simulations cannot be applied directly to isogeometric models. We present a novel approach for interactive visualization of isogeometric analysis results, ensuring correct, i.e., pixel-accurate geometry of the volume including its bounding surfaces. The entire OpenGL pipeline is used in a multi-stage algorithm leveraging techniques from surface rendering, order-independent transparency, as well as theory and numerical methods for ordinary differential equations. We showcase the efficiency of our approach on different models relevant to industry, ranging from quality inspection of the parametrization of the geometry, to stress analysis in linear elasticity, to visualization of computational fluid dynamics results. PMID:26731454

  12. Interactive Isogeometric Volume Visualization with Pixel-Accurate Geometry.

    PubMed

    Fuchs, Franz G; Hjelmervik, Jon M

    2016-02-01

    A recent development, called isogeometric analysis, provides a unified approach for design, analysis and optimization of functional products in industry. Traditional volume rendering methods for inspecting the results from the numerical simulations cannot be applied directly to isogeometric models. We present a novel approach for interactive visualization of isogeometric analysis results, ensuring correct, i.e., pixel-accurate geometry of the volume including its bounding surfaces. The entire OpenGL pipeline is used in a multi-stage algorithm leveraging techniques from surface rendering, order-independent transparency, as well as theory and numerical methods for ordinary differential equations. We showcase the efficiency of our approach on different models relevant to industry, ranging from quality inspection of the parametrization of the geometry, to stress analysis in linear elasticity, to visualization of computational fluid dynamics results.

  13. Accurate ionization potential of semiconductors from efficient density functional calculations

    NASA Astrophysics Data System (ADS)

    Ye, Lin-Hui

    2016-07-01

    Despite its huge successes in total-energy-related applications, the Kohn-Sham scheme of density functional theory cannot get reliable single-particle excitation energies for solids. In particular, it has not been able to calculate the ionization potential (IP), one of the most important material parameters, for semiconductors. We illustrate that an approximate exact-exchange optimized effective potential (EXX-OEP), the Becke-Johnson exchange, can be used to largely solve this long-standing problem. For a group of 17 semiconductors, we have obtained the IPs to an accuracy similar to that of the much more sophisticated G W approximation (GWA), with the computational cost of only local-density approximation/generalized gradient approximation. The EXX-OEP, therefore, is likely as useful for solids as for finite systems. For solid surfaces, the asymptotic behavior of the vx c has effects similar to those of finite systems which, when neglected, typically cause the semiconductor IPs to be underestimated. This may partially explain why standard GWA systematically underestimates the IPs and why using the same GWA procedures has not been able to get an accurate IP and band gap at the same time.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

    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 12CH4 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.

  15. 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. PMID:27634258

  16. 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.

  17. Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential.

    PubMed

    Zhang, Chi; Liu, Song; Zhou, Yaoqi

    2004-02-01

    The conformations of loops are determined by the water-mediated interactions between amino acid residues. Energy functions that describe the interactions can be derived either from physical principles (physical-based energy function) or statistical analysis of known protein structures (knowledge-based statistical potentials). It is commonly believed that statistical potentials are appropriate for coarse-grained representation of proteins but are not as accurate as physical-based potentials when atomic resolution is required. Several recent applications of physical-based energy functions to loop selections appear to support this view. In this article, we apply a recently developed DFIRE-based statistical potential to three different loop decoy sets (RAPPER, Jacobson, and Forrest-Woolf sets). Together with a rotamer library for side-chain optimization, the performance of DFIRE-based potential in the RAPPER decoy set (385 loop targets) is comparable to that of AMBER/GBSA for short loops (two to eight residues). The DFIRE is more accurate for longer loops (9 to 12 residues). Similar trend is observed when comparing DFIRE with another physical-based OPLS/SGB-NP energy function in the large Jacobson decoy set (788 loop targets). In the Forrest-Woolf decoy set for the loops of membrane proteins, the DFIRE potential performs substantially better than the combination of the CHARMM force field with several solvation models. The results suggest that a single-term DFIRE-statistical energy function can provide an accurate loop prediction at a fraction of computing cost required for more complicate physical-based energy functions. A Web server for academic users is established for loop selection at the softwares/services section of the Web site http://theory.med.buffalo.edu/.

  18. Accurate global potential energy surface for the H + OH+ collision

    NASA Astrophysics Data System (ADS)

    Gannouni, M. A.; Jaidane, N. E.; Halvick, P.; Stoecklin, T.; Hochlaf, M.

    2014-05-01

    We mapped the global three-dimensional potential energy surface (3D-PES) of the water cation at the MRCI/aug-cc-pV5Z including the basis set superposition (BSSE) correction. This PES covers the molecular region and the long ranges close to the H + OH+(X3Σ-), the O + H2+(X2Σg+), and the hydrogen exchange channels. The quality of the PES is checked after comparison to previous experimental and theoretical results of the spectroscopic constants of H2O+(tilde X2B1) and of the diatomic fragments, the vibronic spectrum, the dissociation energy, and the barrier to linearity for H2O+(tilde X2B1). Our data nicely approach those measured and computed previously. The long range parts reproduce quite well the diatomic potentials. In whole, a good agreement is found, which validates our 3D-PES.

  19. 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.

  20. 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

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

    PubMed

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

    2016-08-01

    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. PMID:27332140

  3. Accurate intermolecular ground state potential of the Ne-N2 van der Waals complex.

    PubMed

    Munteanu, Cristian R; López Cacheiro, Javier; Fernández, Berta

    2004-05-15

    Ab initio ground state potential energy surfaces are obtained from interaction energies calculated with the coupled cluster singles and doubles model including connected triples corrections [CCSD(T)] and the aug-cc-pVXZ (X=5,Q,T,D) basis sets augmented with two different sets of midbond functions (denoted 33221 and 33211). The aug-cc-pV5Z-33221 surface is characterized by a T-shaped 49.5 cm(-1) minimum at Re=3.38 Angstroms and a linear saddle point at 3.95 Angstroms with De=36.6 cm(-1). These results agree well with the values provided by the accurate semiempirical potentials available. The rovibronic spectroscopic properties are determined and compared to the available experimental data and previous theoretical results. We study the basis set convergence of the intermolecular potentials and the rotational frequencies. The aug-cc-pVTZ basis sets provide reasonable binding parameters, but seem not to be converged enough for the evaluation of the microwave spectra. The aug-cc-pVQZ basis sets considerably improve the triple zeta results. The differences between the results obtained with the aug-cc-pVTZ-33221 basis set surface and those with the aug-cc-pVQZ-33221 are smaller than those of the corresponding bases with the set of 33211 midbond functions. The aug-cc-pVQZ surfaces are close to the aug-cc-pV5Z, that are expected to be close to convergence. With our best surfaces the errors in the frequencies with respect to the accurate experimental results go down to 0.6%.

  4. Low-energy structures of benzene clusters with a novel accurate potential surface.

    PubMed

    Bartolomei, M; Pirani, F; Marques, J M C

    2015-12-01

    The benzene-benzene (Bz-Bz) interaction is present in several chemical systems and it is known to be crucial in understanding the specificity of important biological phenomena. In this work, we propose a novel Bz-Bz analytical potential energy surface which is fine-tuned on accurate ab initio calculations in order to improve its reliability. Once the Bz-Bz interaction is modeled, an analytical function for the energy of the Bzn clusters may be obtained by summing up over all pair potentials. We apply an evolutionary algorithm (EA) to discover the lowest-energy structures of Bzn clusters (for n=2-25), and the results are compared with previous global optimization studies where different potential functions were employed. Besides the global minimum, the EA also gives the structures of other low-lying isomers ranked by the corresponding energy. Additional ab initio calculations are carried out for the low-lying isomers of Bz3 and Bz4 clusters, and the global minimum is confirmed as the most stable structure for both sizes. Finally, a detailed analysis of the low-energy isomers of the n = 13 and 19 magic-number clusters is performed. The two lowest-energy Bz13 isomers show S6 and C3 symmetry, respectively, which is compatible with the experimental results available in the literature. The Bz19 structures reported here are all non-symmetric, showing two central Bz molecules surrounded by 12 nearest-neighbor monomers in the case of the five lowest-energy structures.

  5. Accurate analytical approximation of the OTFTs surface potential by means of the Lagrange Reversion Theorem

    NASA Astrophysics Data System (ADS)

    Colalongo, Luigi; Ghittorelli, Matteo; Torricelli, Fabrizio; Kovács-Vajna, Zsolt Miklos

    2015-12-01

    Surface-potential-based mathematical models are among the most accurate and physically based compact models of Thin-Film Transistors (TFTs) and, in turn, of Organic Thin-Film Transistors (OTFTs), available today. However, the need for 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 enough accurate to model OTFTs and, in particular, transconductances and transcapacitances. In this paper we present an accurate and computationally efficient closed-form approximation of the surface potential, based on the Lagrange Reversion Theorem, that can be exploited in advanced surface-potential-based OTFTs and TFTs device models.

  6. Navier-Stokes simulations of blade-vortex interaction using high-order accurate upwind schemes

    NASA Technical Reports Server (NTRS)

    Rai, Man Mohan

    1987-01-01

    Conventional, spatially second-order-accurate, finite-difference schemes are much too dissipative for calculations involving vortices that travel large distances (relative to some measure of the size of the vortex). This study presents a fifth-order-accurate upwind-biased scheme that preserves vortex structure for much longer times than existing second-order-accurate central and upwind difference schemes. Vortex calculations demonstrating this aspect of the fifth-order scheme are also presented. The method is then applied to the blade-vortex interaction problem. Results for strong interactions wherein the vortex impinges directly on the airfoil or a shock associated with the airfoil are presented. None of these calculations required any modeling of the shape, size, and trajectory of the interacting vortex.

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

    SciTech Connect

    Dawes, Richard E-mail: hguo@unm.edu; Lolur, Phalgun; Li, Anyang; Jiang, Bin; Guo, Hua E-mail: hguo@unm.edu

    2013-11-28

    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-range 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.

  8. Accurate identification of waveform of evoked potentials by component decomposition using discrete cosine transform modeling.

    PubMed

    Bai, O; Nakamura, M; Kanda, M; Nagamine, T; Shibasaki, H

    2001-11-01

    This study introduces a method for accurate identification of the waveform of the evoked potentials by decomposing the component responses. The decomposition was achieved by zero-pole modeling of the evoked potentials in the discrete cosine transform (DCT) domain. It was found that the DCT coefficients of a component response in the evoked potentials could be modeled sufficiently by a second order transfer function in the DCT domain. The decomposition of the component responses was approached by using partial expansion of the estimated model for the evoked potentials, and the effectiveness of the decomposition method was evaluated both qualitatively and quantitatively. Because of the overlap of the different component responses, the proposed method enables an accurate identification of the evoked potentials, which is useful for clinical and neurophysiological investigations.

  9. Accurate, noninvasive detection of Helicobacter pylori DNA from stool samples: potential usefulness for monitoring treatment.

    PubMed

    Shuber, Anthony P; Ascaño, Jennifer J; Boynton, Kevin A; Mitchell, Anastasia; Frierson, Henry F; El-Rifai, Wa'el; Powell, Steven M

    2002-01-01

    A novel DNA assay demonstrating sensitive and accurate detection of Helicobacter pylori from stool samples is reported. Moreover, in three individuals tested for therapeutic response, the assay showed the disappearance of H. pylori DNA during treatment. Thus, this noninvasive molecular biology-based assay has the potential to be a powerful diagnostic tool given its ability to specifically identify H. pylori DNA.

  10. Accurate intermolecular ground state potential of the Ar-N2 van der Waals complex.

    PubMed

    Munteanu, Cristian R; Cacheiro, Javier López; Fernández, Berta

    2004-12-01

    After carrying out a systematic basis set convergence study, we evaluate several ground state potential energy surfaces of the Ar-N(2) van der Waals complex at the coupled cluster singles and doubles model including connected triples corrections. We use the aug-cc-pVXZ (X=5,Q,D) and the daug-cc-pVQZ basis sets augmented with a set of 3s3p2d1f1g (denoted 33211) and 3s3p2d2f1g (denoted 33221) midbond functions, respectively. aug-cc-pVTZ-33211 results were available in the literature. The aug-cc-pV5Z-33211 (daug-cc-pVQZ-33221) surface is characterized by a T-shaped minimum at R(e)=3.709 (3.701) A and of 99.01 (102.50) cm(-1), and a linear saddle point at 4.260 (4.257) A and D(e)=75.28 (79.73) cm(-1). These results are compared with the values provided by the semiempirical potentials available, and those of previous theoretical studies. The basis set convergence of the intermolecular potentials is also analyzed. From the potentials the rovibronic spectroscopic properties are determined. We study the basis set convergence of the rotational frequencies. The binding parameters that characterized the aug-cc-pVTZ-33211 surface are reasonable, but the surface is not good enough to evaluate the microwave spectra. The aug-cc-pVQZ-33211 basis set results considerably improve the triple zeta and are close to the aug-cc-pV5Z-33211. Considering the small differences between the quadruple and the quintuple zeta surfaces, the latter results can be expected to be close to convergence. At this level the differences with respect to the accurate experimental frequencies are in the order of 0.7%. In the case of the daug-cc-pVXZ-33211,33221 (X=5,Q,T,D) series, the convergence of the interaction energies with respect to basis set improvement is not so smooth. The errors in the frequencies obtained with the daug-cc-pVQZ-33221 basis set with respect to experiment are in the order of 0.4%.

  11. Accurate control of a Bose-Einstein condensate by managing the atomic interaction

    SciTech Connect

    Morales-Molina, L.; Arevalo, E.

    2010-07-15

    We exploit the variation of the atomic interaction in order to move ultracold atoms with attractive interaction across an ac-driven periodic lattice. By breaking relevant symmetries, a gathering of atoms is achieved. Accurate control of the gathered atoms' positions can be demonstrated via the control of the atomic localization process. The localization process is analyzed with the help of the nonlinear Floquet states where the Landau-Zener tunneling between states is observed and controlled. Transport effects in the presence of disorder are discussed.

  12. JCZS: An Intermolecular Potential Database for Performing Accurate Detonation and Expansion Calculations

    SciTech Connect

    Baer, M.R.; Hobbs, M.L.; McGee, B.C.

    1998-11-03

    Exponential-13,6 (EXP-13,6) potential pammeters for 750 gases composed of 48 elements were determined and assembled in a database, referred to as the JCZS database, for use with the Jacobs Cowperthwaite Zwisler equation of state (JCZ3-EOS)~l) The EXP- 13,6 force constants were obtained by using literature values of Lennard-Jones (LJ) potential functions, by using corresponding states (CS) theory, by matching pure liquid shock Hugoniot data, and by using molecular volume to determine the approach radii with the well depth estimated from high-pressure isen- tropes. The JCZS database was used to accurately predict detonation velocity, pressure, and temperature for 50 dif- 3 Accurate predictions were also ferent explosives with initial densities ranging from 0.25 glcm3 to 1.97 g/cm . obtained for pure liquid shock Hugoniots, static properties of nitrogen, and gas detonations at high initial pressures.

  13. Construction of an accurate potential energy surface by interpolation with Cartesian weighting coordinates

    NASA Astrophysics Data System (ADS)

    Rhee, Young Min

    2000-10-01

    A modified method to construct an accurate potential energy surface by interpolation is presented. The modification is based on the use of Cartesian coordinates in the weighting function. The translational and rotational invariance of the potential is incorporated by a proper definition of the distance between two Cartesian configurations. A numerical algorithm to find the distance is developed. It is shown that the present method is more exact in describing a planar system compared to the previous methods with weightings in internal coordinates. The applicability of the method to reactive systems is also demonstrated by performing classical trajectory simulations on the surface.

  14. 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).

  15. Accurate Potential Energy Curves for the Ground Electronic States of NeH^{+} and ArH^{+}

    NASA Astrophysics Data System (ADS)

    Coxon, John A.; Hajigeorgiou, Photos G.

    2013-06-01

    All available microwave and infrared spectroscopic line positions for the ground electronic states of the molecular cations NeH^{+} and ArH^{+} were employed in a direct potential fitting procedure to determine compact analytical potential curves and radial functions describing breakdown of the Born-Oppenheimer approximation. For NeH^{+}, 17 adjustable parameters were required to represent a total of 183 line positions for 4 isotopologues, whereas for ArH^{+}, 23 adjustable parameters were required to represent 440 line positions for 6 isotopologues. The MLR3 potential energy functional form was employed, taking full account of the proper 1/r{^4} limiting long-range dependence of the ion-atom dispersion energy interactions. Accurate vibrational energies, rotational constants and centrifugal distortion constants have been calculated for both diatomic cations.

  16. Material interactions with the low earth orbital environment Accurate reaction rate measurements

    NASA Technical Reports Server (NTRS)

    Visentine, J. T.; Leger, L. J.

    1985-01-01

    Interactions between spacecraft surfaces and atomic oxygen within the low earth orbital (LEO) environment have been observed and measured during Space Shuttle flights over the past 3 yr. The results of these experiments have demonstrated that interaction rates for many materials proposed for spacecraft applications are high and that protective coatings must be developed to enable long-lived operation of spacecraft structures in the LEO environment. A flight experiment discussed herein uses the Space Shuttle as an orbiting exposure laboratory to obtain accurate reaction rate measurements for materials typically used in spacecraft construction. An ion-neutral mass spectrometer, installed in the Orbiter cargo bay, will measure diurnal ambient oxygen densities while material samples are exposed at low altitude (222 km) to the orbital environment. From in situ atomic oxygen density information and postflight material recession measurements, accurate reaction rates can be derived to update the Space Station materials interaction data base. Additionally, gases evolved from a limited number of material surfaces subjected to direct oxygen impingement will be identified using the mass spectrometer. These measurements will aid in mechanistic definitions of chemical reactions which cause atom-surface interactions and in validating results of upcoming degradation studies conducted in ground-based neutral beam laboratories.

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

    SciTech Connect

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

    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]. 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.

  18. Developing a general interaction potential for hydrophobic and hydrophilic interactions.

    PubMed

    Donaldson, Stephen H; Røyne, Anja; Kristiansen, Kai; Rapp, Michael V; Das, Saurabh; Gebbie, Matthew A; Lee, Dong Woog; Stock, Philipp; Valtiner, Markus; Israelachvili, Jacob

    2015-02-24

    We review direct force measurements on a broad class of hydrophobic and hydrophilic surfaces. These measurements have enabled the development of a general interaction potential per unit area, W(D) = -2γ(i)Hy exp(-D/D(H)) in terms of a nondimensional Hydra parameter, Hy, that applies to both hydrophobic and hydrophilic interactions between extended surfaces. This potential allows one to quantitatively account for additional attractions and repulsions not included in the well-known combination of electrostatic double layer and van der Waals theories, the so-called Derjaguin-Landau-Verwey-Overbeek (DLVO) theory. The interaction energy is exponentially decaying with decay length D(H) ≈ 0.3-2 nm for both hydrophobic and hydrophilic interactions, with the exact value of D(H) depending on the precise system and conditions. The pre-exponential factor depends on the interfacial tension, γ(i), of the interacting surfaces and Hy. For Hy > 0, the interaction potential describes interactions between partially hydrophobic surfaces, with the maximum hydrophobic interaction (i.e., two fully hydrophobic surfaces) corresponding to Hy = 1. Hydrophobic interactions between hydrophobic monolayer surfaces measured with the surface forces apparatus (SFA) are shown to be well described by the proposed interaction potential. The potential becomes repulsive for Hy < 0, corresponding to partially hydrophilic (hydrated) interfaces. Hydrated surfaces such as mica, silica, and lipid bilayers are discussed and reviewed in the context of the values of Hy appropriate for each system.

  19. Benchmark data base for accurate van der Waals interaction in inorganic fragments

    NASA Astrophysics Data System (ADS)

    Brndiar, Jan; Stich, Ivan

    2012-02-01

    A range of inorganic materials, such as Sb, As, P, S, Se are built from van der Waals (vdW) interacting units forming the crystals, which neither the standard DFT GGA description as well as cheap quantum chemistry methods, such as MP2, do not describe correctly. We use this data base, for which have performed ultra accurate CCSD(T) calculations in complete basis set limit, to test the alternative approximate theories, such as Grimme [1], Langreth-Lundqvist [2], and Tkachenko-Scheffler [3]. While none of these theories gives entirely correct description, Grimme consistently provides more accurate results than Langreth-Lundqvist, which tend to overestimate the distances and underestimate the interaction energies for this set of systems. Contrary Tkachenko-Scheffler appear to yield surprisingly accurate and computationally cheap and convenient description applicable also for systems with appreciable charge transfer. [4pt] [1] S. Grimme, J. Comp. Chem. 27, 1787 (2006) [0pt] [2] K. Lee, et al., Phys. Rev. B 82 081101 (R) (2010) [0pt] [3] Tkachenko and M. Scheffler Phys. Rev. Lett. 102 073005 (2009).

  20. 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.

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

    SciTech Connect

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

    2014-01-28

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

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

    PubMed

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

    2015-06-18

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

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

    SciTech Connect

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

    2015-06-04

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

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

    DOE PAGES

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

    2015-06-04

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

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

    PubMed Central

    2015-01-01

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

  7. Potential interactions between alternative therapies and warfarin.

    PubMed

    Heck, A M; DeWitt, B A; Lukes, A L

    2000-07-01

    Potential and documented interactions between alternative therapy agents and warfarin are discussed. An estimated one third of adults in the United States use alternative therapies, including herbs. A major safety concern is potential interactions of alternative medicine products with prescription medications. This issue is especially important with respect to drugs with narrow therapeutic indexes, such as warfarin. Herbal products that may potentially increase the risk of bleeding or potentiate the effects of warfarin therapy include angelica root, arnica flower, anise, asafoetida, bogbean, borage seed oil, bromelain, capsicum, celery, chamomile, clove, fenugreek, feverfew, garlic, ginger ginkgo, horse chestnut, licorice root, lovage root, meadowsweet, onion, parsley, passionflower herb, poplar, quassia, red clover, rue, sweet clover, turmeric, and willow bark. Products that have been associated with documented reports of potential interactions with warfarin include coenzyme Q10, danshen, devil's claw, dong quai, ginseng, green tea, papain, and vitamin E. Interpretation of the available information on herb-warfarin interactions is difficult because nearly all of it is based on in vitro data, animal studies, or individual case reports. More study is needed to confirm and assess the clinical significance of these potential interactions. There is evidence that a wide range of alternative therapy products have the potential to interact with warfarin. Pharmacists and other health care professionals should question all patients about use of alternative therapies and report documented interactions to FDA's MedWatch program. PMID:10902065

  8. Potential interactions between alternative therapies and warfarin.

    PubMed

    Heck, A M; DeWitt, B A; Lukes, A L

    2000-07-01

    Potential and documented interactions between alternative therapy agents and warfarin are discussed. An estimated one third of adults in the United States use alternative therapies, including herbs. A major safety concern is potential interactions of alternative medicine products with prescription medications. This issue is especially important with respect to drugs with narrow therapeutic indexes, such as warfarin. Herbal products that may potentially increase the risk of bleeding or potentiate the effects of warfarin therapy include angelica root, arnica flower, anise, asafoetida, bogbean, borage seed oil, bromelain, capsicum, celery, chamomile, clove, fenugreek, feverfew, garlic, ginger ginkgo, horse chestnut, licorice root, lovage root, meadowsweet, onion, parsley, passionflower herb, poplar, quassia, red clover, rue, sweet clover, turmeric, and willow bark. Products that have been associated with documented reports of potential interactions with warfarin include coenzyme Q10, danshen, devil's claw, dong quai, ginseng, green tea, papain, and vitamin E. Interpretation of the available information on herb-warfarin interactions is difficult because nearly all of it is based on in vitro data, animal studies, or individual case reports. More study is needed to confirm and assess the clinical significance of these potential interactions. There is evidence that a wide range of alternative therapy products have the potential to interact with warfarin. Pharmacists and other health care professionals should question all patients about use of alternative therapies and report documented interactions to FDA's MedWatch program.

  9. Parallel kinetic Monte Carlo simulation framework incorporating accurate models of adsorbate lateral interactions

    NASA Astrophysics Data System (ADS)

    Nielsen, Jens; d'Avezac, Mayeul; Hetherington, James; Stamatakis, Michail

    2013-12-01

    Ab initio kinetic Monte Carlo (KMC) simulations have been successfully applied for over two decades to elucidate the underlying physico-chemical phenomena on the surfaces of heterogeneous catalysts. These simulations necessitate detailed knowledge of the kinetics of elementary reactions constituting the reaction mechanism, and the energetics of the species participating in the chemistry. The information about the energetics is encoded in the formation energies of gas and surface-bound species, and the lateral interactions between adsorbates on the catalytic surface, which can be modeled at different levels of detail. The majority of previous works accounted for only pairwise-additive first nearest-neighbor interactions. More recently, cluster-expansion Hamiltonians incorporating long-range interactions and many-body terms have been used for detailed estimations of catalytic rate [C. Wu, D. J. Schmidt, C. Wolverton, and W. F. Schneider, J. Catal. 286, 88 (2012)]. In view of the increasing interest in accurate predictions of catalytic performance, there is a need for general-purpose KMC approaches incorporating detailed cluster expansion models for the adlayer energetics. We have addressed this need by building on the previously introduced graph-theoretical KMC framework, and we have developed Zacros, a FORTRAN2003 KMC package for simulating catalytic chemistries. To tackle the high computational cost in the presence of long-range interactions we introduce parallelization with OpenMP. We further benchmark our framework by simulating a KMC analogue of the NO oxidation system established by Schneider and co-workers [J. Catal. 286, 88 (2012)]. We show that taking into account only first nearest-neighbor interactions may lead to large errors in the prediction of the catalytic rate, whereas for accurate estimates thereof, one needs to include long-range terms in the cluster expansion.

  10. Doubly hybrid density functional for accurate descriptions of nonbond interactions, thermochemistry, and thermochemical kinetics

    PubMed Central

    Zhang, Ying; Xu, Xin; Goddard, William A.

    2009-01-01

    We develop and validate a density functional, XYG3, based on the adiabatic connection formalism and the Görling–Levy coupling-constant perturbation expansion to the second order (PT2). XYG3 is a doubly hybrid functional, containing 3 mixing parameters. It has a nonlocal orbital-dependent component in the exchange term (exact exchange) plus information about the unoccupied Kohn–Sham orbitals in the correlation part (PT2 double excitation). XYG3 is remarkably accurate for thermochemistry, reaction barrier heights, and nonbond interactions of main group molecules. In addition, the accuracy remains nearly constant with system size. PMID:19276116

  11. The goal of forming accurate impressions during social interactions: attenuating the impact of negative expectancies.

    PubMed

    Neuberg, S L

    1989-03-01

    Investigated the idea that impression formation goals may regulate the impact that perceiver expectancies have on social interactions. In simulated interviews, interviewers Ss were given a negative expectancy about one applicant S and no expectancy about another. Half the interviewers were encouraged to form accurate impressions; the others were not. As predicted, no-goal interviewers exhibited a postinteraction impression bias against the negative-expectancy applicants, whereas the accuracy-goal interviewers did not. Moreover, the ability of the accuracy goal to reduce this bias was apparently mediated by more extensive and less biased interviewer information-gathering, which in turn elicited an improvement in negative-expectancy applicants' performances. These findings stress the theoretical and practical importance of considering the motivational context within which expectancy-tinged social interactions occur.

  12. The goal of forming accurate impressions during social interactions: attenuating the impact of negative expectancies.

    PubMed

    Neuberg, S L

    1989-03-01

    Investigated the idea that impression formation goals may regulate the impact that perceiver expectancies have on social interactions. In simulated interviews, interviewers Ss were given a negative expectancy about one applicant S and no expectancy about another. Half the interviewers were encouraged to form accurate impressions; the others were not. As predicted, no-goal interviewers exhibited a postinteraction impression bias against the negative-expectancy applicants, whereas the accuracy-goal interviewers did not. Moreover, the ability of the accuracy goal to reduce this bias was apparently mediated by more extensive and less biased interviewer information-gathering, which in turn elicited an improvement in negative-expectancy applicants' performances. These findings stress the theoretical and practical importance of considering the motivational context within which expectancy-tinged social interactions occur. PMID:2926635

  13. Conformation of a flexible polymer in explicit solvent: Accurate solvation potentials for Lennard-Jones chains.

    PubMed

    Taylor, Mark P; Ye, Yuting; Adhikari, Shishir R

    2015-11-28

    The conformation of a polymer chain in solution is coupled to the local structure of the surrounding solvent and can undergo large changes in response to variations in solvent density and temperature. The many-body effects of solvent on the structure of an n-mer polymer chain can be formally mapped to an exact n-body solvation potential. Here, we use a pair decomposition of this n-body potential to construct a set of two-body potentials for a Lennard-Jones (LJ) polymer chain in explicit LJ solvent. The solvation potentials are built from numerically exact results for 5-mer chains in solvent combined with an approximate asymptotic expression for the solvation potential between sites that are distant along the chain backbone. These potentials map the many-body chain-in-solvent problem to a few-body single-chain problem and can be used to study a chain of arbitrary length, thereby dramatically reducing the computational complexity of the polymer chain-in-solvent problem. We have constructed solvation potentials at a large number of state points across the LJ solvent phase diagram including the vapor, liquid, and super-critical regions. We use these solvation potentials in single-chain Monte Carlo (MC) simulations with n ≤ 800 to determine the size, intramolecular structure, and scaling behavior of chains in solvent. To assess our results, we have carried out full chain-in-solvent MC simulations (with n ≤ 100) and find that our solvation potential approach is quantitatively accurate for a wide range of solvent conditions for these chain lengths. PMID:26627969

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

    SciTech Connect

    Heinrich, Martin; Kluska, Sven; Binder, Sebastian; Hameiri, Ziv; Hoex, Bram; Aberle, Armin G.

    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 on how to obtain accurate potential drop sheet resistance measurements on laser-doped regions.

  16. Extensions and applications of the A24 data set of accurate interaction energies.

    PubMed

    Řezáč, Jan; Dubecký, Matúš; Jurečka, Petr; Hobza, Pavel

    2015-07-15

    The A24 data set (Řezáč and Hobza, J. Chem. Theory Comput. 2013, 9, 2151-2155) is a set of noncovalent complexes large enough to showcase various types of interactions yet small enough to make highly accurate calculations possible. It is intended for the testing of accurate computational methods which are then used as a benchmark in larger model systems. In this work, we improve the best estimate of the interaction energies in the set by updating their CCSD(T)/CBS and CCSDT(Q) components with calculations in larger basis sets. The data set is then used to test a large number of composite CCSD(T) approaches. Special attention is paid to the use of the explicitly correlated MP2-F12 method in these composite calculations. It is shown that an accuracy of 1-2% can be achieved with setups applicable to larger molecules. The effect of frozen natural orbital approximation on the accuracy of composite CCSD(T)/CBS calculations is also quantified. In four trivially saturated complexes where CCSDT(Q)/CBS data are now available, the convergence of the many-body correlation effects is assessed by fixed-node diffusion Monte Carlo (FN-DMC) calculations. A good agreement is achieved between FN-DMC and high-level coupled-cluster which represents an important cross-check of both approaches.

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

    SciTech Connect

    Shvab, I.; Sadus, Richard J.

    2013-11-21

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

  18. Accurate Intermolecular Interactions at Dramatically Reduced Cost and a Many-Body Energy Decomposition Scheme for XPol+SAPT

    NASA Astrophysics Data System (ADS)

    Lao, Ka Un; Herbert, John M.

    2013-06-01

    An efficient, monomer-based electronic structure method is introduced for computing non-covalent interactions in molecular and ionic clusters. It builds upon our ``explicit polarization" (XPol) with pairwise-additive symmetry-adapted perturbation theory (SAPT) using the Kohn-Sham (KS) version of SAPT, but replaces the problematic and expensive sum-over-states dispersion terms with empirical potentials. This modification reduces the scaling from {O}(N^5) to {O}(N^3) and also facilitates the use of Kohn-Sham density functional theory (KS-DFT) as a low-cost means to capture intramolecular electron correlation. Accurate binding energies are obtained for benchmark databases of dimer binding energies, and potential energy curves are also captured accurately, for a variety of challenging systems. As compared to traditional DFT-SAPT or SAPT(DFT) methods, it removes the limitation to dimers and extends SAPT-based methodology to many-body systems. For many-body systems such as water clusters and halide-water cluster anions, the new method is superior to established density-functional methods for non-covalent interactions. We suggest that using different asymptotic corrections for different monomers is necessary to get good binding energies in general, as DFT-SAPT or SAPT(DFT), especially for hydrogen-bonded complexes. We also introduce a decomposition scheme for the interaction energy that extends traditional SAPT energy decomposition analysis to systems containing more than two monomers, and we find that the various energy components (electrostatic, exchange, induction, and dispersion) are in very good agreement with high-level SAPT benchmarks for dimers. For (H_2O)_6, the many-body contribution to the interaction energy agrees well with that obtained from traditional Kitaura-Morokuma energy decomposition analysis.

  19. Accurate Kohn-Sham ionization potentials from scaled-opposite-spin second-order optimized effective potential methods.

    PubMed

    Śmiga, Szymon; Della Sala, Fabio; Buksztel, Adam; Grabowski, Ireneusz; Fabiano, Eduardo

    2016-08-15

    One important property of Kohn-Sham (KS) density functional theory is the exact equality of the energy of the highest occupied KS orbital (HOMO) with the negative ionization potential of the system. This exact feature is out of reach for standard density-dependent semilocal functionals. Conversely, accurate results can be obtained using orbital-dependent functionals in the optimized effective potential (OEP) approach. In this article, we investigate the performance, in this context, of some advanced OEP methods, with special emphasis on the recently proposed scaled-opposite-spin OEP functional. Moreover, we analyze the impact of the so-called HOMO condition on the final quality of the HOMO energy. Results are compared to reference data obtained at the CCSD(T) level of theory. © 2016 Wiley Periodicals, Inc.

  20. 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).

  1. Exact kinetic energy enables accurate evaluation of weak interactions by the FDE-vdW method

    SciTech Connect

    Sinha, Debalina; Pavanello, Michele

    2015-08-28

    The correlation energy of interaction is an elusive and sought-after interaction between molecular systems. By partitioning the response function of the system into subsystem contributions, the Frozen Density Embedding (FDE)-vdW method provides a computationally amenable nonlocal correlation functional based on the adiabatic connection fluctuation dissipation theorem applied to subsystem density functional theory. In reproducing potential energy surfaces of weakly interacting dimers, we show that FDE-vdW, either employing semilocal or exact nonadditive kinetic energy functionals, is in quantitative agreement with high-accuracy coupled cluster calculations (overall mean unsigned error of 0.5 kcal/mol). When employing the exact kinetic energy (which we term the Kohn-Sham (KS)-vdW method), the binding energies are generally closer to the benchmark, and the energy surfaces are also smoother.

  2. Simple and accurate modelling of the gravitational potential produced by thick and thin exponential discs

    NASA Astrophysics Data System (ADS)

    Smith, R.; Flynn, C.; Candlish, G. N.; Fellhauer, M.; Gibson, B. K.

    2015-04-01

    We present accurate models of the gravitational potential produced by a radially exponential disc mass distribution. The models are produced by combining three separate Miyamoto-Nagai discs. Such models have been used previously to model the disc of the Milky Way, but here we extend this framework to allow its application to discs of any mass, scalelength, and a wide range of thickness from infinitely thin to near spherical (ellipticities from 0 to 0.9). The models have the advantage of simplicity of implementation, and we expect faster run speeds over a double exponential disc treatment. The potentials are fully analytical, and differentiable at all points. The mass distribution of our models deviates from the radial mass distribution of a pure exponential disc by <0.4 per cent out to 4 disc scalelengths, and <1.9 per cent out to 10 disc scalelengths. We tabulate fitting parameters which facilitate construction of exponential discs for any scalelength, and a wide range of disc thickness (a user-friendly, web-based interface is also available). Our recipe is well suited for numerical modelling of the tidal effects of a giant disc galaxy on star clusters or dwarf galaxies. We consider three worked examples; the Milky Way thin and thick disc, and a discy dwarf galaxy.

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

    PubMed Central

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

    2014-01-01

    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. Database Coordinates and structure factors for the real data have been submitted to the Protein Data Bank under accession 4tws. PMID:25040949

  4. An accurate nucleon-nucleon potential with charge-independence breaking

    SciTech Connect

    Wiringa, R.B.; Stoks, V.G.J.; Schiavilla, R.

    1995-08-01

    We constructed a new NN potential, designated Argonne v{sub 18}, with explicit charge-independence breaking. It supersedes our older v{sub 14} model, which was our standard nonrelativistic NN potential for most of the last decade. The main part of the new potential is charge-independent, like the old v{sub 14} model, with 14 components, each consisting of a radial function v{sub p}(r{sub 12}) multiplied by an operator: 1, {sigma}{sub 1}{center_dot}{sigma}{sub 2}, S{sub 12}, L{center_dot}S, L{sup 2}, L{sup 2}{sigma}{sub 1}{center_dot}{sigma}{sub 2}, and (L{center_dot}S){sup 2}, and each of these times {tau}{sub l}{center_dot}{tau}{sub 2}. Three charge-dependent and one charge-asymmetric operators are added along with a complete electromagnetic interaction, resulting in a model that fits pp, np, and nn data simultaneously. The charge-dependent operators are obtained by multiplying the spin operators 1, {sigma}{sub 1}{center_dot}{sigma}{sub 2}, and S{sub 12} by the isotensor T{sub 12} = 3{tau}{sub 1z}{tau}{sub 2z} - {tau}{sub 1}{center_dot}{tau}{sub 2}, which differentiates between np and pp or nn T = 1 states. A major source of charge dependence in NN interactions is the mass difference of the charged and neutral pions, which is carefully treated in the new model. The charge-asymmetric operator is {tau}{sub 1z}+{tau}{sub 2z} which splits pp and nn states; it is constrained by the difference between nn and pp scattering lengths. The electromagnetic interaction includes Coulomb, Darwin-Foldy, vacuum polarization, and magnetic moment terms. The potential was fit directly to the Nijmegen pp and np scattering database as well as the nn scattering length and deuteron binding energy. With {approximately}40 adjustable parameters it gives an excellent {chi}{sup 2}/degree of freedom of 1.09 for 4301 pp and np data in the range 0-350 MeV. A consistent set of two-body charge and current operators has also been derived to evaluate the deuteron electromagnetic form factors.

  5. A new interaction potential for swarming models

    NASA Astrophysics Data System (ADS)

    Carrillo, J. A.; Martin, S.; Panferov, V.

    2013-10-01

    We consider a self-propelled particle system which has been used to describe certain types of collective motion of animals, such as fish schools and bird flocks. Interactions between particles are specified by means of a pairwise potential, repulsive at short ranges and attractive at longer ranges. The exponentially decaying Morse potential is a typical choice, and is known to reproduce certain types of collective motion observed in nature, particularly aligned flocks and rotating mills. We introduce a class of interaction potentials, that we call Quasi-Morse, for which flock and rotating mills states are also observed numerically, however in that case the corresponding macroscopic equations allow for explicit solutions in terms of special functions, with coefficients that can be obtained numerically without solving the particle evolution. We compare the obtained solutions with long-time dynamics of the particle systems and find a close agreement for several types of flock and mill solutions.

  6. Potential interaction between pomegranate juice and warfarin.

    PubMed

    Komperda, Kathy E

    2009-08-01

    To my knowledge, no published reports have described an interaction between pomegranate juice and warfarin. Investigators from previous animal and in vitro studies have reported a potential for pomegranate juice to inhibit metabolism involving the cytochrome P450 system, an effect that could translate into a clinical drug-diet interaction with warfarin. This case report describes a 64-year-old Caucasian woman who was treated with warfarin for recurrent deep vein thrombosis. She had been receiving a relatively stable dosage of warfarin 4 mg/day for several months, with stable international normalized ratios (INRs). During that time, the patient was consuming pomegranate juice 2-3 times/week. She stopped drinking the juice, and her INRs became subtherapeutic. Her dosage of warfarin was increased to maintain therapeutic anticoagulation. No rechallenge with pomegranate juice was performed. Use of the Drug Interaction Probability Scale indicated a possible relationship between the patient's subtherapeutic INR and the pomegranate juice. Although this potential interaction needs to be explored further, clinicians should be aware of the interaction and thoroughly interview and closely monitor their patients who are receiving warfarin.

  7. Properties of metastable alkaline-earth-metal atoms calculated using an accurate effective core potential

    SciTech Connect

    Santra, Robin; Christ, Kevin V.; Greene, Chris H.

    2004-04-01

    The first three electronically excited states in the alkaline-earth-metal atoms magnesium, calcium, and strontium comprise the (nsnp){sup 3}P{sub J}{sup o}(J=0,1,2) fine-structure manifold. All three states are metastable and are of interest for optical atomic clocks as well as for cold-collision physics. An efficient technique--based on a physically motivated potential that models the presence of the ionic core--is employed to solve the Schroedinger equation for the two-electron valence shell. In this way, radiative lifetimes, laser-induced clock shifts, and long-range interaction parameters are calculated for metastable Mg, Ca, and Sr.

  8. Statistical systems with nonintegrable interaction potentials

    NASA Astrophysics Data System (ADS)

    Yukalov, V. I.

    2016-07-01

    Statistical systems composed of atoms interacting with each other trough nonintegrable interaction potentials are considered. Examples of these potentials are hard-core potentials and long-range potentials, for instance, the Lennard-Jones and dipolar potentials. The treatment of such potentials is known to confront several problems, e.g., the impossibility of using the standard mean-field approximations, such as Hartree and Hartree-Fock approximations, the impossibility of directly introducing coherent states, the difficulty in breaking the global gauge symmetry, which is required for describing Bose-Einstein condensed and superfluid systems, the absence of a correctly defined Fourier transform, which hampers the description of uniform matter as well as the use of local-density approximation for nonuniform systems. A novel iterative procedure for describing such systems is developed, starting from a correlated mean-field approximation, allowing for a systematic derivation of higher orders, and meeting no problems listed above. The procedure is applicable to arbitrary systems, whether equilibrium or nonequilibrium. The specification for equilibrium systems is presented. The method of extrapolating the expressions for observable quantities from weak coupling to strong coupling is described.

  9. Statistical systems with nonintegrable interaction potentials.

    PubMed

    Yukalov, V I

    2016-07-01

    Statistical systems composed of atoms interacting with each other trough nonintegrable interaction potentials are considered. Examples of these potentials are hard-core potentials and long-range potentials, for instance, the Lennard-Jones and dipolar potentials. The treatment of such potentials is known to confront several problems, e.g., the impossibility of using the standard mean-field approximations, such as Hartree and Hartree-Fock approximations, the impossibility of directly introducing coherent states, the difficulty in breaking the global gauge symmetry, which is required for describing Bose-Einstein condensed and superfluid systems, the absence of a correctly defined Fourier transform, which hampers the description of uniform matter as well as the use of local-density approximation for nonuniform systems. A novel iterative procedure for describing such systems is developed, starting from a correlated mean-field approximation, allowing for a systematic derivation of higher orders, and meeting no problems listed above. The procedure is applicable to arbitrary systems, whether equilibrium or nonequilibrium. The specification for equilibrium systems is presented. The method of extrapolating the expressions for observable quantities from weak coupling to strong coupling is described. PMID:27575076

  10. Measuring three-dimensional interaction potentials using optical interference.

    PubMed

    Mojarad, Nassir; Sandoghdar, Vahid; Krishnan, Madhavi

    2013-04-22

    We describe the application of three-dimensional (3D) scattering interferometric (iSCAT) imaging to the measurement of spatial interaction potentials for nano-objects in solution. We study electrostatically trapped gold particles in a nanofluidic device and present details on axial particle localization in the presence of a strongly reflecting interface. Our results demonstrate high-speed (~kHz) particle tracking with subnanometer localization precision in the axial and average 2.5 nm in the lateral dimension. A comparison of the measured levitation heights of trapped particles with the calculated values for traps of various geometries reveals good agreement. Our work demonstrates that iSCAT imaging delivers label-free, high-speed and accurate 3D tracking of nano-objects conducive to probing weak and long-range interaction potentials in solution. PMID:23609648

  11. Tissue resonance interaction accurately detects colon lesions: A double-blind pilot study

    PubMed Central

    Dore, Maria P; Tufano, Marcello O; Pes, Giovanni M; Cuccu, Marianna; Farina, Valentina; Manca, Alessandra; Graham, David Y

    2015-01-01

    AIM: To investigated the performance of the tissue resonance interaction method (TRIM) for the non-invasive detection of colon lesions. METHODS: We performed a prospective single-center blinded pilot study of consecutive adults undergoing colonoscopy at the University Hospital in Sassari, Italy. Before patients underwent colonoscopy, they were examined by the TRIMprobe which detects differences in electromagnetic properties between pathological and normal tissues. All patients had completed the polyethylene glycol-containing bowel prep for the colonoscopy procedure before being screened. During the procedure the subjects remained fully dressed. A hand-held probe was moved over the abdomen and variations in electromagnetic signals were recorded for 3 spectral lines (462-465 MHz, 930 MHz, and 1395 MHz). A single investigator, blind to any clinical information, performed the test using the TRIMprob system. Abnormal signals were identified and recorded as malignant or benign (adenoma or hyperplastic polyps). Findings were compared with those from colonoscopy with histologic confirmation. Statistical analysis was performed by χ2 test. RESULTS: A total of 305 consecutive patients fulfilling the inclusion criteria were enrolled over a period of 12 months. The most frequent indication for colonoscopy was abdominal pain (33%). The TRIMprob was well accepted by all patients; none spontaneously complained about the procedure, and no adverse effects were observed. TRIM proved inaccurate for polyp detection in patients with inflammatory bowel disease (IBD) and they were excluded leaving 281 subjects (mean age 59 ± 13 years; 107 males). The TRIM detected and accurately characterized all 12 adenocarcinomas and 135/137 polyps (98.5%) including 64 adenomatous (100%) found. The method identified cancers and polyps with 98.7% sensitivity, 96.2% specificity, and 97.5% diagnostic accuracy, compared to colonoscopy and histology analyses. The positive predictive value was 96.7% and the

  12. Nanoparticle interaction potentials constructed by multiscale computation.

    PubMed

    Lee, Cheng K; Hua, Chi C

    2010-06-14

    The van der Waals (vdW) potentials governing macroscopic objects have long been formulated in the context of classical theories, such as Hamaker's microscopic theory and Lifshitz's continuum theory. This work addresses the possibility of constructing the vdW interaction potentials of nanoparticle species using multiscale simulation schemes. Amorphous silica nanoparticles were considered as a benchmark example for which a series of (SiO(2))(n) (n being an integer) has been systematically surveyed as the potential candidates of the packing units that reproduce known bulk material properties in atomistic molecular dynamics simulations. This strategy led to the identification of spherical Si(6)O(12) molecules, later utilized as the elementary coarse-grained (CG) particles to compute the pair interaction potentials of silica nanoparticles ranging from 0.62 to 100 nm in diameter. The model nanoparticles so built may, in turn, serve as the children CG particles to construct nanoparticles assuming arbitrary sizes and shapes. Major observations are as follows. The pair interaction potentials for all the investigated spherical silica nanoparticles can be cast into a semiempirical, generalized Lennard-Jones 2alpha-alpha potential (alpha being a size-dependent, large integral number). In its reduced form, we discuss the implied universalities for the vdW potentials governing a certain range of amorphous nanoparticle species as well as how thermodynamic transferability can be fulfilled automatically. In view of future applications with colloidal suspensions, we briefly evaluated the vdW potential in the presence of a "screening" medium mimicking the effects of electrical double layers or grafting materials atop the nanoparticle core. The general observations shed new light on strategies to attain a microscopic control over interparticle attractions. In future perspectives, the proposed multiscale computation scheme shall help bridge the current gap between the modeling of

  13. Capturing the Interaction Potential of Amyloidogenic Proteins

    SciTech Connect

    Javid, Nadeem; Vogtt, Karsten; Winter, Roland; Krywka, Christina; Tolan, Metin

    2007-07-13

    Experimentally derived static structure factors obtained for the aggregation-prone protein insulin were analyzed with a statistical mechanical model based on the Derjaguin-Landau-Verwey-Overbeek potential. The data reveal that the protein self-assembles into equilibrium clusters already at low concentrations. Furthermore, striking differences regarding interaction forces between aggregation-prone proteins such as insulin in the preaggregated regime and natively stable globular proteins are found.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

  17. A time-accurate adaptive grid method and the numerical simulation of a shock-vortex interaction

    NASA Technical Reports Server (NTRS)

    Bockelie, Michael J.; Eiseman, Peter R.

    1990-01-01

    A time accurate, general purpose, adaptive grid method is developed that is suitable for multidimensional steady and unsteady numerical simulations. The grid point movement is performed in a manner that generates smooth grids which resolve the severe solution gradients and the sharp transitions in the solution gradients. The temporal coupling of the adaptive grid and the PDE solver is performed with a grid prediction correction method that is simple to implement and ensures the time accuracy of the grid. Time accurate solutions of the 2-D Euler equations for an unsteady shock vortex interaction demonstrate the ability of the adaptive method to accurately adapt the grid to multiple solution features.

  18. Towards a spectroscopically accurate set of potentials for heavy hydride laser cooling candidates: Effective core potential calculations of BaH

    NASA Astrophysics Data System (ADS)

    Moore, Keith; McLaughlin, Brendan M.; Lane, Ian C.

    2016-04-01

    BaH (and its isotopomers) is an attractive molecular candidate for laser cooling to ultracold temperatures and a potential precursor for the production of ultracold gases of hydrogen and deuterium. The theoretical challenge is to simulate the laser cooling cycle as reliably as possible and this paper addresses the generation of a highly accurate ab initio 2Σ+ potential for such studies. The performance of various basis sets within the multi-reference configuration-interaction (MRCI) approximation with the Davidson correction is tested and taken to the Complete Basis Set (CBS) limit. It is shown that the calculated molecular constants using a 46 electron effective core-potential and even-tempered augmented polarized core-valence basis sets (aug-pCVnZ-PP, n = 4 and 5) but only including three active electrons in the MRCI calculation are in excellent agreement with the available experimental values. The predicted dissociation energy De for the X2Σ+ state (extrapolated to the CBS limit) is 16 895.12 cm-1 (2.094 eV), which agrees within 0.1% of a revised experimental value of <16 910.6 cm-1, while the calculated re is within 0.03 pm of the experimental result.

  19. [Potential interactions between drugs and dietary supplements].

    PubMed

    Farghali, Hassan; Kameníková, Ludmila; Hodis, Jiří; Kutinová Canová, Nikolina

    2014-01-01

    Purified active plant constituents were isolated and assessed for their pharmacological activities that constitute a basis of modern drug development. The situation with herbal supplements is different because the extract or dried herb or mixture of herbs contains several substances beside the beneficial one(s) that might produce drug interaction with the conventional medicine(s). Most patients are misinformed and believe that anything "natural" must be safe. This article is focusing on plant-based substances referred as dietary supplements (DS). Examples of reported drug interactions and contraindications associated with DS with two case studies are presented. As supplements are typically not prescribed, many doctors seem to have no interest in drug-DS interactions since a typical medical history of the patients does not include any questions about self-prescribed remedies of this nature. Rather, patients are left alone when they are tempted to try this or that DS and tend to rely on advice from friends, or on material they read on internet. A better quality control, compliance, public awareness and healthcare professionals vigilance for potential interactions are needed. It is of utmost importance to appreciate the impact of supplements on different stages of pharmacokinetics, especially on drug absorption and metabolism.

  20. Towards an accurate representation of electrostatics in classical force fields: Efficient implementation of multipolar interactions in biomolecular simulations

    NASA Astrophysics Data System (ADS)

    Sagui, Celeste; Pedersen, Lee G.; Darden, Thomas A.

    2004-01-01

    The accurate simulation of biologically active macromolecules faces serious limitations that originate in the treatment of electrostatics in the empirical force fields. The current use of "partial charges" is a significant source of errors, since these vary widely with different conformations. By contrast, the molecular electrostatic potential (MEP) obtained through the use of a distributed multipole moment description, has been shown to converge to the quantum MEP outside the van der Waals surface, when higher order multipoles are used. However, in spite of the considerable improvement to the representation of the electronic cloud, higher order multipoles are not part of current classical biomolecular force fields due to the excessive computational cost. In this paper we present an efficient formalism for the treatment of higher order multipoles in Cartesian tensor formalism. The Ewald "direct sum" is evaluated through a McMurchie-Davidson formalism [L. McMurchie and E. Davidson, J. Comput. Phys. 26, 218 (1978)]. The "reciprocal sum" has been implemented in three different ways: using an Ewald scheme, a particle mesh Ewald (PME) method, and a multigrid-based approach. We find that even though the use of the McMurchie-Davidson formalism considerably reduces the cost of the calculation with respect to the standard matrix implementation of multipole interactions, the calculation in direct space remains expensive. When most of the calculation is moved to reciprocal space via the PME method, the cost of a calculation where all multipolar interactions (up to hexadecapole-hexadecapole) are included is only about 8.5 times more expensive than a regular AMBER 7 [D. A. Pearlman et al., Comput. Phys. Commun. 91, 1 (1995)] implementation with only charge-charge interactions. The multigrid implementation is slower but shows very promising results for parallelization. It provides a natural way to interface with continuous, Gaussian-based electrostatics in the future. It is

  1. Towards an accurate representation of electrostatics in classical force fields: efficient implementation of multipolar interactions in biomolecular simulations.

    PubMed

    Sagui, Celeste; Pedersen, Lee G; Darden, Thomas A

    2004-01-01

    The accurate simulation of biologically active macromolecules faces serious limitations that originate in the treatment of electrostatics in the empirical force fields. The current use of "partial charges" is a significant source of errors, since these vary widely with different conformations. By contrast, the molecular electrostatic potential (MEP) obtained through the use of a distributed multipole moment description, has been shown to converge to the quantum MEP outside the van der Waals surface, when higher order multipoles are used. However, in spite of the considerable improvement to the representation of the electronic cloud, higher order multipoles are not part of current classical biomolecular force fields due to the excessive computational cost. In this paper we present an efficient formalism for the treatment of higher order multipoles in Cartesian tensor formalism. The Ewald "direct sum" is evaluated through a McMurchie-Davidson formalism [L. McMurchie and E. Davidson, J. Comput. Phys. 26, 218 (1978)]. The "reciprocal sum" has been implemented in three different ways: using an Ewald scheme, a particle mesh Ewald (PME) method, and a multigrid-based approach. We find that even though the use of the McMurchie-Davidson formalism considerably reduces the cost of the calculation with respect to the standard matrix implementation of multipole interactions, the calculation in direct space remains expensive. When most of the calculation is moved to reciprocal space via the PME method, the cost of a calculation where all multipolar interactions (up to hexadecapole-hexadecapole) are included is only about 8.5 times more expensive than a regular AMBER 7 [D. A. Pearlman et al., Comput. Phys. Commun. 91, 1 (1995)] implementation with only charge-charge interactions. The multigrid implementation is slower but shows very promising results for parallelization. It provides a natural way to interface with continuous, Gaussian-based electrostatics in the future. It is

  2. Accurate energies of hydrogen bonded nucleic acid base pairs and triplets in tRNA tertiary interactions

    PubMed Central

    2006-01-01

    Tertiary interactions are crucial in maintaining the tRNA structure and functionality. We used a combined sequence analysis and quantum mechanics approach to calculate accurate energies of the most frequent tRNA tertiary base pairing interactions. Our analysis indicates that six out of the nine classical tertiary interactions are held in place mainly by H-bonds between the bases. In the remaining three cases other effects have to be considered. Tertiary base pairing interaction energies range from −8 to −38 kcal/mol in yeast tRNAPhe and are estimated to contribute roughly 25% of the overall tRNA base pairing interaction energy. Six analyzed posttranslational chemical modifications were shown to have minor effect on the geometry of the tertiary interactions. Modifications that introduce a positive charge strongly stabilize the corresponding tertiary interactions. Non-additive effects contribute to the stability of base triplets. PMID:16461956

  3. Toward Accurate Modeling of the Effect of Ion-Pair Formation on Solute Redox Potential.

    PubMed

    Qu, Xiaohui; Persson, Kristin A

    2016-09-13

    A scheme to model the dependence of a solute redox potential on the supporting electrolyte is proposed, and the results are compared to experimental observations and other reported theoretical models. An improved agreement with experiment is exhibited if the effect of the supporting electrolyte on the redox potential is modeled through a concentration change induced via ion pair formation with the salt, rather than by only considering the direct impact on the redox potential of the solute itself. To exemplify the approach, the scheme is applied to the concentration-dependent redox potential of select molecules proposed for nonaqueous flow batteries. However, the methodology is general and enables rational computational electrolyte design through tuning of the operating window of electrochemical systems by shifting the redox potential of its solutes; including potentially both salts as well as redox active molecules. PMID:27500744

  4. Potential Flow Interactions With Directional Solidification

    NASA Technical Reports Server (NTRS)

    Buddhavarapu, Sudhir S.; Meiburg, Eckart

    1999-01-01

    The effect of convective melt motion on the growth of morphological instabilities in crystal growth has been the focus of many studies in the past decade. While most of the efforts have been directed towards investigating the linear stability aspects, relatively little attention has been devoted to experimental and numerical studies. In a pure morphological case, when there is no flow, morphological changes in the solid-liquid interface are governed by heat conduction and solute distribution. Under the influence of a convective motion, both heat and solute are redistributed, thereby affecting the intrinsic morphological phenomenon. The overall effect of the convective motion could be either stabilizing or destabilizing. Recent investigations have predicted stabilization by a flow parallel to the interface. In the case of non-parallel flows, e.g., stagnation point flow, Brattkus and Davis have found a new flow-induced morphological instability that occurs at long wavelengths and also consists of waves propagating against the flow. Other studies have addressed the nonlinear aspects (Konstantinos and Brown, Wollkind and Segel)). In contrast to the earlier studies, our present investigation focuses on the effects of the potential flow fields typically encountered in Hele-Shaw cells. Such a Hele-Shaw cell can simulate a gravity-free environment in the sense that buoyancy-driven convection is largely suppressed, and hence negligible. Our interest lies both in analyzing the linear stability of the solidification process in the presence of potential flow fields, as well as in performing high-accuracy nonlinear simulations. Linear stability analysis can be performed for the flow configuration mentioned above. It is observed that a parallel potential flow is stabilizing and gives rise to waves traveling downstream. We have built a highly accurate numerical scheme which is validated at small amplitudes by comparing with the analytically predicted results for the pure

  5. Accurate interatomic potentials for Ni, Al and Ni/sub 3/Al

    SciTech Connect

    Voter, A.F.; Chen, Shao Ping

    1986-01-01

    To obtain meaningful results from atomistic simulations of materials, the interatomic potentials must be capable of reproducing the thermodynamic properties of the system of interest. Pairwise potentials have known deficiencies that make them unsuitable for quantitative investigations of defective regions such as crack tips and free surfaces. Daw and Baskes (Phys. Rev. B 29, 6443 (1984)) have shown that including a local ''volume'' term for each atom gives the necessary many-body character without the severe computational dependence of explicit n-body potential terms. Using a similar approach, we have fit an interatomic potential to the Ni/sub 3/Al alloy system. This potential can treat diatomic Ni/sub 2/, diatomic Al/sub 2/, fcc Ni, fcc Al and L1/sub 2/ Ni/sub 3/Al on an equal footing. Details of the fitting procedure are presented, along with the calculation of some properties not included in the fit.

  6. 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

  7. Nuclear structure with accurate chiral perturbation theory nucleon-nucleon potential: Application to 6Li and 10B

    SciTech Connect

    Navratil, P; Caurier, E

    2003-10-14

    The authors calculate properties of A = 6 system using the accurate charge-dependent nucleon-nucleon (NN) potential at fourth order of chiral perturbation theory. By application of the ab initio no-core shell model (NCSM) and a variational calculation in the harmonic oscillator basis with basis size up to 16 {h_bar}{Omega} they obtain the {sup 6}Li binding energy of 28.5(5) MeV and a converged excitation spectrum. Also, they calculate properties of {sup 10}B using the same NN potential in a basis space of up to 8 {h_bar}{Omega}. The results are consistent with results obtained by standard accurate NN potentials and demonstrate a deficiency of Hamiltonians consisting of only two-body terms. At this order of chiral perturbation theory three-body terms appear. It is expected that inclusion of such terms in the Hamiltonian will improve agreement with experiment.

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

    PubMed Central

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

    2015-01-01

    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. PMID:26543241

  9. Accurate spectroscopic characterization of protonated oxirane: a potential prebiotic species in Titan's atmosphere

    SciTech Connect

    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{sup –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.

  10. Reliable Spectroscopic Constants for CCH-, NH2- and Their Isotopomers from an Accurate Potential Energy Function

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Dateo, Christopher E.; Schwenke, David W.; Chaban, Galina M.

    2005-01-01

    Accurate quartic force fields have been determined for the CCH- and NH2- molecular anions using the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations, CCSD(T). Very large one-particle basis sets have been used including diffuse functions and up through g-type functions. Correlation of the nitrogen and carbon core electrons has been included, as well as other "small" effects, such as the diagonal Born-Oppenheimer correction, and basis set extrapolation, and corrections for higher-order correlation effects and scalar relativistic effects. Fundamental vibrational frequencies have been computed using standard second-order perturbation theory as well as variational methods. Comparison with the available experimental data is presented and discussed. The implications of our research for the astronomical observation of molecular anions will be discussed.

  11. Effective Potential Energies and Transport Cross Sections for Interactions of Hydrogen and Nitrogen

    NASA Technical Reports Server (NTRS)

    Stallcop, James R.; Partridge, Harry; Levin, Eugene; Arnold, James R. (Technical Monitor)

    2000-01-01

    The interaction energies for N2-He and N2-H2 are calculated by accurate ab initio methods. The virial coefficient and differential scattering cross section for N2-H2 are calculated; the theoretical results are compared with experimental data. The transport collision integrals for N2-H2 and N2-N2 interactions are calculated and tabulated; the results yield transport coefficients that compare well with measured data. Transport coefficients are found to be determined accurately from the interaction energies for a specific configuration of the molecule formed from the interaction partners. Comparisons with results of measurement and accurate calculations demonstrate that the transport properties of complex molecular interactions can be determined rapidly and fairly accurately from the interaction energies of simpler system using combination rules for the short-range parameters of effective interaction energies and the coefficients for the long-range forces. The coefficients for a two-parameter temperature expansion of diffusion and viscosity are tabulated for a realistic universal potential energy that is based primarily on the results of very accurate calculations of the He-He interaction energy.

  12. 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.

  13. Quantum Dynamics of Vinylidene Photodetachment on an Accurate Global Acetylene-Vinylidene Potential Energy Surface.

    PubMed

    Guo, Lifen; Han, Huixian; Ma, Jianyi; Guo, Hua

    2015-08-01

    Vinylidene is a high-energy isomer of acetylene, and the rearrangement of bonds in the two species serves as a prototype for isomerization reactions. Here, a full-dimensional quantum mechanical study of the vinylidene vibration is carried out on a recently developed global acetylene-vinylidene potential energy surface by simulating the photodetachment dynamics of the vinylidene anion. Several low-lying vibrational levels of the anion were first determined on a new ab initio based potential energy surface, and their photoelectron spectra were obtained within the Condon approximation. The vibrational features of the vinylidene isomer are found to agree well with the experiment in both positions and intensities, validating the global acetylene-vinylidene potential energy surface.

  14. 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.

  15. Material interactions with the Low Earth Orbital (LEO) environment: Accurate reaction rate measurements

    NASA Technical Reports Server (NTRS)

    Visentine, James T.; Leger, Lubert J.

    1987-01-01

    To resolve uncertainties in estimated LEO atomic oxygen fluence and provide reaction product composition data for comparison to data obtained in ground-based simulation laboratories, a flight experiment has been proposed for the space shuttle which utilizes an ion-neutral mass spectrometer to obtain in-situ ambient density measurements and identify reaction products from modeled polymers exposed to the atomic oxygen environment. An overview of this experiment is presented and the methodology of calibrating the flight mass spectrometer in a neutral beam facility prior to its use on the space shuttle is established. The experiment, designated EOIM-3 (Evaluation of Oxygen Interactions with Materials, third series), will provide a reliable materials interaction data base for future spacecraft design and will furnish insight into the basic chemical mechanisms leading to atomic oxygen interactions with surfaces.

  16. Accurate and efficient method for many-body van der Waals interactions.

    PubMed

    Tkatchenko, Alexandre; DiStasio, Robert A; Car, Roberto; Scheffler, Matthias

    2012-06-01

    An efficient method is developed for the microscopic description of the frequency-dependent polarizability of finite-gap molecules and solids. This is achieved by combining the Tkatchenko-Scheffler van der Waals (vdW) method [Phys. Rev. Lett. 102, 073005 (2009)] with the self-consistent screening equation of classical electrodynamics. This leads to a seamless description of polarization and depolarization for the polarizability tensor of molecules and solids. The screened long-range many-body vdW energy is obtained from the solution of the Schrödinger equation for a system of coupled oscillators. We show that the screening and the many-body vdW energy play a significant role even for rather small molecules, becoming crucial for an accurate treatment of conformational energies for biomolecules and binding of molecular crystals. The computational cost of the developed theory is negligible compared to the underlying electronic structure calculation.

  17. Accurate formula for dissipative interaction in frequency modulation atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Suzuki, Kazuhiro; Kobayashi, Kei; Labuda, Aleksander; Matsushige, Kazumi; Yamada, Hirofumi

    2014-12-01

    Much interest has recently focused on the viscosity of nano-confined liquids. Frequency modulation atomic force microscopy (FM-AFM) is a powerful technique that can detect variations in the conservative and dissipative forces between a nanometer-scale tip and a sample surface. We now present an accurate formula to convert the dissipation power of the cantilever measured during the experiment to damping of the tip-sample system. We demonstrated the conversion of the dissipation power versus tip-sample separation curve measured using a colloidal probe cantilever on a mica surface in water to the damping curve, which showed a good agreement with the theoretical curve. Moreover, we obtained the damping curve from the dissipation power curve measured on the hydration layers on the mica surface using a nanometer-scale tip, demonstrating that the formula allows us to quantitatively measure the viscosity of a nano-confined liquid using FM-AFM.

  18. Screened exchange hybrid density functional for accurate and efficient structures and interaction energies.

    PubMed

    Brandenburg, Jan Gerit; Caldeweyher, Eike; Grimme, Stefan

    2016-06-21

    We extend the recently introduced PBEh-3c global hybrid density functional [S. Grimme et al., J. Chem. Phys., 2015, 143, 054107] by a screened Fock exchange variant based on the Henderson-Janesko-Scuseria exchange hole model. While the excellent performance of the global hybrid is maintained for small covalently bound molecules, its performance for computed condensed phase mass densities is further improved. Most importantly, a speed up of 30 to 50% can be achieved and especially for small orbital energy gap cases, the method is numerically much more robust. The latter point is important for many applications, e.g., for metal-organic frameworks, organic semiconductors, or protein structures. This enables an accurate density functional based electronic structure calculation of a full DNA helix structure on a single core desktop computer which is presented as an example in addition to comprehensive benchmark results. PMID:27240749

  19. Accurate formula for dissipative interaction in frequency modulation atomic force microscopy

    SciTech Connect

    Suzuki, Kazuhiro; Matsushige, Kazumi; Yamada, Hirofumi; Kobayashi, Kei; Labuda, Aleksander

    2014-12-08

    Much interest has recently focused on the viscosity of nano-confined liquids. Frequency modulation atomic force microscopy (FM-AFM) is a powerful technique that can detect variations in the conservative and dissipative forces between a nanometer-scale tip and a sample surface. We now present an accurate formula to convert the dissipation power of the cantilever measured during the experiment to damping of the tip-sample system. We demonstrated the conversion of the dissipation power versus tip-sample separation curve measured using a colloidal probe cantilever on a mica surface in water to the damping curve, which showed a good agreement with the theoretical curve. Moreover, we obtained the damping curve from the dissipation power curve measured on the hydration layers on the mica surface using a nanometer-scale tip, demonstrating that the formula allows us to quantitatively measure the viscosity of a nano-confined liquid using FM-AFM.

  20. An accurate binding interaction model in de novo computational protein design of interactions: if you build it, they will bind.

    PubMed

    London, Nir; Ambroggio, Xavier

    2014-02-01

    Computational protein design efforts aim to create novel proteins and functions in an automated manner and, in the process, these efforts shed light on the factors shaping natural proteins. The focus of these efforts has progressed from the interior of proteins to their surface and the design of functions, such as binding or catalysis. Here we examine progress in the development of robust methods for the computational design of non-natural interactions between proteins and molecular targets such as other proteins or small molecules. This problem is referred to as the de novo computational design of interactions. Recent successful efforts in de novo enzyme design and the de novo design of protein-protein interactions open a path towards solving this problem. We examine the common themes in these efforts, and review recent studies aimed at understanding the nature of successes and failures in the de novo computational design of interactions. While several approaches culminated in success, the use of a well-defined structural model for a specific binding interaction in particular has emerged as a key strategy for a successful design, and is therefore reviewed with special consideration.

  1. Accurate one-dimensional potential energy curve of the linear (H2)2 cluster

    NASA Astrophysics Data System (ADS)

    Tung, Wei-Cheng; Pavanello, Michele; Adamowicz, Ludwik

    2010-09-01

    We present a sub-0.3 K accuracy, ground-state one-dimensional potential energy curve of the metastable linear configuration of the (H2)2 cluster calculated exclusively with explicitly correlated Gaussian functions with shifted centers. The H2 internuclear distance is kept at the isolated H2 vibrational ground-state average value of 1.448 736 bohr and the intermonomer separation is varied between 2 and 100 bohrs. The analytical gradient of the energy with respect to the nonlinear parameters of the Gaussians (i.e., the exponents and the coordinates of the shifts) has been employed in the variational optimization of the wave function. Procedures for enlarging the basis set and for adjusting the centers of the Gaussians to the varying intermonomer separation have been developed and used in the calculations.

  2. Accurate ab initio potential for the krypton dimer and transport properties of the low-density krypton gas.

    PubMed

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

    2015-05-28

    A new highly accurate potential energy curve for the krypton dimer was constructed using coupled-cluster calculations up to the singles, doubles, triples, and perturbative quadruples level, including corrections for core-core and core-valence correlation and for relativistic effects. The ab initio data points were fitted to an analytic potential which was used to compute the most important transport properties of the krypton gas. The viscosity, thermal conductivity, self-diffusion coefficient, and thermal diffusion factor were calculated by the kinetic theory at low density and temperatures from 116 to 5000 K. The comparisons with literature experimental data as well as with values from other pair potentials indicate that our new potential is superior to all previous ones. The transport property values computed in this work are recommended as standard values over the complete temperature range.

  3. Accurate ab initio potential for the krypton dimer and transport properties of the low-density krypton gas.

    PubMed

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

    2015-05-28

    A new highly accurate potential energy curve for the krypton dimer was constructed using coupled-cluster calculations up to the singles, doubles, triples, and perturbative quadruples level, including corrections for core-core and core-valence correlation and for relativistic effects. The ab initio data points were fitted to an analytic potential which was used to compute the most important transport properties of the krypton gas. The viscosity, thermal conductivity, self-diffusion coefficient, and thermal diffusion factor were calculated by the kinetic theory at low density and temperatures from 116 to 5000 K. The comparisons with literature experimental data as well as with values from other pair potentials indicate that our new potential is superior to all previous ones. The transport property values computed in this work are recommended as standard values over the complete temperature range. PMID:26026447

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

    NASA Astrophysics Data System (ADS)

    Liu, Qianlong; Reifsnider, Kenneth

    2012-11-01

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

  5. Properties of alkali-metal atoms and alkaline-earth-metal ions for an accurate estimate of their long-range interactions

    NASA Astrophysics Data System (ADS)

    Kaur, Jasmeet; Nandy, D. K.; Arora, Bindiya; Sahoo, B. K.

    2015-01-01

    Accurate knowledge of interaction potentials among the alkali-metal atoms and alkaline-earth ions is very useful in the studies of cold atom physics. Here we carry out theoretical studies of the long-range interactions among the Li, Na, K, and Rb alkali-metal atoms with the Ca+, Ba+, Sr+, and Ra+ alkaline-earth ions systematically, which are largely motivated by their importance in a number of applications. These interactions are expressed as a power series in the inverse of the internuclear separation R . Both the dispersion and induction components of these interactions are determined accurately from the algebraic coefficients corresponding to each power combination in the series. Ultimately, these coefficients are expressed in terms of the electric multipole polarizabilities of the above-mentioned systems, which are calculated using the matrix elements obtained from a relativistic coupled-cluster method and core contributions to these quantities from the random-phase approximation. We also compare our estimated polarizabilities with the other available theoretical and experimental results to verify accuracies in our calculations. In addition, we also evaluate the lifetimes of the first two low-lying states of the ions using the above matrix elements. Graphical representations of the dispersion coefficients versus R are given among all the alkaline ions with Rb.

  6. Three-dimensional Euler time accurate simulations of fan rotor-stator interactions

    NASA Technical Reports Server (NTRS)

    Boretti, A. A.

    1990-01-01

    A numerical method useful to describe unsteady 3-D flow fields within turbomachinery stages is presented. The method solves the compressible, time dependent, Euler conservation equations with a finite volume, flux splitting, total variation diminishing, approximately factored, implicit scheme. Multiblock composite gridding is used to partition the flow field into a specified arrangement of blocks with static and dynamic interfaces. The code is optimized to take full advantage of the processing power and speed of the Cray Y/MP supercomputer. The method is applied to the computation of the flow field within a single stage, axial flow fan, thus reproducing the unsteady 3-D rotor-stator interaction.

  7. Interpolation method for accurate affinity ranking of arrayed ligand-analyte interactions.

    PubMed

    Schasfoort, Richard B M; Andree, Kiki C; van der Velde, Niels; van der Kooi, Alex; Stojanović, Ivan; Terstappen, Leon W M M

    2016-05-01

    The values of the affinity constants (kd, ka, and KD) that are determined by label-free interaction analysis methods are affected by the ligand density. This article outlines a surface plasmon resonance (SPR) imaging method that yields high-throughput globally fitted affinity ranking values using a 96-plex array. A kinetic titration experiment without a regeneration step has been applied for various coupled antibodies binding to a single antigen. Globally fitted rate (kd and ka) and dissociation equilibrium (KD) constants for various ligand densities and analyte concentrations are exponentially interpolated to the KD at Rmax = 100 RU response level (KD(R100)).

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

    SciTech Connect

    Han, Huixian; Li, Anyang; Guo, Hua

    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 up 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.

  9. An accurate global potential energy surface, dipole moment surface, and rovibrational frequencies for NH3

    NASA Astrophysics Data System (ADS)

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

    2008-12-01

    A global potential energy surface (PES) that includes short and long range terms has been determined for the NH3 molecule. The singles and doubles coupled-cluster method that includes a perturbational estimate of connected triple excitations and the internally contracted averaged coupled-pair functional electronic structure methods have been used in conjunction with very large correlation-consistent basis sets, including diffuse functions. Extrapolation to the one-particle basis set limit was performed and core correlation and scalar relativistic contributions were included directly, while the diagonal Born-Oppenheimer correction was added. Our best purely ab initio PES, denoted "mixed," is constructed from two PESs which differ in whether the ic-ACPF higher-order correlation correction was added or not. Rovibrational transition energies computed from the mixed PES agree well with experiment and the best previous theoretical studies, but most importantly the quality does not deteriorate even up to 10300cm-1 above the zero-point energy (ZPE). The mixed PES was improved further by empirical refinement using the most reliable J =0-2 rovibrational transitions in the HITRAN 2004 database. Agreement between high-resolution experiment and rovibrational transition energies computed from our refined PES for J =0-6 is excellent. Indeed, the root mean square (rms) error for 13 HITRAN 2004 bands for J =0-2 is 0.023cm-1 and that for each band is always ⩽0.06cm-1. For J =3-5 the rms error is always ⩽0.15cm-1. This agreement means that transition energies computed with our refined PES should be useful in the assignment of new high-resolution NH3 spectra and in correcting mistakes in previous assignments. Ideas for further improvements to our refined PES and for extension to other isotopolog are discussed.

  10. Full Dimensional Vibrational Calculations for Methane Using AN Accurate New AB Initio Based Potential Energy Surface

    NASA Astrophysics Data System (ADS)

    Majumder, Moumita; Dawes, Richard; Wang, Xiao-Gang; Carrington, Tucker; Li, Jun; Guo, Hua; Manzhos, Sergei

    2014-06-01

    New potential energy surfaces for methane were constructed, represented as analytic fits to about 100,000 individual high-level ab initio data. Explicitly-correlated multireference data (MRCI-F12(AE)/CVQZ-F12) were computed using Molpro [1] and fit using multiple strategies. Fits with small to negligible errors were obtained using adaptations of the permutation-invariant-polynomials (PIP) approach [2,3] based on neural-networks (PIP-NN) [4,5] and the interpolative moving least squares (IMLS) fitting method [6] (PIP-IMLS). The PESs were used in full-dimensional vibrational calculations with an exact kinetic energy operator by representing the Hamiltonian in a basis of products of contracted bend and stretch functions and using a symmetry adapted Lanczos method to obtain eigenvalues and eigenvectors. Very close agreement with experiment was produced from the purely ab initio PESs. References 1- H.-J. Werner, P. J. Knowles, G. Knizia, 2012.1 ed. 2012, MOLPRO, a package of ab initio programs. see http://www.molpro.net. 2- Z. Xie and J. M. Bowman, J. Chem. Theory Comput 6, 26, 2010. 3- B. J. Braams and J. M. Bowman, Int. Rev. Phys. Chem. 28, 577, 2009. 4- J. Li, B. Jiang and Hua Guo, J. Chem. Phys. 139, 204103 (2013). 5- S Manzhos, X Wang, R Dawes and T Carrington, JPC A 110, 5295 (2006). 6- R. Dawes, X-G Wang, A.W. Jasper and T. Carrington Jr., J. Chem. Phys. 133, 134304 (2010).

  11. Accurate calculations of the hydration free energies of druglike molecules using the reference interaction site model.

    PubMed

    Palmer, David S; Sergiievskyi, Volodymyr P; Jensen, Frank; Fedorov, Maxim V

    2010-07-28

    We report on the results of testing the reference interaction site model (RISM) for the estimation of the hydration free energy of druglike molecules. The optimum model was selected after testing of different RISM free energy expressions combined with different quantum mechanics and empirical force-field methods of structure optimization and atomic partial charge calculation. The final model gave a systematic error with a standard deviation of 2.6 kcal/mol for a test set of 31 molecules selected from the SAMPL1 blind challenge set [J. P. Guthrie, J. Phys. Chem. B 113, 4501 (2009)]. After parametrization of this model to include terms for the excluded volume and the number of atoms of different types in the molecule, the root mean squared error for a test set of 19 molecules was less than 1.2 kcal/mol.

  12. 4-Component correlated all-electron study on Eka-actinium Fluoride (E121F) including Gaunt interaction: Accurate analytical form, bonding and influence on rovibrational spectra

    NASA Astrophysics Data System (ADS)

    Amador, Davi H. T.; de Oliveira, Heibbe C. B.; Sambrano, Julio R.; Gargano, Ricardo; de Macedo, Luiz Guilherme M.

    2016-10-01

    A prolapse-free basis set for Eka-Actinium (E121, Z = 121), numerical atomic calculations on E121, spectroscopic constants and accurate analytical form for the potential energy curve of diatomic E121F obtained at 4-component all-electron CCSD(T) level including Gaunt interaction are presented. The results show a strong and polarized bond (≈181 kcal/mol in strength) between E121 and F, the outermost frontier molecular orbitals from E121F should be fairly similar to the ones from AcF and there is no evidence of break of periodic trends. Moreover, the Gaunt interaction, although small, is expected to influence considerably the overall rovibrational spectra.

  13. Mitotic Protein CSPP1 Interacts with CENP-H Protein to Coordinate Accurate Chromosome Oscillation in Mitosis.

    PubMed

    Zhu, Lijuan; Wang, Zhikai; Wang, Wenwen; Wang, Chunli; Hua, Shasha; Su, Zeqi; Brako, Larry; Garcia-Barrio, Minerva; Ye, Mingliang; Wei, Xuan; Zou, Hanfa; Ding, Xia; Liu, Lifang; Liu, Xing; Yao, Xuebiao

    2015-11-01

    Mitotic chromosome segregation is orchestrated by the dynamic interaction of spindle microtubules with the kinetochores. During chromosome alignment, kinetochore-bound microtubules undergo dynamic cycles between growth and shrinkage, leading to an oscillatory movement of chromosomes along the spindle axis. Although kinetochore protein CENP-H serves as a molecular control of kinetochore-microtubule dynamics, the mechanistic link between CENP-H and kinetochore microtubules (kMT) has remained less characterized. Here, we show that CSPP1 is a kinetochore protein essential for accurate chromosome movements in mitosis. CSPP1 binds to CENP-H in vitro and in vivo. Suppression of CSPP1 perturbs proper mitotic progression and compromises the satisfaction of spindle assembly checkpoint. In addition, chromosome oscillation is greatly attenuated in CSPP1-depleted cells, similar to what was observed in the CENP-H-depleted cells. Importantly, CSPP1 depletion enhances velocity of kinetochore movement, and overexpression of CSPP1 decreases the speed, suggesting that CSPP1 promotes kMT stability during cell division. Specific perturbation of CENP-H/CSPP1 interaction using a membrane-permeable competing peptide resulted in a transient mitotic arrest and chromosome segregation defect. Based on these findings, we propose that CSPP1 cooperates with CENP-H on kinetochores to serve as a novel regulator of kMT dynamics for accurate chromosome segregation.

  14. Cobra cardiotoxins: membrane interactions and pharmacological potential.

    PubMed

    Dubovskii, P V; Konshina, A G; Efremov, R G

    2014-01-01

    Natural polycationic membrane-active peptides typically lack disulfide bonds and exhibit fusion, cell-penetrating, antimicrobial activities. They are mostly unordered in solution, but adopt a helical structure, when bound to phospholipid membranes. Structurally different are cardiotoxins (or cytotoxins, CTs) from cobra venom. They are fully β- structured molecules, characterized by the three-finger fold (TFF). Affinity of CTs to lipid bilayer was shown to depend on amino acid sequence in the tips of the three loops. In the present review, CT-membrane interactions are analyzed through the prism of data on binding of the toxins to phospholipid liposomes and detergent micelles, as well as their structural and computational studies in membrane mimicking environments. We assess different hydrophobicity scales to compare membrane partitioning of various CTs and their membrane effects. A comparison of hydrophobic/hydrophilic properties of CTs and linear polycationic peptides provides a key to their biological activity and creates a fundamental basis for rational design of new membrane-interacting compounds, including new promising drugs. For instance, from the viewpoint of the data obtained on model lipid membranes, cytotoxic activity of CTs against cancer cells is discussed.

  15. Quantum chemical tests of water-water potential for interaction site water models.

    PubMed

    Huš, Matej; Urbič, Tomaž

    2012-09-01

    Accuracy of different simple interaction site water models was tested. Instead of assessing their quality through the calculations of various water physical properties (dipole moment, dielectric constant, phase-equilibria diagrams, etc.) and comparison with experimental values, we calculated water-water potential and compared it with the potential from quantum chemical calculations. Using density functional theory (DFT) water-water potential was calculated for different positions of two water molecules, which was compared with the interaction used in water models. Different simple interaction site water models were then evaluated and assessed. Special emphasis is placed on angle and distance dependence of water-water potential around minima in the potential. Among three-, four-and five-site electrostatic water models, TIP3P, TIP4P/2005 and TIP5P were found to be the most accurate.

  16. Accurate potential energy curve of the LiH{sup +} molecule calculated with explicitly correlated Gaussian functions

    SciTech Connect

    Tung, Wei-Cheng; Adamowicz, Ludwik

    2014-03-28

    Very accurate calculations of the ground-state potential energy curve (PEC) of the LiH{sup +} ion performed with all-electron explicitly correlated Gaussian functions with shifted centers are presented. The variational method is employed. The calculations involve optimization of nonlinear exponential parameters of the Gaussians performed with the aid of the analytical first derivatives of the energy determined with respect to the parameters. The diagonal adiabatic correction is also calculated for each PEC point. The PEC is then used to calculate the vibrational energies of the system. In that calculation, the non-adiabatic effects are accounted for by using an effective vibrational mass obtained by the minimization of the difference between the vibrational energies obtained from the calculations where the Born-Oppenheimer approximation was not assumed and the results of the present calculations.

  17. Progress Towards the Accurate Calculation of Anharmonic Vibrational States of Fluxional Molecules and Clusters Without a Potential Energy Surface

    NASA Astrophysics Data System (ADS)

    Petit, Andrew S.; McCoy, Anne B.

    2011-06-01

    The accurate calculation of anharmonic vibrational states of highly fluxional systems is complicated by the need to first obtain the full-dimensional potential energy surface(PES). Although commonly exploited as a way around this problem, grid-based methodologies scale exponentially with system size while reduced dimensional approaches are highly system dependent, both in terms of the details of their application and in terms of their suitability. Moreover, the achievement of converged variational calculations of highly anharmonic systems is complicated by the necessity of using a very large basis and hence the construction and diagonalization of enormous Hamiltonian matrices. We report here our recent efforts to develop an algorithm capable of accurately calculating anharmonic vibrational energies, even for very floppy systems, without first obtaining a PES and using only a handful of basis functions per degree of freedom. More specifically, the potential energy and G-matrix elements are calculated on a set of points obtained from a Monte Carlo sampling of the most important regions of configuration space, allowing for a significant reduction in the number of required sampling points. The Hamiltonian matrix is then constructed using an evolving basis which, with each iteration, captures the effect of building H from an ever-expanding basis despite the fact that the actual dimensionality of H is fixed throughout the calculation. This latter property of the algorithm also greatly reduces the size of basis needed for the calculation relative to more traditional variational approaches. The results obtained from the application of our method to several test systems, including ion water complexes, will be reported along with its observed convergence properties.

  18. Accurate high level ab initio-based global potential energy surface and dynamics calculations for ground state of CH2(+).

    PubMed

    Li, Y Q; Zhang, P Y; Han, K L

    2015-03-28

    A global many-body expansion potential energy surface is reported for the electronic ground state of CH2 (+) by fitting high level ab initio energies calculated at the multireference configuration interaction level with the aug-cc-pV6Z basis set. The topographical features of the new global potential energy surface are examined in detail and found to be in good agreement with those calculated directly from the raw ab initio energies, as well as previous calculations available in the literature. In turn, in order to validate the potential energy surface, a test theoretical study of the reaction CH(+)(X(1)Σ(+))+H((2)S)→C(+)((2)P)+H2(X(1)Σg (+)) has been carried out with the method of time dependent wavepacket on the title potential energy surface. The total integral cross sections and the rate coefficients have been calculated; the results determined that the new potential energy surface can both be recommended for dynamics studies of any type and as building blocks for constructing the potential energy surfaces of larger C(+)/H containing systems.

  19. Wake potentials of the ILC Interaction Region

    SciTech Connect

    Novokhatski, A.; /SLAC

    2011-08-16

    The vacuum chamber of the ILC Interaction Region (IR) is optimized for best detector performance. It has special shaping to minimize additional backgrounds due to the metal part of the chamber. Also, for the same reason this thin vacuum chamber does not have water cooling. Therefore, small amounts of power, which may be deposited in the chamber, can be enough to raise the chamber to a high temperature. One of the sources of 'heating' power is the electromagnetic field of the beam. This field diffracts by non-regularities of the beam pipe and excites free-propagating fields, which are then absorbed by the pipe wall. In addition we have a heating power of the image currents due to finite conductivity of the metallic wall. We will discuss these effects as updating the previous results. The conclusions of this report are: (1) The amount of the beam energy loss in IR is almost equal to the energy loss in one ILC (TESLA) accelerating cryo-module; (2) Addition energy spread at IR is very small; (3) Spectrum of the wake fields is limited 300 GHz; (4) Average power of the wake fields excited in IR is 30 W for nominal ILC parameters; and (5) Pulse power in this case is 6 kilowatts.

  20. Van der Waals interactions: accuracy of pair potential approximations.

    PubMed

    Cole, Milton W; Kim, Hye-Young; Liebrecht, Michael

    2012-11-21

    Van der Waals interactions between single atoms and solids are discussed for the regime of large separation. A commonly employed approximation is to evaluate this interaction as a sum of two-body interactions between the adatom and the constituent atoms of the solid. The resulting potentials are here compared with known results in various geometries. Analogous comparisons are made for diatomic molecules near either single atoms or semi-infinite surfaces and for triatomic molecules' interactions with single atoms. PMID:23181315

  1. Quantum chemical approach for condensed-phase thermochemistry (III): Accurate evaluation of proton hydration energy and standard hydrogen electrode potential

    NASA Astrophysics Data System (ADS)

    Ishikawa, Atsushi; Nakai, Hiromi

    2016-04-01

    Gibbs free energy of hydration of a proton and standard hydrogen electrode potential were evaluated using high-level quantum chemical calculations. The solvent effect was included using the cluster-continuum model, which treated short-range effects by quantum chemical calculations of proton-water complexes, and the long-range effects by a conductor-like polarizable continuum model. The harmonic solvation model (HSM) was employed to estimate enthalpy and entropy contributions due to nuclear motions of the clusters by including the cavity-cluster interactions. Compared to the commonly used ideal gas model, HSM treatment significantly improved the contribution of entropy, showing a systematic convergence toward the experimental data.

  2. Effective Potential Energies and Transport Cross Sections for Atom-Molecule Interactions of Nitrogen and Nitrogen

    NASA Technical Reports Server (NTRS)

    Stallcop, James R.; Partridge, Harry; Levin, Eugene; Arnold, Jim (Technical Monitor)

    2001-01-01

    The potential energy surfaces for H2-N and N2-N interactions are calculated by accurate ab initio methods and applied to determine transport data. The results confirm that an effective potential energy for accurately determining transport properties can be calculated using a single orientation. A simple method is developed to determine the dispersion coefficients of effective potential energies Effective potential energies required for O2-O collisions are determ=ined. The H2-N, N2-N, O2-H, and O2-O collision integrals are calculated and tabulated for a large range of temperatures. The theoretical values of the N2-N and O2-O diffusion coefficients compare well with measured data available at room temperature.

  3. Proton-silicon interaction potential extracted from high-resolution measurements of crystal rainbows

    NASA Astrophysics Data System (ADS)

    Petrović, S.; Nešković, N.; Ćosić, M.; Motapothula, M.; Breese, M. B. H.

    2015-10-01

    This study provides a way to produce very accurate ion-atom interaction potentials. We present the high-resolution measurements of angular distributions of protons of energies between 2.0 and 0.7 MeV channeled in a 55 nm thick (0 0 1) silicon membrane. Analysis is performed using the theory of crystal rainbows in which the Molière's interaction potential is modified to make it accurate both close to the channel axis and close to the atomic strings defining the channel. This modification is based on adjusting the shapes of the rainbow lines appearing in the transmission angle plane, with the resulting theoretical angular distributions of transmitted protons being in excellent agreement with the corresponding experimental distributions.

  4. Accurate multireference configuration interaction calculations of the 24 Λ-S states and 60 Ω states of the BO+ cation

    NASA Astrophysics Data System (ADS)

    Liu, Hui; Shi, Deheng; Sun, Jinfeng; Zhu, Zunlue

    2016-11-01

    The potential energy curves were calculated for the 24 Λ-S states correlating with the lowest four dissociation channels of the BO+ cation. The potential energy curves were also computed for the 60 Ω states generated from the 24 Λ-S states. Calculations were made for internuclear separations from 0.08 to 1.05 nm using the CASSCF method, which was followed by the icMRCI approach with the correlation-consistent basis sets. Core-valence correlation, scalar relativistic and basis extrapolation were accounted for. Of the 24 Λ-S states, only three states (25Π, 15Σ-, and 25Σ-) were found to be repulsive; only the 15Δ state was found to be a very weakly-bound state; and the E1Π, 23Π, and 15Π states were found to be very strong bound. In addition, the B1Σ+ and 31Σ+ states have double wells by the avoided crossing between the two states. The a3Π, 13Σ-, and 23Σ- states are inverted with the spin-orbit coupling effect included. The spectroscopic parameters were determined and the vibrational properties of several Λ-S states were predicted. Comparison with available experimental data shows that the methodology employed is highly accurate for this system.

  5. Accurate multireference configuration interaction calculations of the 24 Λ-S states and 60 Ω states of the BO(+) cation.

    PubMed

    Liu, Hui; Shi, Deheng; Sun, Jinfeng; Zhu, Zunlue

    2016-11-01

    The potential energy curves were calculated for the 24 Λ-S states correlating with the lowest four dissociation channels of the BO(+) cation. The potential energy curves were also computed for the 60 Ω states generated from the 24 Λ-S states. Calculations were made for internuclear separations from 0.08 to 1.05nm using the CASSCF method, which was followed by the icMRCI approach with the correlation-consistent basis sets. Core-valence correlation, scalar relativistic and basis extrapolation were accounted for. Of the 24 Λ-S states, only three states (2(5)Π, 1(5)Σ(-), and 2(5)Σ(-)) were found to be repulsive; only the 1(5)Δ state was found to be a very weakly-bound state; and the E(1)Π, 2(3)Π, and 1(5)Π states were found to be very strong bound. In addition, the B(1)Σ(+) and 3(1)Σ(+) states have double wells by the avoided crossing between the two states. The a(3)Π, 1(3)Σ(-), and 2(3)Σ(-) states are inverted with the spin-orbit coupling effect included. The spectroscopic parameters were determined and the vibrational properties of several Λ-S states were predicted. Comparison with available experimental data shows that the methodology employed is highly accurate for this system. PMID:27289351

  6. Interaction potential between a helium atom and metal surfaces

    NASA Technical Reports Server (NTRS)

    Takada, Y.; Kohn, W.

    1985-01-01

    By employing an S-matrix theory for evanescent waves, the repulsive potential between a helium atom and corrugated metal surfaces has been calculated. P-wave interactions and intra-atomic correlation effects were found to be very important. The corrugation part of the interaction potential is much weaker than predicted by the effective-medium theory. Application to Cu, Ni, and Ag (110) surfaces gives good agreement with experiment without any adjustable parameters.

  7. Ring polymer molecular dynamics fast computation of rate coefficients on accurate potential energy surfaces in local configuration space: Application to the abstraction of hydrogen from methane

    NASA Astrophysics Data System (ADS)

    Meng, Qingyong; Chen, Jun; Zhang, Dong H.

    2016-04-01

    To fast and accurately compute rate coefficients of the H/D + CH4 → H2/HD + CH3 reactions, we propose a segmented strategy for fitting suitable potential energy surface (PES), on which ring-polymer molecular dynamics (RPMD) simulations are performed. On the basis of recently developed permutation invariant polynomial neural-network approach [J. Li et al., J. Chem. Phys. 142, 204302 (2015)], PESs in local configuration spaces are constructed. In this strategy, global PES is divided into three parts, including asymptotic, intermediate, and interaction parts, along the reaction coordinate. Since less fitting parameters are involved in the local PESs, the computational efficiency for operating the PES routine is largely enhanced by a factor of ˜20, comparing with that for global PES. On interaction part, the RPMD computational time for the transmission coefficient can be further efficiently reduced by cutting off the redundant part of the child trajectories. For H + CH4, good agreements among the present RPMD rates and those from previous simulations as well as experimental results are found. For D + CH4, on the other hand, qualitative agreement between present RPMD and experimental results is predicted.

  8. An interatomic potential for W-N interactions

    NASA Astrophysics Data System (ADS)

    Polvi, J.; Heinola, K.; Nordlund, K.

    2016-08-01

    N2 gas is routinely used as a seeding species in fusion plasma to control the amount of power emitted from the plasma by radiation to the tungsten walls of an ITER-like divertor. Nitrogen atoms interact with the plasma-facing materials beryllium and tungsten, and form chemical bonds with the wall surfaces, as well as with plasma hydrogen isotopes, thus raising a special interest in W-N and N-H interactions in the fusion community. In this work we describe the development of an analytical interatomic potential for W-N interactions and benchmark the potential against DFT calculation results for N defects in tungsten.

  9. An interatomic potential for W–N interactions

    NASA Astrophysics Data System (ADS)

    Polvi, J.; Heinola, K.; Nordlund, K.

    2016-08-01

    N2 gas is routinely used as a seeding species in fusion plasma to control the amount of power emitted from the plasma by radiation to the tungsten walls of an ITER-like divertor. Nitrogen atoms interact with the plasma-facing materials beryllium and tungsten, and form chemical bonds with the wall surfaces, as well as with plasma hydrogen isotopes, thus raising a special interest in W–N and N–H interactions in the fusion community. In this work we describe the development of an analytical interatomic potential for W–N interactions and benchmark the potential against DFT calculation results for N defects in tungsten.

  10. Interactive Video Systems: Their Promise and Educational Potential.

    ERIC Educational Resources Information Center

    Seal-Wanner, Carla

    1988-01-01

    Hypotheses about the potential educational benefits of interactive video systems (IVS) are described. IVS, if properly designed and applied, has the potential to increase learning, encourage student-initiated learning, and provide a context for what has been learned. A call for research is made. (JL)

  11. Dense neuron system interacting with the gravitational potential.

    PubMed

    Thuraisingham, R A

    2015-10-01

    A theoretical model is developed to study the role of the gravitational potential between neurons in the brain under conditions of zero gravity. The model includes firing and non-firing neurons in a neural network where the source of interaction is the gravitational potential. The importance of this study is its ability to examine the role of the weak gravitational potential alone without the inclusion of other interactions between neurons. The results of the study show density fluctuations contain components from thermal effects and gravitational interactions. It also shows collective oscillatory behavior amongst neurons from gravitational interactions. The study provides a simple alternate mechanism to understand organized behavior of neurons in the brain under conditions of zero gravity.

  12. Potential Drug - Drug Interactions among Medications Prescribed to Hypertensive Patients

    PubMed Central

    Ganguly, Barna

    2014-01-01

    Context: Drug-drug interactions(DDIs) are significant but avoidable causes of iatrogenic morbidity and hospital admission. Aim: To detect potential drug-drug interactions among medications received by hypertensive patients. Materials and Methods: Patients of both sex and all adult age groups, who were attending medicine out -patient department (OPD) of a tertiary care teaching rural hospital since last six months and were being prescribed antihypertensive drug/s for essential hypertension, were selected for the study. Hypertensive patient with co-morbities diabetes mellitus, ischemic heart diseases, congestive heart failure, and chronic renal diseases were also included in the study. Potential drug drug interactions were checked with medscape drug interaction software. Results: With the help of medscape drug interaction software, 71.50% prescriptions were identified having atleast one drug-drug interaction. Total 918 DDIs were found in between 58 drug pairs. 55.23% DDIs were pharmacodynamic, 4.79% pharmacokinetic type of DDIs. 32.24% DDIs were found affecting serum potassium level. 95.42% DDIs were found significant type of DDIs. Drug drug interaction between atenolol & amlodipine was the most common DDI (136) followed by metoprolol and amlodine (88) in this study. Atenolol and amlodipine ( 25.92%) was the most common drugs to cause DDIs in our study. Conclusion: We detected a significant number of drug drug interaction in hypertensive patients. These interactions were between antihypertensive agents or between hypertensive and drug for co-morbid condition. PMID:25584241

  13. Accurate and Reliable Quantification of Total Microalgal Fuel Potential as Fatty Acid Methyl Esters by in situ Transesterfication

    SciTech Connect

    Laurens, L. M. L.; Quinn, M.; Van Wychen, S.; Templeton, D. W.; Wolfrum, E. J.

    2012-04-01

    In the context of algal biofuels, lipids, or better aliphatic chains of the fatty acids, are perhaps the most important constituents of algal biomass. Accurate quantification of lipids and their respective fuel yield is crucial for comparison of algal strains and growth conditions and for process monitoring. As an alternative to traditional solvent-based lipid extraction procedures, we have developed a robust whole-biomass in situ transesterification procedure for quantification of algal lipids (as fatty acid methyl esters, FAMEs) that (a) can be carried out on a small scale (using 4-7 mg of biomass), (b) is applicable to a range of different species, (c) consists of a single-step reaction, (d) is robust over a range of different temperature and time combinations, and (e) tolerant to at least 50% water in the biomass. Unlike gravimetric lipid quantification, which can over- or underestimate the lipid content, whole biomass transesterification reflects the true potential fuel yield of algal biomass. We report here on the comparison of the yield of FAMEs by using different catalysts and catalyst combinations, with the acid catalyst HCl providing a consistently high level of conversion of fatty acids with a precision of 1.9% relative standard deviation. We investigate the influence of reaction time, temperature, and biomass water content on the measured FAME content and profile for 4 different samples of algae (replete and deplete Chlorella vulgaris, replete Phaeodactylum tricornutum, and replete Nannochloropsis sp.). We conclude by demonstrating a full mass balance closure of all fatty acids around a traditional lipid extraction process.

  14. Accurate and reliable quantification of total microalgal fuel potential as fatty acid methyl esters by in situ transesterification.

    PubMed

    Laurens, Lieve M L; Quinn, Matthew; Van Wychen, Stefanie; Templeton, David W; Wolfrum, Edward J

    2012-04-01

    In the context of algal biofuels, lipids, or better aliphatic chains of the fatty acids, are perhaps the most important constituents of algal biomass. Accurate quantification of lipids and their respective fuel yield is crucial for comparison of algal strains and growth conditions and for process monitoring. As an alternative to traditional solvent-based lipid extraction procedures, we have developed a robust whole-biomass in situ transesterification procedure for quantification of algal lipids (as fatty acid methyl esters, FAMEs) that (a) can be carried out on a small scale (using 4-7 mg of biomass), (b) is applicable to a range of different species, (c) consists of a single-step reaction, (d) is robust over a range of different temperature and time combinations, and (e) tolerant to at least 50% water in the biomass. Unlike gravimetric lipid quantification, which can over- or underestimate the lipid content, whole biomass transesterification reflects the true potential fuel yield of algal biomass. We report here on the comparison of the yield of FAMEs by using different catalysts and catalyst combinations, with the acid catalyst HCl providing a consistently high level of conversion of fatty acids with a precision of 1.9% relative standard deviation. We investigate the influence of reaction time, temperature, and biomass water content on the measured FAME content and profile for 4 different samples of algae (replete and deplete Chlorella vulgaris, replete Phaeodactylum tricornutum, and replete Nannochloropsis sp.). We conclude by demonstrating a full mass balance closure of all fatty acids around a traditional lipid extraction process. PMID:22349344

  15. Charge Central Interpretation of the Full Nonlinear PB Equation: Implications for Accurate and Scalable Modeling of Solvation Interactions.

    PubMed

    Xiao, Li; Wang, Changhao; Ye, Xiang; Luo, Ray

    2016-08-25

    Continuum solvation modeling based upon the Poisson-Boltzmann equation (PBE) is widely used in structural and functional analysis of biomolecules. In this work, we propose a charge-central interpretation of the full nonlinear PBE electrostatic interactions. The validity of the charge-central view or simply charge view, as formulated as a vacuum Poisson equation with effective charges, was first demonstrated by reproducing both electrostatic potentials and energies from the original solvated full nonlinear PBE. There are at least two benefits when the charge-central framework is applied. First the convergence analyses show that the use of polarization charges allows a much faster converging numerical procedure for electrostatic energy and forces calculation for the full nonlinear PBE. Second, the formulation of the solvated electrostatic interactions as effective charges in vacuum allows scalable algorithms to be deployed for large biomolecular systems. Here, we exploited the charge-view interpretation and developed a particle-particle particle-mesh (P3M) strategy for the full nonlinear PBE systems. We also studied the accuracy and convergence of solvation forces with the charge-view and the P3M methods. It is interesting to note that the convergence of both the charge-view and the P3M methods is more rapid than the original full nonlinear PBE method. Given the developments and validations documented here, we are working to adapt the P3M treatment of the full nonlinear PBE model to molecular dynamics simulations.

  16. Interaction potential between discrete solitons in waveguide arrays.

    PubMed

    Al Khawaja, U; Al-Marzoug, S M; Bahlouli, H; Baizakov, B

    2016-08-01

    Using a variational approach, we obtained the interaction potential between two discrete solitons in optical waveguide arrays. The resulting potential bears the two features of soliton-soliton and soliton-waveguide interaction potentials where the former is similar to that of the continuum case and the latter is similar to the effective Pierls-Nabarro potential. The interplay between the two interaction potentials is investigated by studying its effect on the soliton molecule formation. It is found that the two solitons bind if their initial separation equals an odd number of waveguides, while they do not bind if their separation is an even number, which is a consequence of the two solitons being both either at the intersites (unstable) or being onsite (stable). We derived the equations of motion for the solitons' centre of mass and relative separation and provided analytic solutions for some specific cases. Favourable agreement between the analytical and numerical interaction potentials is obtained. Possible applications of our results to all-optical logic gates are pointed out. PMID:27505780

  17. Universal scaling of potential energy functions describing intermolecular interactions. II. The halide-water and alkali metal-water interactions

    SciTech Connect

    Werhahn, Jasper C.; Akase, Dai; Xantheas, Sotiris S.

    2014-08-14

    The scaled versions of the newly introduced [S. S. Xantheas and J. C. Werhahn, J. Chem. Phys.141, 064117 (2014)] generalized forms of some popular potential energy functions (PEFs) describing intermolecular interactions – Mie, Lennard-Jones, Morse, and Buckingham exponential-6 – have been used to fit the ab initio relaxed approach paths and fixed approach paths for the halide-water, X-(H2O), X = F, Cl, Br, I, and alkali metal-water, M+(H2O), M = Li, Na, K, Rb, Cs, interactions. The generalized forms of those PEFs have an additional parameter with respect to the original forms and produce fits to the ab initio data that are between one and two orders of magnitude better in the χ2 than the original PEFs. They were found to describe both the long-range, minimum and repulsive wall of the respective potential energy surfaces quite accurately. Overall the 4-parameter extended Morse (eM) and generalized Buckingham exponential-6 (gBe-6) potentials were found to best fit the ab initio data for these two classes of ion-water interactions. Finally, the fitted values of the parameter of the (eM) and (gBe-6) PEFs that control the repulsive wall of the potential correlate remarkably well with the ionic radii of the halide and alkali metal ions.

  18. The Potential for Accurately Measuring Behavioral and Economic Dimensions of Consumption, Prices, and Markets for Illegal Drugs

    PubMed Central

    Johnson, Bruce D.; Golub, Andrew

    2007-01-01

    There are numerous analytic and methodological limitations to current measures of drug market activity. This paper explores the structure of markets and individual user behavior to provide an integrated understanding of behavioral and economic (and market) aspects of illegal drug use with an aim toward developing improved procedures for measurement. This involves understanding the social processes that structure illegal distribution networks and drug users’ interactions with them. These networks are where and how social behaviors, prices, and markets for illegal drugs intersect. Our focus is upon getting an up close measurement of these activities. Building better measures of consumption behaviors necessitates building better rapport with subjects than typically achieved with one-time surveys in order to overcome withholding and underreporting and to get a comprehensive understanding of the processes involved. This can be achieved through repeated interviews and observations of behaviors. This paper also describes analytic advances that could be adopted to direct this inquiry including behavioral templates, and insights into the economic valuation of labor inputs and cash expenditures for various illegal drugs. Additionally, the paper makes recommendations to funding organizations for developing the mechanisms that would support behavioral scientists to weigh specimens and to collect small samples for laboratory analysis—by providing protection from the potential for arrest. The primary focus is upon U.S. markets. The implications for other countries are discussed. PMID:16978801

  19. The potential for accurately measuring behavioral and economic dimensions of consumption, prices, and markets for illegal drugs.

    PubMed

    Johnson, Bruce D; Golub, Andrew

    2007-09-01

    There are numerous analytic and methodological limitations to current measures of drug market activity. This paper explores the structure of markets and individual user behavior to provide an integrated understanding of behavioral and economic (and market) aspects of illegal drug use with an aim toward developing improved procedures for measurement. This involves understanding the social processes that structure illegal distribution networks and drug users' interactions with them. These networks are where and how social behaviors, prices, and markets for illegal drugs intersect. Our focus is upon getting an up close measurement of these activities. Building better measures of consumption behaviors necessitates building better rapport with subjects than typically achieved with one-time surveys in order to overcome withholding and underreporting and to get a comprehensive understanding of the processes involved. This can be achieved through repeated interviews and observations of behaviors. This paper also describes analytic advances that could be adopted to direct this inquiry including behavioral templates, and insights into the economic valuation of labor inputs and cash expenditures for various illegal drugs. Additionally, the paper makes recommendations to funding organizations for developing the mechanisms that would support behavioral scientists to weigh specimens and to collect small samples for laboratory analysis-by providing protection from the potential for arrest. The primary focus is upon U.S. markets. The implications for other countries are discussed. PMID:16978801

  20. Generation of directional EOF by interactive oscillatory zeta potential.

    PubMed

    Kuo, Chih-Yu; Wang, Chang-Yi; Chang, Chien-Cheng

    2008-11-01

    A steady directional EOF due to a nonlinear interaction between oscillatory axial electrical fields and oscillatory wall potentials (zeta potentials) is presented. This is a new mechanism to produce such a mean flow. It is found that the flow velocity depends not on the external driving frequency but on the phase angle difference between the electric fields and the zeta potentials. The formulation can also be reduced to the static EOF straightforwardly. For the purpose of theoretical demonstration, we use the Debye-Huckel approximation for the zeta potential. Results of planar and cylindrical capillaries are given.

  1. Electron interactions in graphene through an effective Coulomb potential

    NASA Astrophysics Data System (ADS)

    Rodrigues, Joao N. B.; Adam, Shaffique

    A recent numerical work [H.-K. Tang et al, PRL 115, 186602 (2015)] considering graphene's π-electrons interacting through an effective Coulomb potential that is finite at short-distances, stressed the importance of the sp2 -electrons in determining the semimetal to Mott insulator phase transition in graphene. Some years ago, I. F. Herbut [PRL 97, 146401 (2006)] studied such a transition by mapping graphene's π-electrons into a Gross-Neveu model. From a different perspective, D. T. Son [PRB 75, 235423 (2007)] put the emphasis on the long-range interactions by modelling graphene as Dirac fermions interacting through a bare Coulomb potential. Here we build on these works and explore the phase diagram of Dirac fermions interacting through an effective Coulomb-like potential screened at short-distances. The interaction potential used allows for analytic results that controllably switch between the two perspectives above. This work was supported by the Singapore National Research Foundation (NRF-NRFF2012-01 and CA2DM medium-sized centre program) and by the Singapore Ministry of Education and Yale-NUS College (R-607-265-01312).

  2. OBSERVATIONAL EVIDENCE FOR DARK MATTER INTERACTING THROUGH A YUKAWA POTENTIAL

    SciTech Connect

    Chan, M. H.

    2013-05-20

    Recent observations in galaxies and clusters indicate that dark matter density profiles exhibit core-like structures which contradict the numerical simulation results of collisionless cold dark matter (CDM). On the other hand, it has been shown that CDM particles interacting through a Yukawa potential could naturally explain the cores in dwarf galaxies. In this Letter, I use the Yukawa potential interacting dark matter model to derive two simple scaling relations on the galactic and cluster scales, respectively, which give excellent agreements with observations. Also, in our model, the masses of the force carrier and dark matter particle can be constrained by the observational data.

  3. Accurate intermolecular ground-state potential-energy surfaces of the HCCH-He, Ne, and Ar van der Waals complexes.

    PubMed

    Munteanu, Cristian Robert; Fernández, Berta

    2005-07-01

    Accurate ground-state intermolecular potential-energy surfaces are obtained for the HCCH-He, Ne, and Ar van der Waals complexes. The interaction energies are calculated at the coupled cluster singles and doubles including connected triple excitations level and fitted to analytic functions. For the three complexes we start with systematic basis set studies carried out at several intermolecular geometries, and using augmented correlation consistent polarized valence basis sets x-aug-cc-pVXZ (x=-,d; X=D,T,Q,5), also extended with a set of 3s3p2d1f1g midbond functions. The aug-cc-pVQZ-33211 surfaces of HCCH-He, Ne, and Ar complexes are characterized by absolute minima of -24.22, -50.20, and -122.17 cm(-1) at distances R between the rare-gas atom and the HCCH centers of mass of 4.35, 3.95, and 3.99 A, respectively; and at angles between the vector R and the HCCH main symmetry axis of 0 degrees , 43.3 degrees , and 60.6 degrees . The results are compared and considerably improve those previously available.

  4. Study of interaction in silica glass via model potential approach

    NASA Astrophysics Data System (ADS)

    Mann, Sarita; Rani, Pooja

    2016-05-01

    Silica is one of the most commonly encountered substances in daily life and in electronics industry. Crystalline SiO2 (in several forms: quartz, cristobalite, tridymite) is an important constituent of many minerals and gemstones, both in pure form and mixed with related oxides. Cohesive energy of amorphous SiO2 has been investigated via intermolecular potentials i.e weak Van der Waals interaction and Morse type short-range interaction. We suggest a simple atom-atom based Van der Waals as well as Morse potential to find cohesive energy of glass. It has been found that the study of silica structure using two different model potentials is significantly different. Van der Waals potential is too weak (P.E =0.142eV/molecule) to describe the interaction between silica molecules. Morse potential is a strong potential, earlier given for intramolecular bonding, but if applied for intermolecular bonding, it gives a value of P.E (=-21.92eV/molecule) to appropriately describe the structure of silica.

  5. 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

    2016-03-01

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

    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+(2Sg) + H(2Sg), Zn(1Sg) + H+(1Sg), and Zn+(2Pu) + H(2Sg), respectively (The Λ-S state is labeled as 2S + 1Λ, 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.

  7. Interacting Bose gas confined in a Kronig-Penney potential

    NASA Astrophysics Data System (ADS)

    Rodríguez, O. A.; Solís, M. A.

    We analyze the effect of the 1D periodic Kronig-Penney potential, composed of barriers of width b and separated a distance a, over an interacting Bose gas. At T = 0 , the Gross-Pitaevskii equation is solved analytically in terms of the Jacobi elliptic functions for repulsive or attractive interaction between bosons. By applying the boundary conditions for periodic solutions as well as the normalization of the wave function, we arrive to a set of nonlinear equations from which we obtain the density profile and the chemical potential of the condensate as a function of the particle momentum. The profiles for attractive and repulsive interactions are compared with that of the non-interacting case. For attractive interaction we are able to observe a pronounced spatial localization in the middle of every two barriers. We reproduce the well known results when the Kronig-Penney potential becomes a Dirac Comb. We acknowledge partial support from Grants PAPIIT IN111613 and CONACyT 221030.

  8. Optimizing Interacting Potentials to Form Targeted Materials Structures

    SciTech Connect

    Torquato, Salvatore

    2015-09-28

    Conventional applications of the principles of statistical mechanics (the "forward" problems), start with particle interaction potentials, and proceed to deduce local structure and macroscopic properties. Other applications (that may be classified as "inverse" problems), begin with targeted configurational information, such as low-order correlation functions that characterize local particle order, and attempt to back out full-system configurations and/or interaction potentials. To supplement these successful experimental and numerical "forward" approaches, we have focused on inverse approaches that make use of analytical and computational tools to optimize interactions for targeted self-assembly of nanosystems. The most original aspect of our work is its inherently inverse approach: instead of predicting structures that result from given interaction potentials among particles, we determine the optimal potential that most robustly stabilizes a given target structure subject to certain constraints. Our inverse approach could revolutionize the manner in which materials are designed and fabricated. There are a number of very tangible properties (e.g. zero thermal expansion behavior), elastic constants, optical properties for photonic applications, and transport properties.

  9. Potential disruption of protein-protein interactions by graphene oxide.

    PubMed

    Feng, Mei; Kang, Hongsuk; Yang, Zaixing; Luan, Binquan; Zhou, Ruhong

    2016-06-14

    Graphene oxide (GO) is a promising novel nanomaterial with a wide range of potential biomedical applications due to its many intriguing properties. However, very little research has been conducted to study its possible adverse effects on protein-protein interactions (and thus subsequent toxicity to human). Here, the potential cytotoxicity of GO is investigated at molecular level using large-scale, all-atom molecular dynamics simulations to explore the interaction mechanism between a protein dimer and a GO nanosheet oxidized at different levels. Our theoretical results reveal that GO nanosheet could intercalate between the two monomers of HIV-1 integrase dimer, disrupting the protein-protein interactions and eventually lead to dimer disassociation as graphene does [B. Luan et al., ACS Nano 9(1), 663 (2015)], albeit its insertion process is slower when compared with graphene due to the additional steric and attractive interactions. This study helps to better understand the toxicity of GO to cell functions which could shed light on how to improve its biocompatibility and biosafety for its wide potential biomedical applications.

  10. Potential disruption of protein-protein interactions by graphene oxide

    NASA Astrophysics Data System (ADS)

    Feng, Mei; Kang, Hongsuk; Yang, Zaixing; Luan, Binquan; Zhou, Ruhong

    2016-06-01

    Graphene oxide (GO) is a promising novel nanomaterial with a wide range of potential biomedical applications due to its many intriguing properties. However, very little research has been conducted to study its possible adverse effects on protein-protein interactions (and thus subsequent toxicity to human). Here, the potential cytotoxicity of GO is investigated at molecular level using large-scale, all-atom molecular dynamics simulations to explore the interaction mechanism between a protein dimer and a GO nanosheet oxidized at different levels. Our theoretical results reveal that GO nanosheet could intercalate between the two monomers of HIV-1 integrase dimer, disrupting the protein-protein interactions and eventually lead to dimer disassociation as graphene does [B. Luan et al., ACS Nano 9(1), 663 (2015)], albeit its insertion process is slower when compared with graphene due to the additional steric and attractive interactions. This study helps to better understand the toxicity of GO to cell functions which could shed light on how to improve its biocompatibility and biosafety for its wide potential biomedical applications.

  11. Microscopic Theory of Heavy-Ion Interaction Potentials.

    NASA Astrophysics Data System (ADS)

    Katoot, Mohammad Walid

    Heavy-ion interaction potentials are calculated in a realistic, fully microscopic theory. The theory is based on the nonrelativistic quantum theory of many-body systems and is formulated in the language of second quantization; it utilizes a molecular set of basis states (two-center shell model) rather than selfconsistent wavefunctions. These basis states depend on two collective parameters: internuclear distance and fragment deformation. In constructing the ground state of the interacting many-body system, we assume, for simplicity, that the nucleons remain in the lowest possible molecular energy levels throughout the reaction. This adiabaticity assumption appears to be justified at bombarding energies near the Coulomb barrier. For computational reasons, the effective nucleon -nucleon interaction is described by a Skyrme force without spin-orbit coupling. The 5 parameters of the Skyrme interaction are fitted to measured binding energies. Heavy-ion interaction potentials are calculated for the following systems: ('28)Si + ('28)Si, ('40)Ca + ('40)Ca, ('90)Zr + ('90)Zr and ('238)U + ('238)U. At large internuclear distances, our theory approaches the double -folding model, which reproduces elastic and inelastic scattering data. However, at smaller distances, it is much more realistic than these phenomenological models, because (a) exchange energy and kinetic energy contributions are calculated consistently and (b) shell effects are taken into account. Possible improvements of the theory are discussed in the last chapter.

  12. Testing ion-neutral interaction potentials using calculated ion transport coefficients.

    PubMed

    Hogan, M J

    2006-10-28

    Several commonly measured ion transport coefficients were investigated in order to determine their sensitivity for testing and comparing proposed ion-neutral interaction potentials. A variety of positive ions, negative ions, neutrals, and temperatures were included in order to draw as general a conclusion as possible. All transport coefficients considered were found to be sufficiently sensitive to be used to clearly distinguish between less and more accurate interaction potentials. It was also found that the longitudinal diffusion coefficient is the most sensitive test, followed by both the transverse diffusion coefficient and the ratio of the longitudinal diffusion coefficient to mobility, followed by the ratio of the transverse diffusion coefficient to mobility and that the mobility is the least sensitive test. When presently achievable levels of experimental error were also taken into account, however, there was no significant difference in the sensitivities. PMID:17092091

  13. Multireference configuration interaction calculations of the first six ionization potentials of the uranium atom

    NASA Astrophysics Data System (ADS)

    Bross, David H.; Parmar, Payal; Peterson, Kirk A.

    2015-11-01

    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 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 IP3 through IP6.

  14. Multireference configuration interaction calculations of the first six ionization potentials of the uranium atom

    SciTech Connect

    Bross, David H.; Parmar, Payal; Peterson, Kirk A.

    2015-11-14

    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 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{sub 3} through IP{sub 6}.

  15. 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.

  16. Comparison of Cluster, Slab, and Analytic Potential Models for the Dimethyl Methylphosphonate (DMMP)/TiO2 (110) Intermolecular Interaction

    SciTech Connect

    Yang, Li; Tunega, Daniel; Xu, Lai; Govind, Niranjan; Sun, Rui; Taylor, Ramona; Lischka, Hans; De Jong, Wibe A.; Hase, William L.

    2013-08-29

    In a previous study (J. Phys. Chem. C 2011, 115, 12403) cluster models for the TiO2 rutile (110) surface and MP2 calculations were used to develop an analytic potential energy function for dimethyl methylphosphonate (DMMP) interacting with this surface. In the work presented here, this analytic potential and MP2 cluster models are compared with DFT "slab" calculations for DMMP interacting with the TiO2 (110) surface and with DFT cluster models for the TiO2 (110) surface. The DFT slab calculations were performed with the PW91 and PBE functionals. The analytic potential gives DMMP/ TiO2 (110) potential energy curves in excellent agreement with those obtained from the slab calculations. The cluster models for the TiO2 (110) surface, used for the MP2 calculations, were extended to DFT calculations with the B3LYP, PW91, and PBE functional. These DFT calculations do not give DMMP/TiO2 (110) interaction energies which agree with those from the DFT slab calculations. Analyses of the wave functions for these cluster models show that they do not accurately represent the HOMO and LUMO for the surface, which should be 2p and 3d orbitals, respectively, and the models also do not give an accurate band gap. The MP2 cluster models do not accurately represent the LUMO and that they give accurate DMMP/TiO2 (110) interaction energies is apparently fortuitous, arising from their highly inaccurate band gaps. Accurate cluster models, consisting of 7, 10, and 15 Ti-atoms and which have the correct HOMO and LUMO properties, are proposed. The work presented here illustrates the care that must be taken in "constructing" cluster models which accurately model surfaces.

  17. He-LiF surface interaction potential from fast atom diffraction

    SciTech Connect

    Schueller, A.; Winter, H.; Gravielle, M. S.; Miraglia, J. E.; Pruneda, J. M.

    2009-12-15

    Diffraction patterns produced by grazing scattering of fast atoms from insulator surfaces are used to examine the atom-surface interaction. The method is applied to He atoms colliding with a LiF(001) surface along axial crystallographic channels. The projectile-surface potential is obtained from an accurate density-functional theory calculation, which includes polarization effects and surface relaxation. For the description of the collision process we employ the surface eikonal approximation, which takes into account quantum interference between different projectile paths. The dependence of projectile spectra on the parallel and perpendicular incident energies is experimentally and theoretically analyzed, demonstrating the range of applicability of the proposed model.

  18. Optimal construction of a fast and accurate polarisable water potential based on multipole moments trained by machine learning.

    PubMed

    Handley, Chris M; Hawe, Glenn I; Kell, Douglas B; Popelier, Paul L A

    2009-08-14

    To model liquid water correctly and to reproduce its structural, dynamic and thermodynamic properties warrants models that account accurately for electronic polarisation. We have previously demonstrated that polarisation can be represented by fluctuating multipole moments (derived by quantum chemical topology) predicted by multilayer perceptrons (MLPs) in response to the local structure of the cluster. Here we further develop this methodology of modeling polarisation enabling control of the balance between accuracy, in terms of errors in Coulomb energy and computing time. First, the predictive ability and speed of two additional machine learning methods, radial basis function neural networks (RBFNN) and Kriging, are assessed with respect to our previous MLP based polarisable water models, for water dimer, trimer, tetramer, pentamer and hexamer clusters. Compared to MLPs, we find that RBFNNs achieve a 14-26% decrease in median Coulomb energy error, with a factor 2.5-3 slowdown in speed, whilst Kriging achieves a 40-67% decrease in median energy error with a 6.5-8.5 factor slowdown in speed. Then, these compromises between accuracy and speed are improved upon through a simple multi-objective optimisation to identify Pareto-optimal combinations. Compared to the Kriging results, combinations are found that are no less accurate (at the 90th energy error percentile), yet are 58% faster for the dimer, and 26% faster for the pentamer.

  19. Accurate combined-hyperbolic-inverse-power-representation of ab initio potential energy surface for the hydroperoxyl radical and dynamics study of O + OH reaction.

    PubMed

    Varandas, A J C

    2013-04-01

    The Combined-Hyperbolic-Inverse-Power-Representation method, which treats evenly both short- and long-range interactions, is used to fit an extensive set of ab initio points for HO2 previously utilized [Xu et al., J. Chem. Phys. 122, 244305 (2005)] to develop a spline interpolant. The novel form is shown to perform accurately when compared with others, while quasiclassical trajectory calculations of the O + OH reaction clearly pinpoint the role of long-range forces at low temperatures. PMID:23574218

  20. Studying bubble-particle interactions by zeta potential distribution analysis.

    PubMed

    Wu, Chendi; Wang, Louxiang; Harbottle, David; Masliyah, Jacob; Xu, Zhenghe

    2015-07-01

    Over a decade ago, Xu and Masliyah pioneered an approach to characterize the interactions between particles in dynamic environments of multicomponent systems by measuring zeta potential distributions of individual components and their mixtures. Using a Zetaphoremeter, the measured zeta potential distributions of individual components and their mixtures were used to determine the conditions of preferential attachment in multicomponent particle suspensions. The technique has been applied to study the attachment of nano-sized silica and alumina particles to sub-micron size bubbles in solutions with and without the addition of surface active agents (SDS, DAH and DF250). The degree of attachment between gas bubbles and particles is shown to be a function of the interaction energy governed by the dispersion, electrostatic double layer and hydrophobic forces. Under certain chemical conditions, the attachment of nano-particles to sub-micron size bubbles is shown to be enhanced by in-situ gas nucleation induced by hydrodynamic cavitation for the weakly interacting systems, where mixing of the two individual components results in negligible attachment. Preferential interaction in complex tertiary particle systems demonstrated strong attachment between micron-sized alumina and gas bubbles, with little attachment between micron-sized alumina and silica, possibly due to instability of the aggregates in the shear flow environment.

  1. A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions

    PubMed Central

    Paulsen, Jonas; Rødland, Einar A.; Holden, Lars; Holden, Marit; Hovig, Eivind

    2014-01-01

    Identification of three-dimensional (3D) interactions between regulatory elements across the genome is crucial to unravel the complex regulatory machinery that orchestrates proliferation and differentiation of cells. ChIA-PET is a novel method to identify such interactions, where physical contacts between regions bound by a specific protein are quantified using next-generation sequencing. However, determining the significance of the observed interaction frequencies in such datasets is challenging, and few methods have been proposed. Despite the fact that regions that are close in linear genomic distance have a much higher tendency to interact by chance, no methods to date are capable of taking such dependency into account. Here, we propose a statistical model taking into account the genomic distance relationship, as well as the general propensity of anchors to be involved in contacts overall. Using both real and simulated data, we show that the previously proposed statistical test, based on Fisher's exact test, leads to invalid results when data are dependent on genomic distance. We also evaluate our method on previously validated cell-line specific and constitutive 3D interactions, and show that relevant interactions are significant, while avoiding over-estimating the significance of short nearby interactions. PMID:25114054

  2. Potential interaction and potential investigation of science center exhibits and visitors' interest

    NASA Astrophysics Data System (ADS)

    Busque, Laurier

    This research consisted of studying the characteristics of interaction and investigation potential present in museum or science center exhibits. Categories (strong and weak) for the characteristics of interaction potential and investigation potential were established. Fifteen exhibits were chosen from the Museum of Science (Ottawa) and from two science centers (Sudbury and Toronto); these were representative of the established characteristics and categories. A test was constructed that measured the interest in an exhibit in a museum or a science center. The final analysis of the test (20 items) reflects a coefficient of homogeneity (Cronbach alpha) of 0.97 (n = 278). In terms of the characteristics of interaction potential and investigation potential, a significant difference among the ranks of interest was not found once they were regrouped under the categories of strong and weak. The hypothesis of a relationship between the interaction potential and visitors' interest in an exhibit in a museum or science center and the hypothesis of a relationship between the investigation potential and the interest aroused were both rejected. In regards to the interaction potential, median ranks of interest in exhibits of 8.6 for the strong category and of 7.5 for the weak category were observed. In terms of the investigation potential, median ranks of interest of 7.0 for the strong category and of 9.1 for the weak category were observed. In the case of investigation potential, even if the difference is not significant, there is an indication that the strong investigation potential seems to have the effect of creating disinterest in the presentation of an exhibit in a museum or in a science center. In the context of new museum and science centers, the view of developing exhibits which are primarily objects which stimulate interest must be maintained. If this is done with exhibits that arc interactive and have an investigative approach, it is necessary for those in charge of

  3. PRN prescribing in psychiatric inpatients: potential for pharmacokinetic drug interactions.

    PubMed

    Davies, Simon J C; Lennard, Martin S; Ghahramani, Parviz; Pratt, Peter; Robertson, Andrea; Potokar, John

    2007-03-01

    Medications are commonly prescribed to psychiatric inpatients on a PRN (pro re nata/as required) basis, allowing drugs to be administered on patient request or at nurses' discretion for psychiatric symptoms, treatment side effects or physical complaints. However, there has been no formal study of the pharmacokinetic implications of PRN prescribing. The objective of the study was to determine the prevalence of PRN drug prescription and administration, and to assess the potential for interactions involving CYP2D6 and CYP3A4 between drugs prescribed and administered to inpatients on psychiatry wards.A cross-sectional survey of prescriptions on general adult and functional elderly psychiatric wards in one city was carried out. Data were recorded from prescription charts of 323 inpatients (236 on general adult and 87 on functional elderly wards). Of 2089 prescriptions, 997 (48%) of prescriptions were on a PRN basis (most commonly benzodiazepines and other hypnotic agents, antipsychotics, analgesics and anticholinergic agents), but only 143 (14%) of these had been administered in the previous 24 hours. One fifth of patients were prescribed drug combinations interacting with CYP2D6 or CYP3A4 of potential clinical importance which included one or more drugs prescribed on a PRN basis.PRN prescribing is common among inpatients in psychiatry, and may lead to cytochrome P450 mediated interactions. Prescribers should be aware of the potential for unpredictability in plasma concentrations, side effects and efficacy which PRN prescribing may cause through these interactions, particularly in old age psychiatry and in treatment of acute psychosis.

  4. Comparing Extended System Interactions with Motions in Softened Potentials

    NASA Astrophysics Data System (ADS)

    Barnes, Eric I.

    2016-08-01

    Using an N-body evolution code that does not rely on softened potentials, I have created a suite of unbound interacting cluster pair simulations. The motions of the centers of mass of the clusters have been tracked and compared to the trajectories of point masses interacting via one of four different softened potential prescriptions. I find that the relationship between the impact parameter of the cluster interaction and the point-mass softening length that best approximates each cluster’s center-of-mass motion depends on the adopted prescription. In general, the range of allowed softening lengths grows roughly linearly with the impact parameter, but zero softening is acceptable in the majority of situations. In an N-body simulation that adopts a fixed softening length, such relationships lead to the possibility of two-body effects, like dynamical friction, being either larger or smaller than the corresponding cluster situation. Further consideration of more specific N-body situations leads to estimating that a very small fraction of point-mass encounters experience two-body effects significantly different from those of equivalent clusters.

  5. Interaction potentials from arbitrary multi-particle trajectory data.

    PubMed

    Jenkins, Ian C; Crocker, John C; Sinno, Talid

    2015-09-21

    Understanding the complex physics of particle-based systems at the nanoscale and mesoscale increasingly relies on simulation methods, empowered by exponential advances in computing speed. A major impediment to progress lies in reliably obtaining the interaction potential functions that control system behavior - which are key inputs for any simulation approach - and which are often difficult or impossible to obtain directly using traditional experimental methods. Here, we present a straightforward methodology for generating pair potential functions from large multi-particle trajectory datasets, with no operational constraints regarding their state of equilibration, degree of damping or presence of hydrodynamic interactions. Using simulated datasets, we demonstrate that the method is highly robust against trajectory perturbations from Brownian motion and common errors introduced by particle tracking algorithms. Given the recent rapid pace of advancement in high-speed and three-dimensional microscopy and associated particle tracking algorithms, we anticipate a near future experimental regime where easily collected high-dimensional trajectory sets can be rapidly converted to the detailed interaction and hydrodynamic force fields required to replicate the system's physics in simulation.

  6. An accurate potential energy surface for the F + H2 → HF + H reaction by the coupled-cluster method

    NASA Astrophysics Data System (ADS)

    Chen, Jun; Sun, Zhigang; Zhang, Dong H.

    2015-01-01

    A three dimensional potential energy surface for the F + H2 → HF + H reaction has been computed by the spin unrestricted coupled cluster method with singles, doubles, triples, and perturbative quadruples [UCCSDT(2)Q] using the augmented correlation-consistent polarised valence quadruple zeta basis set for the fluorine atom and the correlation-consistent polarised valence quadruple zeta basis set for the hydrogen atom. All the calculations are based on the restricted open-shell Hartree-Fock orbitals, together with the frozen core approximations, and the UCCSD(T)/complete basis set (CBS) correction term was included. The global potential energy surface was calculated by fitting the sampled ab initio points without any scaling factor for the correlation energy part using a neutral network function method. Extensive dynamics calculations have been carried out on the potential energy surface. The reaction rate constants, integral cross sections, product rotational states distribution, and forward and backward scattering as a function of collision energy of the F + HD → HF + D, F + HD → DF + H, and F + H2 reaction, were calculated by the time-independent quantum dynamics scattering theory using the new surface. The satisfactory agreement with the reported experimental observations previously demonstrates the accuracy of the new potential energy surface.

  7. An accurate potential energy surface for the F + H2 → HF + H reaction by the coupled-cluster method.

    PubMed

    Chen, Jun; Sun, Zhigang; Zhang, Dong H

    2015-01-14

    A three dimensional potential energy surface for the F + H2 → HF + H reaction has been computed by the spin unrestricted coupled cluster method with singles, doubles, triples, and perturbative quadruples [UCCSDT(2)Q] using the augmented correlation-consistent polarised valence quadruple zeta basis set for the fluorine atom and the correlation-consistent polarised valence quadruple zeta basis set for the hydrogen atom. All the calculations are based on the restricted open-shell Hartree-Fock orbitals, together with the frozen core approximations, and the UCCSD(T)/complete basis set (CBS) correction term was included. The global potential energy surface was calculated by fitting the sampled ab initio points without any scaling factor for the correlation energy part using a neutral network function method. Extensive dynamics calculations have been carried out on the potential energy surface. The reaction rate constants, integral cross sections, product rotational states distribution, and forward and backward scattering as a function of collision energy of the F + HD → HF + D, F + HD → DF + H, and F + H2 reaction, were calculated by the time-independent quantum dynamics scattering theory using the new surface. The satisfactory agreement with the reported experimental observations previously demonstrates the accuracy of the new potential energy surface.

  8. The multiscale coarse-graining method. XI. Accurate interactions based on the centers of charge of coarse-grained sites.

    PubMed

    Cao, Zhen; Voth, Gregory A

    2015-12-28

    It is essential to be able to systematically construct coarse-grained (CG) models that can efficiently and accurately reproduce key properties of higher-resolution models such as all-atom. To fulfill this goal, a mapping operator is needed to transform the higher-resolution configuration to a CG configuration. Certain mapping operators, however, may lose information related to the underlying electrostatic properties. In this paper, a new mapping operator based on the centers of charge of CG sites is proposed to address this issue. Four example systems are chosen to demonstrate this concept. Within the multiscale coarse-graining framework, CG models that use this mapping operator are found to better reproduce the structural correlations of atomistic models. The present work also demonstrates the flexibility of the mapping operator and the robustness of the force matching method. For instance, important functional groups can be isolated and emphasized in the CG model. PMID:26723601

  9. The multiscale coarse-graining method. XI. Accurate interactions based on the centers of charge of coarse-grained sites

    SciTech Connect

    Cao, Zhen; Voth, Gregory A.

    2015-12-28

    It is essential to be able to systematically construct coarse-grained (CG) models that can efficiently and accurately reproduce key properties of higher-resolution models such as all-atom. To fulfill this goal, a mapping operator is needed to transform the higher-resolution configuration to a CG configuration. Certain mapping operators, however, may lose information related to the underlying electrostatic properties. In this paper, a new mapping operator based on the centers of charge of CG sites is proposed to address this issue. Four example systems are chosen to demonstrate this concept. Within the multiscale coarse-graining framework, CG models that use this mapping operator are found to better reproduce the structural correlations of atomistic models. The present work also demonstrates the flexibility of the mapping operator and the robustness of the force matching method. For instance, important functional groups can be isolated and emphasized in the CG model.

  10. Gender differences, polypharmacy, and potential pharmacological interactions in the elderly

    PubMed Central

    Venturini, Carina Duarte; Engroff, Paula; Ely, Luísa Scheer; de Araújo Zago, Luísa Faria; Schroeter, Guilherme; Gomes, Irenio; De Carli, Geraldo Attilio; Morrone, Fernanda Bueno

    2011-01-01

    OBJECTIVE: This study aims to analyze pharmacological interactions among drugs taken by elderly patients and their age and gender differences in a population from Porto Alegre, Brazil. METHODS: We retrospectively analyzed the database provided by the Institute of Geriatric and Gerontology, Porto Alegre, Brazil. The database was composed of 438 elderly and includes information about the patients' disease, therapy regimens, utilized drugs. All drugs reported by the elderly patients were classified using the Anatomical Therapeutic and Chemical Classification System. The drug-drug interactions and their severity were assessed using the Micromedex® Healthcare Series. RESULTS: Of the 438 elderly patients in the data base, 376 (85.8%) used pharmacotherapy, 274 were female, and 90.4% of females used drugs. The average number of drugs used by each individual younger than 80 years was 3.2±2.6. Women younger than 80 years old used more drugs than men in the same age group whereas men older than 80 years increased their use of drugs in relation to other age groups. Therefore, 32.6% of men and 49.2% of women described at least one interaction, and 8.1% of men and 10.6% of women described four or more potential drug-drug interactions. Two-thirds of drug-drug interactions were moderate in both genders, and most of them involved angiotensin-converting enzyme inhibitor, non-steroidal anti-inflammatory, loop and thiazide diuretics, and β-blockers. CONCLUSION: Elderly patients should be closely monitored, based on drug class, gender, age group and nutritional status. PMID:22086515

  11. PETs: A Stable and Accurate Predictor of Protein-Protein Interacting Sites Based on Extremely-Randomized Trees.

    PubMed

    Xia, Bin; Zhang, Hong; Li, Qianmu; Li, Tao

    2015-12-01

    Protein-protein interaction (PPI) plays crucial roles in the performance of various biological processes. A variety of methods are dedicated to identify whether proteins have interaction residues, but it is often more crucial to recognize each amino acid. In practical applications, the stability of a prediction model is as important as its accuracy. However, random sampling, which is widely used in previous prediction models, often brings large difference between each training model. In this paper, a Predictor of protein-protein interaction sites based on Extremely-randomized Trees (PETs) is proposed to improve the prediction accuracy while maintaining the prediction stability. In PETs, a cluster-based sampling strategy is proposed to ensure the model stability: first, the training dataset is divided into subsets using specific features; second, the subsets are clustered using K-means; and finally the samples are selected from each cluster. Using the proposed sampling strategy, samples which have different types of significant features could be selected independently from different clusters. The evaluation shows that PETs is able to achieve better accuracy while maintaining a good stability. The source code and toolkit are available at https://github.com/BinXia/PETs.

  12. Three-way interactions between mosquito population, viral strain and temperature underlying chikungunya virus transmission potential

    PubMed Central

    Zouache, Karima; Fontaine, Albin; Vega-Rua, Anubis; Mousson, Laurence; Thiberge, Jean-Michel; Lourenco-De-Oliveira, Ricardo; Caro, Valérie; Lambrechts, Louis; Failloux, Anna-Bella

    2014-01-01

    Interactions between pathogens and their insect vectors in nature are under the control of both genetic and non-genetic factors, yet most studies on mosquito vector competence for human pathogens are conducted in laboratory systems that do not consider genetic and/or environmental variability. Evaluating the risk of emergence of arthropod-borne viruses (arboviruses) of public health importance such as chikungunya virus (CHIKV) requires a more realistic appraisal of genetic and environmental contributions to vector competence. In particular, sources of variation do not necessarily act independently and may combine in the form of interactions. Here, we measured CHIKV transmission potential by the mosquito Aedes albopictus in all combinations of six worldwide vector populations, two virus strains and two ambient temperatures (20°C and 28°C). Overall, CHIKV transmission potential by Ae. albopictus strongly depended on the three-way combination of mosquito population, virus strain and temperature. Such genotype-by-genotype-by-environment (G × G × E) interactions question the relevance of vector competence studies conducted with a simpler set of conditions. Our results highlight the need to account for the complex interplay between vectors, pathogens and environmental factors to accurately assess the potential of vector-borne diseases to emerge. PMID:25122228

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

    SciTech Connect

    Mizukami, Wataru Tew, David P.; Habershon, Scott

    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 to 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}.

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

    NASA Astrophysics Data System (ADS)

    Mizukami, Wataru; Habershon, Scott; Tew, David P.

    2014-10-01

    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 to 25 000 cm-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-1 and hydrogen transfer tunnelling splittings of 21.0(4) and 3.2(4) cm-1, respectively, which are in excellent agreement with the experimental values of 21.583 and 2.915(4) cm-1.

  15. Accurate Analytic Potential Functions for the a ^3Π_1 and X ^1Σ^+ States of {IBr}

    NASA Astrophysics Data System (ADS)

    Yukiya, Tokio; Nishimiya, Nobuo; Suzuki, Masao; Le Roy, Robert

    2014-06-01

    Spectra of IBr in various wavelength regions have been measured by a number of researchers using traditional diffraction grating and microwave methods, as well as using high-resolution laser techniques combined with a Fourier transform spectrometer. In a previous paper at this meeting, we reported a preliminary determination of analytic potential energy functions for the A ^3Π_1 and X ^1Σ^+ states of IBr from a direct-potential-fit (DPF) analysis of all of the data available at that time. That study also confirmed the presence of anomalous fluctuations in the v--dependence of the first differences of the inertial rotational constant, Δ Bv=Bv+1-Bv in the A ^3Π_1 state for vibrational levels with v'(A) in the mid 20's. However, our previous experience in a recent study of the analogous A ^3Π_1-X ^1Σ_g^+ system of Br_2 suggested that the effect of such fluctuations may be overcome if sufficient data are available. The present work therefore reports new measurements of transitions to levels in the v'(A)=23-26 region, together with a new global DPF analysis that uses ``robust" least-squares fits to average properly over the effect of such fluctuations in order to provide an optimum delineation of the underlying potential energy curve(s). L.E.Selin,Ark. Fys. 21,479(1962) E. Tiemann and Th. Moeller, Z. Naturforsch. A 30,986 (1975) E.M. Weinstock and A. Preston, J. Mol. Spectrosc. 70, 188 (1978) D.R.T. Appadoo, P.F. Bernath, and R.J. Le Roy, Can. J. Phys. 72, 1265 (1994) N. Nishimiya, T. Yukiya and M. Suzuki, J. Mol. Spectrosc. 173, 8 (1995). T. Yukiya, N. Nishimiya, and R.J. Le Roy, Paper MF12 at the 65th Ohio State University International Symposium on Molecular Spectroscopy, Columbus, Ohio, June 20-24, 2011. T. Yukiya, N. Nishimiya, Y. Samajima, K. Yamaguchi, M. Suzuki, C.D. Boone, I. Ozier and R.J. Le Roy, J. Mol. Spectrosc. 283, 32 (2013) J.K.G. Watson, J. Mol. Spectrosc. 219, 326 (2003).

  16. High-Accurate Intermolecular Potential Energy Surface of HCN-H_2 Complex with Intramolecular Vibrational Mode of HCN Included

    NASA Astrophysics Data System (ADS)

    Zhai, Yu; Li, Hui

    2016-06-01

    ydrogen is one of the most abundant interstellar species. Observation of rotational and vibrational spectra of H_2 containing complexes is of great importance because they are possible candidates for radio-astronomical detection. CO, HCN, HCCH are as isoelectronic molecules of N_2, each with a strong triple bond. It had been a big challenge to predict reliable theoretical rovibrational spectra of complexes including such species because the higher order electron correlation energy plays a non-negligible role in improving the accuracy. However, recent works on CO-H_2 have shown that it is possible to reproduce the experimental spectra quantitatively. In this work, we calculate a five-dimension potential energy surface (PES) of HCN-H_2 complex which explicitly include the intramolecular asymmetric stretching vibrational mode(C-H,Q_3) coordinate at CCSD(T)/aug-cc-pVQZ+3s3p2d1f1g level, corrected with electron correlation energy from the triple and quadruple excitation. Vibrational average over intramolecular vibration mode is made with HCN monomer at ground and the first excited vibrational states respectively, and the averaged data are fitted to two four-dimension Morse/Long-Range (MLR) potential energy functions. Based on the MLR PESs, for the first time, we calculated the spectra of HCN-{para}H_2} and {HCN-{ortho}H_2}. The results for HCN-{ortho}H_2} are in good agreement with the published experimental data with root-mean-square-difference (RMSD) only 0.01wn, which validates the accuracy of the PESs. J. Chem. Phys., 139, 164315 (2013); Science, 336, 1147 (2012). J. Chem. Phys., 115, 5137 (2001).

  17. Modeling theta-theta Interactions with the Effective Fragment Potential Method: The Benzene Dimer and Substituents

    SciTech Connect

    Toni Smithl; Lyudmila V. Slipchenko; Mark S. Gordon

    2008-02-27

    This study compares the results of the general effective fragment potential (EFP2) method to the results of a previous combined coupled cluster with single, double, and perturbative triple excitations [CCSD(T)] and symmetry-adapted perturbation theory (SAPT) study [Sinnokrot and Sherrill, J. Am. Chem. Soc., 2004, 126, 7690] on substituent effects in {pi}-{pi} interactions. EFP2 is found to accurately model the binding energies of the benzene-benzene, benzene-phenol, benzene-toluene, benzene-fluorobenzene, and benzene-benzonitrile dimers, as compared with high-level methods [Sinnokrot and Sherrill, J. Am. Chem. Soc., 2004, 126, 7690], but at a fraction of the computational cost of CCSD(T). In addition, an EFP-based Monte Carlo/simulated annealing study was undertaken to examine the potential energy surface of the substituted dimers.

  18. Accurate combined-hyperbolic-inverse-power-representation of ab initio potential energy surface for the hydroperoxyl radical and dynamics study of O+OH reaction

    NASA Astrophysics Data System (ADS)

    Varandas, A. J. C.

    2013-04-01

    The Combined-Hyperbolic-Inverse-Power-Representation method, which treats evenly both short- and long-range interactions, is used to fit an extensive set of ab initio points for HO2 previously utilized [Xu et al., J. Chem. Phys. 122, 244305 (2005), 10.1063/1.1944290] to develop a spline interpolant. The novel form is shown to perform accurately when compared with others, while quasiclassical trajectory calculations of the O + OH reaction clearly pinpoint the role of long-range forces at low temperatures.

  19. Accurately characterizing the importance of wave-particle interactions in radiation belt dynamics: The pitfalls of statistical wave representations

    NASA Astrophysics Data System (ADS)

    Murphy, Kyle R.; Mann, Ian R.; Rae, I. Jonathan; Sibeck, David G.; Watt, Clare E. J.

    2016-08-01

    Wave-particle interactions play a crucial role in energetic particle dynamics in the Earth's radiation belts. However, the relative importance of different wave modes in these dynamics is poorly understood. Typically, this is assessed during geomagnetic storms using statistically averaged empirical wave models as a function of geomagnetic activity in advanced radiation belt simulations. However, statistical averages poorly characterize extreme events such as geomagnetic storms in that storm-time ultralow frequency wave power is typically larger than that derived over a solar cycle and Kp is a poor proxy for storm-time wave power.

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

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

  1. Understanding the Composition and Reactivity of Au/Cu Electrocatalyst Nanoparticles in Solution Using Highly Accurate Reactive Potentials

    NASA Astrophysics Data System (ADS)

    Artrith, Nongnuch; Kolpak, Alexie

    2014-03-01

    The shape, size, and composition of catalyst nanoparticles can have a significant influence on their catalytic activity. Understanding such structure-reactivity relationships is crucial for the optimization of industrial catalysts and the design of novel catalysts with enhanced properties. In this work, we investigate the equilibrium shape and surface structure/composition of Au/Cu nanoparticles in solution, which have recently been shown to be stable and efficient catalysts for CO2 reduction. Using a combination of density functional theory calculations and large-scale Monte-Carlo and molecular dynamics simulations with reactive atomistic potentials, we determine how the nanoparticle shape, surface structure, and surface stoichiometry (i.e., fraction of Au at the surface relative to overall composition), evolve as a function of varying catalytic conditions. We discuss the effects of these changes on the surface electronic structure and binding energies of CO2, H2, and CH3OH. Our results emphasize the important relationships between catalytic environment (e.g., solvent effects), catalyst structure, and catalytic activity. We thank the Schlumberger Foundation Faculty for the Future for financial support. Computing time at XSEDE and NERSC clusters are gratefully acknowledged.

  2. Accurate all-electron G0W0 quasiparticle energies employing the full-potential augmented plane-wave method

    NASA Astrophysics Data System (ADS)

    Nabok, Dmitrii; Gulans, Andris; Draxl, Claudia

    2016-07-01

    The G W approach of many-body perturbation theory has become a common tool for calculating the electronic structure of materials. However, with increasing number of published results, discrepancies between the values obtained by different methods and codes become more and more apparent. For a test set of small- and wide-gap semiconductors, we demonstrate how to reach the numerically best electronic structure within the framework of the full-potential linearized augmented plane-wave (FLAPW) method. We first evaluate the impact of local orbitals in the Kohn-Sham eigenvalue spectrum of the underlying starting point. The role of the basis-set quality is then further analyzed when calculating the G0W0 quasiparticle energies. Our results, computed with the exciting code, are compared to those obtained using the projector-augmented plane-wave formalism, finding overall good agreement between both methods. We also provide data produced with a typical FLAPW basis set as a benchmark for other G0W0 implementations.

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

    SciTech Connect

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

    2014-09-14

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

  4. HubAlign: an accurate and efficient method for global alignment of protein–protein interaction networks

    PubMed Central

    Hashemifar, Somaye; Xu, Jinbo

    2014-01-01

    Motivation: High-throughput experimental techniques have produced a large amount of protein–protein interaction (PPI) data. The study of PPI networks, such as comparative analysis, shall benefit the understanding of life process and diseases at the molecular level. One way of comparative analysis is to align PPI networks to identify conserved or species-specific subnetwork motifs. A few methods have been developed for global PPI network alignment, but it still remains challenging in terms of both accuracy and efficiency. Results: This paper presents a novel global network alignment algorithm, denoted as HubAlign, that makes use of both network topology and sequence homology information, based upon the observation that topologically important proteins in a PPI network usually are much more conserved and thus, more likely to be aligned. HubAlign uses a minimum-degree heuristic algorithm to estimate the topological and functional importance of a protein from the global network topology information. Then HubAlign aligns topologically important proteins first and gradually extends the alignment to the whole network. Extensive tests indicate that HubAlign greatly outperforms several popular methods in terms of both accuracy and efficiency, especially in detecting functionally similar proteins. Availability: HubAlign is available freely for non-commercial purposes at http://ttic.uchicago.edu/∼hashemifar/software/HubAlign.zip Contact: jinboxu@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25161231

  5. Learning to write without writing: writing accurate descriptions of interactions after learning graph-printed description relations.

    PubMed

    Spear, Jack; Fields, Lanny

    2015-12-01

    Interpreting and describing complex information shown in graphs are essential skills to be mastered by students in many disciplines; both are skills that are difficult to learn. Thus, interventions that produce these outcomes are of great value. Previous research showed that conditional discrimination training that established stimulus control by some elements of graphs and their printed descriptions produced some improvement in the accuracy of students' written descriptions of graphs. In the present experiment, students wrote nearly perfect descriptions of the information conveyed in interaction-based graphs after the establishment of conditional relations between graphs and their printed descriptions. This outcome was achieved with the use of special conditional discrimination training procedures that required participants to attend to many of the key elements of the graphs and the phrases in the printed descriptions that corresponded to the elements in the graphs. Thus, students learned to write full descriptions of the information represented by complex graphs by an automated training procedure that did not involve the direct training of writing.

  6. Mineral-microbe interactions: biotechnological potential of bioweathering.

    PubMed

    Mapelli, Francesca; Marasco, Ramona; Balloi, Annalisa; Rolli, Eleonora; Cappitelli, Francesca; Daffonchio, Daniele; Borin, Sara

    2012-02-20

    Mineral-microbe interaction has been a key factor shaping the lithosphere of our planet since the Precambrian. Detailed investigation has been mainly focused on the role of bioweathering in biomining processes, leading to the selection of highly efficient microbial inoculants for the recovery of metals. Here we expand this scenario, presenting additional applications of bacteria and fungi in mineral dissolution, a process with novel biotechnological potential that has been poorly investigated. The ability of microorganisms to trigger soil formation and to sustain plant establishment and growth are suggested as invaluable tools to counteract the expansion of arid lands and to increase crop productivity. Furthermore, interesting exploitations of mineral weathering microbes are represented by biorestoration and bioremediation technologies, innovative and competitive solutions characterized by economical and environmental advantages. Overall, in the future the study and application of the metabolic properties of microbial communities capable of weathering can represent a driving force in the expanding sector of environmental biotechnology. PMID:22138043

  7. Assessment of a sponge layer as a non-reflective boundary treatment with highly accurate gust–airfoil interaction results

    NASA Astrophysics Data System (ADS)

    Crivellini, A.

    2016-02-01

    This paper deals with the numerical performance of a sponge layer as a non-reflective boundary condition. This technique is well known and widely adopted, but only recently have the reasons for a sponge failure been recognised, in analysis by Mani. For multidimensional problems, the ineffectiveness of the method is due to the self-reflections of the sponge occurring when it interacts with an oblique acoustic wave. Based on his theoretical investigations, Mani gives some useful guidelines for implementing effective sponge layers. However, in our opinion, some practical indications are still missing from the current literature. Here, an extensive numerical study of the performance of this technique is presented. Moreover, we analyse a reduced sponge implementation characterised by undamped partial differential equations for the velocity components. The main aim of this paper relies on the determination of the minimal width of the layer, as well as of the corresponding strength, required to obtain a reflection error of no more than a few per cent of that observed when solving the same problem on the same grid, but without employing the sponge layer term. For this purpose, a test case of computational aeroacoustics, the single airfoil gust response problem, has been addressed in several configurations. As a direct consequence of our investigation, we present a well documented and highly validated reference solution for the far-field acoustic intensity, a result that is not well established in the literature. Lastly, the proof of the accuracy of an algorithm for coupling sub-domains solved by the linear and non-liner Euler governing equations is given. This result is here exploited to adopt a linear-based sponge layer even in a non-linear computation.

  8. Assessment of a sponge layer as a non-reflective boundary treatment with highly accurate gust-airfoil interaction results

    NASA Astrophysics Data System (ADS)

    Crivellini, A.

    2016-02-01

    This paper deals with the numerical performance of a sponge layer as a non-reflective boundary condition. This technique is well known and widely adopted, but only recently have the reasons for a sponge failure been recognised, in analysis by Mani. For multidimensional problems, the ineffectiveness of the method is due to the self-reflections of the sponge occurring when it interacts with an oblique acoustic wave. Based on his theoretical investigations, Mani gives some useful guidelines for implementing effective sponge layers. However, in our opinion, some practical indications are still missing from the current literature. Here, an extensive numerical study of the performance of this technique is presented. Moreover, we analyse a reduced sponge implementation characterised by undamped partial differential equations for the velocity components. The main aim of this paper relies on the determination of the minimal width of the layer, as well as of the corresponding strength, required to obtain a reflection error of no more than a few per cent of that observed when solving the same problem on the same grid, but without employing the sponge layer term. For this purpose, a test case of computational aeroacoustics, the single airfoil gust response problem, has been addressed in several configurations. As a direct consequence of our investigation, we present a well documented and highly validated reference solution for the far-field acoustic intensity, a result that is not well established in the literature. Lastly, the proof of the accuracy of an algorithm for coupling sub-domains solved by the linear and non-liner Euler governing equations is given. This result is here exploited to adopt a linear-based sponge layer even in a non-linear computation.

  9. A divide and conquer real-space approach for all-electron molecular electrostatic potentials and interaction energies.

    PubMed

    Losilla, S A; Sundholm, D

    2012-06-01

    A computational scheme to perform accurate numerical calculations of electrostatic potentials and interaction energies for molecular systems has been developed and implemented. Molecular electron and energy densities are divided into overlapping atom-centered atomic contributions and a three-dimensional molecular remainder. The steep nuclear cusps are included in the atom-centered functions making the three-dimensional remainder smooth enough to be accurately represented with a tractable amount of grid points. The one-dimensional radial functions of the atom-centered contributions as well as the three-dimensional remainder are expanded using finite element functions. The electrostatic potential is calculated by integrating the Coulomb potential for each separate density contribution, using our tensorial finite element method for the three-dimensional remainder. We also provide algorithms to compute accurate electron-electron and electron-nuclear interactions numerically using the proposed partitioning. The methods have been tested on all-electron densities of 18 reasonable large molecules containing elements up to Zn. The accuracy of the calculated Coulomb interaction energies is in the range of 10(-3) to 10(-6) E(h) when using an equidistant grid with a step length of 0.05 a(0).

  10. A DPF Analysis Yields Quantum Mechanically Accurate Analytic Potential Energy Functions for the a ^1Σ^+ and X ^1Σ^+ States of NaH

    NASA Astrophysics Data System (ADS)

    Le Roy, Robert J.; Walji, Sadru; Sentjens, Katherine

    2013-06-01

    Alkali hydride diatomic molecules have long been the object of spectroscopic studies. However, their small reduced mass makes them species for which the conventional semiclassical-based methods of analysis tend to have the largest errors. To date, the only quantum-mechanically accurate direct-potential-fit (DPF) analysis for one of these molecules was the one for LiH reported by Coxon and Dickinson. The present paper extends this level of analysis to NaH, and reports a DPF analysis of all available spectroscopic data for the A ^1Σ^+-X ^1Σ^+ system of NaH which yields analytic potential energy functions for these two states that account for those data (on average) to within the experimental uncertainties. W.C. Stwalley, W.T. Zemke and S.C. Yang, J. Phys. Chem. Ref. Data {20}, 153-187 (1991). J.A. Coxon and C.S. Dickinson, J. Chem. Phys. {121}, 8378 (2004).

  11. Communication: Rate coefficients of the H + CH4 → H2 + CH3 reaction from ring polymer molecular dynamics on a highly accurate potential energy surface.

    PubMed

    Meng, Qingyong; Chen, Jun; Zhang, Dong H

    2015-09-14

    The ring polymer molecular dynamics (RPMD) calculations are performed to calculate rate constants for the title reaction on the recently constructed potential energy surface based on permutation invariant polynomial (PIP) neural-network (NN) fitting [J. Li et al., J. Chem. Phys. 142, 204302 (2015)]. By inspecting convergence, 16 beads are used in computing free-energy barriers at 300 K ≤ T ≤ 1000 K, while different numbers of beads are used for transmission coefficients. The present RPMD rates are in excellent agreement with quantum rates computed on the same potential energy surface, as well as with the experimental measurements, demonstrating further that the RPMD is capable of producing accurate rates for polyatomic chemical reactions even at rather low temperatures.

  12. Communication: Rate coefficients of the H + CH4 → H2 + CH3 reaction from ring polymer molecular dynamics on a highly accurate potential energy surface

    NASA Astrophysics Data System (ADS)

    Meng, Qingyong; Chen, Jun; Zhang, Dong H.

    2015-09-01

    The ring polymer molecular dynamics (RPMD) calculations are performed to calculate rate constants for the title reaction on the recently constructed potential energy surface based on permutation invariant polynomial (PIP) neural-network (NN) fitting [J. Li et al., J. Chem. Phys. 142, 204302 (2015)]. By inspecting convergence, 16 beads are used in computing free-energy barriers at 300 K ≤ T ≤ 1000 K, while different numbers of beads are used for transmission coefficients. The present RPMD rates are in excellent agreement with quantum rates computed on the same potential energy surface, as well as with the experimental measurements, demonstrating further that the RPMD is capable of producing accurate rates for polyatomic chemical reactions even at rather low temperatures.

  13. Isolating the non-polar contributions to the intermolecular potential for water-alkane interactions.

    PubMed

    Ballal, Deepti; Venkataraman, Pradeep; Fouad, Wael A; Cox, Kenneth R; Chapman, Walter G

    2014-08-14

    Intermolecular potential models for water and alkanes describe pure component properties fairly well, but fail to reproduce properties of water-alkane mixtures. Understanding interactions between water and non-polar molecules like alkanes is important not only for the hydrocarbon industry but has implications to biological processes as well. Although non-polar solutes in water have been widely studied, much less work has focused on water in non-polar solvents. In this study we calculate the solubility of water in different alkanes (methane to dodecane) at ambient conditions where the water content in alkanes is very low so that the non-polar water-alkane interactions determine solubility. Only the alkane-rich phase is simulated since the fugacity of water in the water rich phase is calculated from an accurate equation of state. Using the SPC/E model for water and TraPPE model for alkanes along with Lorentz-Berthelot mixing rules for the cross parameters produces a water solubility that is an order of magnitude lower than the experimental value. It is found that an effective water Lennard-Jones energy ε(W)/k = 220 K is required to match the experimental water solubility in TraPPE alkanes. This number is much higher than used in most simulation water models (SPC/E-ε(W)/k = 78.2 K). It is surprising that the interaction energy obtained here is also higher than the water-alkane interaction energy predicted by studies on solubility of alkanes in water. The reason for this high water-alkane interaction energy is not completely understood. Some factors that might contribute to the large interaction energy, such as polarizability of alkanes, octupole moment of methane, and clustering of water at low concentrations in alkanes, are examined. It is found that, though important, these factors do not completely explain the anomalously strong attraction between alkanes and water observed experimentally. PMID:25134597

  14. Isolating the non-polar contributions to the intermolecular potential for water-alkane interactions.

    PubMed

    Ballal, Deepti; Venkataraman, Pradeep; Fouad, Wael A; Cox, Kenneth R; Chapman, Walter G

    2014-08-14

    Intermolecular potential models for water and alkanes describe pure component properties fairly well, but fail to reproduce properties of water-alkane mixtures. Understanding interactions between water and non-polar molecules like alkanes is important not only for the hydrocarbon industry but has implications to biological processes as well. Although non-polar solutes in water have been widely studied, much less work has focused on water in non-polar solvents. In this study we calculate the solubility of water in different alkanes (methane to dodecane) at ambient conditions where the water content in alkanes is very low so that the non-polar water-alkane interactions determine solubility. Only the alkane-rich phase is simulated since the fugacity of water in the water rich phase is calculated from an accurate equation of state. Using the SPC/E model for water and TraPPE model for alkanes along with Lorentz-Berthelot mixing rules for the cross parameters produces a water solubility that is an order of magnitude lower than the experimental value. It is found that an effective water Lennard-Jones energy ε(W)/k = 220 K is required to match the experimental water solubility in TraPPE alkanes. This number is much higher than used in most simulation water models (SPC/E-ε(W)/k = 78.2 K). It is surprising that the interaction energy obtained here is also higher than the water-alkane interaction energy predicted by studies on solubility of alkanes in water. The reason for this high water-alkane interaction energy is not completely understood. Some factors that might contribute to the large interaction energy, such as polarizability of alkanes, octupole moment of methane, and clustering of water at low concentrations in alkanes, are examined. It is found that, though important, these factors do not completely explain the anomalously strong attraction between alkanes and water observed experimentally.

  15. Permutation invariant polynomial neural network approach to fitting potential energy surfaces. III. Molecule-surface interactions.

    PubMed

    Jiang, Bin; Guo, Hua

    2014-07-21

    The permutation invariant polynomial-neural network (PIP-NN) method for constructing highly accurate potential energy surfaces (PESs) for gas phase molecules is extended to molecule-surface interaction PESs. The symmetry adaptation in the NN fitting of a PES is achieved by employing as the input symmetry functions that fulfill both the translational symmetry of the surface and permutation symmetry of the molecule. These symmetry functions are low-order PIPs of the primitive symmetry functions containing the surface periodic symmetry. It is stressed that permutationally invariant cross terms are needed to avoid oversymmetrization. The accuracy and efficiency are demonstrated in fitting both a model PES for the H2 + Cu(111) system and density functional theory points for the H2 + Ag(111) system.

  16. Permutation invariant polynomial neural network approach to fitting potential energy surfaces. III. Molecule-surface interactions

    NASA Astrophysics Data System (ADS)

    Jiang, Bin; Guo, Hua

    2014-07-01

    The permutation invariant polynomial-neural network (PIP-NN) method for constructing highly accurate potential energy surfaces (PESs) for gas phase molecules is extended to molecule-surface interaction PESs. The symmetry adaptation in the NN fitting of a PES is achieved by employing as the input symmetry functions that fulfill both the translational symmetry of the surface and permutation symmetry of the molecule. These symmetry functions are low-order PIPs of the primitive symmetry functions containing the surface periodic symmetry. It is stressed that permutationally invariant cross terms are needed to avoid oversymmetrization. The accuracy and efficiency are demonstrated in fitting both a model PES for the H2 + Cu(111) system and density functional theory points for the H2 + Ag(111) system.

  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. Running of the contact interactions in chiral N3LO potentials from subtractive renormalization

    NASA Astrophysics Data System (ADS)

    Batista, E. F.; Szpigel, S.; Timóteo, V. S.

    2015-07-01

    In this work a subtracted kernel renormalization procedure (SKM) is applied to the chiral NN potential up to next-to-next-to-next-to-leading-order (N3 LO) to obtain the running of the renormalized contact strengths with the subtraction scale μ and the phase shifts for all uncoupled waves with contact interaction (S,P,D). We use two potentials constructed within the framework of Weinberg's approach to ChEFT, which provide a very accurate description of NN scattering data below laboratory energies E ∼ 350 MeV, namely Epelbaum, Glöckle and Meissner (N3LO-EGM) and Entem and Machleidt (N3LO-EM). For both potentials, we consider a large cutoff (30 fm-1) and analyze the phases and the running of the contact strengths with the subtraction point μ by making a fit of the K-matrix with five subtractions to the K-matrix from the Nijmegen II potential at low energies (E ≤ 20 MeV).

  19. Probiotics: Interaction with gut microbiome and antiobesity potential.

    PubMed

    Arora, Tulika; Singh, Satvinder; Sharma, Raj Kumar

    2013-04-01

    Obesity is a metabolic disorder afflicting people globally. There has been a pivotal advancement in the understanding of the intestinal microbiota composition and its implication in extraintestinal (metabolic) diseases. Therefore, any agent modulating gut microbiota may produce an influential effect in preventing the pathogenesis of disease. Probiotics are live microbes that, when administered in adequate amounts, have been shown to confer health benefits to the host. Over the years, probiotics have been a part of the human diet in the form of different fermented foods consumed around the world. Their influence on different physiologic functions in the host is increasingly being documented. The antiobesity potential of probiotics is also gaining wide attention because of increasing evidence of the role of gut microbiota in energy homeostasis and fat accumulation. Probiotics have also been shown to interact with the resident bacterial members already present in the gut by altering their properties, which may also affect the metabolic pathways involved in the regulation of fat metabolism. The underlying pathways governing the antiobesity effects of probiotics remain unclear. However, it is hoped that the evidence presented and discussed in this review will encourage and thus drive more extensive research in this field.

  20. Commercially available interactive video games in burn rehabilitation: therapeutic potential.

    PubMed

    Parry, Ingrid S; Bagley, Anita; Kawada, Jason; Sen, Soman; Greenhalgh, David G; Palmieri, Tina L

    2012-06-01

    Commercially available interactive video games (IVG) like the Nintendo Wii™ (NW) and PlayStation™II Eye Toy (PE) are increasingly used in the rehabilitation of patients with burn. Such games have gained popularity in burn rehabilitation because they encourage range of motion (ROM) while distracting from pain. However, IVGs were not originally designed for rehabilitation purposes but rather for entertainment and may lack specificity for achieving rehabilitative goals. Objectively evaluating the specific demands of IVGs in relation to common burn therapy goals will determine their true therapeutic benefit and guide their use in burn rehabilitation. Upper extremity (UE) motion of 24 normal children was measured using 3D motion analysis during play with the two types of IVGs most commonly described for use after burn: NW and PE. Data was analyzed using t-tests and One-way Analysis of Variance. Active range of motion for shoulder flexion and abduction during play with both PE and NW was within functional range, thus supporting the idea that IVGs offer activities with therapeutic potential to improve ROM. PE resulted in higher demands and longer duration of UE motion than NW, and therefore may be the preferred tool when UE ROM or muscular endurance are the goals of rehabilitation. When choosing a suitable IVG for application in rehabilitation, the user's impairment together with the therapeutic attributes of the IVG should be considered to optimize outcome.

  1. Pollution, Climate and Their Potential Interactions in China

    NASA Astrophysics Data System (ADS)

    Li, Z.

    2009-05-01

    As the largest, most populated and fastest developing country of the world, China is most susceptible to pollution and climate changes. Some preliminary model studies have implied significant effects, but few of the studies were founded on actual observational data. By modulating atmospheric heating profile, surface energy balance and cloud microphysics, atmospheric pollutants, especially aerosols (particle pollutants) have been hypothesized to interact with the Asian monsoon system and play a significant role in observed changes in precipitation, temperature and atmospheric circulation. Testing the hypotheses requires extensive and reliable measurements concerning their properties, radiative fluxes, cloud microphysics, precipitation, and other atmospheric variables, which is the primary goal of two major ongoing field campaigns conducted before, during and after the Beijing Olympic Games under the East Asian Study of Tropospheric Aerosols: an International Regional Experiment (EAST-AIRE) and the ARM Mobile Facility deployment in China (AMF-China). In my talk, I will review the status of the two observation campaigns; present some preliminary findings; elaborate the potential usage of the data in dealing with the aforementioned issues.

  2. Breit interaction contribution to parity violating potentials in chiral molecules containing light nuclei.

    PubMed

    Berger, Robert

    2008-10-21

    The importance of the Breit interaction for an accurate prediction of parity violating energy differences between enantiomers is studied within electroweak quantum chemical frameworks. Besides two-electron orbit-orbit and spin-spin coupling contributions, the Breit interaction gives rise to the spin-other-orbit coupling term of the Breit-Pauli Hamiltonian. The present numerical study demonstrates that neglect of this latter term leads in hydrogen peroxide (H(2)O(2)) to relative deviations in the parity violating potential (V(pv)) by about 10%, whereas further relativistic corrections accounted for within a four-component Dirac-Hartree-Fock-Coulomb (DHFC) framework remain smaller, below 5%. Thus, the main source of discrepancy between previous one-component based (coupled perturbed) Hartree-Fock (HF) and four-component Dirac-Hartree-Fock results for parity violating potentials in H(2)O(2) is the neglect of the Breit contribution in DHFC. In heavier homologs of hydrogen peroxide the relative contribution of the spin-other-orbit coupling term to V(pv) decreases with increasing nuclear charge, whereas other relativistic effects become increasingly important. As shown for the H(2)X(2) (X = O,S,Se,Te,Po) series of molecules and for CHBrClF, to a good approximation these other relativistic influences on V(pv) can be accounted for in one-component based HF calculations with the help of relativistic enhancement factors proposed earlier in the theory of atomic parity violation.

  3. Multireference configuration interaction calculations of the first six ionization potentials of the uranium atom

    DOE PAGES

    Bross, David H.; Parmar, Payal; Peterson, Kirk A.

    2015-11-12

    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 IP3 through IP6.« less

  4. Multireference configuration interaction calculations of the first six ionization potentials of the uranium atom

    SciTech Connect

    Bross, David H.; Parmar, Payal; Peterson, Kirk A.

    2015-11-12

    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 a 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 IP3 through IP6.

  5. Intermolecular Interactions and Cooperative Effects from Electronic Structure Calculations: An Effective Means for Developing Interaction Potentials for Condensed Phase Simulations

    SciTech Connect

    Xantheas, Sotiris S.

    2004-05-01

    The modeling of the macroscopic properties of homogeneous and inhomogeneous systems via atomistic simulations such as molecular dynamics (MD) or Monte Carlo (MC) techniques is based on the accurate description of the relevant solvent-solute and solvent-solvent intermolecular interactions. The total energy (U) of an n-body molecular system can be formally written as [1,2,3

  6. Asymptotic near-nucleus structure of the electron-interaction potential in local effective potential theories

    SciTech Connect

    Qian, Zhixin; Sahni, Viraht

    2007-03-15

    In local effective potential theories of electronic structure, the electron correlations due to the Pauli exclusion principle, Coulomb repulsion, and correlation-kinetic effects, are all incorporated in the local electron-interaction potential v{sub ee}(r). In previous work, it has been shown that for spherically symmetric or sphericalized systems, the asymptotic near-nucleus expansion of this potential is v{sub ee}(r)=v{sub ee}(0)+{beta}r+O(r{sup 2}), with v{sub ee}(0) being finite. By assuming that the Schroedinger and local effective potential theory wave functions are analytic near the nucleus of atoms, we prove the following via quantal density functional theory (QDFT): (i) Correlations due to the Pauli principle and Coulomb correlations do not contribute to the linear structure; (ii) these Pauli and Coulomb correlations contribute quadratically; (iii) the linear structure is solely due to correlation-kinetic effects, the contributions of these effects being determined analytically. We also derive by application of adiabatic coupling constant perturbation theory via QDFT (iv) the asymptotic near-nucleus expansion of the Hohenberg-Kohn-Sham theory exchange v{sub x}(r) and correlation v{sub c}(r) potentials. These functions also approach the nucleus linearly with the linear term of v{sub x}(r) being solely due to the lowest-order correlation kinetic effects, and the linear term of v{sub c}(r) being due solely to the higher-order correlation kinetic contributions. The above conclusions are equally valid for systems of arbitrary symmetry, provided spherical averages of the properties are employed.

  7. Interaction of NH(X 3Sigma-) with He: potential energy surface, bound states, and collisional Zeeman relaxation.

    PubMed

    Cybulski, H; Krems, R V; Sadeghpour, H R; Dalgarno, A; Kłos, J; Groenenboom, G C; van der Avoird, A; Zgid, D; Chałasiński, G

    2005-03-01

    A detailed analysis of the He-NH((3)Sigma(-)) van der Waals complex is presented. We discuss ab initio calculations of the potential energy surface and fitting procedures with relevance to cold collisions, and we present accurate calculations of bound energy levels of the triatomic complex as well as collisional properties of NH molecules in a buffer gas of (3)He. The influence of the external magnetic field used to trap the NH molecules and the effect of the atom-molecule interaction potential on the collisionally induced Zeeman relaxation are explored. It is shown that minute variations of the interaction potential due to different fitting procedures may alter the Zeeman relaxation rate at ultralow temperatures by as much as 50%.

  8. Comparative study of collision cross-sections and ion transport coefficients from several He+/He interaction potentials

    NASA Astrophysics Data System (ADS)

    Chicheportiche, A.; Lepetit, B.; Benhenni, M.; Gadea, F. X.; Yousfi, M.

    2013-03-01

    Ion-atom collision cross-sections and transport coefficients are computed from several He2+ interaction potentials. Differential and integral momentum transfer cross-sections are obtained with a close-coupling quantum method using several literature interaction potentials. These collision cross-sections are used in an optimized Monte Carlo code to calculate the ion transport coefficients over a wide range of reduced electric field considering first the scattering anisotropy by using a differential cross-section and then an isotropic scattering approximation based on momentum transfer cross-section. Reduced mobilities are compared with available experimental data. This allows us to segregate accurate potentials which provide reduced mobilities falling within experimental error bars.

  9. Accurate high level ab initio-based global potential energy surface and dynamics calculations for ground state of CH{sub 2}{sup +}

    SciTech Connect

    Li, Y. Q.; Zhang, P. Y.; Han, K. L.

    2015-03-28

    A global many-body expansion potential energy surface is reported for the electronic ground state of CH{sub 2}{sup +} by fitting high level ab initio energies calculated at the multireference configuration interaction level with the aug-cc-pV6Z basis set. The topographical features of the new global potential energy surface are examined in detail and found to be in good agreement with those calculated directly from the raw ab initio energies, as well as previous calculations available in the literature. In turn, in order to validate the potential energy surface, a test theoretical study of the reaction CH{sup +}(X{sup 1}Σ{sup +})+H({sup 2}S)→C{sup +}({sup 2}P)+H{sub 2}(X{sup 1}Σ{sub g}{sup +}) has been carried out with the method of time dependent wavepacket on the title potential energy surface. The total integral cross sections and the rate coefficients have been calculated; the results determined that the new potential energy surface can both be recommended for dynamics studies of any type and as building blocks for constructing the potential energy surfaces of larger C{sup +}/H containing systems.

  10. Potential for the dynamics of pedestrians in a socially interacting group

    NASA Astrophysics Data System (ADS)

    Zanlungo, Francesco; Ikeda, Tetsushi; Kanda, Takayuki

    2014-01-01

    We introduce a simple potential to describe the dynamics of the relative motion of two pedestrians socially interacting in a walking group. We show that the proposed potential, based on basic empirical observations and theoretical considerations, can qualitatively describe the statistical properties of pedestrian behavior. In detail, we show that the two-dimensional probability distribution of the relative distance is determined by the proposed potential through a Boltzmann distribution. After calibrating the parameters of the model on the two-pedestrian group data, we apply the model to three-pedestrian groups, showing that it describes qualitatively and quantitatively well their behavior. In particular, the model predicts that three-pedestrian groups walk in a V-shaped formation and provides accurate values for the position of the three pedestrians. Furthermore, the model correctly predicts the average walking velocity of three-person groups based on the velocity of two-person ones. Possible extensions to larger groups, along with alternative explanations of the social dynamics that may be implied by our model, are discussed at the end of the paper.

  11. Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions.

    PubMed

    Cisneros, Gerardo Andrés; Wikfeldt, Kjartan Thor; Ojamäe, Lars; Lu, Jibao; Xu, Yao; Torabifard, Hedieh; Bartók, Albert P; Csányi, Gábor; Molinero, Valeria; Paesani, Francesco

    2016-07-13

    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.

  12. Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions.

    PubMed

    Cisneros, Gerardo Andrés; Wikfeldt, Kjartan Thor; Ojamäe, Lars; Lu, Jibao; Xu, Yao; Torabifard, Hedieh; Bartók, Albert P; Csányi, Gábor; Molinero, Valeria; Paesani, Francesco

    2016-07-13

    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

  13. Exploring the potential of algae/bacteria interactions.

    PubMed

    Kouzuma, Atsushi; Watanabe, Kazuya

    2015-06-01

    Algae are primary producers in aquatic ecosystems, where heterotrophic bacteria grow on organics produced by algae and recycle nutrients. Ecological studies have identified the co-occurrence of particular species of algae and bacteria, suggesting the presence of their specific interactions. Algae/bacteria interactions are categorized into nutrient exchange, signal transduction and gene transfer. Studies have examined how these interactions shape aquatic communities and influence geochemical cycles in the natural environment. In parallel, efforts have been made to exploit algae for biotechnology processes, such as water treatment and bioenergy production, where bacteria influence algal activities in various ways. We suggest that better understanding of mechanisms underlying algae/bacteria interactions will facilitate the development of more efficient and/or as-yet-unexploited biotechnology processes.

  14. A simple but accurate potential for the naphthalene-argon complex: applications to collisional energy transfer and matrix isolated IR spectroscopy.

    PubMed

    Calvo, F; Falvo, Cyril; Parneix, Pascal

    2013-01-21

    An explicit polarizable potential for the naphthalene-argon complex has been derived assuming only atomic contributions, aiming at large scale simulations of naphthalene under argon environment. The potential was parametrized from dedicated quantum chemical calculations at the CCSD(T) level, and satisfactorily reproduces available structural and energetic properties. Combining this potential with a tight-binding model for naphthalene, collisional energy transfer is studied by means of dedicated molecular dynamics simulations, nuclear quantum effects being accounted for in the path-integral framework. Except at low target temperature, nuclear quantum effects do not alter the average energies transferred by the collision or the collision duration. However, the distribution of energy transferred is much broader in the quantum case due to the significant zero-point energy and the higher density of states. Using an ab initio potential for the Ar-Ar interaction, the IR absorption spectrum of naphthalene solvated by argon clusters or an entire Ar matrix is computed via classical and centroid molecular dynamics. The classical spectra exhibit variations with growing argon environment that are absent from quantum spectra. This is interpreted by the greater fluxional character experienced by the argon atoms due to vibrational delocalization.

  15. Structural properties of fluids interacting via piece-wise constant potentials with a hard core

    NASA Astrophysics Data System (ADS)

    Santos, Andrés; Yuste, Santos B.; de Haro, Mariano López; Bárcenas, Mariana; Orea, Pedro

    2013-08-01

    The structural properties of fluids whose molecules interact via potentials with a hard core plus two piece-wise constant sections of different widths and heights are presented. These follow from the more general development previously introduced for potentials with a hard core plus n piece-wise constant sections [A. Santos, S. B. Yuste, and M. Lopez de Haro, Condens. Matter Phys. 15, 23602 (2012)], 10.5488/CMP.15.23602 in which use was made of a semi-analytic rational-function approximation method. The results of illustrative cases comprising eight different combinations of wells and shoulders are compared both with simulation data and with those that follow from the numerical solution of the Percus-Yevick and hypernetted-chain integral equations. It is found that the rational-function approximation generally predicts a more accurate radial distribution function than the Percus-Yevick theory and is comparable or even superior to the hypernetted-chain theory. This superiority over both integral equation theories is lost, however, at high densities, especially as the widths of the wells and/or the barriers increase.

  16. Accurate ab initio potential energy surface, thermochemistry, and dynamics of the Br(2P, 2P(3∕2)) + CH4 → HBr + CH3 reaction.

    PubMed

    Czakó, Gábor

    2013-04-01

    Chemically accurate full-dimensional non-spin-orbit and spin-orbit (SO) ground-state potential energy surfaces (PESs) are obtained for the Br + CH4 → HBr + CH3 reaction by fitting 21 574 composite ab initio energy points. The composite method considers electron correlation methods up to CCSD(T), basis sets up to aug-cc-pwCVTZ-PP, correlation of the core electrons, scalar relativistic effects via an effective core potential (ECP), and SO corrections, thereby achieving an accuracy better than 0.5 kcal∕mol. Benchmark structures and relative energies are computed for the stationary points using the ab initio focal-point analysis (FPA) scheme based on both ECP and Douglas-Kroll approaches providing all-electron relativistic CCSDT(Q)∕complete-basis-set quality energies. The PESs accurately describe the saddle point of the abstraction reaction and the van der Waals complexes in the entrance and product channels. The SO-corrected PES provides a classical barrier height of 7285(7232 ± 50) cm(-1), De values of 867(799 ± 10) and 399(344 ± 10) cm(-1) for the complexes CH3-HBr and CH3-BrH, respectively, and reaction endothermicity of 7867(7857 ± 50) cm(-1), in excellent agreement with the new, FPA-based benchmark data shown in parentheses. The difference between the Br + CH4 asymptotes of the non-SO and SO PESs is 1240 cm(-1), in good agreement with the experiment (1228 cm(-1)). Quasiclassical trajectory calculations based on more than 13 million trajectories for the late-barrier Br + CH4(vk = 0, 1) [k = 1, 2, 3, 4] reactions show that the vibrational energy, especially the excitation of the stretching modes, activates the reaction much more efficiently than translational energy, in agreement with the extended Polanyi rules. Angular distributions show dominant backward scattering for the ground-state reaction and forward scattering for the stretching-excited reactions. The reactivity on the non-SO PES is about 3-5 times larger than that on the SO PES in a wide

  17. Modeling Earth materials from crustal to lower mantle conditions: A transferable set of interaction potentials for the CMAS system

    NASA Astrophysics Data System (ADS)

    Jahn, Sandro; Madden, Paul A.

    2007-06-01

    A fully flexible ionic interaction model (Aspherical Ion Model, AIM) is presented and applied to various relevant minerals and melts of the Ca-Mg-Al-Si-O (CMAS) system. The model reproduces accurately lattice parameters and thermoelastic properties of minerals in a wide range of compositions. Furthermore, its transferability range extends from the pressure and temperature conditions of the Earth's crust to the lower mantle. Thus, the AIM extends greatly the applicability of classical models in nanoscale computer simulations of Earth materials. The increased transferability compared to other interatomic potentials and the much more efficient calculation of interaction energies compared to first principles electronic structure calculations will allow larger scale simulations. The potential applications of the AIM to new fields of atomistic modeling in Earth sciences is discussed.

  18. Studies on pharmacokinetic drug interaction potential of vinpocetine

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Vinpocetine, a semi-synthetic derivative of vincamine, is a popular dietary supplement used for the treatment of several central nervous system related disorders. Despite its wide use, no pharmacokinetic drug interaction studies are reported in literature. Due to increasing use of dietar...

  19. Classroom Interaction: Potential or Problem? The Case of Karagwe

    ERIC Educational Resources Information Center

    Wedin, Asa

    2010-01-01

    This paper discusses interactional patterns in classrooms in primary school in rural Tanzania, based on an ethnographic study on literacy practices. The paper argues that the official policy of Swahili-only in primary school, together with the huge gap between high expectations on educational outcome and lack of resources, have resulted in the…

  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. A Quasiclassical Study of the F((2)P) + CHD3 (ν1 = 0,1) Reactive System on an Accurate Potential Energy Surface.

    PubMed

    Palma, Juliana; Manthe, Uwe

    2015-12-17

    Quasiclassical trajectories (QCT) have been employed to elucidate the effect of exciting the C-H bond in F + CHD3 collisions. The calculations were performed on a new potential energy surface that accurately describes the van der Waals complexes in the entrance channel of the reaction. It was found that exciting the C-H bond significantly enhances the yield of HF + CD3, whereas it has a minor effect on the production of DF + CHD2. Therefore, the net effect is that the total reactivity increases upon excitation. This result strongly contradicts recent experimental findings. Significant differences in regard to the yield of each product channel were also found between QCT results calculated with the new surface and those obtained with the surface previously developed by Czakó et al. This shows that relatively small variations in the topography of the entrance channel can result in huge discrepancies in the predicted DF/HF branching ratio. However, in regard to other attributes of the reaction, the agreement between QCT results computed with different surfaces, and between them and experimental results, is good. For the F + CHD3 → HF + CD3 reaction, at a collisional energy of 9.0 kcal/mol, experiments and QCT calculations agree, indicating that the extra energy deposited in the C-H bond is channelled into the HF product. In addition, the angular distribution of CD3 is backward oriented and is not sensitive to the excitation of the C-H bond. PMID:26270126

  2. Highly accurate potential energy surface, dipole moment surface, rovibrational energy levels, and infrared line list for ³²S¹⁶O₂ up to 8000 cm⁻¹.

    PubMed

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

    2014-03-21

    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 (σ(RMS)) for all J = 0-80 rovibrational energy levels computed on the refined PES (denoted Ames-1) is 0.013 cm(-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(-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(-1) with 0.01-0.03 cm(-1) uncertainties, and the Ames-296K line list provides continuous, reliable and accurate IR simulations. The K(a)-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. PMID:24655184

  3. Effective Semi-empirical Interaction Potential for Dusty Particles

    SciTech Connect

    Ramazanov, T. S.; Dzhumagulova, K. N.; Omarbakiyeva, Y. A.; Dosbolayev, M. K.; Jumabekov, A. N.

    2008-09-07

    The Poisson equation was numerically solved on the basis of the experimental correlation functions of dusty particles. Calculations were performed with real parameters of dusty plasma. Reconstructed potential has oscillated character; the minimums coincide to maximums of correlation functions.

  4. Solubility of methane in water: the significance of the methane-water interaction potential.

    PubMed

    Konrad, Oliver; Lankau, Timm

    2005-12-15

    The influence of the methane-water interaction potential on the value of the Henry constant obtained from molecular dynamics simulations was investigated. The SPC, SPC/E, MSPC/E, and TIP3P potentials were used to describe water and the OPLS-UA and TraPPE potentials for methane. Nonbonding interactions between unlike atoms were calculated both with one of four mixing rules and with our new methane-water interaction potential. The Henry constants obtained from simulations using any of the mixing rules differed significantly from the experimental ones. Good agreement between simulation and experiment was achieved with the new potential over the whole temperature range. PMID:16375336

  5. Solubility of methane in water: the significance of the methane-water interaction potential.

    PubMed

    Konrad, Oliver; Lankau, Timm

    2005-12-15

    The influence of the methane-water interaction potential on the value of the Henry constant obtained from molecular dynamics simulations was investigated. The SPC, SPC/E, MSPC/E, and TIP3P potentials were used to describe water and the OPLS-UA and TraPPE potentials for methane. Nonbonding interactions between unlike atoms were calculated both with one of four mixing rules and with our new methane-water interaction potential. The Henry constants obtained from simulations using any of the mixing rules differed significantly from the experimental ones. Good agreement between simulation and experiment was achieved with the new potential over the whole temperature range.

  6. Full-potential modeling of blade-vortex interactions

    NASA Technical Reports Server (NTRS)

    Jones, H. E.; Caradonna, F. X.

    1986-01-01

    A comparison is made of four different models for predicting the unsteady loading induced by a vortex passing close to an airfoil. (1) The first model approximates the vortex effect as a change in the airfoil angle of attack. (2) The second model is related to the first but, instead of imposing only a constant velocity on the airfoil, the distributed effect of the vortex is computed and used. This is analogous to a lifting surface method. (3) The third model is to specify a branch cut discontinuity in the potential field. The vortex is modeled as a jump in potential across the branch cut, the edge of which represents the center of the vortex. (4) The fourth method models the vortex expressing the potential as the sum of a known potential due to the vortex and an unknown perturbation due to the airfoil. The purpose of the current study is to investigate the four vortex models described above and to determine their relative merits and suitability for use in large three-dimensional codes.

  7. Calculation of interaction-induced spectra using complex absorbing potentials

    SciTech Connect

    Gustafsson, Magnus; Antipov, Sergey V.

    2010-10-29

    A complex absorbing potential method is implemented for calculation of collision-induced spectra. The scheme provides a way to avoid the integration of the Schroedinger equation to very large separations of the collisional pair. The method is tested by reproducing a previously computed absorption spectrum for H-He at two different temperatures.

  8. i-TTM Model for Ab Initio-Based Ion-Water Interaction Potentials. 1. Halide-Water Potential Energy Functions.

    PubMed

    Arismendi-Arrieta, Daniel J; Riera, Marc; Bajaj, Pushp; Prosmiti, Rita; Paesani, Francesco

    2016-03-01

    New potential energy functions (i-TTM) describing the interactions between halide ions and water molecules are reported. The i-TTM potentials are derived from fits to electronic structure data and include an explicit treatment of two-body repulsion, electrostatics, and dispersion energy. Many-body effects are represented through classical polarization within an extended Thole-type model. By construction, the i-TTM potentials are compatible with the flexible and fully ab initio MB-pol potential, which has recently been shown to accurately predict the properties of water from the gas to the condensed phase. The accuracy of the i-TTM potentials is assessed through extensive comparisons with CCSD(T)-F12, DF-MP2, and DFT data as well as with results obtained with common polarizable force fields for X(-)(H2O)n clusters with X(-) = F(-), Cl(-), Br(-), and I(-), and n = 1-8. By construction, the new i-TTM potentials will enable direct simulations of vibrational spectra of halide-water systems from clusters to bulk and interfaces.

  9. Modeling Intermolecular Interactions in Nanotubes, Fullerenes and Graphite using a New Long-Range Potential

    NASA Technical Reports Server (NTRS)

    Jaffe, Richard; Halicioglu, Timur; Han, Jie; Yang, Liu; Huo, Winifred (Technical Monitor)

    1998-01-01

    The cohesive energy and compressibility of strands of a single-wall nanotube rope has been computed using a new long-range potential energy function derived from accurate ab initio quantum chemistry calculations of the benzene dimer and calibrated for energetic and mechanical properties of graphite (at pressures up to 12 GPa). We also use this potential to calculate a variety of properties of carbon nanotubes (both single- and multi-wall) and fullerenes. Extensive comparisons are made with previously published potentials.

  10. Bubble-bubble interaction: A potential source of cavitation noise

    NASA Astrophysics Data System (ADS)

    Ida, Masato

    2009-01-01

    The interaction between microbubbles through pressure pulses has been studied to show that it can be a source of cavitation noise. A recent report demonstrated that the acoustic noise generated by a shrimp originates from the collapse of a cavitation bubble produced when the shrimp closes its snapper claw. The recorded acoustic signal contains a broadband noise that consists of positive and negative pulses, but a theoretical model for single bubbles fails to reproduce the negative ones. Using a nonlinear multibubble model, we have shown here that the negative pulses can be explained by considering the interaction of microbubbles formed after the cavitation bubble has collapsed and fragmented: Positive pulses produced at the collapse of the microbubbles hit and impulsively compress neighboring microbubbles to generate reflected pulses whose amplitudes are negative. Discussing the details of the noise generation process, we have found that no negative pulses are generated if the internal pressure of the reflecting bubble is very high when hit by a positive pulse.

  11. A constructive model potential method for atomic interactions

    NASA Technical Reports Server (NTRS)

    Bottcher, C.; Dalgarno, A.

    1974-01-01

    A model potential method is presented that can be applied to many electron single centre and two centre systems. The development leads to a Hamiltonian with terms arising from core polarization that depend parametrically upon the positions of the valence electrons. Some of the terms have been introduced empirically in previous studies. Their significance is clarified by an analysis of a similar model in classical electrostatics. The explicit forms of the expectation values of operators at large separations of two atoms given by the model potential method are shown to be equivalent to the exact forms when the assumption is made that the energy level differences of one atom are negligible compared to those of the other.

  12. Interacting He and Ar atoms: Revised theoretical interaction potential, dipole moment, and collision-induced absorption spectra

    SciTech Connect

    Meyer, Wilfried; Frommhold, Lothar

    2015-09-21

    Coupled cluster quantum chemical calculations of the potential energy surface and the induced dipole surface are reported for the He–Ar van der Waals collisional complex. Spectroscopic parameters are derived from global analytical fits while an accurate value for the long-range dipole coefficient D{sub 7} is obtained by perturbation methods. Collision-induced absorption spectra are computed quantum mechanically and compared with existing measurements.

  13. Charge transfer interaction using quasiatomic minimal-basis orbitals in the effective fragment potential method

    SciTech Connect

    Xu, Peng; Gordon, Mark S.

    2013-11-21

    The charge transfer (CT) interaction, the most time-consuming term in the general effective fragment potential method, is made much more computationally efficient. This is accomplished by the projection of the quasiatomic minimal-basis-set orbitals (QUAMBOs) as the atomic basis onto the self-consistent field virtual molecular orbital (MO) space to select a subspace of the full virtual space called the valence virtual space. The diagonalization of the Fock matrix in terms of QUAMBOs recovers the canonical occupied orbitals and, more importantly, gives rise to the valence virtual orbitals (VVOs). The CT energies obtained using VVOs are generally as accurate as those obtained with the full virtual space canonical MOs because the QUAMBOs span the valence part of the virtual space, which can generally be regarded as “chemically important.” The number of QUAMBOs is the same as the number of minimal-basis MOs of a molecule. Therefore, the number of VVOs is significantly smaller than the number of canonical virtual MOs, especially for large atomic basis sets. This leads to a dramatic decrease in the computational cost.

  14. Development and validation of a sensitive solid phase extraction/hydrophilic interaction liquid chromatography/mass spectrometry method for the accurate determination of glucosamine in dog plasma.

    PubMed

    Hubert, C; Houari, S; Lecomte, F; Houbart, V; De Bleye, C; Fillet, M; Piel, G; Rozet, E; Hubert, Ph

    2010-05-01

    A sensitive and accurate LC/MS method was developed for the monitoring of glucosamine (GLcN) dog plasmatic concentration. In this scope, relatively low plasmatic concentrations of GLcN were expected, ranging from 50 to 1000 ng/mL. Liquid chromatography coupled to simple quadrupole mass spectrometry detection (LC/MS) was selected bringing the selectivity and the sensitivity needed for this application. Additionally, a solid phase extraction (SPE) step was performed to reduce matrix and ion suppression effects. Due to the ionisable character of the compound of interest, a mixed-mode strong cation exchange (Plexa PCX) disposable extraction cartridge (DEC) was selected. The separation was carried out on a Zorbax SB-CN column (5 microm, 4.6mm i.d. x 250 mm), considering hydrophilic interaction liquid chromatography (HILIC). Indeed, the mobile phase was made of methanol and 5mM ammonium hydrogen carbonate buffer at pH 7.5 (95/5, v/v). The detection was led at m/z ratios of 180.0 and 417.0, for GLcN and IS, respectively. Reliability of the results was demonstrated through the validation of the method using an approach based on the accuracy profile allowing managing the risk associated to the use of these methods in routine analysis: it is thus guaranteed that each future result will fall in the +/-30% acceptance limits with a probability of at least 90%. Successful application of the method to a preliminary pharmacokinetic study illustrated the usefulness of the method for pre-clinical studies.

  15. Neural correlates of the behavioral-autonomic interaction response to potentially threatening stimuli

    PubMed Central

    Farrow, Tom F. D.; Johnson, Naomi K.; Hunter, Michael D.; Barker, Anthony T.; Wilkinson, Iain D.; Woodruff, Peter W. R.

    2013-01-01

    Subjective assessment of emotional valence is typically associated with both brain activity and autonomic arousal. Accurately assessing emotional salience is particularly important when perceiving threat. We sought to characterize the neural correlates of the interaction between behavioral and autonomic responses to potentially threatening visual and auditory stimuli. Twenty-five healthy male subjects underwent fMRI scanning whilst skin conductance responses (SCR) were recorded. One hundred and eighty pictures, sentences, and sounds were assessed as “harmless” or “threatening.” Individuals' stimulus-locked, phasic SCRs and trial-by-trial behavioral assessments were entered as regressors into a flexible factorial design to establish their separate autonomic and behavioral neural correlates, and convolved to examine psycho-autonomic interaction (PAI) effects. Across all stimuli, “threatening,” compared with “harmless” behavioral assessments were associated with mainly frontal and precuneus activation with specific within-modality activations including bilateral parahippocampal gyri (pictures), bilateral anterior cingulate cortex (ACC) and frontal pole (sentences), and right Heschl's gyrus and bilateral temporal gyri (sounds). Across stimulus modalities SCRs were associated with activation of parieto-occipito-thalamic regions, an activation pattern which was largely replicated within-modality. In contrast, PAI analyses revealed modality-specific activations including right fusiform/parahippocampal gyrus (pictures), right insula (sentences), and mid-cingulate gyrus (sounds). Phasic SCR activity was positively correlated with an individual's propensity to assess stimuli as “threatening.” SCRs may modulate cognitive assessments on a “harmless–threatening” dimension, thereby modulating affective tone and hence behavior. PMID:23335893

  16. Experimental observation of enhanced interaction of magnetic solitons with potential barriers and wells

    NASA Astrophysics Data System (ADS)

    Demidov, Vladislav E.; Hansen, Ulf-Hendrik; Demokritov, Sergej O.

    2008-08-01

    We have studied experimentally the interaction of nonlinear packets of spin waves with strongly localized nonuniformities of the static magnetic field representing magnetic potential barriers and wells. We have found that the nonlinearity in the system causes a noticeable modification of this interaction in comparison to the linear case. The strongest modification is observed under conditions where spin-wave envelope solitons are formed. Our findings show that for the case of potential barriers the solitons demonstrate an enhanced tunneling, whereas for potential wells they show an enhanced reflection. Moreover, the nonlinear enhancement of the interaction was found to be stronger for potential wells, which was associated with its resonant character.

  17. Pharmacological potential of biogenic amine–polyamine interactions beyond neurotransmission

    PubMed Central

    Sánchez-Jiménez, F; Ruiz-Pérez, M V; Urdiales, J L; Medina, M A

    2013-01-01

    Histamine, serotonin and dopamine are biogenic amines involved in intercellular communication with multiple effects on human pathophysiology. They are products of two highly homologous enzymes, histidine decarboxylase and l-aromatic amino acid decarboxylase, and transmit their signals through different receptors and signal transduction mechanisms. Polyamines derived from ornithine (putrescine, spermidine and spermine) are mainly involved in intracellular effects related to cell proliferation and death mechanisms. This review summarizes structural and functional evidence for interactions between components of all these amine metabolic and signalling networks (decarboxylases, transporters, oxidases, receptors etc.) at cellular and tissue levels, distinct from nervous and neuroendocrine systems, where the crosstalk among these amine-related components can also have important pathophysiological consequences. The discussion highlights aspects that could help to predict and discuss the effects of intervention strategies. Linked Articles This article is part of a themed issue on Histamine Pharmacology Update. To view the other articles in this issue visit http://dx.doi.org/10.1111/bph.2013.170.issue-1 PMID:23347064

  18. Dactinomycin potentiation of radiation pneumonitis: A forgotten interaction

    SciTech Connect

    Cohen, I.J.; Loven, D.; Schoenfeld, T.; Sandbank, J.; Kaplinsky, C.; Yaniv, Y.; Jaber, L.; Zaizov, R. )

    1991-04-01

    No mention of dactinomycin potentiation of pulmonary radiation was found in a review of the literature of the past 12 years. Before that, this complication was well described and investigators had calculated that dactinomycin increased the toxic effect of lung radiation by a factor of 1.3 and reduced the radiation tolerance of the lung by at least 20%. An example of such a toxic effect is described in the treatment of a 7-year-old girl with lung metastases from Ewing's sarcoma. The chemotherapy protocol followed contained cyclophosphamide, vincristine, dactinomycin, adriamycin, cisplatinum, VP16, and radiotherapy. The treatment was associated with fatal pulmonary fibrosis following the reintroduction of dactinomycin after radiotherapy. The authors experience suggests that there is clinical significance to this complication in sarcoma therapy when dactinomycin-containing protocols are used with radiation in the treatment of pulmonary metastases. 20 references.

  19. Severe potential drug-drug interactions in older adults with dementia and associated factors

    PubMed Central

    Bogetti-Salazar, Michele; González-González, Cesar; Juárez-Cedillo, Teresa; Sánchez-García, Sergio; Rosas-Carrasco, Oscar

    2016-01-01

    OBJECTIVE: To identify the main severe potential drug-drug interactions in older adults with dementia and to examine the factors associated with these interactions. METHOD: This was a cross-sectional study. The enrolled patients were selected from six geriatrics clinics of tertiary care hospitals across Mexico City. The patients had received a clinical diagnosis of dementia based on the current standards and were further divided into the following two groups: those with severe drug-drug interactions (contraindicated/severe) (n=64) and those with non-severe drug-drug interactions (moderate/minor/absent) (n=117). Additional socio-demographic, clinical and caregiver data were included. Potential drug-drug interactions were identified using Micromedex Drug Reax 2.0® database. RESULTS: A total of 181 patients were enrolled, including 57 men (31.5%) and 124 women (68.5%) with a mean age of 80.11±8.28 years. One hundred and seven (59.1%) patients in our population had potential drug-drug interactions, of which 64 (59.81%) were severe/contraindicated. The main severe potential drug-drug interactions were caused by the combinations citalopram/anti-platelet (11.6%), clopidogrel/omeprazole (6.1%), and clopidogrel/aspirin (5.5%). Depression, the use of a higher number of medications, dementia severity and caregiver burden were the most significant factors associated with severe potential drug-drug interactions. CONCLUSIONS: Older people with dementia experience many severe potential drug-drug interactions. Anti-depressants, antiplatelets, anti-psychotics and omeprazole were the drugs most commonly involved in these interactions. Despite their frequent use, anti-dementia drugs were not involved in severe potential drug-drug interactions. The number and type of medications taken, dementia severity and depression in patients in addition to caregiver burden should be considered to avoid possible drug interactions in this population. PMID:26872079

  20. Orchid-pollinator interactions and potential vulnerability to biological invasion.

    PubMed

    Chupp, Adam D; Battaglia, Loretta L; Schauber, Eric M; Sipes, Sedonia D

    2015-01-01

    an indirect threat to plant-pollinator interactions. PMID:26286221

  1. Evaluation of a Potential Clinical Interaction between Ceftriaxone and Calcium▿

    PubMed Central

    Steadman, Emily; Raisch, Dennis W.; Bennett, Charles L.; Esterly, John S.; Becker, Tischa; Postelnick, Michael; McKoy, June M.; Trifilio, Steve; Yarnold, Paul R.; Scheetz, Marc H.

    2010-01-01

    In April 2009, the FDA retracted a warning asserting that ceftriaxone and intravenous calcium products should not be coadministered to any patient to prevent precipitation events leading to end-organ damage. Following that announcement, we sought to evaluate if the retraction was justified. A search of the FDA Adverse Event Reporting System was conducted to identify any ceftriaxone-calcium interactions that resulted in serious adverse drug events. Ceftazidime-calcium was used as a comparator agent. One hundred four events with ceftriaxone-calcium and 99 events with ceftazidime-calcium were identified. Adverse drug events were recorded according to the listed description of drug involvement (primary or secondary suspect) and were interpreted as probable, possible, unlikely, or unrelated. For ceftriaxone-calcium-related adverse events, 7.7% and 20.2% of the events were classified as probable and possible for embolism, respectively. Ceftazidime-calcium resulted in fewer probable embolic events (4%) but more possible embolic events (30.3%). Among cases that considered ceftriaxone or ceftazidime and calcium as the primary or secondary drug, one case was classified as a probable embolic event. That patient received ceftriaxone-calcium and died, although an attribution of causality was not possible. Our analysis suggests a lack of support for the occurrence of ceftriaxone-calcium precipitation events in adults. The results of the current analysis reinforce the revised FDA recommendations suggesting that patients >28 days old may receive ceftriaxone and calcium sequentially and provide a transparent and reproducible methodology for such evaluations. PMID:20086152

  2. Orchid-pollinator interactions and potential vulnerability to biological invasion.

    PubMed

    Chupp, Adam D; Battaglia, Loretta L; Schauber, Eric M; Sipes, Sedonia D

    2015-08-17

    an indirect threat to plant-pollinator interactions.

  3. Orchid–pollinator interactions and potential vulnerability to biological invasion

    PubMed Central

    Chupp, Adam D.; Battaglia, Loretta L.; Schauber, Eric M.; Sipes, Sedonia D.

    2015-01-01

    an indirect threat to plant–pollinator interactions. PMID:26286221

  4. Cold NH–NH collisions in a magnetic field: Basis set convergence versus sensitivity to the interaction potential

    NASA Astrophysics Data System (ADS)

    Suleimanov, Yu V.; Tscherbul, Timur V.

    2016-10-01

    We explore the combined effect of the uncertainties due to the interaction potential and basis set convergence on low-temperature collisional properties of spin-polarized NH molecules in a magnetic field. We show that quantum scattering calculations with different rotational basis sets and λ-scaled interaction potentials produce qualitatively different ratios of elastic to inelastic cross sections for collision energies above 10‑3 cm‑1, leading to favorable (unfavorable) prospects for sympathetic cooling of NH molecules depending on the basis set cutoff parameter {N}{{\\max }}. The physical reason behind this effect is that the resonance widths, which determine the maximum variation of the scattering cross sections with λ, tend to depend strongly on {N}{{\\max }}. At ultralow collision energies, all basis sets produce highly uncertain (and statistically indistinguishable) elastic and inelastic cross sections; however, their ratio γ is much less sensitive to small variations of the interaction potential. Our results highlight the importance of basis set convergence in quantum scattering calculations and establish the existence of parameter regimes where unconverged calculations can still be used to make qualitatively accurate predictions of scattering observables.

  5. Insights in the electronic structure and redox reaction energy in LiFePO{sub 4} battery material from an accurate Tran-Blaha modified Becke Johnson potential

    SciTech Connect

    Araujo, Rafael B.; Almeida, J. de S; Ferreira da Silva, A.; Ahuja, Rajeev

    2015-09-28

    The main goals of this paper are to investigate the accuracy of the Tran-Blaha modified Becke Johnson (TB-mBJ) potential to predict the electronic structure of lithium iron phosphate and the related redox reaction energy with the lithium deintercalation process. The computed electronic structures show that the TB-mBJ method is able to partially localize Fe-3d electrons in LiFePO{sub 4} and FePO{sub 4} which usually is a problem for the generalized gradient approximation (GGA) due to the self interaction error. The energy band gap is also improved by the TB-mBJ calculations in comparison with the GGA results. It turned out, however, that the redox reaction energy evaluated by the TB-mBJ technique is not in good agreement with the measured one. It is speculated that this disagreement in the computed redox energy and the experimental value is due to the lack of a formal expression to evaluate the exchange and correlation energy. Therefore, the TB-mBJ is an efficient method to improve the prediction of the electronic structures coming form the standard GGA functional in LiFePO{sub 4} and FePO{sub 4}. However, it does not appear to have the same efficiency for evaluating the redox reaction energies for the investigated system.

  6. MULTIMODE quantum calculations of vibrational energies and IR spectrum of the NO{sup +}(H{sub 2}O) cluster using accurate potential energy and dipole moment surfaces

    SciTech Connect

    Homayoon, Zahra

    2014-09-28

    A new, full (nine)-dimensional potential energy surface and dipole moment surface to describe the NO{sup +}(H{sub 2}O) cluster is reported. The PES is based on fitting of roughly 32 000 CCSD(T)-F12/aug-cc-pVTZ electronic energies. The surface is a linear least-squares fit using a permutationally invariant basis with Morse-type variables. The PES is used in a Diffusion Monte Carlo study of the zero-point energy and wavefunction of the NO{sup +}(H{sub 2}O) and NO{sup +}(D{sub 2}O) complexes. Using the calculated ZPE the dissociation energies of the clusters are reported. Vibrational configuration interaction calculations of NO{sup +}(H{sub 2}O) and NO{sup +}(D{sub 2}O) using the MULTIMODE program are performed. The fundamental, a number of overtone, and combination states of the clusters are reported. The IR spectrum of the NO{sup +}(H{sub 2}O) cluster is calculated using 4, 5, 7, and 8 modes VSCF/CI calculations. The anharmonic, coupled vibrational calculations, and IR spectrum show very good agreement with experiment. Mode coupling of the water “antisymmetric” stretching mode with the low-frequency intermolecular modes results in intensity borrowing.

  7. Accurate ab initio potential energy surface, thermochemistry, and dynamics of the F- + CH3F SN2 and proton-abstraction reactions

    NASA Astrophysics Data System (ADS)

    Szabó, István; Telekes, Hajnalka; Czakó, Gábor

    2015-06-01

    We develop a full-dimensional global analytical potential energy surface (PES) for the F- + CH3F reaction by fitting about 50 000 energy points obtained by an explicitly correlated composite method based on the second-order Møller-Plesset perturbation-F12 and coupled-cluster singles, doubles, and perturbative triples-F12a methods and the cc-pVnZ-F12 [n = D, T] basis sets. The PES accurately describes the (a) back-side attack Walden inversion mechanism involving the pre- and post-reaction (b) ion-dipole and (c) hydrogen-bonded complexes, the configuration-retaining (d) front-side attack and (e) double-inversion substitution pathways, as well as (f) the proton-abstraction channel. The benchmark quality relative energies of all the important stationary points are computed using the focal-point analysis (FPA) approach considering electron correlation up to coupled-cluster singles, doubles, triples, and perturbative quadruples method, extrapolation to the complete basis set limit, core-valence correlation, and scalar relativistic effects. The FPA classical(adiabatic) barrier heights of (a), (d), and (e) are -0.45(-0.61), 46.07(45.16), and 29.18(26.07) kcal mol-1, respectively, the dissociation energies of (b) and (c) are 13.81(13.56) and 13.73(13.52) kcal mol-1, respectively, and the endothermicity of (f) is 42.54(38.11) kcal mol-1. Quasiclassical trajectory computations of cross sections, scattering (θ) and initial attack (α) angle distributions, as well as translational and internal energy distributions are performed for the F- + CH3F(v = 0) reaction using the new PES. Apart from low collision energies (Ecoll), the SN2 excitation function is nearly constant, the abstraction cross sections rapidly increase with Ecoll from a threshold of ˜40 kcal mol-1, and retention trajectories via double inversion are found above Ecoll = ˜ 30 kcal mol-1, and at Ecoll = ˜ 50 kcal mol-1, the front-side attack cross sections start to increase very rapidly. At low Ecoll, the

  8. Accurate ab initio potential energy surface, thermochemistry, and dynamics of the F(-) + CH3F SN2 and proton-abstraction reactions.

    PubMed

    Szabó, István; Telekes, Hajnalka; Czakó, Gábor

    2015-06-28

    We develop a full-dimensional global analytical potential energy surface (PES) for the F(-) + CH3F reaction by fitting about 50 000 energy points obtained by an explicitly correlated composite method based on the second-order Møller-Plesset perturbation-F12 and coupled-cluster singles, doubles, and perturbative triples-F12a methods and the cc-pVnZ-F12 [n = D, T] basis sets. The PES accurately describes the (a) back-side attack Walden inversion mechanism involving the pre- and post-reaction (b) ion-dipole and (c) hydrogen-bonded complexes, the configuration-retaining (d) front-side attack and (e) double-inversion substitution pathways, as well as (f) the proton-abstraction channel. The benchmark quality relative energies of all the important stationary points are computed using the focal-point analysis (FPA) approach considering electron correlation up to coupled-cluster singles, doubles, triples, and perturbative quadruples method, extrapolation to the complete basis set limit, core-valence correlation, and scalar relativistic effects. The FPA classical(adiabatic) barrier heights of (a), (d), and (e) are -0.45(-0.61), 46.07(45.16), and 29.18(26.07) kcal mol(-1), respectively, the dissociation energies of (b) and (c) are 13.81(13.56) and 13.73(13.52) kcal mol(-1), respectively, and the endothermicity of (f) is 42.54(38.11) kcal mol(-1). Quasiclassical trajectory computations of cross sections, scattering (θ) and initial attack (α) angle distributions, as well as translational and internal energy distributions are performed for the F(-) + CH3F(v = 0) reaction using the new PES. Apart from low collision energies (Ecoll), the SN2 excitation function is nearly constant, the abstraction cross sections rapidly increase with Ecoll from a threshold of ∼40 kcal mol(-1), and retention trajectories via double inversion are found above Ecoll = ∼ 30 kcal mol(-1), and at Ecoll = ∼ 50 kcal mol(-1), the front-side attack cross sections start to increase very rapidly. At

  9. Ab initio wavenumber accurate spectroscopy : {sup 1}CH{sub 2} and HCN vibrational levels on automatically generated IMLS potential energy surfaces.

    SciTech Connect

    Dawes, R.; Wagner, A. F.; Thompson, D. L.; Chemical Sciences and Engineering Division; Univ. of Missouri at Columbia

    2009-04-23

    We report here calculated J = 0 vibrational frequencies for {sup 1}CH{sub 2} and HCN with root-mean-square error relative to available measurements of 2.0 cm{sup -1} and 3.2 cm{sup -1}, respectively. These results are obtained with DVR calculations with a dense grid on ab initio potential energy surfaces (PESs). The ab initio electronic structure calculations employed are Davidson-corrected MRCI calculations with double-, triple-, and quadruple-{zeta} basis sets extrapolated to the complete basis set (CBS) limit. In the {sup 1}CH{sub 2} case, Full CI tests of the Davidson correction at small basis set levels lead to a scaling of the correction with the bend angle that can be profitably applied at the CBS limit. Core-valence corrections are added derived from CCSD(T) calculations with and without frozen cores. Relativistic and non-Born-Oppenheimer corrections are available for HCN and were applied. CBS limit CCSD(T) and CASPT2 calculations with the same basis sets were also tried for HCN. The CCSD(T) results are noticeably less accurate than the MRCI results while the CASPT2 results are much poorer. The PESs were generated automatically using the local interpolative moving least-squares method (L-IMLS). A general triatomic code is described where the L-IMLS method is interfaced with several common electronic structure packages. All PESs were computed with this code running in parallel on eight processors. The L-IMLS method provides global and local fitting error measures important in automatically growing the PES from initial ab initio seed points. The reliability of this approach was tested for {sup 1}CH{sub 2} by comparing DVR-calculated vibrational levels on an L-IMLS ab initio surface with levels generated by an explicit ab initio calculation at each DVR grid point. For all levels ({approx}200) below 20000 cm{sup -1}, the mean unsigned difference between the levels of these two calculations was 0.1 cm{sup -1}, consistent with the L-IMLS estimated mean unsigned

  10. Accurate ab initio potential energy surface, thermochemistry, and dynamics of the F(-) + CH3F SN2 and proton-abstraction reactions.

    PubMed

    Szabó, István; Telekes, Hajnalka; Czakó, Gábor

    2015-06-28

    We develop a full-dimensional global analytical potential energy surface (PES) for the F(-) + CH3F reaction by fitting about 50 000 energy points obtained by an explicitly correlated composite method based on the second-order Møller-Plesset perturbation-F12 and coupled-cluster singles, doubles, and perturbative triples-F12a methods and the cc-pVnZ-F12 [n = D, T] basis sets. The PES accurately describes the (a) back-side attack Walden inversion mechanism involving the pre- and post-reaction (b) ion-dipole and (c) hydrogen-bonded complexes, the configuration-retaining (d) front-side attack and (e) double-inversion substitution pathways, as well as (f) the proton-abstraction channel. The benchmark quality relative energies of all the important stationary points are computed using the focal-point analysis (FPA) approach considering electron correlation up to coupled-cluster singles, doubles, triples, and perturbative quadruples method, extrapolation to the complete basis set limit, core-valence correlation, and scalar relativistic effects. The FPA classical(adiabatic) barrier heights of (a), (d), and (e) are -0.45(-0.61), 46.07(45.16), and 29.18(26.07) kcal mol(-1), respectively, the dissociation energies of (b) and (c) are 13.81(13.56) and 13.73(13.52) kcal mol(-1), respectively, and the endothermicity of (f) is 42.54(38.11) kcal mol(-1). Quasiclassical trajectory computations of cross sections, scattering (θ) and initial attack (α) angle distributions, as well as translational and internal energy distributions are performed for the F(-) + CH3F(v = 0) reaction using the new PES. Apart from low collision energies (Ecoll), the SN2 excitation function is nearly constant, the abstraction cross sections rapidly increase with Ecoll from a threshold of ∼40 kcal mol(-1), and retention trajectories via double inversion are found above Ecoll = ∼ 30 kcal mol(-1), and at Ecoll = ∼ 50 kcal mol(-1), the front-side attack cross sections start to increase very rapidly. At

  11. An isotopic-independent highly accurate potential energy surface for CO2 isotopologues and an initial (12)C(16)O2 infrared line list.

    PubMed

    Huang, Xinchuan; Schwenke, David W; Tashkun, Sergey A; Lee, Timothy J

    2012-03-28

    An isotopic-independent, highly accurate potential energy surface (PES) has been determined for CO(2) by refining a purely ab initio PES with selected, purely experimentally determined rovibrational energy levels. The purely ab initio PES is denoted Ames-0, while the refined PES is denoted Ames-1. Detailed tests are performed to demonstrate the spectroscopic accuracy of the Ames-1 PES. It is shown that Ames-1 yields σ(rms) (root-mean-squares error) = 0.0156 cm(-1) for 6873 J = 0-117 (12)C(16)O(2) experimental energy levels, even though less than 500 (12)C(16)O(2) energy levels were included in the refinement procedure. It is also demonstrated that, without any additional refinement, Ames-1 yields very good agreement for isotopologues. Specifically, for the (12)C(16)O(2) and (13)C(16)O(2) isotopologues, spectroscopic constants G(v) computed from Ames-1 are within ±0.01 and 0.02 cm(-1) of reliable experimentally derived values, while for the (16)O(12)C(18)O, (16)O(12)C(17)O, (16)O(13)C(18)O, (16)O(13)C(17)O, (12)C(18)O(2), (17)O(12)C(18)O, (12)C(17)O(2), (13)C(18)O(2), (13)C(17)O(2), (17)O(13)C(18)O, and (14)C(16)O(2) isotopologues, the differences are between ±0.10 and 0.15 cm(-1). To our knowledge, this is the first time a polyatomic PES has been refined using such high J values, and this has led to new challenges in the refinement procedure. An initial high quality, purely ab initio dipole moment surface (DMS) is constructed and used to generate a 296 K line list. For most bands, experimental IR intensities are well reproduced for (12)C(16)O(2) using Ames-1 and the DMS. For more than 80% of the bands, the experimental intensities are reproduced with σ(rms)(ΔI) < 20% or σ(rms)(ΔI∕δ(obs)) < 5. A few exceptions are analyzed and discussed. Directions for future improvements are discussed, though it is concluded that the current Ames-1 and the DMS should be useful in analyzing and assigning high-resolution laboratory or astronomical spectra. PMID:22462861

  12. Phase transition of strongly interacting matter with a chemical potential dependent Polyakov loop potential

    NASA Astrophysics Data System (ADS)

    Shao, Guo-yun; Tang, Zhan-duo; Di Toro, Massimo; Colonna, Maria; Gao, Xue-yan; Gao, Ning

    2016-07-01

    We construct a hadron-quark two-phase model based on the Walecka-quantum hadrodynamics and the improved Polyakov-Nambu-Jona-Lasinio (PNJL) model with an explicit chemical potential dependence of Polyakov loop potential (μ PNJL model). With respect to the original PNJL model, the confined-deconfined phase transition is largely affected at low temperature and large chemical potential. Using the two-phase model, we investigate the equilibrium transition between hadronic and quark matter at finite chemical potentials and temperatures. The numerical results show that the transition boundaries from nuclear to quark matter move towards smaller chemical potential (lower density) when the μ -dependent Polyakov loop potential is taken. In particular, for charge asymmetric matter, we compute the local asymmetry of u , d quarks in the hadron-quark coexisting phase, and analyze the isospin-relevant observables possibly measurable in heavy-ion collision (HIC) experiments. In general new HIC data on the location and properties of the mixed phase would bring relevant information on the expected chemical potential dependence of the Polyakov loop contribution.

  13. Potential Energy Curves and Transport Properties for the Interaction of He with Other Ground-state Atoms

    NASA Technical Reports Server (NTRS)

    Partridge, Harry; Stallcop, James R.; Levin, Eugene; Arnold, Jim (Technical Monitor)

    2001-01-01

    The interactions of a He atom with a heavier atom are examined for 26 different elements, which are consecutive members selected from three rows (Li - Ne, Na - Ar, and K,Ca, Ga - Kr) and column 12 (Zn,Cd) of the periodic table. Interaction energies are determined wing high-quality ab initio calculations for the states of the molecule that would be formed from each pair of atoms in their ground states. Potential energies are tabulated for a broad range of Interatomic separation distances. The results show, for example, that the energy of an alkali interaction at small separations is nearly the same as that of a rare-gas interaction with the same electron configuration for the dosed shells. Furthermore, the repulsive-range parameter for this region is very short compared to its length for the repulsion dominated by the alkali-valence electron at large separations (beyond about 3-4 a(sub 0)). The potential energies in the region of the van der Waals minimum agree well with the most accurate results available. The ab initio energies are applied to calculate scattering cross sections and obtain the collision integrals that are needed to determine transport properties to second order. The theoretical values of Li-He total scattering cross sections and the rare-gas atom-He transport properties agree well (to within about 1%) with the corresponding measured data. Effective potential energies are constructed from the ab initio energies; the results have been shown to reproduce known transport data and can be readily applied to predict unknown transport properties for like-atom interactions.

  14. An accurate full-dimensional potential energy surface for H-Au(111): Importance of nonadiabatic electronic excitation in energy transfer and adsorption.

    PubMed

    Janke, Svenja M; Auerbach, Daniel J; Wodtke, Alec M; Kandratsenka, Alexander

    2015-09-28

    We have constructed a potential energy surface (PES) for H-atoms interacting with fcc Au(111) based on fitting the analytic form of the energy from Effective Medium Theory (EMT) to ab initio energy values calculated with density functional theory. The fit used input from configurations of the H-Au system with Au atoms at their lattice positions as well as configurations with the Au atoms displaced from their lattice positions. It reproduces the energy, in full dimension, not only for the configurations used as input but also for a large number of additional configurations derived from ab initio molecular dynamics (AIMD) trajectories at finite temperature. Adiabatic molecular dynamics simulations on this PES reproduce the energy loss behavior of AIMD. EMT also provides expressions for the embedding electron density, which enabled us to develop a self-consistent approach to simulate nonadiabatic electron-hole pair excitation and their effect on the motion of the incident H-atoms. For H atoms with an energy of 2.7 eV colliding with Au, electron-hole pair excitation is by far the most important energy loss pathway, giving an average energy loss ≈3 times that of the adiabatic case. This increased energy loss enhances the probability of the H-atom remaining on or in the Au slab by a factor of 2. The most likely outcome for H-atoms that are not scattered also depends prodigiously on the energy transfer mechanism; for the nonadiabatic case, more than 50% of the H-atoms which do not scatter are adsorbed on the surface, while for the adiabatic case more than 50% pass entirely through the 4 layer simulation slab.

  15. An accurate full-dimensional potential energy surface for H–Au(111): Importance of nonadiabatic electronic excitation in energy transfer and adsorption

    SciTech Connect

    Janke, Svenja M.; Auerbach, Daniel J.; Kandratsenka, Alexander; Wodtke, Alec M.

    2015-09-28

    We have constructed a potential energy surface (PES) for H-atoms interacting with fcc Au(111) based on fitting the analytic form of the energy from Effective Medium Theory (EMT) to ab initio energy values calculated with density functional theory. The fit used input from configurations of the H–Au system with Au atoms at their lattice positions as well as configurations with the Au atoms displaced from their lattice positions. It reproduces the energy, in full dimension, not only for the configurations used as input but also for a large number of additional configurations derived from ab initio molecular dynamics (AIMD) trajectories at finite temperature. Adiabatic molecular dynamics simulations on this PES reproduce the energy loss behavior of AIMD. EMT also provides expressions for the embedding electron density, which enabled us to develop a self-consistent approach to simulate nonadiabatic electron-hole pair excitation and their effect on the motion of the incident H-atoms. For H atoms with an energy of 2.7 eV colliding with Au, electron-hole pair excitation is by far the most important energy loss pathway, giving an average energy loss ≈3 times that of the adiabatic case. This increased energy loss enhances the probability of the H-atom remaining on or in the Au slab by a factor of 2. The most likely outcome for H-atoms that are not scattered also depends prodigiously on the energy transfer mechanism; for the nonadiabatic case, more than 50% of the H-atoms which do not scatter are adsorbed on the surface, while for the adiabatic case more than 50% pass entirely through the 4 layer simulation slab.

  16. Student Interactions with CD-ROM Storybooks: A Look at Potential Relationships between Multiple Intelligence Strengths and Levels of Interaction

    ERIC Educational Resources Information Center

    Huffman, Celia A.

    2012-01-01

    This study looked at the potential relationship that may exist between students' intelligence strengths, in particular their spatial and kinesthetic strengths, and their combined cognitive and metacognitive levels of interaction with a CD-ROM storybook. The multiple intelligence strengths of a sample of students, measured via the MIDAS/My…

  17. Kirkwood-Buff Integrals for Aqueous Urea Solutions Based upon the Quantum Chemical Electrostatic Potential and Interaction Energies.

    PubMed

    Chiba, Shuntaro; Furuta, Tadaomi; Shimizu, Seishi

    2016-08-11

    Cosolvents, such as urea, affect protein folding and binding, and the solubility of solutes. The modeling of cosolvents has been facilitated significantly by the rigorous Kirkwood-Buff (KB) theory of solutions, which can describe structural thermodynamics over the entire composition range of aqueous cosolvent mixtures based only on the solution density and the KB integrals (KBIs), i.e., the net excess radial distribution functions from the bulk. Using KBIs to describe solution thermodynamics has given rise to a clear guideline that an accurate prediction of KBIs is equivalent to accurate modeling of cosolvents. Taking urea as an example, here we demonstrate that an improvement in the prediction of KBIs comes from an improved reproduction of high-level quantum chemical (QC) electrostatic potential and molecular pairwise interaction energies. This rational approach to the improvement of the KBI prediction stems from a comparison of existing force fields, AMOEBA, and the generalized AMBER force field, as well as the further optimization of the former to enable better agreement with QC interaction energies. Such improvements would pave the way toward a rational and systematic determination of the transferable force field parameters for a number of important small molecule cosolvents. PMID:27434200

  18. Potential of the neutron lloyd's mirror interferometer for the search for new interactions

    SciTech Connect

    Pokotilovski, Yu. N.

    2013-04-15

    We discuss the potential of the neutron Lloyd's mirror interferometer in a search for new interactions at small scales. We consider three hypothetical interactions that may be tested using the interferometer. The chameleon scalar field proposed to solve the enigma of accelerating expansion of the Universe produces interaction between particles and matter. The axion-like spin-dependent coupling between a neutron and nuclei or/and electrons may result in a P- and T-noninvariant interaction with matter. Hypothetical non-Newtonian gravitational interactions mediates an additional short-range potential between neutrons and bulk matter. These interactions between the neutron and the mirror of a Lloyd-type neutron interferometer cause a phase shift of neutron waves. We estimate the sensitivity and systematic effects of possible experiments.

  19. Ab initio Potential-Energy Surfaces and Electron-Spin-Exchange Cross Sections for H-O2 Interactions

    NASA Technical Reports Server (NTRS)

    Stallcop, James R.; Partridge, Harry; Levin, Eugene

    1996-01-01

    Accurate quartet- and doublet-state potential-energy surfaces for the interaction of a hydrogen atom and an oxygen molecule in their ground states have been determined from an ab initio calculation using large-basis sets and the internally contracted multireference configuration interaction method. These potential surfaces have been used to calculate the H-O2 electron-spin-exchange cross section; the square root of the cross section (in a(sub 0)), not taking into account inelastic effects, can be obtained approximately from the expressions 2.390E(sup -1/6) and 5.266-0.708 log10(E) at low and high collision energies E (in E(sub h)), respectively. These functional forms, as well as the oscillatory structure of the cross section found at high energies, are expected from the nature of the interaction energy. The mean cross section (the cross section averaged over a Maxwellian velocity distribution) agrees reasonably well with the results of measurements.

  20. Spin-polarized Rb2 interacting with bosonic He atoms: potential energy surface and quantum structures of small clusters.

    PubMed

    Rodríguez-Cantano, R; López-Durán, David; González-Lezana, T; Delgado-Barrio, G; Villarreal, P; Yurtsever, E; Gianturco, F A

    2012-03-15

    A new full-dimension potential energy surface of the three-body He-Rb₂(³Σ(u)(+)) complex and a quantum study of small (⁴He)(N)-Rb₂(³Σ(u)(+)) clusters, 1 ≤ N ≤ 4, are presented. We have accurately fitted the ab initio points of the interaction to an analytical form and addressed the dopant's vibration, which is found to be negligible. A Variational approach and a Diffusion Monte Carlo technique have been applied to yield energy and geometric properties of the selected species. Our quantum structure calculations show a transition in the arrangements of the helium atoms from N = 2, where they tend to be separated across the diatomic bond, to N = 4, in which a closer packing of the rare gas particles is reached, guided by the dominance of the He-He potential over the weaker interaction of the latter adatoms with the doping dimer. The deepest well of the He-Rb₂ interaction is placed at the T-shape configuration, a feature which causes the dopant to be located as parallel to the helium "minidroplet". Our results are shown to agree with previous findings on this and on similar systems.

  1. Peculiar features of the interaction potential between hydrogen and antihydrogen at intermediate separations

    SciTech Connect

    Lee, Teck G; Wong, Cheuk-Yin; Wang, Lee-Shien

    2008-01-01

    This paper evaluates the interaction potential between a hydrogen and an antihydrogen using the second-order perturbation theory within the framework of the four-body system in a separable two-body basis. It finds that the H interaction potential possesses the peculiar features of a shallow local minimum located around interatomic separations of r ~ 6 a.u. and a barrier rising at r 5 a.u.

  2. Susceptibility based upon Chemical Interaction with Disease Processes: Potential Implications for Risk Assessment

    EPA Science Inventory

    One of the challenges facing toxicology and risk assessment is that numerous host and environmental factors may modulate vulnerability and risk. An area of increasing interest is the potential for chemicals to interact with background aging and disease processes, an interaction...

  3. Potential-derived point-charge model study of electrostatic interaction energies in some hydrogen-bonded systems.

    PubMed

    Ray, N K; Shibata, M; Bolis, G; Rein, R

    1985-01-01

    Mulliken's atomic changes (MC) and potential derived (PD) point charges obtained from STO-3G wave functions are used to study the electrostatic interaction energies for a series of representative hydrogen-bonded complexes. The results of the above-mentioned models are compared with the more accurate results of segmental multipole moment (SMM) expansion, and it is shown that the PD model is superior to the MC model. The results of PD model are shown to be well correlated with the results of SMM expansion technique. Results of our calculations using 6-31G and 6-31G** PD charges are also reported here. Electrostatic interaction energies obtained using 6-31G** PD charges are compared with the 6-31G** SCF interaction energies available for the nine hydrogen-bonded dimers of ammonia, water, and hydrogen fluoride and a good correlation between the two is shown. The interrelationship between the results of different basis sets are also examined for the PD point-charge model. The electrostatic interaction energies obtained using STO-3G PD model are shown to be well correlated to the results of 6-31G and 6-31G** PD models.

  4. Double Folding Potential of Different Interaction Models for 16O + 12C Elastic Scattering

    NASA Astrophysics Data System (ADS)

    Hamada, Sh.; Bondok, I.; Abdelmoatmed, M.

    2016-08-01

    The elastic scattering angular distributions for 16O + 12C nuclear system have been analyzed using double folding potential of different interaction models: CDM3Y1, CDM3Y6, DDM3Y1 and BDM3Y1. We have extracted the renormalization factor N r for the different concerned interaction models. Potential created by BDM3Y1 model of interaction has the shallowest depth which reflects the necessity to use higher renormalization factor. The experimental angular distributions for 16O + 12C nuclear system in the energy range 115.9-230 MeV exhibited unmistakable refractive features and rainbow phenomenon.

  5. A note on the binary interaction potential in complex (dusty) plasmas

    SciTech Connect

    Khrapak, S. A.; Morfill, G. E.

    2008-08-15

    The effect of ion-neutral collisions on the potential of interaction between a pair of negatively charged grains in isotropic weakly collisional plasmas is investigated. Two interaction mechanisms are considered: Electric repulsion between like-charged grains and attraction due to the so-called ''ion shadow'' effect. It is demonstrated that in the presence of collisions, both interaction potentials exhibit Coulomb-like {proportional_to}r{sup -1} decay at large distances. A necessary condition for the existence of long-range attraction is derived. The obtained results are then used to reconsider the possibility of liquid-vapor critical point occurrence in complex plasmas.

  6. Evaluation of comprehensive two-dimensional gas chromatography with accurate mass time-of-flight mass spectrometry for the metabolic profiling of plant-fungus interaction in Aquilaria malaccensis.

    PubMed

    Wong, Yong Foo; Chin, Sung-Tong; Perlmutter, Patrick; Marriott, Philip J

    2015-03-27

    To explore the possible obligate interactions between the phytopathogenic fungus and Aquilaria malaccensis which result in generation of a complex array of secondary metabolites, we describe a comprehensive two-dimensional gas chromatography (GC × GC) method, coupled to accurate mass time-of-flight mass spectrometry (TOFMS) for the untargeted and comprehensive metabolic profiling of essential oils from naturally infected A. malaccensis trees. A polar/non-polar column configuration was employed, offering an improved separation pattern of components when compared to other column sets. Four different grades of the oils displayed quite different metabolic patterns, suggesting the evolution of a signalling relationship between the host tree (emergence of various phytoalexins) and fungi (activation of biotransformation). In total, ca. 550 peaks/metabolites were detected, of which tentative identification of 155 of these compounds was reported, representing between 20.1% and 53.0% of the total ion count. These are distributed over the chemical families of monoterpenic and sesquiterpenic hydrocarbons, oxygenated monoterpenes and sesquiterpenes (comprised of ketone, aldehyde, oxide, alcohol, lactone, keto-alcohol and diol), norterpenoids, diterpenoids, short chain glycols, carboxylic acids and others. The large number of metabolites detected, combined with the ease with which they are located in the 2D separation space, emphasises the importance of a comprehensive analytical approach for the phytochemical analysis of plant metabolomes. Furthermore, the potential of this methodology in grading agarwood oils by comparing the obtained metabolic profiles (pattern recognition for unique metabolite chemical families) is discussed. The phytocomplexity of the agarwood oils signified the production of a multitude of plant-fungus mediated secondary metabolites as chemical signals for natural ecological communication. To the best of our knowledge, this is the most complete

  7. Potential drug interaction between Rho(D) immune globulin and live virus vaccine.

    PubMed

    Holmes, Amy; Wright, Debra

    2014-12-01

    Women often receive Rho(D) immune globulin as well as a live virus vaccine in the immediate postpartum period. The immune globulin product has the potential to interfere with appropriate immune response to the vaccine. Here we describe our approach to identifying and following up on this often overlooked potential drug interaction. PMID:25495973

  8. Potential drug interaction between Rho(D) immune globulin and live virus vaccine.

    PubMed

    Holmes, Amy; Wright, Debra

    2014-12-01

    Women often receive Rho(D) immune globulin as well as a live virus vaccine in the immediate postpartum period. The immune globulin product has the potential to interfere with appropriate immune response to the vaccine. Here we describe our approach to identifying and following up on this often overlooked potential drug interaction.

  9. Collisional interactions between self-interacting nonrelativistic boson stars: Effective potential analysis and numerical simulations

    NASA Astrophysics Data System (ADS)

    Cotner, Eric

    2016-09-01

    Scalar particles are a common prediction of many beyond the Standard Model theories. If they are light and cold enough, there is a possibility they may form Bose-Einstein condensates, which will then become gravitationally bound. These boson stars are solitonic solutions to the Einstein-Klein-Gordon equations but may be approximated in the nonrelativistic regime with a coupled Schrödinger-Poisson system. General properties of single soliton states are derived, including the possibility of quartic self-interactions. Binary collisions between two solitons are then studied, and the effects of different mass ratios, relative phases, self-couplings, and separation distances are characterized, leading to an easy conceptual understanding of how these parameters affect the collision outcome in terms of conservation of energy. Applications to dark matter are discussed.

  10. Homology-Based Prediction of Potential Protein–Protein Interactions between Human Erythrocytes and Plasmodium falciparum

    PubMed Central

    Ramakrishnan, Gayatri; Srinivasan, Narayanaswamy; Padmapriya, Ponnan; Natarajan, Vasant

    2015-01-01

    Plasmodium falciparum, a causative agent of malaria, is a well-characterized obligate intracellular parasite known for its ability to remodel host cells, particularly erythrocytes, to successfully persist in the host environment. However, the current levels of understanding from the laboratory experiments on the host–parasite interactions and the strategies pursued by the parasite to remodel host erythrocytes are modest. Several computational means developed in the recent past to predict host–parasite/pathogen interactions have generated testable hypotheses on feasible protein–protein interactions. We demonstrate the utility of protein structure-based protocol in the recognition of potential interacting proteins across P. falciparum and host erythrocytes. In concert with the information on the expression and subcellular localization of host and parasite proteins, we have identified 208 biologically feasible interactions potentially brought about by 59 P. falciparum and 30 host erythrocyte proteins. For selected cases, we have evaluated the physicochemical viability of the predicted interactions in terms of surface complementarity, electrostatic complementarity, and interaction energies at protein interface regions. Such careful inspection of molecular and mechanistic details generates high confidence on the predicted host–parasite protein–protein interactions. The predicted host–parasite interactions generate many experimentally testable hypotheses that can contribute to the understanding of possible mechanisms undertaken by the parasite in host erythrocyte remodeling. Thus, the key protein players recognized in P. falciparum can be explored for their usefulness as targets for chemotherapeutic intervention. PMID:26740742

  11. Constraining density functional approximations to yield self-interaction free potentials.

    PubMed

    Gidopoulos, Nikitas I; Lathiotakis, Nektarios N

    2012-06-14

    Self-interactions (SIs) are a major problem in density functional approximations and the source of serious divergence from experimental results. Here, we propose to optimize density functional total energies in terms of the effective local potential, under constraints for the effective potential that guarantee it is free from SI errors and consequently asymptotically correct. More specifically, we constrain the Hartree, exchange and correlation potential to be the electrostatic potential of a non-negative effective repulsive density of N - 1 electrons. In this way, the optimal effective potentials exhibit the correct asymptotic decay, resulting in significantly improved one-electron properties. PMID:22713038

  12. Interaction networks in coastal soft-sediments highlight the potential for change in ecological resilience.

    PubMed

    Thrush, S F; Hewitt, J E; Lohrer, A M

    2012-06-01

    Recent studies emphasize the role of indirect relationships and feedback loops in maintaining ecosystem resilience. Environmental changes that impact on the organisms involved in these processes have the potential to initiate threshold responses and fundamentally shift the interactions within an ecosystem. However, empirical studies are hindered by the difficulty of designing appropriate manipulative experiments to capture this complexity. Here we employ structural equation modeling to define and test the architecture of ecosystem interaction networks. Using survey data from 19 estuaries we investigate the interactions between biological (abundance of large bioturbating macrofauna, microphytobenthos, and detrital matter) and physical (sediment grain size) processes. We assess the potential for abrupt changes in the architecture of the network and the strength of interactions to occur across environmental gradients. Our analysis identified a potential threshold in the relationship between sediment mud content and benthic chlorophyll a, at -12 microg/g, using quantile regression. Below this threshold, the interaction network involved different variables and fewer feedbacks than above. This approach has potential to improve our empirical understanding of thresholds in ecological systems and our ability to design manipulative experiments that test how and when a threshold will be passed. It can also be used to indicate to resource managers that a particular system has the potential to exhibit threshold responses to environmental change, emphasizing precautionary management and facilitating a better understanding of how persistent multiple stressors threaten the resilience and long-term use of natural ecosystems.

  13. Cross-species conservation of complementary amino acid-ribonucleobase interactions and their potential for ribosome-free encoding

    PubMed Central

    Cannon, John G. D.; Sherman, Rachel M.; Wang, Victoria M. Y.; Newman, Grace A.

    2015-01-01

    The role of amino acid-RNA nucleobase interactions in the evolution of RNA translation and protein-mRNA autoregulation remains an open area of research. We describe the inference of pairwise amino acid-RNA nucleobase interaction preferences using structural data from known RNA-protein complexes. We observed significant matching between an amino acid’s nucleobase affinity and corresponding codon content in both the standard genetic code and mitochondrial variants. Furthermore, we showed that knowledge of nucleobase preferences allows statistically significant prediction of protein primary sequence from mRNA using purely physiochemical information. Interestingly, ribosomal primary sequences were more accurately predicted than non-ribosomal sequences, suggesting a potential role for direct amino acid-nucleobase interactions in the genesis of amino acid-based ribosomal components. Finally, we observed matching between amino acid-nucleobase affinities and corresponding mRNA sequences in 35 evolutionarily diverse proteomes. We believe these results have important implications for the study of the evolutionary origins of the genetic code and protein-mRNA cross-regulation. PMID:26656258

  14. Ab initio interaction potentials and scattering lengths for ultracold mixtures of metastable helium and alkali-metal atoms

    NASA Astrophysics Data System (ADS)

    Kedziera, Dariusz; Mentel, Łukasz; Żuchowski, Piotr S.; Knoop, Steven

    2015-06-01

    We have obtained accurate ab initio +4Σ quartet potentials for the diatomic metastable triplet helium+alkali-metal (Li, Na, K, Rb) systems, using all-electron restricted open-shell coupled cluster singles and doubles with noniterative triples corrections CCSD(T) calculations and accurate calculations of the long-range C6 coefficients. These potentials provide accurate ab initio quartet scattering lengths, which for these many-electron systems is possible, because of the small reduced masses and shallow potentials that result in a small amount of bound states. Our results are relevant for ultracold metastable triplet helium+alkali-metal mixture experiments.

  15. A comparison of interatomic potentials for modeling tungsten-hydrogen-helium plasma-surface interactions

    NASA Astrophysics Data System (ADS)

    Cusentino, Mary Alice; Hammond, Karl D.; Sefta, Faiza; Juslin, Niklas; Wirth, Brian D.

    2015-08-01

    We compare the hydrogen and helium clustering characteristics of three interatomic potential energy models intended for simulation of plasma-facing materials for fusion applications. Our simulations compare a Finnis-Sinclair potential and two different Tersoff-style bond order potentials created by Juslin et al. (2005) and Li et al. (2011), respectively, with respect to both helium and hydrogen clustering behavior in tungsten. We find significant differences between the Juslin and Li potentials in terms of both hydrogen and helium clustering behavior as well as the spatial distribution of hydrogen below the surface. These simulations are an important test on the road to more accurate models of gas clustering and surface evolution of tungsten divertors in ITER and other plasma devices.

  16. Size effects in aerosol particle interactions: the van der Waals potential and collision rates

    SciTech Connect

    Marlow, W H

    1980-01-01

    Three effects which are explicitly dependent on aerosol particle size are identified and discussed. They are focussed about the particle collision rate and how it relates to the properties of the gas, the particle, and the particle's interaction potential energy which play roles in particle-particle collision rates. By incorporating the conduction electronic free path effect for conductors into the frequency-dependent dielectric constants of silver and graphite, particle size effects in the Lifshitz-van der Waals potentials for identical pairs of 1 nm and 100 nm particles are evaluated. Water and tetradecane particle interaction potentials for the same size particles are also calculated to illustrate size effects due to the retardation of the interaction. These potentials are then used to calculate the enhancement of the particle collision rates above their values in the absence of any potential at various gas pressures. The roles of the interaction potential in collision among identical pairs of particles of differing compositions is also briefly discussed.

  17. A review: potential usage of cellulose nanofibers (CNF) for enzyme immobilization via covalent interactions.

    PubMed

    Sulaiman, Safwan; Mokhtar, Mohd Noriznan; Naim, Mohd Nazli; Baharuddin, Azhari Samsu; Sulaiman, Alawi

    2015-02-01

    Nanobiocatalysis is a new frontier of emerging nanosized material support in enzyme immobilization application. This paper is about a comprehensive review on cellulose nanofibers (CNF), including their structure, surface modification, chemical coupling for enzyme immobilization, and potential applications. The CNF surface consists of mainly -OH functional group that can be directly interacted weakly with enzyme, and its binding can be improved by surface modification and interaction of chemical coupling that forms a strong and stable covalent immobilization of enzyme. The knowledge of covalent interaction for enzyme immobilization is important to provide more efficient interaction between CNF support and enzyme molecule. Enzyme immobilization onto CNF is having potential for improving enzymatic performance and production yield, as well as contributing toward green technology and sustainable sources.

  18. Consistency of multi-time Dirac equations with general interaction potentials

    NASA Astrophysics Data System (ADS)

    Deckert, Dirk-André; Nickel, Lukas

    2016-07-01

    In 1932, Dirac proposed a formulation in terms of multi-time wave functions as candidate for relativistic many-particle quantum mechanics. A well-known consistency condition that is necessary for existence of solutions strongly restricts the possible interaction types between the particles. It was conjectured by Petrat and Tumulka that interactions described by multiplication operators are generally excluded by this condition, and they gave a proof of this claim for potentials without spin-coupling. Under suitable assumptions on the differentiability of possible solutions, we show that there are potentials which are admissible, give an explicit example, however, show that none of them fulfills the physically desirable Poincaré invariance. We conclude that in this sense, Dirac's multi-time formalism does not allow to model interaction by multiplication operators, and briefly point out several promising approaches to interacting models one can instead pursue.

  19. A systematic approach for the accurate non-invasive estimation of blood glucose utilizing a novel light-tissue interaction adaptive modelling scheme

    NASA Astrophysics Data System (ADS)

    Rybynok, V. O.; Kyriacou, P. A.

    2007-10-01

    Diabetes is one of the biggest health challenges of the 21st century. The obesity epidemic, sedentary lifestyles and an ageing population mean prevalence of the condition is currently doubling every generation. Diabetes is associated with serious chronic ill health, disability and premature mortality. Long-term complications including heart disease, stroke, blindness, kidney disease and amputations, make the greatest contribution to the costs of diabetes care. Many of these long-term effects could be avoided with earlier, more effective monitoring and treatment. Currently, blood glucose can only be monitored through the use of invasive techniques. To date there is no widely accepted and readily available non-invasive monitoring technique to measure blood glucose despite the many attempts. This paper challenges one of the most difficult non-invasive monitoring techniques, that of blood glucose, and proposes a new novel approach that will enable the accurate, and calibration free estimation of glucose concentration in blood. This approach is based on spectroscopic techniques and a new adaptive modelling scheme. The theoretical implementation and the effectiveness of the adaptive modelling scheme for this application has been described and a detailed mathematical evaluation has been employed to prove that such a scheme has the capability of extracting accurately the concentration of glucose from a complex biological media.

  20. Comment on 'Intermolecular interaction potentials of the methane dimer from the local density approximation'

    SciTech Connect

    Li, Arvin H.-T.; Chao, S.D.

    2006-01-15

    To verify the recently calculated intermolecular interaction potentials of the methane dimer within the density functional theory using the (Perdew) local density approximation (LDA) [Chen et al., Phys. Rev. A 69, 034701 (2004)], we have performed a parallel series of calculations using the LDA/6-311++G (3df, 3pd) level of theory with selected exchange functionals (B, G96, MPW, O, PBE, PW91, S, and XA). None of the above calculated intermolecular interaction potentials from the local density approximation reproduce the results reported in the commented paper. In addition, we point out the inappropriateness of using the Lennard-Jones function to model the long-range parts of the calculated intermolecular interaction potentials, as suggested positively by Chen et al.

  1. Random interactions in the geometric collective model and the E(5) potential

    SciTech Connect

    Zhang, Jing-Ye; Zamfir, N. V.; Casten, R. F.; Caprio, M. A.

    2001-07-01

    In a study parallel to one recently carried out for the interacting boson model, the behavior of the geometric collective model (GCM) with (partially restricted) random interactions is studied. In particular, we study the frequency distribution of E(4{sub 1}{sup +})/E(2{sub 1}{sup +}) ratios. In addition, we characterize those GCM potentials giving E(5) spectra and distinguish them from others giving R{sub 4/2}{approx}2.3 but non-E(5) spectra.

  2. How Accurate Are the Minnesota Density Functionals for Noncovalent Interactions, Isomerization Energies, Thermochemistry, and Barrier Heights Involving Molecules Composed of Main-Group Elements?

    PubMed

    Mardirossian, Narbe; Head-Gordon, Martin

    2016-09-13

    The 14 Minnesota density functionals published between the years 2005 and early 2016 are benchmarked on a comprehensive database of 4986 data points (84 data sets) involving molecules composed of main-group elements. The database includes noncovalent interactions, isomerization energies, thermochemistry, and barrier heights, as well as equilibrium bond lengths and equilibrium binding energies of noncovalent dimers. Additionally, the sensitivity of the Minnesota density functionals to the choice of basis set and integration grid is explored for both noncovalent interactions and thermochemistry. Overall, the main strength of the hybrid Minnesota density functionals is that the best ones provide very good performance for thermochemistry (e.g., M06-2X), barrier heights (e.g., M08-HX, M08-SO, MN15), and systems heavily characterized by self-interaction error (e.g., M06-2X, M08-HX, M08-SO, MN15), while the main weakness is that none of them are state-of-the-art for the full spectrum of noncovalent interactions and isomerization energies (although M06-2X is recommended from the 10 hybrid Minnesota functionals). Similarly, the main strength of the local Minnesota density functionals is that the best ones provide very good performance for thermochemistry (e.g., MN15-L), barrier heights (e.g., MN12-L), and systems heavily characterized by self-interaction error (e.g., MN12-L and MN15-L), while the main weakness is that none of them are state-of-the-art for the full spectrum of noncovalent interactions and isomerization energies (although M06-L is clearly the best from the four local Minnesota functionals). As an overall guide, M06-2X and MN15 are perhaps the most broadly useful hybrid Minnesota functionals, while M06-L and MN15-L are perhaps the most broadly useful local Minnesota functionals, although each has different strengths and weaknesses.

  3. How Accurate Are the Minnesota Density Functionals for Noncovalent Interactions, Isomerization Energies, Thermochemistry, and Barrier Heights Involving Molecules Composed of Main-Group Elements?

    PubMed

    Mardirossian, Narbe; Head-Gordon, Martin

    2016-09-13

    The 14 Minnesota density functionals published between the years 2005 and early 2016 are benchmarked on a comprehensive database of 4986 data points (84 data sets) involving molecules composed of main-group elements. The database includes noncovalent interactions, isomerization energies, thermochemistry, and barrier heights, as well as equilibrium bond lengths and equilibrium binding energies of noncovalent dimers. Additionally, the sensitivity of the Minnesota density functionals to the choice of basis set and integration grid is explored for both noncovalent interactions and thermochemistry. Overall, the main strength of the hybrid Minnesota density functionals is that the best ones provide very good performance for thermochemistry (e.g., M06-2X), barrier heights (e.g., M08-HX, M08-SO, MN15), and systems heavily characterized by self-interaction error (e.g., M06-2X, M08-HX, M08-SO, MN15), while the main weakness is that none of them are state-of-the-art for the full spectrum of noncovalent interactions and isomerization energies (although M06-2X is recommended from the 10 hybrid Minnesota functionals). Similarly, the main strength of the local Minnesota density functionals is that the best ones provide very good performance for thermochemistry (e.g., MN15-L), barrier heights (e.g., MN12-L), and systems heavily characterized by self-interaction error (e.g., MN12-L and MN15-L), while the main weakness is that none of them are state-of-the-art for the full spectrum of noncovalent interactions and isomerization energies (although M06-L is clearly the best from the four local Minnesota functionals). As an overall guide, M06-2X and MN15 are perhaps the most broadly useful hybrid Minnesota functionals, while M06-L and MN15-L are perhaps the most broadly useful local Minnesota functionals, although each has different strengths and weaknesses. PMID:27537680

  4. The potential of inductively coupled plasma mass spectrometry detection for high-performance liquid chromatography combined with accurate mass measurement of organic pharmaceutical compounds.

    PubMed

    Axelsson, B O; Jörnten-Karlsson, M; Michelsen, P; Abou-Shakra, F

    2001-01-01

    Quantification of unknown components in pharmaceutical, metabolic and environmental samples is an important but difficult task. Most commonly used detectors (like UV, RI or MS) require standards of each analyte for accurate quantification. Even if the chemical structure or elemental composition is known, the response from these detectors is difficult to predict with any accuracy. In inductively coupled plasma mass spectrometry (ICP-MS) compounds are atomised and ionised irrespective of the chemical structure(s) incorporating the element of interest. Liquid chromatography coupled with inductively coupled plasma mass spectrometry (LC/ICP-MS) has been shown to provide a generic detection for structurally non-correlated compounds with common elements like phosphorus and iodine. Detection of selected elements gives a better quantification of tested 'unknowns' than UV and organic mass spectrometric detection. It was shown that the ultrasonic nebuliser did not introduce any measurable dead volume and preserves the separation efficiency of the system. ICP-MS can be used in combination with many different mobile phases ranging from 0-100% organic modifier. The dynamic range was found to exceed 2.5 orders of magnitude. The application of LC/ICP-MS to pharmaceutical drugs and formulations has shown that impurities can be quantified below the 0.1 mol-% level.

  5. An accurate potential energy surface for the F + H{sub 2} → HF + H reaction by the coupled-cluster method

    SciTech Connect

    Chen, Jun; Sun, Zhigang E-mail: zhangdh@dicp.ac.cn; Zhang, Dong H. E-mail: zhangdh@dicp.ac.cn

    2015-01-14

    A three dimensional potential energy surface for the F + H{sub 2} → HF + H reaction has been computed by the spin unrestricted coupled cluster method with singles, doubles, triples, and perturbative quadruples [UCCSDT(2){sub Q}] using the augmented correlation-consistent polarised valence quadruple zeta basis set for the fluorine atom and the correlation-consistent polarised valence quadruple zeta basis set for the hydrogen atom. All the calculations are based on the restricted open-shell Hartree-Fock orbitals, together with the frozen core approximations, and the UCCSD(T)/complete basis set (CBS) correction term was included. The global potential energy surface was calculated by fitting the sampled ab initio points without any scaling factor for the correlation energy part using a neutral network function method. Extensive dynamics calculations have been carried out on the potential energy surface. The reaction rate constants, integral cross sections, product rotational states distribution, and forward and backward scattering as a function of collision energy of the F + HD → HF + D, F + HD → DF + H, and F + H{sub 2} reaction, were calculated by the time-independent quantum dynamics scattering theory using the new surface. The satisfactory agreement with the reported experimental observations previously demonstrates the accuracy of the new potential energy surface.

  6. Nonlinear pressure dependence of the interaction potential of dense protein solutions.

    PubMed

    Schroer, Martin A; Markgraf, Jonas; Wieland, D C Florian; Sahle, Christoph J; Möller, Johannes; Paulus, Michael; Tolan, Metin; Winter, Roland

    2011-04-29

    The influence of pressure on the structure and protein-protein interaction potential of dense protein solutions was studied and analyzed using small-angle x-ray scattering in combination with a liquid state theoretical approach. The structural as well as the interaction parameters of dense lysozyme solutions are affected by pressure in a nonlinear way. The structural properties of water lead to a modification of the protein-protein interactions below 4 kbar, which might have significant consequences for the stability of proteins in extreme natural environments.

  7. Nonlinear pressure dependence of the interaction potential of dense protein solutions.

    PubMed

    Schroer, Martin A; Markgraf, Jonas; Wieland, D C Florian; Sahle, Christoph J; Möller, Johannes; Paulus, Michael; Tolan, Metin; Winter, Roland

    2011-04-29

    The influence of pressure on the structure and protein-protein interaction potential of dense protein solutions was studied and analyzed using small-angle x-ray scattering in combination with a liquid state theoretical approach. The structural as well as the interaction parameters of dense lysozyme solutions are affected by pressure in a nonlinear way. The structural properties of water lead to a modification of the protein-protein interactions below 4 kbar, which might have significant consequences for the stability of proteins in extreme natural environments. PMID:21635065

  8. Signal type and signal-to-noise ratio interact to affect cortical auditory evoked potentials.

    PubMed

    Billings, Curtis J; Grush, Leslie D

    2016-08-01

    Use of speech signals and background noise is emerging in cortical auditory evoked potential (CAEP) studies; however, the interaction between signal type and noise level remains unclear. Two experiments determined the interaction between signal type and signal-to-noise ratio (SNR) on CAEPs. Three signals (syllable /ba/, 1000-Hz tone, and the /ba/ envelope with 1000-Hz fine structure) with varying SNRs were used in two experiments, demonstrating signal-by-SNR interactions due to both envelope and spectral characteristics. When using real-world stimuli such as speech to evoke CAEPs, temporal and spectral complexity leads to differences with traditional tonal stimuli, especially when presented in background noise. PMID:27586784

  9. Intermolecular interaction of thiosemicarbazone derivatives to solvents and a potential Aedes aegypti target

    NASA Astrophysics Data System (ADS)

    da Silva, João Bosco P.; Hallwass, Fernando; da Silva, Aluizio G.; Moreira, Diogo Rodrigo; Ramos, Mozart N.; Espíndola, José Wanderlan P.; de Oliveira, Ana Daura T.; Brondani, Dalci José; Leite, Ana Cristina L.; Merz, Kenneth M.

    2015-08-01

    DFT calculations were used to access information about structure, energy and electronic properties of series of phenyl- and phenoxymethyl-(thio)semicarbazone derivatives with demonstrated activity against the larvae of Aedes aegypti in stage L4. The way as the thiosemicarbazone derivatives can interact with solvents like DMSO and water were analyzed from the comparison between calculated and experimental 1H NMR chemical shifts. The evidences of thiosemicarbazone derivatives making H-bond interaction to solvent have provide us insights on how they can interact with a potential A. aegypti's biological target, the Sterol Carrier Protein-2.

  10. Potential Energy Curves and Collisions Integrals of Air Components. 2; Interactions Involving Ionized Atoms

    NASA Technical Reports Server (NTRS)

    Stallcop, James R.; Partridge, Harry; Levin, Eugene; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    Collision integrals are fundamental quantities required to determine the transport properties of the environment surrounding aerospace vehicles in the upper atmosphere. These collision integrals can be determined as a function of temperature from the potential energy curves describing the atomic and molecular collisions. Ab initio calculations provide a practical method of computing the required interaction potentials. In this work we will discuss recent advances in scattering calculations with an emphasis on the accuracy that is obtainable. Results for interactions of the atoms and ionized atoms of nitrogen and oxygen will be reviewed and their application to the determination of transport properties, such as diffusion and viscosity coefficients, will be examined.

  11. Low temperature rate constants for the N + CN → N2 + C reaction: two-dimensional quantum capture calculations on an accurate potential energy surface.

    PubMed

    Ma, Jianyi; Guo, Hua; Dawes, Richard

    2012-09-21

    The title reaction is thought to be responsible for the production of molecular nitrogen in interstellar clouds. In this work, we report quantum capture calculations on a new two-dimensional potential energy surface determined by interpolating high-level ab initio data. The low-temperature rate constant calculated using a capture model is quite large and has a positive temperature dependence, in agreement with a recent experiment. The origin of the aforementioned behaviors of the rate constant is analyzed.

  12. A new algorithm for predicting triplet-triplet energy-transfer activated complex coordinate in terms of accurate potential-energy surfaces

    NASA Astrophysics Data System (ADS)

    Frutos, Luis Manuel; Castaño, Obis

    2005-09-01

    The new algorithm presented here allows, for the first time, the determination of the optimal geometrical distortions that an acceptor molecule in the triplet-triplet energy-transfer process undergoes, as well as the dependence of the activation energy of the process on the triplet energy difference of donor and acceptor molecules. This algorithm makes use of the complete potential-energy surfaces (singlet and triplet states), and contrasts with the first-order approximation already published [L. M. Frutos, O. Castaño, J. L. Andrés, M. Merchán, and A. U. Acuña, J. Chem. Phys. 120, 1208 (2004)] in which an expansion of the potential-energy surfaces was used. This algorithm is gradient based and finds the best trajectory for the acceptor molecule, starting from S0 ground-state equilibrium geometry, to achieve the maximum variation of the singlet-triplet energy gap with the minimum energy of activation on S0. Therefore, the algorithm allows the determination of a "reaction path" for the triplet-triplet energy-transfer processes. Also, the algorithm could also serve eventually to find minimum-energy crossing (singlet-triplet) points on the potential-energy surface, which can play an important role in the intersystem crossing process for the acceptor molecules to recover their initial capacity as acceptors. Also addressed is the misleading use of minimum-energy paths in T1 to describe the energy-transfer process by comparing these results with those obtained using the new algorithm. The implementation of the algorithm is illustrated with different potential-energy surface models and it is discussed in the frame of nonvertical behavior.

  13. Intrapartum Magnesium Sulfate and the Potential for Cardiopulmonary Drug-Drug Interactions

    PubMed Central

    Campbell, Sarah C.; Stockmann, Chris; Balch, Alfred; Clark, Erin A.S.; Kamyar, Manijeh; Varner, Michael; Korgenski, E. Kent; Bonkowsky, Joshua L.; Spigarelli, Michael G.; Sherwin, Catherine M.T.

    2014-01-01

    Objective This study sought to determine the frequency of possible cardiopulmonary drug-drug interactions among pregnant women who received intrapartum magnesium sulfate (MgSO4). Methods Pregnant women admitted to an Intermountain Healthcare facility between January 2009 and October 2011 were studied if they received one or more doses of MgSO4. Concomitant medications were electronically queried from an electronic health records system. Adverse events were identified using administrative discharge codes. The frequency of cardiopulmonary drug-drug interactions was compared among women who did, and did not, receive aminoglycoside antibiotics, antacids / laxatives, calcium channel blockers, corticosteroids, diuretics, neuromuscular blocking agents, and vitamin D analogs, all of which are contraindicated for patients receiving MgSO4. Results Overall, 683 women received intrapartum MgSO4 during the study period. A total of 219 MgSO4 potentially interacting drugs were identified among 155 (23%) unique patients. The most commonly identified potentially interacting agents included calcium channel blockers (26%), diuretics (25%), and antacids / laxatives (19%). Longer hospital stays were significantly associated with increasing numbers of MgSO4 interacting drugs (P<0.001). Three of 53 (6%) women who received furosemide experienced a cardiac arrest, compared to 0 of 618 (0%) women who did not receive furosemide (Fisher’s Exact Test P<0.001). Conclusion Intrapartum administration of drugs that interact with MgSO4 is common and associated with prolonged hospital stays and potentially cardiopulmonary drug-drug interactions. Caution is warranted when prescribing MgSO4 in combination with known interacting medications. PMID:24487252

  14. A Review of Potential Harmful Interactions between Anticoagulant/Antiplatelet Agents and Chinese Herbal Medicines

    PubMed Central

    Tsai, Hsin-Hui; Lin, Hsiang-Wen; Lu, Ying-Hung; Chen, Yi-Ling; Mahady, Gail B.

    2013-01-01

    Background The risks attributed to drug-herb interactions, even when known, are often ignored or underestimated, especially for those involving anti-clotting drugs and Chinese medicines. The aim of this study was to structurally search and evaluate the existing evidence-based data associated with potential drug interactions between anticoagulant/antiplatelet drugs and Chinese herbal medicines (CHMs) and evaluate the documented mechanisms, consequences, and/or severity of interactions. Methodology and Findings Information related to anticoagulant/antiplatelet drug-CHM interactions was retrieved from eight interaction-based textbooks, four web resources and available primary biomedical literature. The primary literature searches were conducted in English and/or Chinese from January 2000 through December 2011 using the secondary databases (e.g., PubMed, Airiti Library, China Journal full-text database). The search terms included the corresponding medical subject headings and key words. Herbs or natural products not used as a single entity CHM or in Chinese Medicinal Prescriptions were excluded from further review. The corresponding mechanisms and severity ratings of interactions were retrieved using MicroMedex®, Lexicomp® and Natural Medicines Comprehensive Database®. Finally, we found 90 single entity CHMs contributed to 306 documented drug-CHM interactions. A total of 194 (63.4%) interactions were verified for its evidence describing possible mechanisms and severity. Of them, 155 interactions (79.9%) were attributable to pharmacodynamic interactions, and almost all were rated as moderate to severe interactions. The major consequences of these interactions were increased bleeding risks due to the additive anticoagulant or antiplatelet effects of the CHMs, specifically danshen, dong quai, ginger, ginkgo, licorice, and turmeric. Conclusions/Significance Conventional anticoagulants and antiplatelet drugs were documented to have harmful interactions with some commonly

  15. Full-dimensional quantum calculations of vibrational levels of NH4+ 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 (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. As a result, the low-lying vibrational levels of all isotopomers are assigned and the agreement with available experimental data is better than 1 cm–1.

  16. 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).

  17. Five ab initio potential energy and dipole moment surfaces for hydrated NaCl and NaF. I. Two-body interactions.

    PubMed

    Wang, Yimin; Bowman, Joel M; Kamarchik, Eugene

    2016-03-21

    We report full-dimensional, ab initio-based potentials and dipole moment surfaces for NaCl, NaF, Na(+)H2O, F(-)H2O, and Cl(-)H2O. The NaCl and NaF potentials are diabatic ones that dissociate to ions. These are obtained using spline fits to CCSD(T)/aug-cc-pV5Z energies. In addition, non-linear least square fits using the Born-Mayer-Huggins potential are presented, providing accurate parameters based strictly on the current ab initio energies. The long-range behavior of the NaCl and NaF potentials is shown to go, as expected, accurately to the point-charge Coulomb interaction. The three ion-H2O potentials are permutationally invariant fits to roughly 20,000 coupled cluster CCSD(T) energies (awCVTZ basis for Na(+) and aVTZ basis for Cl(-) and F(-)), over a large range of distances and H2O intramolecular configurations. These potentials are switched accurately in the long range to the analytical ion-dipole interactions, to improve computational efficiency. Dipole moment surfaces are fits to MP2 data; for the ion-ion cases, these are well described in the intermediate- and long-range by the simple point-charge expression. The performance of these new fits is examined by direct comparison to additional ab initio energies and dipole moments along various cuts. Equilibrium structures, harmonic frequencies, and electronic dissociation energies are also reported and compared to direct ab initio results. These indicate the high fidelity of the new PESs. PMID:27004880

  18. Five ab initio potential energy and dipole moment surfaces for hydrated NaCl and NaF. I. Two-body interactions.

    PubMed

    Wang, Yimin; Bowman, Joel M; Kamarchik, Eugene

    2016-03-21

    We report full-dimensional, ab initio-based potentials and dipole moment surfaces for NaCl, NaF, Na(+)H2O, F(-)H2O, and Cl(-)H2O. The NaCl and NaF potentials are diabatic ones that dissociate to ions. These are obtained using spline fits to CCSD(T)/aug-cc-pV5Z energies. In addition, non-linear least square fits using the Born-Mayer-Huggins potential are presented, providing accurate parameters based strictly on the current ab initio energies. The long-range behavior of the NaCl and NaF potentials is shown to go, as expected, accurately to the point-charge Coulomb interaction. The three ion-H2O potentials are permutationally invariant fits to roughly 20,000 coupled cluster CCSD(T) energies (awCVTZ basis for Na(+) and aVTZ basis for Cl(-) and F(-)), over a large range of distances and H2O intramolecular configurations. These potentials are switched accurately in the long range to the analytical ion-dipole interactions, to improve computational efficiency. Dipole moment surfaces are fits to MP2 data; for the ion-ion cases, these are well described in the intermediate- and long-range by the simple point-charge expression. The performance of these new fits is examined by direct comparison to additional ab initio energies and dipole moments along various cuts. Equilibrium structures, harmonic frequencies, and electronic dissociation energies are also reported and compared to direct ab initio results. These indicate the high fidelity of the new PESs.

  19. Five ab initio potential energy and dipole moment surfaces for hydrated NaCl and NaF. I. Two-body interactions

    NASA Astrophysics Data System (ADS)

    Wang, Yimin; Bowman, Joel M.; Kamarchik, Eugene

    2016-03-01

    We report full-dimensional, ab initio-based potentials and dipole moment surfaces for NaCl, NaF, Na+H2O, F-H2O, and Cl-H2O. The NaCl and NaF potentials are diabatic ones that dissociate to ions. These are obtained using spline fits to CCSD(T)/aug-cc-pV5Z energies. In addition, non-linear least square fits using the Born-Mayer-Huggins potential are presented, providing accurate parameters based strictly on the current ab initio energies. The long-range behavior of the NaCl and NaF potentials is shown to go, as expected, accurately to the point-charge Coulomb interaction. The three ion-H2O potentials are permutationally invariant fits to roughly 20 000 coupled cluster CCSD(T) energies (awCVTZ basis for Na+ and aVTZ basis for Cl- and F-), over a large range of distances and H2O intramolecular configurations. These potentials are switched accurately in the long range to the analytical ion-dipole interactions, to improve computational efficiency. Dipole moment surfaces are fits to MP2 data; for the ion-ion cases, these are well described in the intermediate- and long-range by the simple point-charge expression. The performance of these new fits is examined by direct comparison to additional ab initio energies and dipole moments along various cuts. Equilibrium structures, harmonic frequencies, and electronic dissociation energies are also reported and compared to direct ab initio results. These indicate the high fidelity of the new PESs.

  20. The potential of protein-nanomaterial interaction for advanced drug delivery.

    PubMed

    Peng, Qiang; Mu, Huiling

    2016-03-10

    Nanomaterials, like nanoparticles, micelles, nano-sheets, nanotubes and quantum dots, have great potentials in biomedical fields. However, their delivery is highly limited by the formation of protein corona upon interaction with endogenous proteins. This new identity, instead of nanomaterial itself, would be the real substance the organs and cells firstly encounter. Consequently, the behavior of nanomaterials in vivo is uncontrollable and some undesired effects may occur, like rapid clearance from blood stream; risk of capillary blockage; loss of targeting capacity; and potential toxicity. Therefore, protein-nanomaterial interaction is a great challenge for nanomaterial systems and should be inhibited. However, this interaction can also be used to functionalize nanomaterials by forming a selected protein corona. Unlike other decoration using exogenous molecules, nanomaterials functionalized by selected protein corona using endogenous proteins would have greater promise for clinical use. In this review, we aim to provide a comprehensive understanding of protein-nanomaterial interaction. Importantly, a discussion about how to use such interaction is launched and some possible applications of such interaction for advanced drug delivery are presented.

  1. Can sucrose content in the phloem sap reaching field pea seeds (Pisum sativum L.) be an accurate indicator of seed growth potential?

    PubMed

    Munier-Jolain, Nathalie; Salon, Christophe

    2003-11-01

    The composition of the translocates reaching the seeds of pea plants having various nitrogen (N) nutrition regimes was investigated under field situations. Sucrose flow in the phloem sap increased with the node number, but was not significantly different between N nutrition levels. Because N deficiency reduced the number of flowering nodes and the number of seeds per pod, the sucrose flow bleeding from cut peduncles was divided by the number of seeds to give the amount of assimilates available per seed. The sucrose concentration in phloem sap supplied to seeds at the upper nodes was higher than that at the lower nodes. The flow of sucrose delivered to the seeds during the cell division period was correlated with seed growth potential. Seeds from the more N-stressed plants had both the highest seed growth rate and received a higher sucrose flux per seed during the cell division period. As seed growth rate is highly correlated with the number of cotyledonary cells produced during the cell division period, sucrose flow in phloem sap is proposed to be an important determinant of mitotic activity in seed embryos. The carbon (C)/N ratio of the flow of translocates towards seeds was higher under conditions of N-deficiency than with optimal N nutrition, indicating that N flux towards seeds, in itself, is not the main determinant of seed growth potential.

  2. The Relationship between Fluid Intelligence and Learning Potential: Is There an Interaction with Attentional Control?

    ERIC Educational Resources Information Center

    Filicková, Marta; Ropovik, Ivan; Bobaková, Monika; Kovalcíková, Iveta

    2015-01-01

    The main aim of the study was to explore the relationship between fluid intelligence (gf), attentional control (AC), and learning potential (LP), and to investigate the interaction effect between gf and AC on LP. The sample comprised 210 children attending the fourth grade of a standard elementary school. It was hypothesized that the extent of the…

  3. A simple contact mapping algorithm for identifying potential peptide mimetics in protein–protein interaction partners

    PubMed Central

    Krall, Alex; Brunn, Jonathan; Kankanala, Spandana; Peters, Michael H

    2014-01-01

    A simple, static contact mapping algorithm has been developed as a first step at identifying potential peptide biomimetics from protein interaction partner structure files. This rapid and simple mapping algorithm, “OpenContact” provides screened or parsed protein interaction files based on specified criteria for interatomic separation distances and interatomic potential interactions. The algorithm, which uses all-atom Amber03 force field models, was blindly tested on several unrelated cases from the literature where potential peptide mimetics have been experimentally developed to varying degrees of success. In all cases, the screening algorithm efficiently predicted proposed or potential peptide biomimetics, or close variations thereof, and provided complete atom-atom interaction data necessary for further detailed analysis and drug development. In addition, we used the static parsing/mapping method to develop a peptide mimetic to the cancer protein target, epidermal growth factor receptor. In this case, secondary, loop structure for the peptide was indicated from the intra-protein mapping, and the peptide was subsequently synthesized and shown to exhibit successful binding to the target protein. The case studies, which all involved experimental peptide drug advancement, illustrate many of the challenges associated with the development of peptide biomimetics, in general. Proteins 2014; 82:2253–2262. © 2014 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc. PMID:24756879

  4. Helium-antihydrogen interaction: the Born-Oppenheimer potential energy curve.

    PubMed

    Strasburger, Krzysztof; Chojnacki, Henryk

    2002-04-22

    The interaction of atomic antihydrogen with helium has been studied within the Born-Oppenheimer approximation. The linear combination of explicitly correlated Gaussian functions was used as the ansatz for the wave function of light particles. The potential energy curve with the minimum at 3.63 bohr and the barrier at 2.42 bohr has been obtained.

  5. Potential pharmacokinetic interactions between antiretrovirals and medicinal plants used as complementary and African traditional medicines.

    PubMed

    Müller, Adrienne C; Kanfer, Isadore

    2011-11-01

    The use of traditional/complementary/alternate medicines (TCAMs) in HIV/AIDS patients who reside in Southern Africa is quite common. Those who use TCAMs in addition to antiretroviral (ARV) treatment may be at risk of experiencing clinically significant pharmacokinetic (PK) interactions, particularly between the TCAMs and the protease inhibitors (PIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs). Mechanisms of PK interactions include alterations to the normal functioning of drug efflux transporters, such as P-gp and/or CYP isoenzymes, such a CYP3A4 that mediate the absorption and elimination of drugs in the small intestine and liver. Specific mechanisms include inhibition and activation of these proteins and induction via the pregnane X receptor (PXR). Several clinical studies and case reports involving ARV-herb PK interactions have been reported. St John's Wort, Garlic and Cat's Claw exhibited potentially significant interactions, each with a PI or NNRTI. The potential for these herbs to induce PK interactions with drugs was first identified in reports of in vitro studies. Other in vitro studies have shown that several African traditional medicinal (ATM) plants and extracts may also demonstrate PK interactions with ARVs, through effects on CYP3A4, P-gp and PXR. The most complex effects were exhibited by Hypoxis hemerocallidea, Sutherlandia frutescens, Cyphostemma hildebrandtii, Acacia nilotica, Agauria salicifolia and Elaeodendron buchananii. Despite a high incidence of HIV/AIDs in the African region, only one clinical study, between efavirenz and Hypoxis hemerocallidea has been conducted. However, several issues/concerns still remain to be addressed and thus more studies on ATMs are warranted in order for more meaningful data to be generated and the true potential for such interactions to be determined.

  6. 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.

  7. The role of metabolism in understanding the altitudinal segregation pattern of two potentially interacting lizards.

    PubMed

    Žagar, Anamarija; Simčič, Tatjana; Carretero, Miguel A; Vrezec, Al

    2015-01-01

    Sympatric species from the same ecological guild, that exhibit partial altitudinal segregation, can potentially interact in areas of syntopic occurrence. Besides general species' ecology, physiology can provide important answers about species interactions reflected in altitudinal patterns. Lizards Podarcis muralis and Iberolacerta horvathi exhibit partial altitudinal segregation, while they strongly resemble in overall morphology and ecology (diet, daily and seasonal activity pattern), but show certain degree of physiological dissimilarity. They have similar mean preferred body temperatures and patterns of seasonal and daily variations but differ in the magnitude of seasonal variation. Since an ectotherm metabolism is highly dependent on body temperature, thermoregulation is expected to directly affect their metabolism. We compared metabolic rates of adult males from an area of sympatry, measured under two temperature regimes (20°C and 28°C). Both species increased metabolic rates with temperature in a similar pattern. We also compared electron transport activity from tail tissues which provide values of species' potential metabolic activity (enzymatic capacity). Species clearly differed in potential metabolic activity; I. horvathi attained higher values than P. muralis. No difference was detected in how species exploited this potential (calculated from the ratio of electron transport activity and metabolic rates). However, we observed higher potential metabolic activity I. horvathi which together with the ability to thermoregulate more precisely could represent a higher competitive advantage over P. muralis in thermally more restrictive environments such as higher altitudes. Understanding of metabolism seems to provide valuable information for understanding recent distributional patterns as well as species interactions.

  8. Time evolution of initial states that extend beyond the potential interaction region in quantum decay

    NASA Astrophysics Data System (ADS)

    García-Calderón, Gastón; Villavicencio, Jorge; Hernández-Maldonado, Alberto; Romo, Roberto

    2016-08-01

    We investigate the decay of initial states that possess a tail that extends beyond the interaction potential region, for potentials of arbitrary shape that vanish exactly after a distance. This is the case for a relevant class of artificial quantum structures. We obtain that along the internal interaction region, the time evolution of the decaying wave function is formed by two terms. The first one refers to the proper decay of the internal portion of the initial state, whereas the second one, that arises from the external tail, yields a transient contribution that tunnels into the internal region, builds up to a value, and then decays. We obtain that depending on the parameters of the initial state, the nonexponential tail decaying contribution may be larger than the contribution of the proper nonexponential term. These results are illustrated by an exactly solvable model and the Heidelberg potential for decay of ultracold atoms and open the possibility to control initial states in artificial decaying systems.

  9. Molecular dynamics investigations of ozone on an ab initio potential energy surface with the utilization of pattern-recognition neural network for accurate determination of product formation.

    PubMed

    Le, Hung M; Dinh, Thach S; Le, Hieu V

    2011-10-13

    The singlet-triplet transformation and molecular dissociation of ozone (O(3)) gas is investigated by performing quasi-classical molecular dynamics (MD) simulations on an ab initio potential energy surface (PES) with visible and near-infrared excitations. MP4(SDQ) level of theory with the 6-311g(2d,2p) basis set is executed for three different electronic spin states (singlet, triplet, and quintet). In order to simplify the potential energy function, an approximation is adopted by ignoring the spin-orbit coupling and allowing the molecule to switch favorably and instantaneously to the spin state that is more energetically stable (lowest in energy among the three spin states). This assumption has previously been utilized to study the SiO(2) system as reported by Agrawal et al. (J. Chem. Phys. 2006, 124 (13), 134306). The use of such assumption in this study probably makes the upper limits of computed rate coefficients the true rate coefficients. The global PES for ozone is constructed by fitting 5906 ab initio data points using a 60-neuron two-layer feed-forward neural network. The mean-absolute error and root-mean-squared error of this fit are 0.0446 eV (1.03 kcal/mol) and 0.0756 eV (1.74 kcal/mol), respectively, which reveal very good fitting accuracy. The parameter coefficients of the global PES are reported in this paper. In order to identify the spin state with high confidence, we propose the use of a pattern-recognition neural network, which is trained to predict the spin state of a given configuration (with a prediction accuracy being 95.6% on a set of testing data points). To enhance the prediction effectiveness, a buffer series of five points are validated to confirm the spin state during the MD process to gain better confidence. Quasi-classical MD simulations from 1.2 to 2.4 eV of total internal energy (including zero-point energy) result in rate coefficients of singlet-triplet transformation in the range of 0.027 ps(-1) to 1.21 ps(-1). Also, we find very

  10. Accurate Ionization Potentials and Electron Affinities of Acceptor Molecules I. Reference Data at the CCSD(T) Complete Basis Set Limit.

    PubMed

    Richard, Ryan M; Marshall, Michael S; Dolgounitcheva, O; Ortiz, J V; Brédas, Jean-Luc; Marom, Noa; Sherrill, C David

    2016-02-01

    In designing organic materials for electronics applications, particularly for organic photovoltaics (OPV), the ionization potential (IP) of the donor and the electron affinity (EA) of the acceptor play key roles. This makes OPV design an appealing application for computational chemistry since IPs and EAs are readily calculable from most electronic structure methods. Unfortunately reliable, high-accuracy wave function methods, such as coupled cluster theory with single, double, and perturbative triples [CCSD(T)] in the complete basis set (CBS) limit are too expensive for routine applications to this problem for any but the smallest of systems. One solution is to calibrate approximate, less computationally expensive methods against a database of high-accuracy IP/EA values; however, to our knowledge, no such database exists for systems related to OPV design. The present work is the first of a multipart study whose overarching goal is to determine which computational methods can be used to reliably compute IPs and EAs of electron acceptors. This part introduces a database of 24 known organic electron acceptors and provides high-accuracy vertical IP and EA values expected to be within ±0.03 eV of the true non-relativistic, vertical CCSD(T)/CBS limit. Convergence of IP and EA values toward the CBS limit is studied systematically for the Hartree-Fock, MP2 correlation, and beyond-MP2 coupled cluster contributions to the focal point estimates. PMID:26731487

  11. Small and efficient basis sets for the evaluation of accurate interaction-induced linear and non-linear electric properties in model hydrogen-bonded complexes

    NASA Astrophysics Data System (ADS)

    Baranowska-Łączkowska, Angelika; Fernández, Berta

    2015-11-01

    Interaction-induced electric dipole moment, polarisability and first hyperpolarisability are investigated in model hydrogen-bonded clusters built of hydrogen fluoride molecules organised in three linear chains parallel to each other. The properties are evaluated within the finite field approach, using the second order Møller-Plesset method, and the LPol-m (m = ds, dl) and the optical rotation prediction (ORP) basis sets. These bases and correlation method are selected after a systematic basis set and correlation method convergence study carried out on the smallest of the complexes and taking properties obtained with Dunning's bases and the coupled cluster singles and doubles (CCSD) and the CCSD including connected triple corrections (CCSD(T)) methods as reference. Results are analysed in terms of many-body and cooperative effects.

  12. Insect antimicrobial peptides show potentiating functional interactions against Gram-negative bacteria

    PubMed Central

    Rahnamaeian, Mohammad; Cytryńska, Małgorzata; Zdybicka-Barabas, Agnieszka; Dobslaff, Kristin; Wiesner, Jochen; Twyman, Richard M.; Zuchner, Thole; Sadd, Ben M.; Regoes, Roland R.; Schmid-Hempel, Paul; Vilcinskas, Andreas

    2015-01-01

    Antimicrobial peptides (AMPs) and proteins are important components of innate immunity against pathogens in insects. The production of AMPs is costly owing to resource-based trade-offs, and strategies maximizing the efficacy of AMPs at low concentrations are therefore likely to be advantageous. Here, we show the potentiating functional interaction of co-occurring insect AMPs (the bumblebee linear peptides hymenoptaecin and abaecin) resulting in more potent antimicrobial effects at low concentrations. Abaecin displayed no detectable activity against Escherichia coli when tested alone at concentrations of up to 200 μM, whereas hymenoptaecin affected bacterial cell growth and viability but only at concentrations greater than 2 μM. In combination, as little as 1.25 μM abaecin enhanced the bactericidal effects of hymenoptaecin. To understand these potentiating functional interactions, we investigated their mechanisms of action using atomic force microscopy and fluorescence resonance energy transfer-based quenching assays. Abaecin was found to reduce the minimal inhibitory concentration of hymenoptaecin and to interact with the bacterial chaperone DnaK (an evolutionarily conserved central organizer of the bacterial chaperone network) when the membrane was compromised by hymenoptaecin. These naturally occurring potentiating interactions suggest that combinations of AMPs could be used therapeutically against Gram-negative bacterial pathogens that have acquired resistance to common antibiotics. PMID:25833860

  13. Insect antimicrobial peptides show potentiating functional interactions against Gram-negative bacteria.

    PubMed

    Rahnamaeian, Mohammad; Cytryńska, Małgorzata; Zdybicka-Barabas, Agnieszka; Dobslaff, Kristin; Wiesner, Jochen; Twyman, Richard M; Zuchner, Thole; Sadd, Ben M; Regoes, Roland R; Schmid-Hempel, Paul; Vilcinskas, Andreas

    2015-05-01

    Antimicrobial peptides (AMPs) and proteins are important components of innate immunity against pathogens in insects. The production of AMPs is costly owing to resource-based trade-offs, and strategies maximizing the efficacy of AMPs at low concentrations are therefore likely to be advantageous. Here, we show the potentiating functional interaction of co-occurring insect AMPs (the bumblebee linear peptides hymenoptaecin and abaecin) resulting in more potent antimicrobial effects at low concentrations. Abaecin displayed no detectable activity against Escherichia coli when tested alone at concentrations of up to 200 μM, whereas hymenoptaecin affected bacterial cell growth and viability but only at concentrations greater than 2 μM. In combination, as little as 1.25 μM abaecin enhanced the bactericidal effects of hymenoptaecin. To understand these potentiating functional interactions, we investigated their mechanisms of action using atomic force microscopy and fluorescence resonance energy transfer-based quenching assays. Abaecin was found to reduce the minimal inhibitory concentration of hymenoptaecin and to interact with the bacterial chaperone DnaK (an evolutionarily conserved central organizer of the bacterial chaperone network) when the membrane was compromised by hymenoptaecin. These naturally occurring potentiating interactions suggest that combinations of AMPs could be used therapeutically against Gram-negative bacterial pathogens that have acquired resistance to common antibiotics.

  14. Kinetic and interaction components of the exact time-dependent correlation potential

    SciTech Connect

    Luo, Kai; Fuks, Johanna I.; Sandoval, Ernesto D.; Maitra, Neepa T.; Elliott, Peter

    2014-05-14

    The exact exchange-correlation (xc) potential of time-dependent density functional theory has been shown to have striking features. For example, step and peak features are generically found when the system is far from its ground-state, and these depend nonlocally on the density in space and time. We analyze the xc potential by decomposing it into kinetic and interaction components and comparing each with their exact-adiabatic counterparts, for a range of dynamical situations in model one-dimensional two-electron systems. We find that often, but not always, the kinetic contribution is largely responsible for these features that are missed by the adiabatic approximation. The adiabatic approximation often makes a smaller error for the interaction component, which we write in two parts, one being the Coulomb potential due to the time-dependent xc hole. Non-adiabatic features of the kinetic component were also larger than those of the interaction component in cases that we studied when there is negligible step structure. In ground-state situations, step and peak structures arise in cases of static correlation, when more than one determinant is essential to describe the interacting state. We investigate the time-dependent natural orbital occupation numbers and find the corresponding relation between these and the dynamical step is more complex than for the ground-state case.

  15. Model-specific tests on variance heterogeneity for detection of potentially interacting genetic loci

    PubMed Central

    2012-01-01

    Background Trait variances among genotype groups at a locus are expected to differ in the presence of an interaction between this locus and another locus or environment. A simple maximum test on variance heterogeneity can thus be used to identify potentially interacting single nucleotide polymorphisms (SNPs). Results We propose a multiple contrast test for variance heterogeneity that compares the mean of Levene residuals for each genotype group with their average as an alternative to a global Levene test. We applied this test to a Bogalusa Heart Study dataset to screen for potentially interacting SNPs across the whole genome that influence a number of quantitative traits. A user-friendly implementation of this method is available in the R statistical software package multcomp. Conclusions We show that the proposed multiple contrast test of model-specific variance heterogeneity can be used to test for potential interactions between SNPs and unknown alleles, loci or covariates and provide valuable additional information compared with traditional tests. Although the test is statistically valid for severely unbalanced designs, care is needed in interpreting the results at loci with low allele frequencies. PMID:22808950

  16. Accurate Potential Energy Surface, Rovibrational Energy Levels, and Transitions of Ammonia C_{3v} Isotopologues: ^{14}NH_3, ^{15}NH_3, ^{14}ND_3 and ^{14}NT_3

    NASA Astrophysics Data System (ADS)

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

    2009-06-01

    A further refined, global potential energy surface (PES) is computed for the C_{3v} symmetry isotopologues of ammonia, including ^{14}NH_3, ^{15}NH_3, ^{14}ND_3 and ^{14}NT_3. The refinement procedure was similar to that used in our previously reported PES, but now extends to higher J energy levels and other isotopologues. Both the diagonal Born-Oppenheimer correction and the non-adiabatic correction were included. J=0-6 rovibrational energy levels and transition frequencies of ^{14}NH_3 computed on this PES are in excellent agreement with HITRAN data. Statistics on nearly 4100 transitions and more than 1000 energy levels demonstrate the accuracy achieved by the state-of-the-art "Best Theory + Experiment" strategy. Most transition frequencies are of ±0.01-0.02 cm^{-1} accuracy. Similar accuracy has been found on ^{15}NH_3 J=0-3 rovibrational energy levels. Several transitions and energy levels in HITRAN have been identified as unreliable or suspicious, and some have been re-assigned. For ^{14}ND_3 and ^{14}NT_3, J=0-3 calculations have been performed. Agreement for pure rotation-inversion transitions is nearly perfect, with more reliable energy levels presented. On the other hand, our J=0 results suggest a re-analysis on the ^{14}ND_3 ν_1 band origin is needed. Finally, we will discuss possible future refinements leading to an even better final PES for Ammonia. X. Huang, D.W. Schwenke, and T.J. Lee, J. Chem. Phys. 129, 214304 (2008).

  17. Accurate ab initio potential energy curves and spectroscopic properties of the four lowest singlet states of C2

    SciTech Connect

    Boschen, Jeffery S.; Theis, Daniel; Ruedenberg, Klaus; Windus, Theresa L.

    2013-12-07

    The diatomic carbon molecule has a complex electronic structure with a large number of low-lying electronic excited states. In this work, the potential energy curves (PECs) of the four lowest lying singlet states (X-1 Sigma(+)(g), A(1)Pi(u), B-1 Delta(g), and B'(1)Sigma(+)(g)) were obtained by high-level ab initio calculations. Valence electron correlation was accounted for by the correlation energy extrapolation by intrinsic scaling (CEEIS) method. Additional corrections to the PECs included core-valence correlation and relativistic effects. Spin-orbit corrections were found to be insignificant. The impact of using dynamically weighted reference wave functions in conjunction with CEEIS was examined and found to give indistinguishable results from the even weighted method. The PECs showed multiple curve crossings due to the B-1 Delta(g) state as well as an avoided crossing between the two (1)Sigma(+)(g) states. Vibrational energy levels were computed for each of the four electronic states, as well as rotational constants and spectroscopic parameters. Comparison between the theoretical and experimental results showed excellent agreement overall. Equilibrium bond distances are reproduced to within 0.05 %. The dissociation energies of the states agree with experiment to within similar to 0.5 kcal/mol, achieving "chemical accuracy." Vibrational energy levels show average deviations of similar to 20 cm(-1) or less. The B-1 Delta(g) state shows the best agreement with a mean absolute deviation of 2.41 cm(-1). Calculated rotational constants exhibit very good agreement with experiment, as do the spectroscopic constants.

  18. Potential substrates for nicotine and alcohol interactions: a focus on the mesocorticolimbic dopamine system.

    PubMed

    Doyon, William M; Thomas, Alyse M; Ostroumov, Alexey; Dong, Yu; Dani, John A

    2013-10-15

    Epidemiological studies consistently find correlations between nicotine and alcohol use, yet the neural mechanisms underlying their interaction remain largely unknown. Nicotine and alcohol (i.e., ethanol) share many common molecular and cellular targets that provide potential substrates for nicotine-alcohol interactions. These targets for interaction often converge upon the mesocorticolimbic dopamine system, where the link to drug self-administration and reinforcement is well documented. Both nicotine and alcohol activate the mesocorticolimbic dopamine system, producing downstream dopamine signals that promote the drug reinforcement process. While nicotine primarily acts via nicotinic acetylcholine receptors, alcohol acts upon a wider range of receptors and molecular substrates. The complex pharmacological profile of these two drugs generates overlapping responses that ultimately intersect within the mesocorticolimbic dopamine system to promote drug use. Here we will examine overlapping targets between nicotine and alcohol and provide evidence for their interaction. Based on the existing literature, we will also propose some potential targets that have yet to be directly tested. Mechanistic studies that examine nicotine-alcohol interactions would ultimately improve our understanding of the factors that contribute to the associations between nicotine and alcohol use.

  19. Monomerization of cytosolic mature smac attenuates interaction with IAPs and potentiation of caspase activation.

    PubMed

    Burke, Stephen P; Smith, Jeffrey B

    2010-10-01

    The four residues at the amino-terminus of mature Smac/DIABLO are an IAP binding motif (IBM). Upon exit from mitochondria, mature Smac interacts with inhibitor of apoptosis proteins (IAPs), abrogating caspase inhibition. We used the ubiquitin fusion model to express mature Smac in the cytosol. Transiently expressed mature Smac56-239 (called Smac56) and Smac60-239 (called Smac60), which lacks the IBM, interacted with X-linked inhibitor of apoptosis protein (XIAP). However, stable expression produced wild type Smac56 that failed to homodimerize, interact with XIAP, and potentiate caspase activation. Cytosolic Smac60 retained these functions. Cytosolic Smac56 apparently becomes posttranslationally modified at the dimer interface region, which obliterated the epitope for a monoclonal antibody. Cytosolic Smacδ, which has the IBM but lacks amino acids 62-105, homodimerized and weakly interacted with XIAP, but failed to potentiate apoptosis. These findings suggest that the IBM of Smac is a recognition point for a posttranslational modification(s) that blocks homodimerization and IAP interaction, and that amino acids 62-105 are required for the proapoptotic function of Smac.

  20. Effects of adiabatic, relativistic, and quantum electrodynamics interactions on the pair potential and thermophysical properties of helium.

    PubMed

    Cencek, Wojciech; Przybytek, Michał; Komasa, Jacek; Mehl, James B; Jeziorski, Bogumił; Szalewicz, Krzysztof

    2012-06-14

    The adiabatic, relativistic, and quantum electrodynamics (QED) contributions to the pair potential of helium were computed, fitted separately, and applied, together with the nonrelativistic Born-Oppenheimer (BO) potential, in calculations of thermophysical properties of helium and of the properties of the helium dimer. An analysis of the convergence patterns of the calculations with increasing basis set sizes allowed us to estimate the uncertainties of the total interaction energy to be below 50 ppm for interatomic separations R smaller than 4 bohrs and for the distance R = 5.6 bohrs. For other separations, the relative uncertainties are up to an order of magnitude larger (and obviously still larger near R = 4.8 bohrs where the potential crosses zero) and are dominated by the uncertainties of the nonrelativistic BO component. These estimates also include the contributions from the neglected relativistic and QED terms proportional to the fourth and higher powers of the fine-structure constant α. To obtain such high accuracy, it was necessary to employ explicitly correlated Gaussian expansions containing up to 2400 terms for smaller R (all R in the case of a QED component) and optimized orbital bases up to the cardinal number X = 7 for larger R. Near-exact asymptotic constants were used to describe the large-R behavior of all components. The fitted potential, exhibiting the minimum of -10.996 ± 0.004 K at R = 5.608 0 ± 0.000 1 bohr, was used to determine properties of the very weakly bound (4)He(2) dimer and thermophysical properties of gaseous helium. It is shown that the Casimir-Polder retardation effect, increasing the dimer size by about 2 Å relative to the nonrelativistic BO value, is almost completely accounted for by the inclusion of the Breit-interaction and the Araki-Sucher contributions to the potential, of the order α(2) and α(3), respectively. The remaining retardation effect, of the order of α(4) and higher, is practically negligible for the bound

  1. Interaction of a propagating guided matter wave with a localized potential

    NASA Astrophysics Data System (ADS)

    Gattobigio, G. L.; Couvert, A.; Georgeot, B.; Guéry-Odelin, D.

    2010-08-01

    We provide a theoretical framework to describe the interaction of a propagating guided matter wave with a localized potential in terms of quantum scattering in a confined environment. We analyze how this scattering correlates the longitudinal and transverse degrees of freedom, and work out analytically the output state under the Born approximation using a Gaussian localized potential. In this limit, it is possible to engineer the potential and achieve coherent control of the output channels. The robustness of this approximation is studied by comparing the stationary scattering theory to numerical simulations involving incident wave packets. It remains valid in a domain of weak localized potential that is achievable experimentally. We deduce a possible method to determine the longitudinal coherence length of a guided atom laser. Then, we detail the non-perturbative regime of the interaction of the guided matter wave with the localized potential using a coupled channel approach. This approach is worked out explicitly with a square potential. It yields new non-perturbative effects such as the occurrence of confinement-induced resonances. The perspectives opened up by this work for experiments are discussed.

  2. Potential of interaction between the H1-antagonist astemizole and other drugs.

    PubMed

    Rombaut, N; Heykants, J; Vanden Bussche, G

    1986-11-01

    Astemizole is a potent H1-antagonist devoid of sedative effects, which was found at single oral daily doses to be very effective in the treatment of allergic rhinitis, allergic conjunctivitis, and urticaria. Its interaction potential on other drugs was studied in various ways. Studies on salivary antipyrine clearance, the 6-beta-hydrocortisol excretion, the elimination rate of ethanol and the indocyanine-green clearance are presented. No changes were observed. Astemizole also was given in combination with diazepam or alcohol. Psychomotor performance failed to show any effects. In none of these studies was there any evidence of interaction of astemizole on other drugs. This review summarizes the data available thus far.

  3. Delocalization of Weakly Interacting Bosons in a 1D Quasiperiodic Potential

    NASA Astrophysics Data System (ADS)

    Michal, V. P.; Altshuler, B. L.; Shlyapnikov, G. V.

    2014-07-01

    We consider weakly interacting bosons in a 1D quasiperiodic potential (Aubry-Azbel-Harper model) in the regime where all single-particle states are localized. We show that the interparticle interaction may lead to the many-body delocalization and we obtain the finite-temperature phase diagram. Counterintuitively, in a wide range of parameters the delocalization requires stronger coupling as the temperature increases. This means that the system of bosons can undergo a transition from a fluid to insulator (glass) state under heating.

  4. Potentially significant versus clinically significant drug interactions: pomegranate juice as a case in point.

    PubMed

    Andrade, Chittaranjan

    2014-04-01

    In vitro and in vivo laboratory data show that pomegranate juice consistently inhibits intestinal CYP2C9 and CYP3A4 enzymes. Pomegranate juice may therefore increase the bioavailability of drugs that are metabolized by these enzymes. However, studies in humans find that pomegranate juice does not increase exposure to either CYP2C9 or CYP3A4 substrates. These contradictory findings suggest that potential drug interactions identified in the laboratory may not necessarily translate into clinically significant drug interactions in humans, and hence that laboratory data are insufficient grounds upon which clinical decisions may be based.

  5. Charged patchy particle models in explicit salt: Ion distributions, electrostatic potentials, and effective interactions

    SciTech Connect

    Yigit, Cemil; Dzubiella, Joachim; Heyda, Jan

    2015-08-14

    We introduce a set of charged patchy particle models (CPPMs) in order to systematically study the influence of electrostatic charge patchiness and multipolarity on macromolecular interactions by means of implicit-solvent, explicit-ion Langevin dynamics simulations employing the Gromacs software. We consider well-defined zero-, one-, and two-patched spherical globules each of the same net charge and (nanometer) size which are composed of discrete atoms. The studied mono- and multipole moments of the CPPMs are comparable to those of globular proteins with similar size. We first characterize ion distributions and electrostatic potentials around a single CPPM. Although angle-resolved radial distribution functions reveal the expected local accumulation and depletion of counter- and co-ions around the patches, respectively, the orientation-averaged electrostatic potential shows only a small variation among the various CPPMs due to space charge cancellations. Furthermore, we study the orientation-averaged potential of mean force (PMF), the number of accumulated ions on the patches, as well as the CPPM orientations along the center-to-center distance of a pair of CPPMs. We compare the PMFs to the classical Derjaguin-Verwey-Landau-Overbeek theory and previously introduced orientation-averaged Debye-Hückel pair potentials including dipolar interactions. Our simulations confirm the adequacy of the theories in their respective regimes of validity, while low salt concentrations and large multipolar interactions remain a challenge for tractable theoretical descriptions.

  6. Charged patchy particle models in explicit salt: Ion distributions, electrostatic potentials, and effective interactions.

    PubMed

    Yigit, Cemil; Heyda, Jan; Dzubiella, Joachim

    2015-08-14

    We introduce a set of charged patchy particle models (CPPMs) in order to systematically study the influence of electrostatic charge patchiness and multipolarity on macromolecular interactions by means of implicit-solvent, explicit-ion Langevin dynamics simulations employing the Gromacs software. We consider well-defined zero-, one-, and two-patched spherical globules each of the same net charge and (nanometer) size which are composed of discrete atoms. The studied mono- and multipole moments of the CPPMs are comparable to those of globular proteins with similar size. We first characterize ion distributions and electrostatic potentials around a single CPPM. Although angle-resolved radial distribution functions reveal the expected local accumulation and depletion of counter- and co-ions around the patches, respectively, the orientation-averaged electrostatic potential shows only a small variation among the various CPPMs due to space charge cancellations. Furthermore, we study the orientation-averaged potential of mean force (PMF), the number of accumulated ions on the patches, as well as the CPPM orientations along the center-to-center distance of a pair of CPPMs. We compare the PMFs to the classical Derjaguin-Verwey-Landau-Overbeek theory and previously introduced orientation-averaged Debye-Hückel pair potentials including dipolar interactions. Our simulations confirm the adequacy of the theories in their respective regimes of validity, while low salt concentrations and large multipolar interactions remain a challenge for tractable theoretical descriptions. PMID:26277163

  7. Structure and dynamics of near-threshold leptons driven by dipolar interactions: an accurate computational study for the DNA purinic bases

    NASA Astrophysics Data System (ADS)

    Carelli, Fabio; Gianturco, Francesco Antonio

    2016-06-01

    The interaction of low-energy scattering electrons/positrons with molecular targets characterized by a "supercritical" permanent dipole moment (≳2.0 D) presents special physical characteristics that affect their spatial distributions, around the nuclear network of the molecular partners, both above and below the energy thresholds. Such special states are described as either dipole scattering states (DSS) above thresholds or as dipole bound states (DBS) below thresholds. The details of their respective behaviour will be presented and discussed in this work in the case of the purinic DNA bases of adenine and guanine. The behavior of the additional electron, in particular, will be discussed in detail by providing new computational results that will be related to the findings from recent experiments on the same DNA bases, confirming the transient electron's behaviour surmised by them. This work is affectionately dedicated to Michael Allan on the occasion of his official retirement. We wish to this dear friend and outstanding scientist many years to come in the happy pursuit of his many scientific interests.Contribution to the Topical Issue "Advances in Positron and Electron Scattering", edited by Paulo Limao-Vieira, Gustavo Garcia, E. Krishnakumar, James Sullivan, Hajime Tanuma and Zoran Petrovic.

  8. Natural enemy-mediated indirect interactions among prey species: potential for enhancing biocontrol services in agroecosystems.

    PubMed

    Chailleux, Anaïs; Mohl, Emily K; Teixeira Alves, Mickaël; Messelink, Gerben J; Desneux, Nicolas

    2014-12-01

    Understanding how arthropod pests and their natural enemies interact in complex agroecosystems is essential for pest management programmes. Theory predicts that prey sharing a predator, such as a biological control agent, can indirectly reduce each other's density at equilibrium (apparent competition). From this premise, we (i) discuss the complexity of indirect interactions among pests in agroecosystems and highlight the importance of natural enemy-mediated indirect interactions other than apparent competition, (ii) outline factors that affect the nature of enemy-mediated indirect interactions in the field and (iii) identify the way to manipulate enemy-mediated interactions for biological control. We argue that there is a need to increase the link between community ecology theory and biological control to develop better agroecological methods of crop protection via conservation biological control. In conclusion, we identify (i) interventions to be chosen depending on agroecosystem characteristics and (ii) several lines of research that will improve the potential for enemy-mediated indirect interactions to be applied to biological control.

  9. Inferring coarse-grain histone-DNA interaction potentials from high-resolution structures of the nucleosome

    NASA Astrophysics Data System (ADS)

    Meyer, Sam; Everaers, Ralf

    2015-02-01

    The histone-DNA interaction in the nucleosome is a fundamental mechanism of genomic compaction and regulation, which remains largely unknown despite increasing structural knowledge of the complex. In this paper, we propose a framework for the extraction of a nanoscale histone-DNA force-field from a collection of high-resolution structures, which may be adapted to a larger class of protein-DNA complexes. We applied the procedure to a large crystallographic database extended by snapshots from molecular dynamics simulations. The comparison of the structural models first shows that, at histone-DNA contact sites, the DNA base-pairs are shifted outwards locally, consistent with locally repulsive forces exerted by the histones. The second step shows that the various force profiles of the structures under analysis derive locally from a unique, sequence-independent, quadratic repulsive force-field, while the sequence preferences are entirely due to internal DNA mechanics. We have thus obtained the first knowledge-derived nanoscale interaction potential for histone-DNA in the nucleosome. The conformations obtained by relaxation of nucleosomal DNA with high-affinity sequences in this potential accurately reproduce the experimental values of binding preferences. Finally we address the more generic binding mechanisms relevant to the 80% genomic sequences incorporated in nucleosomes, by computing the conformation of nucleosomal DNA with sequence-averaged properties. This conformation differs from those found in crystals, and the analysis suggests that repulsive histone forces are related to local stretch tension in nucleosomal DNA, mostly between adjacent contact points. This tension could play a role in the stability of the complex.

  10. Family-of-origin interaction and adolescent mothers' potential for child abuse.

    PubMed

    McCullough, M; Scherman, A

    1998-01-01

    This study examined the relationship between family-of-origin interaction and environment and the potential for young mothers to abuse their children. Females aged 14 to 21 from three teen parenting programs completed the Teen Parenting Questionnaire, the Family Environment Scale, and the Child Abuse Potential Inventory. Low scores on family cohesion were found to correlate with high scores on child abuse potential. This suggests that providing the teenager with an accepting and supportive atmosphere may assist her in building a positive identity as a mother. Increased understanding of how family-of-origin issues contribute to young mothers' potential to abuse their children will aid school and community professionals in providing better services for this population.

  11. Accurate determination of pair potentials for a C{sub w}H{sub x}N{sub y}O{sub z} system of molecules: A semiempirical method

    SciTech Connect

    Thiel, M. van; Ree, F.H.; Haselman, L.C.

    1995-03-01

    Statistical mechanical chemical equilibrium calculations of the properties of high-pressure high-temperature reactive C,H,N,O mixtures are made to derive an accurate self-consistent set of inter-molecular potentials for the product molecules. Previous theoretical efforts to predict such properties relied in part on Corresponding States theory and shock wave data of argon. More recent high-pressure Hugoniot measurements on a number of elements and molecules allow more accurate determination of the potentials of these materials, and explicit inclusion of additional dissociation products. The present discussion briefly reviews the previous analysis and the method used to produce a self-consistent set of potentials from shock data on N{sub 2}, O{sub 2}, H{sub 2}, NO, an N{sub 2} + O{sub 2} mixture, carbon, CO{sub 2}, and CO, as well as some simple explosive product mixtures from detonation of hexanitrobenzene, PETN, and a mixture of hydrazine nitrate, hydrazine and water. The results are tested using the data from an HMX explosive formulations. The effect of the non-equilibrium nature of carbon clusters is estimated using data for TNT as a standard to determine a nonequilibrium equation of state for carbon. The resulting parameter set is used in a survey of 27 explosives. For the subset that contains no fluorine or two-phase carbon effects the rms deviation from experimental detonation velocity is 1.2%.

  12. Reconstructing interaction potentials in thin films from real-space images

    NASA Astrophysics Data System (ADS)

    Gienger, Jonas; Severin, Nikolai; Rabe, Jürgen P.; Sokolov, Igor M.

    2016-04-01

    We demonstrate that an inverse Monte Carlo approach allows one to reconstruct effective interaction potentials from real-space images. The method is exemplified on monomolecular ethanol-water films imaged with scanning force microscopy, which provides the spatial distribution of the molecules. Direct Monte Carlo simulations with the reconstructed potential allow for obtaining characteristics of the system which are unavailable in the experiment, such as the heat capacity of the monomolecularly thin film, and for a prediction of the critical temperature of the demixing transition.

  13. The interaction potential of NO-H2 in ground and A Rydberg state

    NASA Astrophysics Data System (ADS)

    Pajón-Suárez, Pedro; Valentín-Rodríguez, Mónica; Hernández-Lamoneda, Ramón

    2016-08-01

    The interaction potential for the ground and A Rydberg state of NO-H2 has been calculated using high level ab initio methods. The complex is very floppy in nature and large amplitude motions are expected to characterize its dynamics. The ground state is characterized by two very close-lying states which exhibit crossings. By analogy with other complexes the Rydberg state is characterized by much smaller well depth and larger intermolecular distance. We compare with model potentials used in previous molecular dynamics simulations of photoexcitation and relaxation and conclude on the importance of performing new studies.

  14. Role of the isovector nucleon-nucleus interaction potential in nonmesonic hypernuclear decay

    SciTech Connect

    Barbero, C.; Mariano, A.; Duarte, S. B.

    2010-12-15

    We develop a theoretical finite nucleus framework for the evaluation of the coincidence number of pairs N{sub nN} and the asymmetry parameter a{sub {Lambda}} in nonmesonic hypernuclear decay {Lambda}N{yields}nN, and introduce the effect of final-state interactions. The primary nonmesonic weak hyperon-nucleon decay process is described through the independent-particle shell model. We work within the 2p1h subspace of final states, assuming a simple approach for finite nuclei based on the eikonal approximation. An optical potential including the nucleon-nucleus isoscalar and isovector interactions is introduced to take into account the minimum nuclear-medium effects. The calculated values for {sub {Lambda}}{sup 5}He and {sub {Lambda}}{sup 12}C show that our treatment of final-state interactions, even those considered as restricted to a subspace of states, brings the independent-particle model results closer to the experimental data.

  15. Analysis of hydrogen-bond interaction potentials from the electron density: Integration of NCI regions

    PubMed Central

    Contreras-García, Julia; Yang, Weitao; Johnson, Erin R.

    2013-01-01

    Hydrogen bonds are of crucial relevance to many problems in chemistry biology and materials science. The recently-developed NCI (Non-Covalent Interactions) index enables real-space visualization of both attractive (van der Waals and hydrogen-bonding) and repulsive (steric) interactions based on properties of the electron density It is thus an optimal index to describe the interplay of stabilizing and de-stabilizing contributions that determine stable minima on hydrogen-bonding potential-energy surfaces (PESs). In the framework of density-functional theory energetics are completely determined by the electron density Consequently NCI will be shown to allow quantitative treatment of hydrogen-bond energetics. The evolution of NCI regions along a PES follows a well-behaved pattern which, upon integration of the electron density is capable of mimicking conventional hydrogen-bond interatomic potentials. PMID:21786796

  16. Life history determines genetic structure and evolutionary potential of host–parasite interactions

    PubMed Central

    Barrett, Luke G.; Thrall, Peter H.; Burdon, Jeremy J.; Linde, Celeste C.

    2009-01-01

    Measures of population genetic structure and diversity of disease-causing organisms are commonly used to draw inferences regarding their evolutionary history and potential to generate new variation in traits that determine interactions with their hosts. Parasite species exhibit a range of population structures and life-history strategies, including different transmission modes, life-cycle complexity, off-host survival mechanisms and dispersal ability. These are important determinants of the frequency and predictability of interactions with host species. Yet the complex causal relationships between spatial structure, life history and the evolutionary dynamics of parasite populations are not well understood. We demonstrate that a clear picture of the evolutionary potential of parasitic organisms and their demographic and evolutionary histories can only come from understanding the role of life history and spatial structure in influencing population dynamics and epidemiological patterns. PMID:18947899

  17. The interaction between nitrobenzene and Microcystis aeruginosa and its potential to impact water quality.

    PubMed

    Liu, Zhiquan; Cui, Fuyi; Ma, Hua; Fan, Zhenqiang; Zhao, Zhiwei; Hou, Zhenling; Liu, Dongmei; Jia, Xuebin

    2013-08-01

    The potential water quality problems caused by the interaction between nitrobezene (NB) and Microcystis aeruginosa was investigated by studying the growth inhibition, the haloacetic acids formation potential (HAAFP) and the secretion of microcystin-LR (MC-LR). The results showed that NB can inhibit the growth of M. aeruginosa, and the value of EC50 increased with the increase of initial algal density. Although NB can hardly react with chlorine to form HAAs, the presence of NB can enhance the HAAFP productivity. The secretion of the intracellular MC-LR is constant under the steady experimental conditions. However, the presence of NB can reduce the MC-LR productivity of M. aeruginosa. Overall, the increased disinfection risk caused by the interaction has more important effect on the safety of drinking water quality than the benefit of the decreased MC-LR productivity, and should be serious considered when the water contained NB and M. aeruginosa is used as drinking water source.

  18. Specific anion effects on the pressure dependence of the protein-protein interaction potential.

    PubMed

    Möller, Johannes; Grobelny, Sebastian; Schulze, Julian; Steffen, Andre; Bieder, Steffen; Paulus, Michael; Tolan, Metin; Winter, Roland

    2014-04-28

    We present a study on ion specific effects on the intermolecular interaction potential V(r) of dense protein solutions under high hydrostatic pressure conditions. Small-angle X-ray scattering in combination with a liquid-state theoretical approach was used to determine the effect of structure breaking/making salt anions (Cl(-), SO4(2-), PO4(3-)) on the intermolecular interaction of lysozyme molecules. It was found that besides the Debye-Hückel charge screening effect, reducing the repulsiveness of the interaction potential V(r) at low salt concentrations, a specific ion effect is observed at high salt concentrations for the multivalent kosmotropic anions, which modulates also the pressure dependence of the protein-protein interaction potential. Whereas sulfate and phosphate strongly influence the pressure dependence of V(r), chloride anions do not. The strong structure-making effect of the multivalent anions, dominating for the triply charged PO4(3-), renders the solution structure less bulk-water-like at high salt concentrations, which leads to an altered behavior of the pressure dependence of V(r). Hence, the particular structural properties of the salt solutions are able to influence the spatial organization and the intermolecular interactions of the proteins, in particular upon compression. These results are of interest for exploring the combined effects of ionic strength, temperature and pressure on the phase behavior of protein solutions, but may also be of relevance for understanding pressure effects on the hydration behavior of biological matter under extreme environmental conditions.

  19. Specific anion effects on the pressure dependence of the protein-protein interaction potential.

    PubMed

    Möller, Johannes; Grobelny, Sebastian; Schulze, Julian; Steffen, Andre; Bieder, Steffen; Paulus, Michael; Tolan, Metin; Winter, Roland

    2014-04-28

    We present a study on ion specific effects on the intermolecular interaction potential V(r) of dense protein solutions under high hydrostatic pressure conditions. Small-angle X-ray scattering in combination with a liquid-state theoretical approach was used to determine the effect of structure breaking/making salt anions (Cl(-), SO4(2-), PO4(3-)) on the intermolecular interaction of lysozyme molecules. It was found that besides the Debye-Hückel charge screening effect, reducing the repulsiveness of the interaction potential V(r) at low salt concentrations, a specific ion effect is observed at high salt concentrations for the multivalent kosmotropic anions, which modulates also the pressure dependence of the protein-protein interaction potential. Whereas sulfate and phosphate strongly influence the pressure dependence of V(r), chloride anions do not. The strong structure-making effect of the multivalent anions, dominating for the triply charged PO4(3-), renders the solution structure less bulk-water-like at high salt concentrations, which leads to an altered behavior of the pressure dependence of V(r). Hence, the particular structural properties of the salt solutions are able to influence the spatial organization and the intermolecular interactions of the proteins, in particular upon compression. These results are of interest for exploring the combined effects of ionic strength, temperature and pressure on the phase behavior of protein solutions, but may also be of relevance for understanding pressure effects on the hydration behavior of biological matter under extreme environmental conditions. PMID:24626853

  20. Herbal medicines in Brazil: pharmacokinetic profile and potential herb-drug interactions

    PubMed Central

    Mazzari, Andre L. D. A.; Prieto, Jose M.

    2014-01-01

    A plethora of active compounds found in herbal medicines can serve as substrate for enzymes involved in the metabolism of xenobiotics. When a medicinal plant is co-administered with a conventional drug and little or no information is known about the pharmacokinetics of the plant metabolites, there is an increased risk of potential herb-drug interactions. Moreover, genetic polymorphisms in a population may act to predispose individuals to adverse reactions. The use of herbal medicines is rapidly increasing in many countries, particularly Brazil where the vast biodiversity is a potential source of new and more affordable treatments for numerous conditions. Accordingly, the Brazilian Unified Public Health System (SUS) produced a list of 71 plant species of interest, which could be made available to the population in the near future. Physicians at SUS prescribe a number of essential drugs and should herbal medicines be added to this system the chance of herb-drug interactions further increases. A review of the effects of these medicinal plants on Phase 1 and Phase 2 metabolic mechanisms and the transporter P-glycoprotein was conducted. The results have shown that approximately half of these medicinal plants lack any pharmacokinetic data. Moreover, most of the studies carried out are in vitro. Only a few reports on herb-drug interactions with essential drugs prescribed by SUS were found, suggesting that very little attention is being given to the safety of herbal medicines. Here we have taken this information to discuss the potential interactions between herbal medicines and essential drugs prescribed to Brazilian patients whilst taking into account the most common polymorphisms present in the Brazilian population. A number of theoretical interactions are pinpointed but more pharmacokinetic studies and pharmacovigilance data are needed to ascertain their clinical significance. PMID:25071580

  1. Potential drug-drug interactions in Alzheimer patients with behavioral symptoms.

    PubMed

    Pasqualetti, Giuseppe; Tognini, Sara; Calsolaro, Valeria; Polini, Antonio; Monzani, Fabio

    2015-01-01

    The use of multi drug regimens among the elderly population has increased tremendously over the last decade although the benefits of medications are always accompanied by potential harm, even when prescribed at recommended doses. The elderly populations are particularly at an increased risk of adverse drug reactions considering comorbidity, poly-therapy, physiological changes affecting the pharmacokinetics and pharmacodynamics of many drugs and, in some cases, poor compliance due to cognitive impairment and/or depression. In this setting, drug-drug interaction may represent a serious and even life-threatening clinical condition. Moreover, the inability to distinguish drug-induced symptoms from a definitive medical diagnosis often results in addition of yet another drug to treat the symptoms, which in turn increases drug-drug interactions. Cognitive enhancers, including acetylcholinesterase inhibitors and memantine, are the most widely prescribed agents for Alzheimer's disease (AD) patients. Behavioral and psychological symptoms of dementia, including psychotic symptoms and behavioral disorders, represent noncognitive disturbances frequently observed in AD patients. Antipsychotic drugs are at high risk of adverse events, even at modest doses, and may interfere with the progression of cognitive impairment and interact with several drugs including anti-arrhythmics and acetylcholinesterase inhibitors. Other medications often used in AD patients are represented by anxiolytic, like benzodiazepine, or antidepressant agents. These agents also might interfere with other concomitant drugs through both pharmacokinetic and pharmacodynamic mechanisms. In this review we focus on the most frequent drug-drug interactions, potentially harmful, in AD patients with behavioral symptoms considering both physiological and pathological changes in AD patients, and potential pharmacodynamic/pharmacokinetic drug interaction mechanisms.

  2. Herbal medicines in Brazil: pharmacokinetic profile and potential herb-drug interactions.

    PubMed

    Mazzari, Andre L D A; Prieto, Jose M

    2014-01-01

    A plethora of active compounds found in herbal medicines can serve as substrate for enzymes involved in the metabolism of xenobiotics. When a medicinal plant is co-administered with a conventional drug and little or no information is known about the pharmacokinetics of the plant metabolites, there is an increased risk of potential herb-drug interactions. Moreover, genetic polymorphisms in a population may act to predispose individuals to adverse reactions. The use of herbal medicines is rapidly increasing in many countries, particularly Brazil where the vast biodiversity is a potential source of new and more affordable treatments for numerous conditions. Accordingly, the Brazilian Unified Public Health System (SUS) produced a list of 71 plant species of interest, which could be made available to the population in the near future. Physicians at SUS prescribe a number of essential drugs and should herbal medicines be added to this system the chance of herb-drug interactions further increases. A review of the effects of these medicinal plants on Phase 1 and Phase 2 metabolic mechanisms and the transporter P-glycoprotein was conducted. The results have shown that approximately half of these medicinal plants lack any pharmacokinetic data. Moreover, most of the studies carried out are in vitro. Only a few reports on herb-drug interactions with essential drugs prescribed by SUS were found, suggesting that very little attention is being given to the safety of herbal medicines. Here we have taken this information to discuss the potential interactions between herbal medicines and essential drugs prescribed to Brazilian patients whilst taking into account the most common polymorphisms present in the Brazilian population. A number of theoretical interactions are pinpointed but more pharmacokinetic studies and pharmacovigilance data are needed to ascertain their clinical significance.

  3. Potential drug–drug interactions in Alzheimer patients with behavioral symptoms

    PubMed Central

    Pasqualetti, Giuseppe; Tognini, Sara; Calsolaro, Valeria; Polini, Antonio; Monzani, Fabio

    2015-01-01

    The use of multi drug regimens among the elderly population has increased tremendously over the last decade although the benefits of medications are always accompanied by potential harm, even when prescribed at recommended doses. The elderly populations are particularly at an increased risk of adverse drug reactions considering comorbidity, poly-therapy, physiological changes affecting the pharmacokinetics and pharmacodynamics of many drugs and, in some cases, poor compliance due to cognitive impairment and/or depression. In this setting, drug–drug interaction may represent a serious and even life-threatening clinical condition. Moreover, the inability to distinguish drug-induced symptoms from a definitive medical diagnosis often results in addition of yet another drug to treat the symptoms, which in turn increases drug–drug interactions. Cognitive enhancers, including acetylcholinesterase inhibitors and memantine, are the most widely prescribed agents for Alzheimer’s disease (AD) patients. Behavioral and psychological symptoms of dementia, including psychotic symptoms and behavioral disorders, represent noncognitive disturbances frequently observed in AD patients. Antipsychotic drugs are at high risk of adverse events, even at modest doses, and may interfere with the progression of cognitive impairment and interact with several drugs including anti-arrhythmics and acetylcholinesterase inhibitors. Other medications often used in AD patients are represented by anxiolytic, like benzodiazepine, or antidepressant agents. These agents also might interfere with other concomitant drugs through both pharmacokinetic and pharmacodynamic mechanisms. In this review we focus on the most frequent drug–drug interactions, potentially harmful, in AD patients with behavioral symptoms considering both physiological and pathological changes in AD patients, and potential pharmacodynamic/pharmacokinetic drug interaction mechanisms. PMID:26392756

  4. Potential drug-drug interactions in Alzheimer patients with behavioral symptoms.

    PubMed

    Pasqualetti, Giuseppe; Tognini, Sara; Calsolaro, Valeria; Polini, Antonio; Monzani, Fabio

    2015-01-01

    The use of multi drug regimens among the elderly population has increased tremendously over the last decade although the benefits of medications are always accompanied by potential harm, even when prescribed at recommended doses. The elderly populations are particularly at an increased risk of adverse drug reactions considering comorbidity, poly-therapy, physiological changes affecting the pharmacokinetics and pharmacodynamics of many drugs and, in some cases, poor compliance due to cognitive impairment and/or depression. In this setting, drug-drug interaction may represent a serious and even life-threatening clinical condition. Moreover, the inability to distinguish drug-induced symptoms from a definitive medical diagnosis often results in addition of yet another drug to treat the symptoms, which in turn increases drug-drug interactions. Cognitive enhancers, including acetylcholinesterase inhibitors and memantine, are the most widely prescribed agents for Alzheimer's disease (AD) patients. Behavioral and psychological symptoms of dementia, including psychotic symptoms and behavioral disorders, represent noncognitive disturbances frequently observed in AD patients. Antipsychotic drugs are at high risk of adverse events, even at modest doses, and may interfere with the progression of cognitive impairment and interact with several drugs including anti-arrhythmics and acetylcholinesterase inhibitors. Other medications often used in AD patients are represented by anxiolytic, like benzodiazepine, or antidepressant agents. These agents also might interfere with other concomitant drugs through both pharmacokinetic and pharmacodynamic mechanisms. In this review we focus on the most frequent drug-drug interactions, potentially harmful, in AD patients with behavioral symptoms considering both physiological and pathological changes in AD patients, and potential pharmacodynamic/pharmacokinetic drug interaction mechanisms. PMID:26392756

  5. Effect of taurine and potential interactions with caffeine on cardiovascular function.

    PubMed

    Schaffer, Stephen W; Shimada, Kayoko; Jong, Chian Ju; Ito, Takashi; Azuma, Junichi; Takahashi, Kyoko

    2014-05-01

    The major impetus behind the rise in energy drink popularity among adults is their ability to heighten mental alertness, improve physical performance and supply energy. However, accompanying the exponential growth in energy drink usage have been recent case reports and analyses from the National Poison Data System, raising questions regarding the safety of energy drinks. Most of the safety concerns have centered on the effect of energy drinks on cardiovascular and central nervous system function. Although the effects of caffeine excess have been widely studied, little information is available on potential interactions between the other active ingredients of energy drinks and caffeine. One of the active ingredients often mentioned as a candidate for interactions with caffeine is the beta-amino acid, taurine. Although taurine is considered a conditionally essential nutrient for humans and is thought to play a key role in several human diseases, clinical studies evaluating the effects of taurine are limited. However, based on this review regarding possible interactions between caffeine and taurine, we conclude that taurine should neutralize several untoward effects of caffeine excess. In agreement with this conclusion, the European Union's Scientific Committee on Food published a report in March 2003 summarizing its investigation into potential interactions of the ingredients in energy drinks. At the cardiovascular level, they concluded that "if there are any interactions between caffeine and taurine, taurine might reduce the cardiovascular effects of caffeine." Although these interactions remain to be further examined in humans, the physiological functions of taurine appear to be inconsistent with the adverse cardiovascular symptoms associated with excessive consumption of caffeine-taurine containing beverages.

  6. Multi-time Schrödinger equations cannot contain interaction potentials

    SciTech Connect

    Petrat, Sören; Tumulka, Roderich

    2014-03-15

    Multi-time wave functions are wave functions that have a time variable for every particle, such as ϕ(t{sub 1},x{sub 1},...,t{sub N},x{sub N}). They arise as a relativistic analog of the wave functions of quantum mechanics but can be applied also in quantum field theory. The evolution of a wave function with N time variables is governed by N Schrödinger equations, one for each time variable. These Schrödinger equations can be inconsistent with each other, i.e., they can fail to possess a joint solution for every initial condition; in fact, the N Hamiltonians need to satisfy a certain commutator condition in order to be consistent. While this condition is automatically satisfied for non-interacting particles, it is a challenge to set up consistent multi-time equations with interaction. We prove for a wide class of multi-time Schrödinger equations that the presence of interaction potentials (given by multiplication operators) leads to inconsistency. We conclude that interaction has to be implemented instead by creation and annihilation of particles, which, in fact, can be done consistently [S. Petrat and R. Tumulka, “Multi-time wave functions for quantum field theory,” Ann. Physics (to be published)]. We also prove the following result: When a cut-off length δ > 0 is introduced (in the sense that the multi-time wave function is defined only on a certain set of spacelike configurations, thereby breaking Lorentz invariance), then the multi-time Schrödinger equations with interaction potentials of range δ are consistent; however, in the desired limit δ → 0 of removing the cut-off, the resulting multi-time equations are interaction-free, which supports the conclusion expressed in the title.

  7. Protein interaction network analysis--approach for potential drug target identification in Mycobacterium tuberculosis.

    PubMed

    Kushwaha, Sandeep K; Shakya, Madhvi

    2010-01-21

    In host-parasite diseases like tuberculosis, non-homologous proteins (enzymes) as drug target are first preference. Most potent drug target can be identified among large number of non-homologous protein through protein interaction network analysis. In this study, the entire promising dimension has been explored for identification of potential drug target. A comparative metabolic pathway analysis of the host Homo sapiens and the pathogen M. tuberculosis H37Rv has been performed with three level of analysis. In first level, the unique metabolic pathways of M. tuberculosis have been identified through its comparative study with H. sapiens and identification of non-homologous proteins has been done through BLAST similarity search. In second level, choke-point analysis has been performed with identified non-homologous proteins of metabolic pathways. In third level, two type of analysis have been performed through protein interaction network. First analysis has been done to find out the most potential metabolic functional associations among all identified choke point proteins whereas second analysis has been performed to find out the functional association of high metabolic interacting proteins to pathogenesis causing proteins. Most interactive metabolic proteins which have highest number of functional association with pathogenesis causing proteins have been considered as potential drug target. A list of 18 potential drug targets has been proposed which are various stages of progress at the TBSGC and proposed drug targets are also studied for other pathogenic strains. As a case study, we have built a homology model of identified drug targets histidinol-phosphate aminotransferase (HisC1) using MODELLER software and various information have been generated through molecular dynamics which will be useful in wetlab structure determination. The generated model could be further explored for insilico docking studies with suitable inhibitors.

  8. [Population potential, spatial interaction, and borders: from two German states to unification].

    PubMed

    Grasland, C

    1990-01-01

    The concept of population potential is used to analyze the spatial dynamics of the populations of East and West Germany from 1960 to 1985. Choosing different functions of spatial interaction allows different hypotheses to be drawn up concerning the location of the geographical center of the German people. Diachronic analysis permits the identification of poles of population growth and decline. The author introduces a barrier effect to allow the demographic impact of reunification to be considered. (SUMMARY IN ENG)

  9. Formation of chain structures in systems of charged grains interacting via isotropic pair potentials

    SciTech Connect

    Vaulina, O. S.; Lisina, I. I.; Koss, K. G.

    2013-05-15

    Conditions for the formation of chain structures of charged grains confined in the gravitational field by external electric fields are studied analytically and numerically. The relationships between the parameters of the pair interaction potential, the number of grains, and the electric field gradient in the trap are found. A criterion for the violation of stable equilibrium in a quasi-one-dimensional chain of grains and the formation of a new configuration in the system is proposed.

  10. "Features of two proteins of Leptospira interrogans with potential role in host-pathogen interactions"

    PubMed Central

    2012-01-01

    Background Leptospirosis is considered a re-emerging infectious disease caused by pathogenic spirochaetes of the genus Leptospira. Pathogenic leptospires have the ability to survive and disseminate to multiple organs after penetrating the host. Leptospires were shown to express surface proteins that interact with the extracellular matrix (ECM) and to plasminogen (PLG). This study examined the interaction of two putative leptospiral proteins with laminin, collagen Type I, collagen Type IV, cellular fibronectin, plasma fibronectin, PLG, factor H and C4bp. Results We show that two leptospiral proteins encoded by LIC11834 and LIC12253 genes interact with laminin in a dose - dependent and saturable mode, with dissociation equilibrium constants (KD) of 367.5 and 415.4 nM, respectively. These proteins were named Lsa33 and Lsa25 (Leptospiral surface adhesin) for LIC11834 and LIC12253, respectively. Metaperiodate - treated laminin reduced Lsa25 - laminin interaction, suggesting that sugar moieties of this ligand participate in this interaction. The Lsa33 is also PLG - binding receptor, with a KD of 23.53 nM, capable of generating plasmin in the presence of an activator. Although in a weak manner, both proteins interact with C4bp, a regulator of complement classical route. In silico analysis together with proteinase K and immunoflorescence data suggest that these proteins might be surface exposed. Moreover, the recombinant proteins partially inhibited leptospiral adherence to immobilized laminin and PLG. Conclusions We believe that these multifunctional proteins have the potential to participate in the interaction of leptospires to hosts by mediating adhesion and by helping the bacteria to escape the immune system and to overcome tissue barriers. To our knowledge, Lsa33 is the first leptospiral protein described to date with the capability of binding laminin, PLG and C4bp in vitro. PMID:22463075

  11. Improving intermolecular interactions in DFTB3 using extended polarization from chemical-potential equalization

    SciTech Connect

    Christensen, Anders S. E-mail: cui@chem.wisc.edu; Cui, Qiang E-mail: cui@chem.wisc.edu; Elstner, Marcus

    2015-08-28

    Semi-empirical quantum mechanical methods traditionally expand the electron density in a minimal, valence-only electron basis set. The minimal-basis approximation causes molecular polarization to be underestimated, and hence intermolecular interaction energies are also underestimated, especially for intermolecular interactions involving charged species. In this work, the third-order self-consistent charge density functional tight-binding method (DFTB3) is augmented with an auxiliary response density using the chemical-potential equalization (CPE) method and an empirical dispersion correction (D3). The parameters in the CPE and D3 models are fitted to high-level CCSD(T) reference interaction energies for a broad range of chemical species, as well as dipole moments calculated at the DFT level; the impact of including polarizabilities of molecules in the parameterization is also considered. Parameters for the elements H, C, N, O, and S are presented. The Root Mean Square Deviation (RMSD) interaction energy is improved from 6.07 kcal/mol to 1.49 kcal/mol for interactions with one charged species, whereas the RMSD is improved from 5.60 kcal/mol to 1.73 for a set of 9 salt bridges, compared to uncorrected DFTB3. For large water clusters and complexes that are dominated by dispersion interactions, the already satisfactory performance of the DFTB3-D3 model is retained; polarizabilities of neutral molecules are also notably improved. Overall, the CPE extension of DFTB3-D3 provides a more balanced description of different types of non-covalent interactions than Neglect of Diatomic Differential Overlap type of semi-empirical methods (e.g., PM6-D3H4) and PBE-D3 with modest basis sets.

  12. Improving intermolecular interactions in DFTB3 using extended polarization from chemical-potential equalization

    PubMed Central

    Christensen, Anders S.; Elstner, Marcus; Cui, Qiang

    2015-01-01

    Semi-empirical quantum mechanical methods traditionally expand the electron density in a minimal, valence-only electron basis set. The minimal-basis approximation causes molecular polarization to be underestimated, and hence intermolecular interaction energies are also underestimated, especially for intermolecular interactions involving charged species. In this work, the third-order self-consistent charge density functional tight-binding method (DFTB3) is augmented with an auxiliary response density using the chemical-potential equalization (CPE) method and an empirical dispersion correction (D3). The parameters in the CPE and D3 models are fitted to high-level CCSD(T) reference interaction energies for a broad range of chemical species, as well as dipole moments calculated at the DFT level; the impact of including polarizabilities of molecules in the parameterization is also considered. Parameters for the elements H, C, N, O, and S are presented. The Root Mean Square Deviation (RMSD) interaction energy is improved from 6.07 kcal/mol to 1.49 kcal/mol for interactions with one charged species, whereas the RMSD is improved from 5.60 kcal/mol to 1.73 for a set of 9 salt bridges, compared to uncorrected DFTB3. For large water clusters and complexes that are dominated by dispersion interactions, the already satisfactory performance of the DFTB3-D3 model is retained; polarizabilities of neutral molecules are also notably improved. Overall, the CPE extension of DFTB3-D3 provides a more balanced description of different types of non-covalent interactions than Neglect of Diatomic Differential Overlap type of semi-empirical methods (e.g., PM6-D3H4) and PBE-D3 with modest basis sets. PMID:26328834

  13. Multisensory interactions elicited by audiovisual stimuli presented peripherally in a visual attention task: a behavioral and event-related potential study in humans.

    PubMed

    Wu, Jinglong; Li, Qi; Bai, Ou; Touge, Tetsuo

    2009-12-01

    We applied behavioral and event-related potential measurements to study human multisensory interactions induced by audiovisual (AV) stimuli presented peripherally in a visual attention task in which an irrelevant auditory stimulus occasionally accompanied the visual stimulus. A stream of visual, auditory, and AV stimuli was randomly presented to the left or right side of the subjects; subjects covertly attended to the visual stimuli on either the left or right side and promptly responded to visual targets on that side. Behavioral results showed that responses to AV stimuli were faster and more accurate than those to visual stimuli only. Three event-related potential components related to AV interactions were identified: (1) over the right temporal area, approximately 200 to 220 milliseconds; (2) over the centromedial area, approximately 290 to 310 milliseconds; and (3) over the left and right ventral temporal area, approximately 290 to 310 milliseconds. We found that these interaction effects occurred slightly later than those reported in previously published AV interaction studies in which AV stimuli were presented centrally. Our results suggest that the retinotopic location of stimuli affects AV interactions occurring at later stages of cognitive processing in response to a visual attention task.

  14. Managing potential drug-drug interactions between gastric acid-reducing agents and antiretroviral therapy: experience from a large HIV-positive cohort.

    PubMed

    Lewis, J M; Stott, K E; Monnery, D; Seden, K; Beeching, N J; Chaponda, M; Khoo, S; Beadsworth, M B J

    2016-02-01

    Drug-drug interactions between antiretroviral therapy and other drugs are well described. Gastric acid-reducing agents are one such class. However, few data exist regarding the frequency of and indications for prescription, nor risk assessment in the setting of an HIV cohort receiving antiretroviral therapy. To assess prevalence of prescription of gastric acid-reducing agents and drug-drug interaction within a UK HIV cohort, we reviewed patient records for the whole cohort, assessing demographic data, frequency and reason for prescription of gastric acid-reducing therapy. Furthermore, we noted potential drug-drug interaction and whether risk had been documented and mitigated. Of 701 patients on antiretroviral therapy, 67 (9.6%) were prescribed gastric acid-reducing therapy. Of these, the majority (59/67 [88.1%]) were prescribed proton pump inhibitors. We identified four potential drug-drug interactions, which were appropriately managed by temporally separating the administration of gastric acid-reducing agent and antiretroviral therapy, and all four of these patients remained virally suppressed. Gastric acid-reducing therapy, in particular proton pump inhibitor therapy, appears common in patients prescribed antiretroviral therapy. Whilst there remains a paucity of published data, our findings are comparable to those in other European cohorts. Pharmacovigilance of drug-drug interactions in HIV-positive patients is vital. Education of patients and staff, and accurate data-gathering tools, will enhance patient safety.

  15. An improved density functional theory description of the Ge(100)c(4×2) surface using the MBJLDA xc potential and spin-orbit interactions.

    PubMed

    Smith, Phillip V; Radny, Marian W; Shah, G Ali

    2013-02-01

    The MBJLDA xc potential (modified Becke-Johnson exchange potential with local density approximation correlation) proposed by Tran and Blaha has been designed and shown to significantly improve the description of the fundamental energy gaps of a wide range of bulk materials. Recently we reported that combining this MBJLDA xc potential with spin-orbit interactions and local density approximation pseudopotentials within the plane wave density functional method led to results for bulk germanium that were at least as accurate as those obtained from far more sophisticated and computationally expensive methods such as the GW method. Here we demonstrate that the application of this approach to the Ge(100)c(4×2) surface yields results that are in excellent agreement with the available experimental data.

  16. Whitebark pine facilitation at treeline: potential interactions for disruption by an invasive pathogen.

    PubMed

    Tomback, Diana F; Blakeslee, Sarah C; Wagner, Aaron C; Wunder, Michael B; Resler, Lynn M; Pyatt, Jill C; Diaz, Soledad

    2016-08-01

    In stressful environments, facilitation often aids plant establishment, but invasive plant pathogens may potentially disrupt these interactions. In many treeline communities in the northern Rocky Mountains of the U.S. and Canada, Pinus albicaulis, a stress-tolerant pine, initiates tree islands at higher frequencies than other conifers - that is, leads to leeward tree establishment more frequently. The facilitation provided by a solitary (isolated) P. albicaulis leading to tree island initiation may be important for different life-history stages for leeward conifers, but it is not known which life-history stages are influenced and protection provided. However, P. albicaulis mortality from the non-native pathogen Cronartium ribicola potentially disrupts these facilitative interactions, reducing tree island initiation. In two Rocky Mountain eastern slope study areas, we experimentally examined fundamental plant-plant interactions which might facilitate tree island formation: the protection offered by P. albicaulis to leeward seed and seedling life-history stages, and to leeward krummholz conifers. In the latter case, we simulated mortality from C. ribicola for windward P. albicaulis to determine whether loss of P. albicaulis from C. ribicola impacts leeward conifers. Relative to other common solitary conifers at treeline, solitary P. albicaulis had higher abundance. More seeds germinated in leeward rock microsites than in conifer or exposed microsites, but the odds of cotyledon seedling survival during the growing season were highest in P. albicaulis microsites. Planted seedling survival was low among all microsites examined. Simulating death of windward P. albicaulis by C. ribicola reduced shoot growth of leeward trees. Loss of P. albicaulis to exotic disease may limit facilitation interactions and conifer community development at treeline and potentially impede upward movement as climate warms. PMID:27551372

  17. Communication: Rate coefficients of the H + CH{sub 4} → H{sub 2} + CH{sub 3} reaction from ring polymer molecular dynamics on a highly accurate potential energy surface

    SciTech Connect

    Meng, Qingyong Chen, Jun Zhang, Dong H.

    2015-09-14

    The ring polymer molecular dynamics (RPMD) calculations are performed to calculate rate constants for the title reaction on the recently constructed potential energy surface based on permutation invariant polynomial (PIP) neural-network (NN) fitting [J. Li et al., J. Chem. Phys. 142, 204302 (2015)]. By inspecting convergence, 16 beads are used in computing free-energy barriers at 300 K ≤ T ≤ 1000 K, while different numbers of beads are used for transmission coefficients. The present RPMD rates are in excellent agreement with quantum rates computed on the same potential energy surface, as well as with the experimental measurements, demonstrating further that the RPMD is capable of producing accurate rates for polyatomic chemical reactions even at rather low temperatures.

  18. Fully Coriolis-coupled quantum studies of the H + O2 (upsilon i = 0-2, j i = 0,1) --> OH + O reaction on an accurate potential energy surface: integral cross sections and rate constants.

    PubMed

    Lin, Shi Ying; Sun, Zhigang; Guo, Hua; Zhang, Dong Hui; Honvault, Pascal; Xie, Daiqian; Lee, Soo-Y

    2008-01-31

    We present accurate quantum calculations of the integral cross section and rate constant for the H + O2 --> OH + O combustion reaction on a recently developed ab initio potential energy surface using parallelized time-dependent and Chebyshev wavepacket methods. Partial wave contributions up to J = 70 were computed with full Coriolis coupling, which enabled us to obtain the initial state-specified integral cross sections up to 2.0 eV of the collision energy and thermal rate constants up to 3000 K. The integral cross sections show a large reaction threshold due to the quantum endothermicity of the reaction, and they monotonically increase with the collision energy. As a result, the temperature dependence of the rate constant is of the Arrhenius type. In addition, it was found that reactivity is enhanced by reactant vibrational excitation. The calculated thermal rate constant shows a significant improvement over that obtained on the DMBE IV potential, but it still underestimates the experimental consensus.

  19. The Δ potential in nuclear matter from the Argonne v28 interaction

    NASA Astrophysics Data System (ADS)

    Baldo, M.; Ferreira, L. S.

    1992-07-01

    The model potential Argonne v28, which allows all possible transitions from NN states to NΔ and ΔΔ ones, is used to calculate the potential energy of the Δ isobar in nuclear matter. All diagrams with one nucleon hole line are summed up in the framework of a G-matrix approach. The Δ potential so obtained was found to be weakly attractive at low density, becoming repulsive at increasing density with a value of 50 MeV at saturation. The repulsion receives the main contribution from the isotropic spin T=2 channels and appears to be in contradiction with the phenomonology on Δ production in nuclei. The possible drawbacks of the interaction or the possible missing physical effects are briefly discussed. Permanent address: Centro de Física, da Matèria Condensada, Avenida Gama Pinto 2, P-1699 Lisbon, Portugal.

  20. Polarizable interaction potential for molecular dynamics simulations of actinoids(III) in liquid water.

    PubMed

    Duvail, Magali; Martelli, Fausto; Vitorge, Pierre; Spezia, Riccardo

    2011-07-28

    In this work, we have developed a polarizable classical interaction potential to study actinoids(III) in liquid water. This potential has the same analytical form as was recently used for lanthanoid(III) hydration [M. Duvail, P. Vitorge, and R. Spezia, J. Chem. Phys. 130, 104501 (2009)]. The hydration structure obtained with this potential is in good agreement with the experimentally measured ion-water distances and coordination numbers for the first half of the actinoid series. In particular, the almost linearly decreasing water-ion distance found experimentally is replicated within the calculations, in agreement with the actinoid contraction behavior. We also studied the hydration of the last part of the series, for which no structural experimental data are available, which allows us to provide some predictive insights on these ions. In particular we found that the ion-water distance decreases almost linearly across the series with a smooth decrease of coordination number from nine to eight at the end.

  1. The hydrogen peroxide-rare gas systems: quantum chemical calculations and hyperspherical harmonic representation of the potential energy surface for atom-floppy molecule interactions.

    PubMed

    Barreto, Patricia R P; Vilela, Alessandra F A; Lombardi, Andrea; Maciel, Glauciete S; Palazzetti, Federico; Aquilanti, Vincenzo

    2007-12-13

    A quantum chemical exploration is reported on the interaction potentials of H2O2 with the rare gases, He, Ne, Ar, Kr, and Xe. Hydrogen peroxide (the simplest example of chiral molecule in its equilibrium geometry) is modeled as rigid except for the torsional mode around the O-O bond. However, on the basis of previous work (Maciel, G. S.; et al. Chem. Phys. Lett. 2006 432, 383), the internal mode description is based, rather than on the vectors of the usual valence picture, on the orthogonal local representation, which was demonstrated useful for molecular dynamics simulations, because the torsion around the vector joining the center-of-mass of the two OH radicals mimics accurately the adiabatic reaction path for chirality changing isomerization, following the torsional potential energy profile from equilibrium through the barriers for the trans and cis geometries. The basic motivation of this work is the determination of potential energy surfaces for the interactions to be used in classical and quantum simulations of molecular collisions, specifically those leading to chirality changes of possible relevance in the modeling of prebiotic phenomena. Particular attention is devoted to the definition of coordinates and expansion formulas for the potentials, allowing for a faithful representation of geometrical and symmetry properties of these systems, prototypical of the interaction of an atom with a floppy molecule.

  2. 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.

  3. Potential interactions between pericytes and oligodendrocyte precursor cells in perivascular regions of cerebral white matter

    PubMed Central

    Maki, Takakuni; Maeda, Mitsuyo; Uemura, Maiko; Lo, Evan K.; Terasaki, Yasukazu; Liang, Anna C.; Shindo, Akihiro; Choi, Yoon Kyung; Taguchi, Akihiko; Matsuyama, Tomohiro; Takahashi, Ryosuke; Ihara, Masafumi; Arai, Ken

    2015-01-01

    Pericytes are embedded within basal lamina and play multiple roles in the perivascular niche in brain. Recently, oligodendrocyte precursor cells (OPCs) have also been reported to associate with cerebral endothelium. Is it possible that within this gliovascular locus, there may also exist potential spatial and functional interactions between pericytes and OPCs? Here, we demonstrated that in the perivascular region of cerebral white matter, pericytes and OPCs may attach and support each other. Immunostaining showed that pericytes and OPCs are localized in close contact with each other in mouse white matter at postnatal days 0, 60 and 240. Electron microscopic analysis confirmed that pericytes attached to OPCs via basal lamina in the perivascular region. The close proximity between these two cell types was also observed in postmortem human brains. Functional interaction between pericytes and OPCs was assessed by in vitro media transfer experiments. When OPC cultures were treated with pericyte-conditioned media, OPC number increased. Similarly, pericyte number increased when pericytes were maintained in OPC-conditioned media. Taken together, our data suggest a potential anatomical and functional interaction between pericytes and OPCs in cerebral white matter. PMID:25936593

  4. Stromal interactions as regulators of tumor growth and therapeutic response: A potential target for photodynamic therapy?

    PubMed Central

    Celli, Jonathan P.

    2013-01-01

    It has become increasingly widely recognized that the stroma plays several vital roles in tumor growth and development and that tumor-stroma interactions can in many cases account poor therapeutic response. Inspired by an emerging body of literature, we consider the potential role of photodynamic therapy (PDT) for targeting interactions with stromal fibroblasts and mechano-sensitive signaling with the extracellular matrix as a means to drive tumors toward a more therapeutically responsive state and synergize with other treatments. This concept is particularly relevant for cancer of the pancreas, which is characterized by tumors with a profoundly dense, rigid fibrous stroma. Here we introduce new in vitro systems to model interactions between pancreatic tumors and their mechanical microenvironment and restore signaling with stromal fibroblasts. Using one such model as a test bed it is shown here that PDT treatment is able to destroy fibroblasts in an in vitro 3D pancreatic tumor-fibroblast co-culture. These results and the literature suggest the further development of PDT as a potential modality for stromal depletion. PMID:23457416

  5. Quantitative assessment of substituent effects on cation-π interactions using molecular electrostatic potential topography.

    PubMed

    Sayyed, Fareed Bhasha; Suresh, Cherumuttathu H

    2011-08-25

    A molecular electrostatic potential (MESP) topography based approach has been proposed to quantify the substituent effects on cation-π interactions in complexes of mono-, di-, tri-, and hexasubstituted benzenes with Li(+), Na(+), K(+), and NH(4)(+). The MESP minimum (V(min)) on the π-region of C(6)H(5)X showed strong linear dependency to the cation-π interaction energy, E(M(+)). Further, cation-π distance correlated well with V(min)-π distance. The difference between V(min) of C(6)H(5)X and C(6)H(6) (ΔV(min)) is proposed as a good parameter to quantify the substituent effect on cation-π interaction. Compared to benzene, electron-donating groups stabilize the di-, tri-, and hexasubstituted cation-π complexes while electron-withdrawing groups destabilize them. In multiple substituted complexes, E(M(+)) is almost equal (∼95%) to the sum of the individual substituent contributions (E(M(+)) ≈ Σ(ΔE(M(+)))), suggesting that substituent effect on cation-π interactions is largely additive. The ΔV(min) of C(6)H(5)X systems and additivity feature have been used to make predictions on the interaction energies of 80 multiple substituted cation-π complexes with above 97% accuracy. The average mean absolute deviation of the V(min)-predicted interaction energy, E(M(+))(V) from the calculated E(M(+)) is -0.18 kcal/mol for Li(+), -0.09 kcal/mol for Na(+), -0.43 kcal/mol for K(+), and -0.67 kcal/mol for NH(4)(+), which emphasize the predictive power of V(min) as well as the additive feature of the substituent effect.

  6. Interaction of green tea polyphenol epigallocatechin-3-gallate with sunitinib: potential risk of diminished sunitinib bioavailability.

    PubMed

    Ge, Jun; Tan, Ben-Xu; Chen, Ye; Yang, Li; Peng, Xing-Chen; Li, Hong-Ze; Lin, Hong-Jun; Zhao, Yu; Wei, Meng; Cheng, Ke; Li, Long-Hao; Dong, Hang; Gao, Feng; He, Jian-Ping; Wu, Yang; Qiu, Meng; Zhao, Ying-Lan; Su, Jing-Mei; Hou, Jian-Mei; Liu, Ji-Yan

    2011-06-01

    Sunitinib, a novel oral multi-targeted tyrosine kinase inhibitor for patients with metastatic renal cell carcinoma (mRCC) and advanced gastrointestinal stromal tumor, has a good prospect for clinical application and is being investigated for the potential therapy of other tumors. We observed the phenomenon that drinking tea interfered with symptom control in an mRCC patient treated with sunitinib and speculated that green tea or its components might interact with sunitinib. This study was performed to investigate whether epigallocatechin-3-gallate (EGCG), the major constituent of green tea, interacted with sunitinib. The interaction between EGCG and sunitinib was examined in vitro and in vivo. (1)H nuclear magnetic resonance ((1)H-NMR) spectroscopy and mass spectrometry (MS) were used to analyze the interaction between these two molecules and whether a new compound was formed. Solutions of sunitinib and EGCG were intragastrically administered to rats to investigate whether the plasma concentrations of sunitinib were affected by EGCG. In this study, we noticed that a precipitate was formed when the solutions of sunitinib and EGCG were mixed under both neutral and acidic conditions. (1)H-NMR spectra indicated an interaction between EGCG and sunitinib, but no new compound was observed by MS. Sticky semisolid contents were found in the stomachs of sunitinib and EGCG co-administrated mice. The AUC(0-∞) and C (max) of plasma sunitinib were markedly reduced by co-administration of EGCG to rats. Our study firstly showed that EGCG interacted with sunitinib and reduced the bioavailability of sunitinib. This finding has significant practical implications for tea-drinking habit during sunitinib administration. PMID:21331509

  7. Erythromycin potentiates PR interval prolonging effect of verapamil in the rat: A pharmacodynamic drug interaction

    SciTech Connect

    Dakhel, Yaman; Jamali, Fakhreddin . E-mail: fjamali@ualberta.ca

    2006-07-01

    Calcium channel blockers and macrolide antibiotics account for many drug interactions. Anecdotal reports suggest interactions between the two resulting in severe side effects. We studied the interaction between verapamil and erythromycin in the rat to see whether it occurs at the pharmacokinetics or pharmacodynamic level. Adult male Sprague-Dawley rats received doses of 1 mg/kg verapamil or 100 mg/kg erythromycin alone or in combination (n = 6/group). Serial blood samples (0-6 h) were taken for determination of the drug concentrations using HPLC. Electrocardiograms were recorded (0-6 h) through subcutaneously inserted lead II. Binding of the drugs to plasma proteins was studied using spiked plasma. Verapamil prolonged PR but not QT interval. Erythromycin prolonged QT but not PR interval. The combination resulted in a significant increase in PR interval prolongation and AV node blocks but did not further prolong QT interval. Pharmacokinetics and protein binding of neither drug were altered by the other. Our rat data confirm the anecdotal human case reports that combination of erythromycin and verapamil can result in potentiation of the cardiovascular response. The interaction appears to be at the pharmacodynamic rather than pharmacokinetic level hence may be extrapolated to other calcium channel antagonists.

  8. Clinical relevancy and risks of potential drug–drug interactions in intensive therapy

    PubMed Central

    Rodrigues, Aline Teotonio; Stahlschmidt, Rebeca; Granja, Silvia; Falcão, Antonio Luis Eiras; Moriel, Patricia; Mazzola, Priscila Gava

    2014-01-01

    Purpose Evaluate the potential Drug–Drug Interactions (pDDI) found in prescription orders of adult Intensive Care Unit (ICU) of a Brazilian public health system hospital; quantify and qualify the pDDI regarding their severity and risks to the critical patient, using the database from Micromedex®. Methods Prospective study (January–December of 2011) collecting and evaluating 369 prescription orders (convenient sampling), one per patient. Results During the study 1844 pDDIs were identified and distributed in 405 pairs (medication A × medication B combination). There was an average of 5.00 ± 5.06 pDDIs per prescription order, the most prevalent being moderate and important interactions, present in 74% and 67% of prescription orders, respectively. In total, there were 9 contraindicated, 129 important and 204 moderate pDDIs. Among them 52 had as management recommendation to “avoid concomitant use” or “suspension of medication”, while 306 had as recommendation “continuous and adequate monitoring”. Conclusion The high number of pDDIs found in the study combined with the evaluation of the clinical relevancy of the most frequent pDDIs in the ICU shows that moderate and important interactions are highly incident. As the majority of them demand monitoring and adequate management, being aware of these interactions is major information for the safe and individualized risk management. PMID:27134536

  9. Entangling spin-spin interactions of ions in individually controlled potential wells

    NASA Astrophysics Data System (ADS)

    Wilson, Andrew; Colombe, Yves; Brown, Kenton; Knill, Emanuel; Leibfried, Dietrich; Wineland, David

    2014-03-01

    Physical systems that cannot be modeled with classical computers appear in many different branches of science, including condensed-matter physics, statistical mechanics, high-energy physics, atomic physics and quantum chemistry. Despite impressive progress on the control and manipulation of various quantum systems, implementation of scalable devices for quantum simulation remains a formidable challenge. As one approach to scalability in simulation, here we demonstrate an elementary building-block of a configurable quantum simulator based on atomic ions. Two ions are trapped in separate potential wells that can individually be tailored to emulate a number of different spin-spin couplings mediated by the ions' Coulomb interaction together with classical laser and microwave fields. We demonstrate deterministic tuning of this interaction by independent control of the local wells and emulate a particular spin-spin interaction to entangle the internal states of the two ions with 0.81(2) fidelity. Extension of the building-block demonstrated here to a 2D-network, which ion-trap micro-fabrication processes enable, may provide a new quantum simulator architecture with broad flexibility in designing and scaling the arrangement of ions and their mutual interactions. This research was funded by the Office of the Director of National Intelligence (ODNI), Intelligence Advanced Research Projects Activity (IARPA), ONR, and the NIST Quantum Information Program.

  10. Assessment of Potential Herb-Drug Interactions among Nigerian Adults with Type-2 Diabetes.

    PubMed

    Ezuruike, Udoamaka; Prieto, Jose M

    2016-01-01

    It is becoming increasingly evident that patients with diabetes do not rely only on prescription drugs for their disease management. The use of herbal medicines is one of the self-management practices adopted by these patients, often without the knowledge of their healthcare practitioners. This study assessed the potential for pharmacokinetic herb-drug interactions (HDIs) amongst Nigerian adult diabetic patients. This was done through a literature analysis of the pharmacokinetic profile of their herbal medicines and prescription drugs, based on information obtained from 112 patients with type-2 diabetes attending two secondary health care facilities in Nigeria. Fifty percent of the informants used herbal medicines alongside their prescription drugs. Worryingly, 60% of the patients taking herbal medicines did not know their identity, thus increasing the risk of unidentified HDIs. By comparing the pharmacokinetic profile of eight identified herbs taken by the patients for the management of diabetes against those of the prescription drugs, several scenarios of potential HDIs were identified and their clinical relevance is discussed. The lack of clinical predictors points toward cultural factors as the influence for herb use, making it more difficult to identify these patients and in turn monitor potential HDIs. In identifying these possible interactions, we have highlighted the need for healthcare professionals to promote a proactive monitoring of patients' use of herbal medicines. PMID:27559312

  11. Assessment of Potential Herb-Drug Interactions among Nigerian Adults with Type-2 Diabetes

    PubMed Central

    Ezuruike, Udoamaka; Prieto, Jose M.

    2016-01-01

    It is becoming increasingly evident that patients with diabetes do not rely only on prescription drugs for their disease management. The use of herbal medicines is one of the self-management practices adopted by these patients, often without the knowledge of their healthcare practitioners. This study assessed the potential for pharmacokinetic herb-drug interactions (HDIs) amongst Nigerian adult diabetic patients. This was done through a literature analysis of the pharmacokinetic profile of their herbal medicines and prescription drugs, based on information obtained from 112 patients with type-2 diabetes attending two secondary health care facilities in Nigeria. Fifty percent of the informants used herbal medicines alongside their prescription drugs. Worryingly, 60% of the patients taking herbal medicines did not know their identity, thus increasing the risk of unidentified HDIs. By comparing the pharmacokinetic profile of eight identified herbs taken by the patients for the management of diabetes against those of the prescription drugs, several scenarios of potential HDIs were identified and their clinical relevance is discussed. The lack of clinical predictors points toward cultural factors as the influence for herb use, making it more difficult to identify these patients and in turn monitor potential HDIs. In identifying these possible interactions, we have highlighted the need for healthcare professionals to promote a proactive monitoring of patients' use of herbal medicines. PMID:27559312

  12. Experimenting with ecosystem interaction networks in search of threshold potentials in real-world marine ecosystems.

    PubMed

    Thrush, Simon F; Hewitt, Judi E; Parkes, Samantha; Lohrer, Andrew M; Pilditch, Conrad; Woodin, Sarah A; Wethey, David S; Chiantore, Mariachiara; Asnaghi, Valentina; De Juan, Silvia; Kraan, Casper; Rodil, Ivan; Savage, Candida; Van Colen, Carl

    2014-06-01

    Thresholds profoundly affect our understanding and management of ecosystem dynamics, but we have yet to develop practical techniques to assess the risk that thresholds will be crossed. Combining ecological knowledge of critical system interdependencies with a large-scale experiment, we tested for breaks in the ecosystem interaction network to identify threshold potential in real-world ecosystem dynamics. Our experiment with the bivalves Macomona liliana and Austrovenus stutchburyi on marine sandflats in New Zealand demonstrated that reductions in incident sunlight changed the interaction network between sediment biogeochemical fluxes, productivity, and macrofauna. By demonstrating loss of positive feedbacks and changes in the architecture of the network, we provide mechanistic evidence that stressors lead to break points in dynamics, which theory predicts predispose a system to a critical transition.

  13. Mechanisms of radiation interaction with DNA: Potential implications for radiation protection

    SciTech Connect

    Sinclair, W.K.; Fry, R.J.M.

    1987-01-01

    An overview of presentations and discussions which took place at the US Department of Energy/Commission of European Communities (DOE/CEC) workshop on ''Mechanisms of Radiation Interaction with DNA: Potential Implications for Radiation Protection,'' held at San Diego, California, January 21-22, 1987, is provided. The Department has traditionally supported fundamental research on interactions of ionizing radiation with different biological systems and at all levels of biological organization. The aim of this workshop was to review the base of knowledge in the area of mechanisms of radiation action at the DNA level, and to explore ways in which this information can be applied to the development of scientifically sound concepts and procedures for use in the field of radiation protection.

  14. Arsenic: A Review of the Element's Toxicity, Plant Interactions, and Potential Methods of Remediation.

    PubMed

    Hettick, Bryan E; Cañas-Carrell, Jaclyn E; French, Amanda D; Klein, David M

    2015-08-19

    Arsenic is a naturally occurring element with a long history of toxicity. Sites of contamination are found worldwide as a result of both natural processes and anthropogenic activities. The broad scope of arsenic toxicity to humans and its unique interaction with the environment have led to extensive research into its physicochemical properties and toxic behavior in biological systems. The purpose of this review is to compile the results of recent studies concerning the metalloid and consider the chemical and physical properties of arsenic in the broad context of human toxicity and phytoremediation. Areas of focus include arsenic's mechanisms of human toxicity, interaction with plant systems, potential methods of remediation, and protocols for the determination of metals in experimentation. This assessment of the literature indicates that controlling contamination of water sources and plants through effective remediation and management is essential to successfully addressing the problems of arsenic toxicity and contamination.

  15. Antinucleon-nucleus interaction near threshold from the Paris N bar N potential

    NASA Astrophysics Data System (ADS)

    Friedman, E.; Gal, A.; Loiseau, B.; Wycech, S.

    2015-11-01

    A general algorithm for handling the energy dependence of hadron-nucleon amplitudes in the nuclear medium, consistently with their density dependence, has been recently applied to antikaons, eta mesons and pions interacting with nuclei. Here we apply this approach to antiprotons below threshold, analyzing experimental results for antiprotonic atoms across the periodic table. It is also applied to antiproton and antineutron interactions with nuclei up to 400 MeV/c, comparing with elastic scattering and annihilation cross sections. The underlying p bar N scattering amplitudes are derived from the Paris N bar N potential, including in-medium modifications. Emphasis is placed on the role of the P-wave amplitudes with respect to the repulsive S-wave amplitudes.

  16. Research on the potential use of interactive materials on astronomy education

    NASA Astrophysics Data System (ADS)

    Voelzke, Marcos Rincon; Macedo, Josue

    2016-07-01

    This study presents results of a survey conducted at the Federal Institution of Education, Science and Technology in the North of Minas Gerais (IFNMG), and aimed to investigate the potentialities of the use of interactive materials in the teaching of astronomy. An advanced training course with involved learning activities about basic concepts of astronomy was offered to thirty-two Licenciate students in Physics, Mathematics and Biological Sciences, using the mixed methodology, combined with the three pedagogical moments. Among other aspects, the viability of the use of resources was noticed, involving digital technologies and interactive materials on teaching of astronomy, which may contribute to the broadening of methodological options for future teachers and meet their training needs.

  17. Predicting potential responses to future climate in an alpine ungulate: interspecific interactions exceed climate effects.

    PubMed

    Mason, Tom H E; Stephens, Philip A; Apollonio, Marco; Willis, Stephen G

    2014-12-01

    The altitudinal shifts of many montane populations are lagging behind climate change. Understanding habitual, daily behavioural rhythms, and their climatic and environmental influences, could shed light on the constraints on long-term upslope range-shifts. In addition, behavioural rhythms can be affected by interspecific interactions, which can ameliorate or exacerbate climate-driven effects on ecology. Here, we investigate the relative influences of ambient temperature and an interaction with domestic sheep (Ovis aries) on the altitude use and activity budgets of a mountain ungulate, the Alpine chamois (Rupicapra rupicapra). Chamois moved upslope when it was hotter but this effect was modest compared to that of the presence of sheep, to which they reacted by moving 89-103 m upslope, into an entirely novel altitudinal range. Across the European Alps, a range-shift of this magnitude corresponds to a 46% decrease in the availability of suitable foraging habitat. This highlights the importance of understanding how factors such as competition and disturbance shape a given species' realised niche when predicting potential future responses to change. Furthermore, it exposes the potential for manipulations of species interactions to ameliorate the impacts of climate change, in this case by the careful management of livestock. Such manipulations could be particularly appropriate for species where competition or disturbance already strongly restricts their available niche. Our results also reveal the potential role of behavioural flexibility in responses to climate change. Chamois reduced their activity when it was warmer, which could explain their modest altitudinal migrations. Considering this behavioural flexibility, our model predicts a small 15-30 m upslope shift by 2100 in response to climate change, less than 4% of the altitudinal shift that would be predicted using a traditional species distribution model-type approach (SDM), which assumes that species' behaviour

  18. Potential Role of Elicitins in the Interaction between Phytophthora Species and Tobacco

    PubMed Central

    Kamoun, Sophien; Young, Mary; Förster, Helga; Coffey, Michael D.; Tyler, Brett M.

    1994-01-01

    The potential role of extracellular elicitor proteins (elicitins) from Phytophthora species as avirulence factors in the interaction between Phytophthora and tobacco was examined. A survey of 85 Phytophthora isolates representing 14 species indicated that production of elicitin is almost ubiquitous except for isolates of Phytophthora parasitica from tobacco. The production of elicitins by isolates of P. parasitica correlated without exception with low or no virulence on tobacco. Genetic analysis was conducted by using a cross between two isolates of P. parasitica, segregating for production of elicitin and virulence on tobacco. Virulence assays of the progeny on tobacco confirmed the correlation between production of elicitin and low virulence. Images PMID:16349258

  19. Milk Thistle Constituents Inhibit Raloxifene Intestinal Glucuronidation: A Potential Clinically Relevant Natural Product-Drug Interaction.

    PubMed

    Gufford, Brandon T; Chen, Gang; Vergara, Ana G; Lazarus, Philip; Oberlies, Nicholas H; Paine, Mary F

    2015-09-01

    Women at high risk of developing breast cancer are prescribed selective estrogen response modulators, including raloxifene, as chemoprevention. Patients often seek complementary and alternative treatment modalities, including herbal products, to supplement prescribed medications. Milk thistle preparations, including silibinin and silymarin, are top-selling herbal products that may be consumed by women taking raloxifene, which undergoes extensive first-pass glucuronidation in the intestine. Key constituents in milk thistle, flavonolignans, were previously shown to be potent inhibitors of intestinal UDP-glucuronosyl transferases (UGTs), with IC50s ≤ 10 μM. Taken together, milk thistle preparations may perpetrate unwanted interactions with raloxifene. The objective of this work was to evaluate the inhibitory effects of individual milk thistle constituents on the intestinal glucuronidation of raloxifene using human intestinal microsomes and human embryonic kidney cell lysates overexpressing UGT1A1, UGT1A8, and UGT1A10, isoforms highly expressed in the intestine that are critical to raloxifene clearance. The flavonolignans silybin A and silybin B were potent inhibitors of both raloxifene 4'- and 6-glucuronidation in all enzyme systems. The Kis (human intestinal microsomes, 27-66 µM; UGT1A1, 3.2-8.3 µM; UGT1A8, 19-73 µM; and UGT1A10, 65-120 µM) encompassed reported intestinal tissue concentrations (20-310 µM), prompting prediction of clinical interaction risk using a mechanistic static model. Silibinin and silymarin were predicted to increase raloxifene systemic exposure by 4- to 5-fold, indicating high interaction risk that merits further evaluation. This systematic investigation of the potential interaction between a widely used herbal product and chemopreventive agent underscores the importance of understanding natural product-drug interactions in the context of cancer prevention.

  20. Milk Thistle Constituents Inhibit Raloxifene Intestinal Glucuronidation: A Potential Clinically Relevant Natural Product–Drug Interaction

    PubMed Central

    Gufford, Brandon T.; Chen, Gang; Vergara, Ana G.; Lazarus, Philip; Oberlies, Nicholas H.

    2015-01-01

    Women at high risk of developing breast cancer are prescribed selective estrogen response modulators, including raloxifene, as chemoprevention. Patients often seek complementary and alternative treatment modalities, including herbal products, to supplement prescribed medications. Milk thistle preparations, including silibinin and silymarin, are top-selling herbal products that may be consumed by women taking raloxifene, which undergoes extensive first-pass glucuronidation in the intestine. Key constituents in milk thistle, flavonolignans, were previously shown to be potent inhibitors of intestinal UDP-glucuronosyl transferases (UGTs), with IC50s ≤ 10 μM. Taken together, milk thistle preparations may perpetrate unwanted interactions with raloxifene. The objective of this work was to evaluate the inhibitory effects of individual milk thistle constituents on the intestinal glucuronidation of raloxifene using human intestinal microsomes and human embryonic kidney cell lysates overexpressing UGT1A1, UGT1A8, and UGT1A10, isoforms highly expressed in the intestine that are critical to raloxifene clearance. The flavonolignans silybin A and silybin B were potent inhibitors of both raloxifene 4′- and 6-glucuronidation in all enzyme systems. The Kis (human intestinal microsomes, 27–66 µM; UGT1A1, 3.2–8.3 µM; UGT1A8, 19–73 µM; and UGT1A10, 65–120 µM) encompassed reported intestinal tissue concentrations (20–310 µM), prompting prediction of clinical interaction risk using a mechanistic static model. Silibinin and silymarin were predicted to increase raloxifene systemic exposure by 4- to 5-fold, indicating high interaction risk that merits further evaluation. This systematic investigation of the potential interaction between a widely used herbal product and chemopreventive agent underscores the importance of understanding natural product–drug interactions in the context of cancer prevention. PMID:26070840

  1. Extending plasma transport theory to strong coupling through the concept of an effective interaction potential

    SciTech Connect

    Baalrud, Scott D.; Daligault, Jérôme

    2014-05-15

    A method for extending traditional plasma transport theories into the strong coupling regime is presented. Like traditional theories, this is based on a binary scattering approximation, but where physics associated with many body correlations is included through the use of an effective interaction potential. The latter is simply related to the pair-distribution function. Modeling many body effects in this manner can extend traditional plasma theory to orders of magnitude stronger coupling. Theoretical predictions are tested against molecular dynamics simulations for electron-ion temperature relaxation as well as diffusion in one component systems. Emphasis is placed on the connection with traditional plasma theory, where it is stressed that the effective potential concept has precedence through the manner in which screening is imposed. The extension to strong coupling requires accounting for correlations in addition to screening. Limitations of this approach in the presence of strong caging are also discussed.

  2. Enabling fast brain-computer interaction by single-trial extraction of visual evoked potentials.

    PubMed

    Chen, Min; Guan, Jinan; Liu, Haihua

    2011-10-01

    This paper investigates the challenging issue of enabling fast brain-computer interaction to construct a mental speller. Exploiting visual evoked potentials as communication carriers, an online paradigm called "imitating-human-natural-reading" is realized. In this online paradigm, single-trial estimation with the intrinsically real-time feature should be used instead of grand average that is traditionally used in the cognitive or clinical experiments. By the use of several montages of component features from four channels with parameter optimization, we explored the support vector machines-based single-trial estimation of evoked potentials. The results on a human-subject show the advantages of the inducing paradigm used in our mental speller with a high classification rate.

  3. Potential disturbance interactions with a single IGV in an F109 turbofan engine

    NASA Astrophysics Data System (ADS)

    Kirk, Joel F.

    A common cause of aircraft engine failure is the high cycle fatigue of engine blades and stators. One of the primary causes of these failures is due to blade row interactions, which cause an aerodynamic excitation to be resonant with a mechanical natural frequency. Traditionally, the primary source of such aerodynamic excitations has been practically limited to viscous wakes from upstream components. However, more advanced designs require that blade rows be very highly loaded and closely spaced. This results in aerodynamic excitation from potential fields of down stream engine components, in addition to the known wake excitations. An experimental investigation of the potential field from the fan of a Honeywell F109 turbofan engine has been completed. The investigation included velocity measurements upstream of the fan, addition of an airfoil shaped probe upstream of the fan on which surface pressure measurements were acquired, and measurement of the velocity in the interaction region between the probe and the fan. This investigation sought to characterize the response on the upstream probe due to the fan potential field and the interaction between a viscous wake and the potential field; as such, all test conditions were for subsonic fan speeds. The results from the collected data show that fan-induced potential disturbances propagate upstream at acoustic velocities, to produce vane surface-pressure amplitudes as high as 40 percent Joel F. Kirk of the inlet, mean total pressure. Further, these fan-induced pressure amplitudes display large variations between the two vane surfaces. An argument is made that the structure of the pressure response is consistent with the presence of two distinct sources of unsteady forcing disturbances. The disturbances on the incoming-rotation-facing surface of the IGV propagated upstream at a different speed than those on the outgoing-rotation-facing surface, indicating that one originated from a rotating source and the other from a

  4. Hb lepore/β0-thalassaemia with α+-thalassaemia interactions, a potential diagnostic pitfall.

    PubMed

    Alauddin, Hafiza; Mohamad Nasir, Suziana; Ahadon, Madzlifah; Raja Sabudin, Raja Zahratul Azma; Ithnin, Azlin; Hussin, Noor Hamidah; Alias, Hamidah; Loh, C-Khai; Abdul Latiff, Zarina; Abdul Murad, Nor Azian; Othman, Ainoon

    2015-12-01

    Haemoglobin (Hb) Lepore is a variant Hb consisting of two α-globin and two δβ-globin chains. In a heterozygote, it is associated with clinical findings of thalassaemia minor, but interactions with other haemoglobinopathies can lead to various clinical phenotypes and pose diagnostic challenges. We reported a pair of siblings from a Malay family, who presented with pallor and hepatosplenomegaly at the ages of 21 months and 14 months old. The red cell indices and peripheral blood smears of both patients showed features of thalassaemia intermedia. Other laboratory investigations of the patients showed conflicting results. However, laboratory investigation results of the parents had led to a presumptive diagnosis of compound heterozygote Hb Lepore/β-thalassaemia and co-inheritance α+-thalassaemia (-α3.7). Hb Lepore has rarely been detected in Southeast Asian countries, particularly in Malaysia. These two cases highlight the importance of family studies for accurate diagnosis, hence appropriate clinical management and genetic counseling. PMID:26712677

  5. Chemical compounds from anthropogenic environment and immune evasion mechanisms: potential interactions

    PubMed Central

    Kravchenko, Julia; Corsini, Emanuela; Williams, Marc A.; Decker, William; Manjili, Masoud H.; Otsuki, Takemi; Singh, Neetu; Al-Mulla, Faha; Al-Temaimi, Rabeah; Amedei, Amedeo; Colacci, Anna Maria; Vaccari, Monica; Mondello, Chiara; Scovassi, A. Ivana; Raju, Jayadev; Hamid, Roslida A.; Memeo, Lorenzo; Forte, Stefano; Roy, Rabindra; Woodrick, Jordan; Salem, Hosni K.; Ryan, Elizabeth P.; Brown, Dustin G.; Lowe, Leroy; Lyerly, H.Kim

    2015-01-01

    An increasing number of studies suggest an important role of host immunity as a barrier to tumor formation and progression. Complex mechanisms and multiple pathways are involved in evading innate and adaptive immune responses, with a broad spectrum of chemicals displaying the potential to adversely influence immunosurveillance. The evaluation of the cumulative effects of low-dose exposures from the occupational and natural environment, especially if multiple chemicals target the same gene(s) or pathway(s), is a challenge. We reviewed common environmental chemicals and discussed their potential effects on immunosurveillance. Our overarching objective was to review related signaling pathways influencing immune surveillance such as the pathways involving PI3K/Akt, chemokines, TGF-β, FAK, IGF-1, HIF-1α, IL-6, IL-1α, CTLA-4 and PD-1/PDL-1 could individually or collectively impact immunosurveillance. A number of chemicals that are common in the anthropogenic environment such as fungicides (maneb, fluoxastrobin and pyroclostrobin), herbicides (atrazine), insecticides (pyridaben and azamethiphos), the components of personal care products (triclosan and bisphenol A) and diethylhexylphthalate with pathways critical to tumor immunosurveillance. At this time, these chemicals are not recognized as human carcinogens; however, it is known that they these chemicalscan simultaneously persist in the environment and appear to have some potential interfere with the host immune response, therefore potentially contributing to promotion interacting with of immune evasion mechanisms, and promoting subsequent tumor growth and progression. PMID:26002081

  6. Chemical compounds from anthropogenic environment and immune evasion mechanisms: potential interactions.

    PubMed

    Kravchenko, Julia; Corsini, Emanuela; Williams, Marc A; Decker, William; Manjili, Masoud H; Otsuki, Takemi; Singh, Neetu; Al-Mulla, Faha; Al-Temaimi, Rabeah; Amedei, Amedeo; Colacci, Anna Maria; Vaccari, Monica; Mondello, Chiara; Scovassi, A Ivana; Raju, Jayadev; Hamid, Roslida A; Memeo, Lorenzo; Forte, Stefano; Roy, Rabindra; Woodrick, Jordan; Salem, Hosni K; Ryan, Elizabeth P; Brown, Dustin G; Bisson, William H; Lowe, Leroy; Lyerly, H Kim

    2015-06-01

    An increasing number of studies suggest an important role of host immunity as a barrier to tumor formation and progression. Complex mechanisms and multiple pathways are involved in evading innate and adaptive immune responses, with a broad spectrum of chemicals displaying the potential to adversely influence immunosurveillance. The evaluation of the cumulative effects of low-dose exposures from the occupational and natural environment, especially if multiple chemicals target the same gene(s) or pathway(s), is a challenge. We reviewed common environmental chemicals and discussed their potential effects on immunosurveillance. Our overarching objective was to review related signaling pathways influencing immune surveillance such as the pathways involving PI3K/Akt, chemokines, TGF-β, FAK, IGF-1, HIF-1α, IL-6, IL-1α, CTLA-4 and PD-1/PDL-1 could individually or collectively impact immunosurveillance. A number of chemicals that are common in the anthropogenic environment such as fungicides (maneb, fluoxastrobin and pyroclostrobin), herbicides (atrazine), insecticides (pyridaben and azamethiphos), the components of personal care products (triclosan and bisphenol A) and diethylhexylphthalate with pathways critical to tumor immunosurveillance. At this time, these chemicals are not recognized as human carcinogens; however, it is known that they these chemicalscan simultaneously persist in the environment and appear to have some potential interfere with the host immune response, therefore potentially contributing to promotion interacting with of immune evasion mechanisms, and promoting subsequent tumor growth and progression. PMID:26002081

  7. Modeling intermolecular interactions of physisorbed organic molecules using pair potential calculations

    SciTech Connect

    Kroeger, Ingo; Stadtmueller, Benjamin; Wagner, Christian; Weiss, Christian; Temirov, Ruslan; Tautz, F. Stefan; Kumpf, Christian

    2011-12-21

    The understanding and control of epitaxial growth of organic thin films is of crucial importance in order to optimize the performance of future electronic devices. In particular, the start of the submonolayer growth plays an important role since it often determines the structure of the first layer and subsequently of the entire molecular film. We have investigated the structure formation of 3,4,9,10-perylene-tetracarboxylic dianhydride and copper-phthalocyanine molecules on Au(111) using pair-potential calculations based on van der Waals and electrostatic intermolecular interactions. The results are compared with the fundamental lateral structures known from experiment and an excellent agreement was found for these weakly interacting systems. Furthermore, the calculations are even suitable for chemisorptive adsorption as demonstrated for copper-phthalocyanine/Cu(111), if the influence of charge transfer between substrate and molecules is known and the corresponding charge redistribution in the molecules can be estimated. The calculations are of general applicability for molecular adsorbate systems which are dominated by electrostatic and van der Waals interaction.

  8. Spatial representation in the social interaction potential metric: an analysis of scale and parameter sensitivity

    NASA Astrophysics Data System (ADS)

    Li, Xiao; Farber, Steven

    2016-10-01

    The social interaction potential (SIP) metric measures urban structural constraints on social interaction opportunities of a metropolitan region based on the time geographic concept of joint accessibility. Previous implementations of the metric used an interaction surface based on census tracts and the locations of their centroids. This has been shown to be a shortcoming, as the metric strongly depends on the scale of the zoning system in the region, making it difficult to compare the SIP metric between metropolitan regions. This research explores the role of spatial representation in the SIP metric and identifies a suitable grid-based representation that allows for comparison between regions while retaining cost-effectiveness with respect to computational burden. We also report on findings from an extensive sensitivity analysis investigating the SIP metric's input parameters such as a travel flow congestion factor and the length of the allowable time budget for social activities. The results provide new insights on the role of the modifiable areal unit problem in the computation of time geographic measures of accessibility.

  9. Rationale for ibuprofen co-administration with antacids: potential interaction mechanisms affecting drug absorption.

    PubMed

    Parojcić, Jelena; Corrigan, Owen I

    2008-06-01

    Ibuprofen is a widely used NSAID which is often co-administered with antacids because of its gastro-irritant effects. Literature data suggest that antacid interactions may increase or decrease the drug's absorption rate and onset of action and that the interaction may be formulation specific. In the present study, literature data on ibuprofen absorption were evaluated in order to gain insight into the nature of the in vivo effect. Solubility determinations in reactive media containing magnesium or aluminium and dissolution studies in the presence of antacid suspension were performed in an attempt to simulate in vitro the effects observed in vivo. The results obtained indicate that magnesium hydroxide enhances ibuprofen solubility, dissolution and bioavailability, while aluminium hydroxide has a retarding effect. Solubility studies indicated formation of a soluble solid ibuprofen phase in the presence of Mg2+, in contrast, an insoluble ibuprofen salt was formed with Al3+. The introduction of magnesium based antacid suspension into the dissolution media resulted in a formulation specific increase in drug dissolution rate with the most pronounced effect observed for the slowest release tablet formulation. The results obtained indicate the potential for in vitro studies to predict physicochemical interactions that are likely to influence drug absorption rate in vivo.

  10. Molecular Insights into the Potential Toxicological Interaction of 2-Mercaptothiazoline with the Antioxidant Enzyme—Catalase

    PubMed Central

    Huang, Zhenxing; Huang, Ming; Mi, Chenyu; Wang, Tao; Chen, Dong; Teng, Yue

    2016-01-01

    2-mercaptothiazoline (2-MT) is widely used in many industrial fields, but its residue is potentially harmful to the environment. In this study, to evaluate the biological toxicity of 2-MT at protein level, the interaction between 2-MT and the pivotal antioxidant enzyme—catalase (CAT) was investigated using multiple spectroscopic techniques and molecular modeling. The results indicated that the CAT fluorescence quenching caused by 2-MT should be dominated by a static quenching mechanism through formation of a 2-MT/CAT complex. Furthermore, the identifications of the binding constant, binding forces, and the number of binding sites demonstrated that 2-MT could spontaneously interact with CAT at one binding site mainly via Van der Waals’ forces and hydrogen bonding. Based on the molecular docking simulation and conformation dynamic characterization, it was found that 2-MT could bind into the junctional region of CAT subdomains and that the binding site was close to enzyme active sites, which induced secondary structural and micro-environmental changes in CAT. The experiments on 2-MT toxicity verified that 2-MT significantly inhibited CAT activity via its molecular interaction, where 2-MT concentration and exposure time both affected the inhibitory action. Therefore, the present investigation provides useful information for understanding the toxicological mechanism of 2-MT at the molecular level. PMID:27537873

  11. Molecular Insights into the Potential Toxicological Interaction of 2-Mercaptothiazoline with the Antioxidant Enzyme-Catalase.

    PubMed

    Huang, Zhenxing; Huang, Ming; Mi, Chenyu; Wang, Tao; Chen, Dong; Teng, Yue

    2016-01-01

    2-mercaptothiazoline (2-MT) is widely used in many industrial fields, but its residue is potentially harmful to the environment. In this study, to evaluate the biological toxicity of 2-MT at protein level, the interaction between 2-MT and the pivotal antioxidant enzyme-catalase (CAT) was investigated using multiple spectroscopic techniques and molecular modeling. The results indicated that the CAT fluorescence quenching caused by 2-MT should be dominated by a static quenching mechanism through formation of a 2-MT/CAT complex. Furthermore, the identifications of the binding constant, binding forces, and the number of binding sites demonstrated that 2-MT could spontaneously interact with CAT at one binding site mainly via Van der Waals' forces and hydrogen bonding. Based on the molecular docking simulation and conformation dynamic characterization, it was found that 2-MT could bind into the junctional region of CAT subdomains and that the binding site was close to enzyme active sites, which induced secondary structural and micro-environmental changes in CAT. The experiments on 2-MT toxicity verified that 2-MT significantly inhibited CAT activity via its molecular interaction, where 2-MT concentration and exposure time both affected the inhibitory action. Therefore, the present investigation provides useful information for understanding the toxicological mechanism of 2-MT at the molecular level. PMID:27537873

  12. Spectroscopic investigations, molecular interactions, and molecular docking studies on the potential inhibitor "thiophene-2-carboxylicacid".

    PubMed

    Karthick, T; Balachandran, V; Perumal, S

    2015-04-15

    Thiophene derivatives have been focused in the past decades due to their remarkable biological and pharmacological activities. In connection with that the conformational stability, spectroscopic characterization, molecular (inter- and intra-) interactions, and molecular docking studies on thiophene-2-carboxylicacid have been performed in this work by experimental FT-IR and theoretical quantum chemical computations. Experimentally recorded FT-IR spectrum in the region 4000-400 cm(-1) has been compared with the scaled theoretical spectrum and the spectral peaks have been assigned on the basis of potential energy distribution results obtained from MOLVIB program package. The conformational stability of monomer and dimer conformers has been examined. The presence of inter- and intramolecular interactions in the monomer and dimer conformers have been explained by natural bond orbital analysis. The UV-Vis spectra of the sample in different solvents have been simulated and solvent effects were predicted by polarisable continuum model with TD-DFT/B3LYP/6-31+G(d,p) method. To test the biological activity of the sample, molecular docking (ligand-protein) simulations have been performed using SWISSDOCK web server. The full fitness (FF) score and binding affinity values revealed that thiophene-2-carboxylicacid can act as potential inhibitor against inflammation.

  13. Pressure Effects on the Intermolecular Interaction Potential of Condensed Protein Solutions.

    PubMed

    Winter, Roland

    2015-01-01

    Knowledge of the intermolecular interaction potential of proteins as a function of their solution conditions is essential for understanding protein aggregation, crystallization, and the phase behavior of proteins in general. Here, we report on a combined small-angle X-ray scattering and liquid-state theoretical approach to study dense lysozyme solutions as a function of temperature and pressure, but also in the presence of salts and osmolytes of different nature. We show that the pressure-dependent interaction potential of lysozyme changes in a nonlinear fashion over a wide range of temperatures, salt and protein concentrations, indicating that changes of the bulk water structure mediate the pressure dependence of the intermolecular forces. We present also results on the effect of high hydrostatic pressure on the phase behavior of dense lysozyme solutions in the liquid-liquid phase-coexistence region. As also shown in this study, the application of pressure can be used to fine-tune the second virial coefficient of protein solutions, which can be used to control nucleation rates and hence protein crystallization, or to prevent protein aggregation. Moreover, these results are also important for understanding the hydration behavior of biological matter under extreme environmental conditions, and the high stability of dense protein solutions (as they occur intracellularly) in organisms thriving under hydrostatic pressure conditions such as in the deep sea, where pressures up to the 100 MPa-level are reached.

  14. Spectroscopic investigations, molecular interactions, and molecular docking studies on the potential inhibitor "thiophene-2-carboxylicacid"

    NASA Astrophysics Data System (ADS)

    Karthick, T.; Balachandran, V.; Perumal, S.

    2015-04-01

    Thiophene derivatives have been focused in the past decades due to their remarkable biological and pharmacological activities. In connection with that the conformational stability, spectroscopic characterization, molecular (inter- and intra-) interactions, and molecular docking studies on thiophene-2-carboxylicacid have been performed in this work by experimental FT-IR and theoretical quantum chemical computations. Experimentally recorded FT-IR spectrum in the region 4000-400 cm-1 has been compared with the scaled theoretical spectrum and the spectral peaks have been assigned on the basis of potential energy distribution results obtained from MOLVIB program package. The conformational stability of monomer and dimer conformers has been examined. The presence of inter- and intramolecular interactions in the monomer and dimer conformers have been explained by natural bond orbital analysis. The UV-Vis spectra of the sample in different solvents have been simulated and solvent effects were predicted by polarisable continuum model with TD-DFT/B3LYP/6-31+G(d,p) method. To test the biological activity of the sample, molecular docking (ligand-protein) simulations have been performed using SWISSDOCK web server. The full fitness (FF) score and binding affinity values revealed that thiophene-2-carboxylicacid can act as potential inhibitor against inflammation.

  15. Optimal aluminum/zirconium: Protein interactions for predicting antiperspirant efficacy using zeta potential measurements.

    PubMed

    Yuan, Shaotang; Vaughn, John; Pappas, Iraklis; Fitzgerald, Michael; Masters, James G; Pan, Long

    2015-01-01

    The interactions between commercial antiperspirant (AP) salts [aluminum chlorohydrate (ACH), activated ACH, aluminum sesquichlorohydrate (ASCH), zirconium aluminum glycine (ZAG), activated ZAG), pure aluminum polyoxocations (Al13-mer, Al30-mer), and the zirconium(IV)-glycine complex Zr6 (O)4 (OH)4 (H2O)8 (Gly)8]12+(-) (CP-2 or ZG) with Bovine serum albumin (BSA) were studied using zeta potential and turbidity measurements. The maximal turbidity, which revealed the optimal interactions between protein and metal salts, for all protein-metal salt samples was observed at the isoelectric point (IEP), where the zeta potential of the solution was zero. Efficacy of AP salts was determined via three parameters: the amount of salt required to flocculate BSA to reach IEP, the turbidity of solution at the IEP, and the pH range over which the turbidity of the solution remains sufficiently high. By comparing active salt performance from this work to traditional prescreening methods, this methodology was able to provide a consistent efficacy assessment for metal actives in APs or in water treatment. PMID:26454974

  16. Oscillatory brain states interact with late cognitive components of the somatosensory evoked potential.

    PubMed

    Reinacher, Matthias; Becker, Robert; Villringer, Arno; Ritter, Petra

    2009-09-30

    The question of interaction between ongoing neuronal activity and evoked responses has been addressed for different species, sensory systems and measurement modalities. Among other findings, there is converging evidence for an interaction of occipital alpha-rhythm amplitude with the visual evoked potential. Here, we test the hypothesis that the modulatory role of an ongoing rhythm might not be confined to the visual system and the occipital alpha rhythm, but instead may be generalized to other sensory systems. Using an online EEG analysis approach, we investigated the influence of the Rolandic alpha-rhythm on the somatosensory evoked potential (SEP). We triggered vibrotactile stimulation during periods of high Rolandic alpha-rhythm amplitude. Analysis revealed significant effects of pre-stimulus Rolandic alpha amplitude on the amplitude of the N140 and P260 components of the SEP, known to be linked to cognitive processing, but not on early sensory components. The N140-P260 complex shows a different focus in topography than the early sensory components and the pre-stimulus Rolandic alpha rhythm. These results indicate an involvement of Rolandic alpha-rhythm in higher cognitive processing. In more general terms--and in the context of similar studies in the visual system--our findings suggest that modulation of late EP components by ongoing rhythms might be a characteristic and possibly universal feature of sensory systems. PMID:19589356

  17. Optimal aluminum/zirconium: Protein interactions for predicting antiperspirant efficacy using zeta potential measurements.

    PubMed

    Yuan, Shaotang; Vaughn, John; Pappas, Iraklis; Fitzgerald, Michael; Masters, James G; Pan, Long

    2015-01-01

    The interactions between commercial antiperspirant (AP) salts [aluminum chlorohydrate (ACH), activated ACH, aluminum sesquichlorohydrate (ASCH), zirconium aluminum glycine (ZAG), activated ZAG), pure aluminum polyoxocations (Al13-mer, Al30-mer), and the zirconium(IV)-glycine complex Zr6 (O)4 (OH)4 (H2O)8 (Gly)8]12+(-) (CP-2 or ZG) with Bovine serum albumin (BSA) were studied using zeta potential and turbidity measurements. The maximal turbidity, which revealed the optimal interactions between protein and metal salts, for all protein-metal salt samples was observed at the isoelectric point (IEP), where the zeta potential of the solution was zero. Efficacy of AP salts was determined via three parameters: the amount of salt required to flocculate BSA to reach IEP, the turbidity of solution at the IEP, and the pH range over which the turbidity of the solution remains sufficiently high. By comparing active salt performance from this work to traditional prescreening methods, this methodology was able to provide a consistent efficacy assessment for metal actives in APs or in water treatment.

  18. The Potential for Signal Integration and Processing in Interacting Map Kinase Cascades

    PubMed Central

    Schwacke, John H.; Voit, Eberhard O.

    2009-01-01

    The cellular response to environmental stimuli requires biochemical information processing through which sensory inputs and cellular status are integrated and translated into appropriate responses by way of interacting networks of enzymes. One such network, the Mitogen Activated Protein (MAP) kinase cascade is a highly conserved signal transduction module that propagates signals from cell surface receptors to various cytosolic and nuclear targets by way of a phosphorylation cascade. We have investigated the potential for signal processing within a network of interacting feed-forward kinase cascades typified by the MAP kinase cascade. A genetic algorithm was used to search for sets of kinetic parameters demonstrating representative key input-output patterns of interest. We discuss two of the networks identified in our study, one implementing the exclusive-or function (XOR) and another implementing what we refer to as an in-band detector (IBD) or two-sided threshold. These examples confirm the potential for logic and amplitude-dependent signal processing in interacting MAP kinase cascades demonstrating limited cross-talk. Specifically, the XOR function allows the network to respond to either one, but not both signals simultaneously, while the IBD permits the network to respond exclusively to signals within a given range of strength, and to suppress signals below as well as above this range. The solution to the XOR problem is interesting in that it requires only two interacting pathways, crosstalk at only one layer, and no feedback or explicit inhibition. These types of responses are not only biologically relevant but constitute signal processing modules that can be combined to create other logical functions and that, in contrast to amplification, cannot be achieved with a single cascade or with two non-interacting cascades. Our computational results revealed surprising similarities between experimental data describing the JNK/MKK4/MKK7 pathway and the solution for

  19. Interaction grand potential between calcium-silicate-hydrate nanoparticles at the molecular level

    NASA Astrophysics Data System (ADS)

    Bonnaud, Patrick A.; Labbez, Christophe; Miura, Ryuji; Suzuki, Ai; Miyamoto, Naoto; Hatakeyama, Nozomu; Miyamoto, Akira; van Vliet, Krystyn J.

    2016-02-01

    Calcium-silicate-hydrate (or C-S-H), an inosilicate, is the major binding phase in cement pastes and concretes and a porous hydrated material made up of a percolated and dense network of crystalline nanoparticles of a mean apparent spherical diameter of ~5 nm that are each stacks of multiple C-S-H layers. Interaction forces between these nanoparticles are at the origin of C-S-H chemical, physical, and mechanical properties at the meso- and macroscales. These particle interactions and the resulting properties may be affected significantly by nanoparticle density and environmental conditions such as the temperature, relative humidity, or concentration of chemical species in the bulk solution. In this study, we combined grand canonical Monte Carlo simulations and an extension of the mean force integration method to derive the pair potentials. This approach enables realistic simulation of the physical environment surrounding the C-S-H particles. We thus constructed the pair potentials for C-S-H nanoparticles of defined chemical stoichiometry at 10% relative humidity (RH), varying the relative crystallographic orientations at a constant particle density of ρpart ~ 2.21 mmol L-1. We found that cohesion between nanoparticles is affected strongly by both the aspect ratio and the crystallographic misorientation of interacting particles. This method and the findings underscore the importance of accounting for relative dimensions and orientation among C-S-H nanoparticles in descriptions of physical and simulated multiparticle aggregates or mesoscale systems.Calcium-silicate-hydrate (or C-S-H), an inosilicate, is the major binding phase in cement pastes and concretes and a porous hydrated material made up of a percolated and dense network of crystalline nanoparticles of a mean apparent spherical diameter of ~5 nm that are each stacks of multiple C-S-H layers. Interaction forces between these nanoparticles are at the origin of C-S-H chemical, physical, and mechanical

  20. Accurate ab initio-based adiabatic global potential energy surface for the 2{sup 2}A″ state of NH{sub 2} by extrapolation to the complete basis set limit

    SciTech Connect

    Li, Y. Q.; Ma, F. C.; Sun, M. T.

    2013-10-21

    A full three-dimensional global potential energy surface is reported first time for the title system, which is important for the photodissociation processes. It is obtained using double many-body expansion theory and an extensive set of accurate ab initio energies extrapolated to the complete basis set limit. Such a work can be recommended for dynamics studies of the N({sup 2}D) + H{sub 2} reaction, a reliable theoretical treatment of the photodissociation dynamics and as building blocks for constructing the double many-body expansion potential energy surface of larger nitrogen/hydrogen containing systems. In turn, a preliminary theoretical study of the reaction N({sup 2}D)+H{sub 2}(X{sup 1}Σ{sub g}{sup +})(ν=0,j=0)→NH(a{sup 1}Δ)+H({sup 2}S) has been carried out with the method of quasi-classical trajectory on the new potential energy surface. Integral cross sections and thermal rate constants have been calculated, providing perhaps the most reliable estimate of the integral cross sections and the rate constants known thus far for such a reaction.

  1. Revealing the potential pathogenesis of glioma by utilizing a glioma associated protein-protein interaction network.

    PubMed

    Pan, Weiran; Li, Gang; Yang, Xiaoxiao; Miao, Jinming

    2015-04-01

    This study aims to explore the potential mechanism of glioma through bioinformatic approaches. The gene expression profile (GSE4290) of glioma tumor and non-tumor samples was downloaded from Gene Expression Omnibus database. A total of 180 samples were available, including 23 non-tumor and 157 tumor samples. Then the raw data were preprocessed using robust multiarray analysis, and 8,890 differentially expressed genes (DEGs) were identified by using t-test (false discovery rate < 0.0005). Furthermore, 16 known glioma related genes were abstracted from Genetic Association Database. After mapping 8,890 DEGs and 16 known glioma related genes to Human Protein Reference Database, a glioma associated protein-protein interaction network (GAPN) was constructed. In addition, 51 sub-networks in GAPN were screened out through Molecular Complex Detection (score ≥ 1), and sub-network 1 was found to have the closest interaction (score = 3). What' more, for the top 10 sub-networks, Gene Ontology (GO) enrichment analysis (p value < 0.05) was performed, and DEGs involved in sub-network 1 and 2, such as BRMS1L and CCNA1, were predicted to regulate cell growth, cell cycle, and DNA replication via interacting with known glioma related genes. Finally, the overlaps of DEGs and human essential, housekeeping, tissue-specific genes were calculated (p value = 1.0, 1.0, and 0.00014, respectively) and visualized by Venn Diagram package in R. About 61% of human tissue-specific genes were DEGs as well. This research shed new light on the pathogenesis of glioma based on DEGs and GAPN, and our findings might provide potential targets for clinical glioma treatment.

  2. Pralatrexate Monitoring Using a Commercially Available Methotrexate Assay to Avoid Potential Drug Interactions.

    PubMed

    McPherson, Jordan P; Vrontikis, Alaina; Sedillo, Courtney; Halwani, Ahmad S; Gilreath, Jeffrey A

    2016-02-01

    Pralatrexate (PDX) is a folate antagonist structurally similar to methotrexate (MTX). Unlike MTX, it is currently not known whether PDX exhibits delayed clearance and heightened toxicity in the setting of fluid overload. A specific serum assay for PDX is not commercially available. To our knowledge, we report the first case using an MTX serum assay as a surrogate for PDX concentrations to avoid a potential drug-drug interaction with pralatrexate. We describe a 76-year-old man with refractory cutaneous T-cell lymphoma who began therapy with weekly PDX 15 mg/m(2) intravenous infusions on days 1, 8, and 15 of a 28-day cycle. He subsequently developed mucositis, a moderate right-sided pleural effusion, and peripheral edema over the next 5 weeks. Aggressive diuresis with furosemide was initiated, which was then withheld the day before his next PDX dose to avoid a potential drug-drug interaction between PDX and furosemide. His baseline MTX/PDX concentration (measured prior to administration of the cycle 2, week 2 PDX dose) was less than 0.20 μmol/L (i.e., undetectable). After PDX administration, his 1-hour peak MTX/PDX concentration increased to 0.58 μmol/L. Aggressive diuresis was withheld until his MTX/PDX concentration was undetectable, 43.5 hours later. PDX is more potent than MTX and displays similar pharmacokinetic properties. PDX concentrations using the serum MTX assay reflect lower values than those reported from PDX-specific assays in clinical studies. Because PDX is approved by the U.S. Food and Drug Administration for the treatment of uncommon malignancies, it is unlikely that a specific assay will be commercially developed. We propose that the MTX serum assay has merit for use in determining when to reinstate possible interacting drug therapies such as loop diuretics.

  3. Are distance-dependent statistical potentials considering three interacting bodies superior to two-body statistical potentials for protein structure prediction?

    PubMed

    Ghomi, Hamed Tabatabaei; Thompson, Jared J; Lill, Markus A

    2014-10-01

    Distance-based statistical potentials have long been used to model condensed matter systems, e.g. as scoring functions in differentiating native-like protein structures from decoys. These scoring functions are based on the assumption that the total free energy of the protein can be calculated as the sum of pairwise free energy contributions derived from a statistical analysis of pair-distribution functions. However, this fundamental assumption has been challenged theoretically. In fact the free energy of a system with N particles is only exactly related to the N-body distribution function. Based on this argument coarse-grained multi-body statistical potentials have been developed to capture higher-order interactions. Having a coarse representation of the protein and using geometric contacts instead of pairwise interaction distances renders these models insufficient in modeling details of multi-body effects. In this study, we investigated if extending distance-dependent pairwise atomistic statistical potentials to corresponding interaction functions that are conditional on a third interacting body, defined as quasi-three-body statistical potentials, could model details of three-body interactions. We also tested if this approach could improve the predictive capabilities of statistical scoring functions for protein structure prediction. We analyzed the statistical dependency between two simultaneous pairwise interactions and showed that there is surprisingly little if any dependency of a third interacting site on pairwise atomistic statistical potentials. Also the protein structure prediction performance of these quasi-three-body potentials is comparable with their corresponding two-body counterparts. The scoring functions developed in this study showed better or comparable performances compared to some widely used scoring functions for protein structure prediction. PMID:25212727

  4. Interaction Between Helminths and Toll-Like Receptors: Possibilities and Potentials for Asthma Therapy.

    PubMed

    Zakeri, Amin; Borji, Hassan; Haghparast, Alireza

    2016-05-01

    Toll-like receptors (TLRs) are essential components of the innate immune system. They play an important role in the pathogenesis of allergic diseases, especially asthma. Since TLRs significantly orchestrate innate and adaptive immune response, their manipulation has widely been considered as a potential approach to control asthma symptoms. It is well established that helminths have immunoregulatory effects on host immune responses, especially innate immunity. They release bioactive molecules such as excretory-secretory (ES) products manipulating TLRs expression and signaling. Thus, given the promising results derived from preclinical studies, harnessing helminth-derived molecules affecting TLRs can be considered as a potential biological therapy for allergic diseases. Prospectively, the data that are available at present suggest that, in the near future, it is possible that helminth antigens will offer new therapeutic strategies and druggable targets for fighting allergic diseases. This review describes the interactions between helminths and TLRs and discusses the potential possibilities for asthma therapy. In this opinion paper, the authors aimed to review the updated literatures on the interplay between helminths, TLRs, and asthma with a view to proposing helminth-based asthma therapy. PMID:27120222

  5. Clinically Relevant Pharmacological Strategies That Reverse MDMA-Induced Brain Hyperthermia Potentiated by Social Interaction.

    PubMed

    Kiyatkin, Eugene A; Ren, Suelynn; Wakabayashi, Ken T; Baumann, Michael H; Shaham, Yavin

    2016-01-01

    MDMA-induced hyperthermia is highly variable, unpredictable, and greatly potentiated by the social and environmental conditions of recreational drug use. Current strategies to treat pathological MDMA-induced hyperthermia in humans are palliative and marginally effective, and there are no specific pharmacological treatments to counteract this potentially life-threatening condition. Here, we tested the efficacy of mixed adrenoceptor blockers carvedilol and labetalol, and the atypical antipsychotic clozapine, in reversing MDMA-induced brain and body hyperthermia. We injected rats with a moderate non-toxic dose of MDMA (9 mg/kg) during social interaction, and we administered potential treatment drugs after the development of robust hyperthermia (>2.5 °C), thus mimicking the clinical situation of acute MDMA intoxication. Brain temperature was our primary focus, but we also simultaneously recorded temperatures from the deep temporal muscle and skin, allowing us to determine the basic physiological mechanisms of the treatment drug action. Carvedilol was modestly effective in attenuating MDMA-induced hyperthermia by moderately inhibiting skin vasoconstriction, and labetalol was ineffective. In contrast, clozapine induced a marked and immediate reversal of MDMA-induced hyperthermia via inhibition of brain metabolic activation and blockade of skin vasoconstriction. Our findings suggest that clozapine, and related centrally acting drugs, might be highly effective for reversing MDMA-induced brain and body hyperthermia in emergency clinical situations, with possible life-saving results.

  6. Clinically Relevant Pharmacological Strategies That Reverse MDMA-Induced Brain Hyperthermia Potentiated by Social Interaction.

    PubMed

    Kiyatkin, Eugene A; Ren, Suelynn; Wakabayashi, Ken T; Baumann, Michael H; Shaham, Yavin

    2016-01-01

    MDMA-induced hyperthermia is highly variable, unpredictable, and greatly potentiated by the social and environmental conditions of recreational drug use. Current strategies to treat pathological MDMA-induced hyperthermia in humans are palliative and marginally effective, and there are no specific pharmacological treatments to counteract this potentially life-threatening condition. Here, we tested the efficacy of mixed adrenoceptor blockers carvedilol and labetalol, and the atypical antipsychotic clozapine, in reversing MDMA-induced brain and body hyperthermia. We injected rats with a moderate non-toxic dose of MDMA (9 mg/kg) during social interaction, and we administered potential treatment drugs after the development of robust hyperthermia (>2.5 °C), thus mimicking the clinical situation of acute MDMA intoxication. Brain temperature was our primary focus, but we also simultaneously recorded temperatures from the deep temporal muscle and skin, allowing us to determine the basic physiological mechanisms of the treatment drug action. Carvedilol was modestly effective in attenuating MDMA-induced hyperthermia by moderately inhibiting skin vasoconstriction, and labetalol was ineffective. In contrast, clozapine induced a marked and immediate reversal of MDMA-induced hyperthermia via inhibition of brain metabolic activation and blockade of skin vasoconstriction. Our findings suggest that clozapine, and related centrally acting drugs, might be highly effective for reversing MDMA-induced brain and body hyperthermia in emergency clinical situations, with possible life-saving results. PMID:26105141

  7. Accurate monotone cubic interpolation

    NASA Technical Reports Server (NTRS)

    Huynh, Hung T.

    1991-01-01

    Monotone piecewise cubic interpolants are simple and effective. They are generally third-order accurate, except near strict local extrema where accuracy degenerates to second-order due to the monotonicity constraint. Algorithms for piecewise cubic interpolants, which preserve monotonicity as well as uniform third and fourth-order accuracy are presented. The gain of accuracy is obtained by relaxing the monotonicity constraint in a geometric framework in which the median function plays a crucial role.

  8. 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.

  9. Accurate, Analytic, Empirical Potentials and Born-Oppenheimer Breakdown Functions for the X(1^1Σ)-STATES of BeH, BeD, and BeT

    NASA Astrophysics Data System (ADS)

    Dattani, Nikesh S.; Welsh, Staszek

    2014-06-01

    Being the simplest neutral open shell molecule, BeH is a very important benchmark system for ab initio calculations. However, the most accurate empirical potentials and Born-Oppenheimer breakdown (BOB) functions for this system are nearly a decade old and are not reliable in the long-range region. Particularly, the uncertainties in their dissociation energies were about ±200 cm-1, and even the number of vibrational levels predicted was at the time very questionable, meaning that no good benchmark exists for ab initio calculations on neutral open shell molecules. We build new empirical potentials for BeH, BeD, and BeT that are much more reliable in the long-range. Being the second lightest heteronuclear molecule with a stable ground electronic state, BeH is also very important for the study of isotope effects, such as BOB. We extensively study isotope effects in this system, and we show that the empirical BOB functions fitted from the data of any two isotopologues, is sufficient to predict crucial properties of the third isotopologue.

  10. Plant-Microbial Interactions Define Potential Mechanisms of Organic Matter Priming in the Rhizosphere

    NASA Astrophysics Data System (ADS)

    Zhalnina, K.; Cho, H. J.; Hao, Z.; Mansoori, N.; Karaoz, U.; Jenkins, S.; White, R. A., III; Lipton, M. S.; Deng, K.; Zhou, J.; Pett-Ridge, J.; Northen, T.; Firestone, M. K.; Brodie, E.

    2015-12-01

    In the rhizosphere, metabolic processes of plants and microorganisms are closely coupled, and together with soil minerals, their interactions regulate the turnover of soil organic C (SOC). Plants provide readily assimilable metabolites for microorganisms through exudation, and it has been hypothesized that increasing concentrations of exudate C may either stimulate or suppress rates of SOC mineralization (rhizosphere priming). Both positive and negative rhizosphere priming has been widely observed, however the underlying mechanisms remain poorly understood. To begin to identify the molecular mechanisms underlying rhizosphere priming, we isolated a broad range of soil bacteria from a Mediterranean grassland dominated by annual grass. Thirty-nine heterotrophic bacteria were selected for genome sequencing and both rRNA gene analysis and metagenome coverage suggest that these isolates represent naturally abundant strain variants. We analyzed their genomes for potential metabolic traits related to life in the rhizosphere and the decomposition of polymeric SOC. While the two dominant groups, Alphaproteobacteria and Actinobacteria, were enriched in polymer degrading enzymes, Alphaproteobacterial isolates contained greater gene copies of transporters related to amino acid, organic acid and auxin uptake or export, suggesting an enhanced metabolic potential for life in the root zone. To verify this metabolic potential, we determined the enzymatic activities of these isolates and revealed preferences of strains to degrade certain polymers (xylan, cellulose or lignin). Fourier Transform Infrared spectroscopy is being used to determine which polymeric components of plant roots are targeted by specific strains and how exudates may impact their degradation. To verify the potential of isolates to assimilate root exudates and export key metabolites we are using LC-MS/MS based exometabolomic profiling. The traits hypothesized and verified here (transporters, enzymes, exudate uptake

  11. Cation Interactions and Membrane Potential Induce Conformational Changes in NaPi-IIb.

    PubMed

    Patti, Monica; Fenollar-Ferrer, Cristina; Werner, Andreas; Forrest, Lucy R; Forster, Ian C

    2016-09-01

    Voltage-dependence of Na(+)-coupled phosphate cotransporters of the SLC34 family arises from displacement of charges intrinsic to the protein and the binding/release of one Na(+) ion in response to changes in the transmembrane electric field. Candidate coordination residues for the cation at the Na1 site were previously predicted by structural modeling using the x-ray structure of dicarboxylate transporter VcINDY as template and confirmed by functional studies. Mutations at Na1 resulted in altered steady-state and presteady-state characteristics that should be mirrored in the conformational changes induced by membrane potential changes. To test this hypothesis by functional analysis, double mutants of the flounder SLC34A2 protein were constructed that contain one of the Na1-site perturbing mutations together with a substituted cysteine for fluorophore labeling, as expressed in Xenopus oocytes. The locations of the mutations were mapped onto a homology model of the flounder protein. The effects of the mutagenesis were characterized by steady-state, presteady-state, and fluorometric assays. Changes in fluorescence intensity (ΔF) in response to membrane potential steps were resolved at three previously identified positions. These fluorescence data corroborated the altered presteady-state kinetics upon perturbation of Na1, and furthermore indicated concomitant changes in the microenvironment of the respective fluorophores, as evidenced by changes in the voltage dependence and time course of ΔF. Moreover, iodide quenching experiments indicated that the aqueous nature of the fluorophore microenvironment depended on the membrane potential. These findings provide compelling evidence that membrane potential and cation interactions induce significant large-scale structural rearrangements of the protein. PMID:27602725

  12. The solar wind interaction with Mars as seen by the Viking retarding potential analyzers

    NASA Technical Reports Server (NTRS)

    Cragin, B. L.; Hanson, W. B.; Sanatani, S.

    1982-01-01

    Both energy spectra and continuous monitoring periods of the total flux above 15 eV are available, from Viking retarding potential analyzer measurements of electron fluxes not exceeding 75 eV out to 16,000 km above the Mars surface. Although the mean electron current at energies above 15 eV increases monotonically by almost two orders of magnitude from 9000 to 700 km in Viking 1 data, no clear signature of the bow shock is seen. Total current wave power shows a peak near 1700 km altitude. It is suggested that there may be a highly turbulent shock structure masking a clear signature of the bow shock in the time-averaged data, and it is concluded that the interaction model consistent with the bow shock at 1700 km, together with ionosphere measurements, indicates a permanent magnetic field able to stand off the solar wind during the Viking 1 entry.

  13. Early-life stress interactions with the epigenome: potential mechanisms driving vulnerability toward psychiatric illness.

    PubMed

    Lewis, Candace R; Olive, M Foster

    2014-09-01

    Throughout the 20th century a body of literature concerning the long-lasting effects of the early environment was produced. Adverse experiences in early life, or early-life stress (ELS), is associated with a higher risk of developing various psychiatric illnesses. The mechanisms driving the complex interplay between ELS and adult phenotype has baffled many investigators for decades. Over the last decade, the new field of neuroepigenetics has emerged as one possible mechanism by which ELS can have far-reaching effects on adult phenotype, behavior, and risk for psychiatric illness. Here we review two commonly investigated epigenetic mechanisms, histone modifications and DNA methylation, and the emerging field of neuroepigenetics as they relate to ELS. We discuss the current animal literature demonstrating ELS-induced epigenetic modulation of gene expression that results in altered adult phenotypes. We also briefly discuss other areas in which neuroepigenetics has emerged as a potential mechanism underlying environmental and genetic interactions.

  14. Potential of mean force for human lysozyme camelid vhh hl6 antibody interaction studies

    NASA Astrophysics Data System (ADS)

    Wang, Yeng-Tseng; Liao, Jun-Min; Chen, Cheng-Lung; Su, Zhi-Yuan; Chen, Chang-Hung; Hu, Jeu-Jiun

    2008-04-01

    Calculating antigen-antibody interaction energies is crucial for understanding antigen-antibody associations in immunology. To shed further light into this equation, we study a separation of human lysozyme-camelid vhh hl6 antibody (cAb-HuL6) complex. The c-terminal end-to-end stretching of the lysozyme-antibody complex structures have been studied using potential of mean force (PMF) calculations based on molecular dynamics (MD) and explicit water model. For the lysozyme-antibody complex, there are six important intermediates in the c-terminal extensions process. Inclusion of our simulations may help to understand the binding mechanics of lysozyme-cAb-HuL6 antibody complex.

  15. [Cell signaling pathways interaction in cellular proliferation: Potential target for therapeutic interventionism].

    PubMed

    Valdespino-Gómez, Víctor Manuel; Valdespino-Castillo, Patricia Margarita; Valdespino-Castillo, Víctor Edmundo

    2015-01-01

    Nowadays, cellular physiology is best understood by analysing their interacting molecular components. Proteins are the major components of the cells. Different proteins are organised in the form of functional clusters, pathways or networks. These molecules are ordered in clusters of receptor molecules of extracellular signals, transducers, sensors and biological response effectors. The identification of these intracellular signaling pathways in different cellular types has required a long journey of experimental work. More than 300 intracellular signaling pathways have been identified in human cells. They participate in cell homeostasis processes for structural and functional maintenance. Some of them participate simultaneously or in a nearly-consecutive progression to generate a cellular phenotypic change. In this review, an analysis is performed on the main intracellular signaling pathways that take part in the cellular proliferation process, and the potential use of some components of these pathways as target for therapeutic interventionism are also underlined. PMID:25986976

  16. The solar wind interaction with Mars as seen by the Viking retarding potential analyzers

    NASA Astrophysics Data System (ADS)

    Cragin, B. L.; Hanson, W. B.; Sanatani, S.

    1982-06-01

    Both energy spectra and continuous monitoring periods of the total flux above 15 eV are available, from Viking retarding potential analyzer measurements of electron fluxes not exceeding 75 eV out to 16,000 km above the Mars surface. Although the mean electron current at energies above 15 eV increases monotonically by almost two orders of magnitude from 9000 to 700 km in Viking 1 data, no clear signature of the bow shock is seen. Total current wave power shows a peak near 1700 km altitude. It is suggested that there may be a highly turbulent shock structure masking a clear signature of the bow shock in the time-averaged data, and it is concluded that the interaction model consistent with the bow shock at 1700 km, together with ionosphere measurements, indicates a permanent magnetic field able to stand off the solar wind during the Viking 1 entry.

  17. Strongly Correlated 2D Quantum Phases with Cold Polar Molecules: Controlling the Shape of the Interaction Potential

    SciTech Connect

    Buechler, H. P.; Micheli, A.; Pupillo, G.; Zoller, P.; Demler, E.; Lukin, M.; Prokof'ev, N.

    2007-02-09

    We discuss techniques to tune and shape the long-range part of the interaction potentials in quantum gases of bosonic polar molecules by dressing rotational excitations with static and microwave fields. This provides a novel tool towards engineering strongly correlated quantum phases in combination with low-dimensional trapping geometries. As an illustration, we discuss the 2D superfluid-crystal quantum phase transition for polar molecules interacting via an electric-field-induced dipole-dipole potential.

  18. Affective processing in natural scene viewing: valence and arousal interactions in eye-fixation-related potentials.

    PubMed

    Simola, Jaana; Le Fevre, Kevin; Torniainen, Jari; Baccino, Thierry

    2015-02-01

    Attention is drawn to emotionally salient stimuli. The present study investigates processing of emotionally salient regions during free viewing of emotional scenes that were categorized according to the two-dimensional model comprising of valence (unpleasant, pleasant) and arousal (high, low). Recent studies have reported interactions between these dimensions, indicative of stimulus-evoked approach or withdrawal tendencies. We addressed the valence and arousal effects when emotional items were embedded in complex real-world scenes by analyzing both eye movement behavior and eye-fixation-related potentials (EFRPs) time-locked to the critical event of fixating the emotionally salient items for the first time. Both data sets showed an interaction between the valence and arousal dimensions. First, the fixation rates and gaze durations on emotionally salient regions were enhanced for unpleasant versus pleasant images in the high arousal condition. In the low arousal condition, both measures were enhanced for pleasant versus unpleasant images. Second, the EFRP results at 140-170 ms [P2] over the central site showed stronger responses for high versus low arousing images in the unpleasant condition. In addition, the parietal LPP responses at 400-500 ms post-fixation were enhanced for stimuli reflecting congruent stimulus dimensions, that is, stronger responses for high versus low arousing images in the unpleasant condition and stronger responses for low versus high arousing images in the pleasant condition. The present findings support the interactive two-dimensional approach, according to which the integration of valence and arousal recruits brain regions associated with action tendencies of approach or withdrawal.

  19. The emotion potential of simple sentences: additive or interactive effects of nouns and adjectives?

    PubMed Central

    Lüdtke, Jana; Jacobs, Arthur M.

    2015-01-01

    The vast majority of studies on affective processes in reading focus on single words. The most robust finding is a processing advantage for positively valenced words, which has been replicated in the rare studies investigating effects of affective features of words during sentence or story comprehension. Here we were interested in how the different valences of words in a sentence influence its processing and supralexical affective evaluation. Using a sentence verification task we investigated how comprehension of simple declarative sentences containing a noun and an adjective depends on the valences of both words. The results are in line with the assumed general processing advantage for positive words. We also observed a clear interaction effect, as can be expected from the affective priming literature: sentences with emotionally congruent words (e.g., The grandpa is clever) were verified faster than sentences containing emotionally incongruent words (e.g., The grandpa is lonely). The priming effect was most prominent for sentences with positive words suggesting that both, early processing as well as later meaning integration and situation model construction, is modulated by affective processing. In a second rating task we investigated how the emotion potential of supralexical units depends on word valence. The simplest hypothesis predicts that the supralexical affective structure is a linear combination of the valences of the nouns and adjectives (Bestgen, 1994). Overall, our results do not support this: The observed clear interaction effect on ratings indicate that especially negative adjectives dominated supralexical evaluation, i.e., a sort of negativity bias in sentence evaluation. Future models of sentence processing thus should take interactive affective effects into account. PMID:26321975

  20. Evaluation of drug interaction potential of Labisia pumila (Kacip Fatimah) and its constituents

    PubMed Central

    Manda, Vamshi K.; Dale, Olivia R.; Awortwe, Charles; Ali, Zulfiqar; Khan, Ikhlas A.; Walker, Larry A.; Khan, Shabana I.

    2014-01-01

    Labisia pumila (Kacip Fatimah) is a popular herb in Malaysia that has been traditionally used in a number of women’s health applications such as to improve libido, relieve postmenopausal symptoms, and to facilitate or hasten delivery in childbirth. In addition, the constituents of this plant have been reported to possess anticancer, antioxidant, and anti-inflammatory properties. Clinical studies have indicated that cytochrome P450s (CYPs), P-glycoprotein (P-gp), and Pregnane X receptor (PXR) are the three main modulators of drug-drug interactions which alter the absorption, distribution, and metabolism of drugs. Given the widespread use of Kacip Fatimah in dietary supplements, the current study focuses on determining the potential of its constituents to affect the activities of CYPs, P-gp, or PXR using in vitro assays which may provide useful information toward the risk of herb-drug interaction with concomitantly used drugs. Six compounds isolated from the roots of L. pumila (2 saponins and 4 alkyl phenols) were tested, in addition to the methanolic extract. The extract of L. pumila showed a significant time dependent inhibition (TDI) of CYP3A4, reversible inhibition of CYP2C9 and 2C19 and a weak inhibition of 1A2 and 2D6 as well as an inhibition of P-gp and rifampicin-induced PXR activation. The alkyl phenols inhibited CYP3A4 (TDI), CYP2C9, and 2C19 (reversible) while saponins inhibited P-gp and PXR. In conclusion, L. pumila and its constituents showed significant modulation of all three regulatory proteins (CYPs, P-gp, and PXR) suggesting a potential to alter the pharmacokinetic and pharmacodynamic properties of conventional drugs if used concomitantly. PMID:25152732

  1. Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions.

    PubMed

    Chow, Cheryl-Emiliane T; Winget, Danielle M; White, Richard A; Hallam, Steven J; Suttle, Curtis A

    2015-01-01

    Viral diversity and virus-host interactions in oxygen-starved regions of the ocean, also known as oxygen minimum zones (OMZs), remain relatively unexplored. Microbial community metabolism in OMZs alters nutrient and energy flow through marine food webs, resulting in biological nitrogen loss and greenhouse gas production. Thus, viruses infecting OMZ microbes have the potential to modulate community metabolism with resulting feedback on ecosystem function. Here, we describe viral communities inhabiting oxic surface (10 m) and oxygen-starved basin (200 m) waters of Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island, British Columbia using viral metagenomics and complete viral fosmid sequencing on samples collected between April 2007 and April 2010. Of 6459 open reading frames (ORFs) predicted across all 34 viral fosmids, 77.6% (n = 5010) had no homology to reference viral genomes. These fosmids recruited a higher proportion of viral metagenomic sequences from Saanich Inlet than from nearby northeastern subarctic Pacific Ocean (Line P) waters, indicating differences in the viral communities between coastal and open ocean locations. While functional annotations of fosmid ORFs were limited, recruitment to NCBI's non-redundant "nr" database and publicly available single-cell genomes identified putative viruses infecting marine thaumarchaeal and SUP05 proteobacteria to provide potential host linkages with relevance to coupled biogeochemical cycling processes in OMZ waters. Taken together, these results highlight the power of coupled analyses of multiple sequence data types, such as viral metagenomic and fosmid sequence data with prokaryotic single cell genomes, to chart viral diversity, elucidate genomic and ecological contexts for previously unclassifiable viral sequences, and identify novel host interactions in natural and engineered ecosystems. PMID:25914678

  2. Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions.

    PubMed

    Chow, Cheryl-Emiliane T; Winget, Danielle M; White, Richard A; Hallam, Steven J; Suttle, Curtis A

    2015-01-01

    Viral diversity and virus-host interactions in oxygen-starved regions of the ocean, also known as oxygen minimum zones (OMZs), remain relatively unexplored. Microbial community metabolism in OMZs alters nutrient and energy flow through marine food webs, resulting in biological nitrogen loss and greenhouse gas production. Thus, viruses infecting OMZ microbes have the potential to modulate community metabolism with resulting feedback on ecosystem function. Here, we describe viral communities inhabiting oxic surface (10 m) and oxygen-starved basin (200 m) waters of Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island, British Columbia using viral metagenomics and complete viral fosmid sequencing on samples collected between April 2007 and April 2010. Of 6459 open reading frames (ORFs) predicted across all 34 viral fosmids, 77.6% (n = 5010) had no homology to reference viral genomes. These fosmids recruited a higher proportion of viral metagenomic sequences from Saanich Inlet than from nearby northeastern subarctic Pacific Ocean (Line P) waters, indicating differences in the viral communities between coastal and open ocean locations. While functional annotations of fosmid ORFs were limited, recruitment to NCBI's non-redundant "nr" database and publicly available single-cell genomes identified putative viruses infecting marine thaumarchaeal and SUP05 proteobacteria to provide potential host linkages with relevance to coupled biogeochemical cycling processes in OMZ waters. Taken together, these results highlight the power of coupled analyses of multiple sequence data types, such as viral metagenomic and fosmid sequence data with prokaryotic single cell genomes, to chart viral diversity, elucidate genomic and ecological contexts for previously unclassifiable viral sequences, and identify novel host interactions in natural and engineered ecosystems.

  3. Final Report - Assessment of Potential Phosphate Ion-Cementitious Materials Interactions

    SciTech Connect

    Naus, Dan J; Mattus, Catherine H; Dole, Leslie Robert

    2007-06-01

    The objectives of this limited study were to: (1) review the potential for degradation of cementitious materials due to exposure to high concentrations of phosphate ions; (2) provide an improved understanding of any significant factors that may lead to a requirement to establish exposure limits for concrete structures exposed to soils or ground waters containing high levels of phosphate ions; (3) recommend, as appropriate, whether a limitation on phosphate ion concentration in soils or ground water is required to avoid degradation of concrete structures; and (4) provide a "primer" on factors that can affect the durability of concrete materials and structures in nuclear power plants. An assessment of the potential effects of phosphate ions on cementitious materials was made through a review of the literature, contacts with concrete research personnel, and conduct of a "bench-scale" laboratory investigation. Results of these activities indicate that: no harmful interactions occur between phosphates and cementitious materials unless phosphates are present in the form of phosphoric acid; phosphates have been incorporated into concrete as set retarders, and phosphate cements have been used for infrastructure repair; no standards or guidelines exist pertaining to applications of reinforced concrete structures in high-phosphate environments; interactions of phosphate ions and cementitious materials has not been a concern of the research community; and laboratory results indicate similar performance of specimens cured in phosphate solutions and those cured in a calcium hydroxide solution after exposure periods of up to eighteen months. Relative to the "primer," a separate NUREG report has been prepared that provides a review of pertinent factors that can affect the durability of nuclear power plant reinforced concrete structures.

  4. Does Curcumin or Pindolol Potentiate Fluoxetine's Antidepressant Effect by a Pharmacokinetic or Pharmacodynamic Interaction?

    PubMed Central

    Murad, H.A.S.; Suliaman, M. I.; Abdallah, H.; Abdulsattar, May

    2014-01-01

    This study was designed to study potentiation of fluoxetine's antidepressant effect by curcumin or pindolol. Twenty eight groups of mice (n=8) were used in three sets of experiments. In the first set, 9 groups were subjected to the forced swimming test after being treated intraperitoneally with three vehicles, fluoxetine (5 and 20 mg/kg), curcumin (20 mg/kg), pindolol (32 mg/kg), curcumin+fluoxetine (5 mg/kg) and pindolol+fluoxetine (5 mg/kg). One hour after the test, serum and brain fluoxetine and norfluoxetine levels were measured in mice receiving fluoxetine (5 and 20 mg/kg), curcumin+fluoxetine (5 mg/kg) and pindolol+fluoxetine (5 mg/kg). In the second set, the test was done after pretreatment with p-chlorophenylalanine. In the third set, the locomotor activity was measured. The immobility duration was significantly decreased in fluoxetine (20 mg/kg), curcumin (20 mg/kg), curcumin+fluoxetine (5 mg/kg) and pindolol+fluoxetine (5 mg/kg) groups. These decreases were reversed with p-chlorophenylalanine. Fluoxetine and norfluoxetine levels were significantly higher in fluoxetine (20 mg/kg) group with no differences in fluoxetine (5 mg/kg), curcumin+fluoxetine (5 mg/kg) and pindolol+fluoxetine (5 mg/kg) groups. Moreover, drugs failed to alter the locomotor activity indicating absence of central stimulation. In conclusion, curcumin, more than pindolol enhanced the antidepressant effect of a subeffective dose of fluoxetine in mice without increasing its serum or brain levels excluding any pharmacokinetic interaction. Reversal of this potentiation with p-chlorophenylalanine suggests a pharmacodynamic interaction through involvement of presynaptic 5-HT1A receptors. PMID:25035531

  5. Genomic insights into the metabolic potential and interactions between marine methanotrophic ANME archaea and associated bacteria

    NASA Astrophysics Data System (ADS)

    Orphan, V. J.; Skennerton, C.; Chadwick, G.; Haroon, F.; Tyson, G. W.; Leu, A.; Hatzenpichler, R.; Woyke, T.; Malmstrom, R.; Yu, H.; Scheller, S.

    2015-12-01

    Cooperative metabolic interactions between multiple groups of methanotrophic 'ANME' archaea and sulfate-reducing bacteria represent the primary sink for methane within continental margin sediments. These syntrophic associations are frequently observed as structured multi-celled consortia in methane seeps, often comprising a substantial proportion of the microbial biomass within near seafloor seep sediments. Since their discovery nearly 15 years ago, a number of distinct ANME groups and multiple sulfate-reducing bacterial partners have been described from seep environments worldwide. Attempts to reconstruct the genomes of some ANME organisms have been reported, however the ecological physiology and metabolic interactions of distinct ANME lineages and their bacterial partners remains poorly understood. Here, we used a fluorescence azide-alkyne click chemistry technique known as BONCAT combined with FAC sorting to examine patterns in microbial membership and the genomes of single, metabolically active ANME-bacterial consortia recovered from methane seep sediments. This targeted consortia-level sequencing approach revealed significant diversity in the ANME-bacterial associations in situ as well as insights into the potential syntrophic mechanisms underpinning these enigmatic methane-fueled partnerships.

  6. Therapeutic potential of mitotic interaction between the nucleoporin Tpr and aurora kinase A.

    PubMed

    Kobayashi, Akiko; Hashizume, Chieko; Dowaki, Takayuki; Wong, Richard W

    2015-01-01

    Spindle poles are defined by centrosomes; therefore, an abnormal number or defective structural organization of centrosomes can lead to loss of spindle bipolarity and genetic integrity. Previously, we showed that Tpr (translocated promoter region), a component of the nuclear pore complex (NPC), interacts with Mad1 and dynein to promote proper chromosome segregation during mitosis. Tpr also associates with p53 to induce autophagy. Here, we report that Tpr depletion induces mitotic catastrophe and enhances the rate of tetraploidy and polyploidy. Mechanistically, Tpr interacts, via its central domain, with Aurora A but not Aurora B kinase. In Tpr-depleted cells, the expression levels, centrosomal localization and phosphorylation of Aurora A were all reduced. Surprisingly, an Aurora A inhibitor, Alisertib (MLN8237), also disrupted centrosomal localization of Tpr and induced mitotic catastrophe and cell death in a time- and dose-dependent manner. Strikingly, over-expression of Aurora A disrupted Tpr centrosomal localization only in cells with supernumerary centrosomes but not in bipolar cells. Our results highlight the mutual regulation between Tpr and Aurora A and further confirm the importance of nucleoporin function in spindle pole organization, bipolar spindle assembly, and mitosis; functions that are beyond the conventional nucleocytoplasmic transport and NPC structural roles of nucleoporins. Furthermore, the central coiled-coil domain of Tpr binds to and sequesters extra Aurora A to safeguard bipolarity. This Tpr domain merits further investigation for its ability to inhibit Aurora kinase and as a potential therapeutic agent in cancer treatment.

  7. Liquid chloroform structure from computer simulation with a full ab initio intermolecular interaction potential

    SciTech Connect

    Yin, Chih-Chien; Li, Arvin Huang-Te; Chao, Sheng D.

    2013-11-21

    We have calculated the intermolecular interaction energies of the chloroform dimer in 12 orientations using the second-order Møller-Plesset perturbation theory. Single point energies of important geometries were calibrated by the coupled cluster with single and double and perturbative triple excitation method. Dunning's correlation consistent basis sets up to aug-cc-pVQZ have been employed in extrapolating the interaction energies to the complete basis set limit values. With the ab initio potential data we constructed a 5-site force field model for molecular dynamics simulations. We compared the simulation results with recent experiments and obtained quantitative agreements for the detailed atomwise radial distribution functions. Our results were also consistent with previous results using empirical force fields with polarization effects. Moreover, the calculated diffusion coefficients reproduced the experimental data over a wide range of thermodynamic conditions. To the best of our knowledge, this is the first ab initio force field which is capable of competing with existing empirical force fields for liquid chloroform.

  8. Visuo-tactile interactions in the congenitally deaf: a behavioral and event-related potential study

    PubMed Central

    Hauthal, Nadine; Debener, Stefan; Rach, Stefan; Sandmann, Pascale; Thorne, Jeremy D.

    2015-01-01

    Auditory deprivation is known to be accompanied by alterations in visual processing. Yet not much is known about tactile processing and the interplay of the intact sensory modalities in the deaf. We presented visual, tactile, and visuo-tactile stimuli to congenitally deaf and hearing individuals in a speeded detection task. Analyses of multisensory responses showed a redundant signals effect that was attributable to a coactivation mechanism in both groups, although the redundancy gain was less in the deaf. In line with these behavioral results, on a neural level, there were multisensory interactions in both groups that were again weaker in the deaf. In hearing but not deaf participants, somatosensory event-related potential N200 latencies were modulated by simultaneous visual stimulation. A comparison of unisensory responses between groups revealed larger N200 amplitudes for visual and shorter N200 latencies for tactile stimuli in the deaf. Furthermore, P300 amplitudes were also larger in the deaf. This group difference was significant for tactile and approached significance for visual targets. The differences in visual and tactile processing between deaf and hearing participants, however, were not reflected in behavior. Both the behavioral and electroencephalography (EEG) results suggest more pronounced multisensory interaction in hearing than in deaf individuals. Visuo-tactile enhancements could not be explained by perceptual deficiency, but could be partly attributable to inverse effectiveness. PMID:25653602

  9. In vivo multispectral photoacoustic and photothermal flow cytometry with multicolor dyes: a potential for real-time assessment of circulation, dye-cell interaction, and blood volume

    PubMed Central

    Proskurnin, Mikhail A.; Zhidkova, Tatyana V.; Volkov, Dmitry S.; Sarimollaoglu, Mustafa; Galanzha, Ekaterina I.; Mock, Donald; Zharov, Vladimir P.

    2011-01-01

    Recently, photoacoustic (PA) flow cytometry (PAFC) has been developed for in vivo detection of circulating tumor cells and bacteria targeted by nanoparticles. Here, we propose multispectral PAFC with multiple dyes having distinctive absorption spectra as multicolor PA contrast agents. As a first step of our proof-of-concept, we characterized high-speed PAFC capability to monitor the clearance of three dyes (ICG, MB, and TB) in an animal model in vivo and in real time. We observed strong dynamic PA signal fluctuations, which can be associated with interactions of dyes with circulating blood cells and plasma proteins. PAFC demonstrated enumeration of circulating red and white blood cells labeled with ICG and MB, respectively, and detection of rare dead cells uptaking TB directly in bloodstream. The possibility for accurate measurements of various dye concentrations including CV and BG were verified in vitro using complementary to PAFC photothermal (PT) technique and spectrophotometry under batch and flow conditions. We further analyze the potential of integrated PAFC/PT spectroscopy with multiple dyes for rapid and accurate measurements of circulating blood volume without a priori information on hemoglobin content, which is impossible with existing optical techniques. This is important in many medical conditions including surgery and trauma with extensive blood loss, rapid fluid administration, transfusion of red blood cells. The potential for developing a robust clinical PAFC prototype that is, safe for human, and its applications for studying the liver function are further highlighted. PMID:21905207

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

    PubMed

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

    2008-06-01

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

  11. In vivo quantification and perturbation of Myc-Max interactions and the impact on oncogenic potential.

    PubMed

    Raffeiner, Philipp; Röck, Ruth; Schraffl, Andrea; Hartl, Markus; Hart, Jonathan R; Janda, Kim D; Vogt, Peter K; Stefan, Eduard; Bister, Klaus

    2014-10-15

    The oncogenic bHLH-LZ transcription factor Myc forms binary complexes with its binding partner Max. These and other bHLH-LZ-based protein-protein interactions (PPI) in the Myc-Max network are essential for the physiological and oncogenic activities of Myc. We have generated a genetically determined and highly specific protein-fragment complementation assay based on Renilla luciferase to analyze the dynamic interplay of bHLH-LZ transcription factors Myc, Max, and Mxd1 in vivo. We also applied this PPI reporter to quantify alterations of nuclear Myc-Max complexes in response to mutational events, competitive binding by the transcriptional repressor Mxd1, or perturbations by small-molecule Myc inhibitors, including recently identified potent PPI inhibitors from a Kröhnke pyridine library. We show that the specificity of Myc-Max PPI reduction by the pyridine inhibitors directly correlates with their efficient and highly specific potential to interfere with the proliferation of human and avian tumor cells displaying deregulated Myc expression. In a direct comparison with known Myc inhibitors using human and avian cell systems, the pyridine compounds reveal a unique inhibitory potential even at sub-micromolar concentrations combined with remarkable specificity for the inhibition of Myc-driven tumor cell proliferation. Furthermore, we show in direct comparisons using defined avian cell systems that different Max PPI profiles for the variant members of the Myc protein family (c-Myc, v-Myc, N-Myc, L-Myc) correlate with their diverse oncogenic potential and their variable sensitivity to the novel pyridine inhibitors.

  12. Full-Potential Modeling of Blade-Vortex Interactions. Degree awarded by George Washington Univ., Feb. 1987

    NASA Technical Reports Server (NTRS)

    Jones, Henry E.

    1997-01-01

    A study of the full-potential modeling of a blade-vortex interaction was made. A primary goal of this study was to investigate the effectiveness of the various methods of modeling the vortex. The model problem restricts the interaction to that of an infinite wing with an infinite line vortex moving parallel to its leading edge. This problem provides a convenient testing ground for the various methods of modeling the vortex while retaining the essential physics of the full three-dimensional interaction. A full-potential algorithm specifically tailored to solve the blade-vortex interaction (BVI) was developed to solve this problem. The basic algorithm was modified to include the effect of a vortex passing near the airfoil. Four different methods of modeling the vortex were used: (1) the angle-of-attack method, (2) the lifting-surface method, (3) the branch-cut method, and (4) the split-potential method. A side-by-side comparison of the four models was conducted. These comparisons included comparing generated velocity fields, a subcritical interaction, and a critical interaction. The subcritical and critical interactions are compared with experimentally generated results. The split-potential model was used to make a survey of some of the more critical parameters which affect the BVI.

  13. Interaction potentials of anisotropic nanocrystals from the trajectory sampling of particle motion using in situ liquid phase transmission electron microscopy

    DOE PAGES

    Chen, Qian; Cho, Hoduk; Manthiram, Karthish; Yoshida, Mark; Ye, Xingchen; Alivisatos, A. Paul

    2015-03-23

    We demonstrate a generalizable strategy to use the relative trajectories of pairs and groups of nanocrystals, and potentially other nanoscale objects, moving in solution which can now be obtained by in situ liquid phase transmission electron microscopy (TEM) to determine the interaction potentials between nanocrystals. Such nanoscale interactions are crucial for collective behaviors and applications of synthetic nanocrystals and natural biomolecules, but have been very challenging to measure in situ at nanometer or sub-nanometer resolution. Here we use liquid phase TEM to extract the mathematical form of interaction potential between nanocrystals from their sampled trajectories. We show the power ofmore » this approach to reveal unanticipated features of nanocrystal–nanocrystal interactions by examining the anisotropic interaction potential between charged rod-shaped Au nanocrystals (Au nanorods); these Au nanorods assemble, in a tip-to-tip fashion in the liquid phase, in contrast to the well-known side-by-side arrangements commonly observed for drying-mediated assembly. These observations can be explained by a long-range and highly anisotropic electrostatic repulsion that leads to the tip-selective attachment. As a result, Au nanorods stay unassembled at a lower ionic strength, as the electrostatic repulsion is even longer-ranged. Our study not only provides a mechanistic understanding of the process by which metallic nanocrystals assemble but also demonstrates a method that can potentially quantify and elucidate a broad range of nanoscale interactions relevant to nanotechnology and biophysics.« less

  14. Interaction Potentials of Anisotropic Nanocrystals from the Trajectory Sampling of Particle Motion using in Situ Liquid Phase Transmission Electron Microscopy

    PubMed Central

    2015-01-01

    We demonstrate a generalizable strategy to use the relative trajectories of pairs and groups of nanocrystals, and potentially other nanoscale objects, moving in solution which can now be obtained by in situ liquid phase transmission electron microscopy (TEM) to determine the interaction potentials between nanocrystals. Such nanoscale interactions are crucial for collective behaviors and applications of synthetic nanocrystals and natural biomolecules, but have been very challenging to measure in situ at nanometer or sub-nanometer resolution. Here we use liquid phase TEM to extract the mathematical form of interaction potential between nanocrystals from their sampled trajectories. We show the power of this approach to reveal unanticipated features of nanocrystal–nanocrystal interactions by examining the anisotropic interaction potential between charged rod-shaped Au nanocrystals (Au nanorods); these Au nanorods assemble, in a tip-to-tip fashion in the liquid phase, in contrast to the well-known side-by-side arrangements commonly observed for drying-mediated assembly. These observations can be explained by a long-range and highly anisotropic electrostatic repulsion that leads to the tip-selective attachment. As a result, Au nanorods stay unassembled at a lower ionic strength, as the electrostatic repulsion is even longer-ranged. Our study not only provides a mechanistic understanding of the process by which metallic nanocrystals assemble but also demonstrates a method that can potentially quantify and elucidate a broad range of nanoscale interactions relevant to nanotechnology and biophysics. PMID:27162944

  15. Potential energy curves for the interaction of Ag(5s) and Ag(5p) with noble gas atoms.

    PubMed

    Loreau, J; Sadeghpour, H R; Dalgarno, A

    2013-02-28

    We investigate the interaction of ground and excited states of a silver atom with noble gases (NG), including helium. Born-Oppenheimer potential energy curves are calculated with quantum chemistry methods and spin-orbit effects in the excited states are included by assuming a spin-orbit splitting independent of the internuclear distance. We compare our results with experimentally available spectroscopic data, as well as with previous calculations. Because of strong spin-orbit interactions, excited Ag-NG potential energy curves cannot be fitted to Morse-like potentials. We find that the labeling of the observed vibrational levels has to be shifted by one unit.

  16. Interaction with Mixed Micelles in the Intestine Attenuates the Permeation Enhancing Potential of Alkyl-Maltosides.

    PubMed

    Gradauer, Kerstin; Nishiumi, Ayano; Unrinin, Kota; Higashino, Haruki; Kataoka, Makoto; Pedersen, Betty L; Buckley, Stephen T; Yamashita, Shinji

    2015-07-01

    The purpose of the present study was to investigate the interaction of intestinal permeation enhancers with lipid and surfactant components present in the milieu of the small intestine. Maltosides of different chain lengths (decyl-, dodecyl-, and tetradecyl-maltoside; DM, DDM, TDM, respectively) were used as examples of nonionic, surfactant-like permeation enhancers, and their effect on the permeation of FD4 across Caco-2 monolayers was monitored. To mimic the environment of the small intestine, modified versions of fasted and fed state simulated intestinal fluid (FaSSIFmod, FeSSIFmod6.5, respectively) were used in addition to standard transport media (TM). Compared to the buffer control, 0.5 mM DDM led to a 200-fold permeation enhancement of FD4 in TM. However, this was dramatically decreased in FaSSIFmod, where a concentration of 5 mM DDM was necessary in order to elicit a moderate, 4-fold, permeation enhancement. Its capacity to promote permeation was diminished further when FeSSIFmod6.5 was employed. Even when cells were exposed to a concentration of 5 mM, no significant permeation enhancement of FD4 was observed. Analogous effects were observed in the case of DM and TDM, with slight deviations on account of differences in their critical micelle concentration (CMC). This observation was corroborated by calculating the amount of maltoside monomer versus micellar bound maltoside in FaSSIFmod and FeSSIFmod6.5, which demonstrated a reduced amount of free monomer in these fluids. To evaluate the in vivo significance of our findings, DDM solutions in TM, FaSSIFmod, and FeSSIFmod6.5 were used for closed intestinal loop studies in rats. Consistent with the results found in in vitro permeation studies, these investigations illustrated the overwhelming impact of sodium taurocholate/lecithin micelles on the permeation enhancing effect of DDM. While DDM led to a 20-fold increase in FD4 bioavailability when it was applied in TM, no significant permeation enhancement was

  17. Structural and Functional Interactions between Transient Receptor Potential Vanilloid Subfamily 1 and Botulinum Neurotoxin Serotype A

    PubMed Central

    2016-01-01

    Background Botulinum neurotoxins are produced by Clostridium botulinum bacteria. There are eight serologically distinct botulinum neurotoxin isoforms (serotypes A–H). Currently, botulinum neurotoxin serotype A (BoNT⁄A) is commonly used for the treatment of many disorders, such as hyperactive musculoskeletal disorders, dystonia, and pain. However, the effectiveness of BoNT⁄A for pain alleviation and the mechanisms that mediate the analgesic effects of BoNT⁄A remain unclear. To define the antinociceptive mechanisms by which BoNT/A functions, the interactions between BoNT⁄A and the transient receptor potential vanilloid subfamily 1 (TRPV1) were investigated using immunofluorescence, co-immunoprecipitation, and western blot analysis in primary mouse embryonic dorsal root ganglion neuronal cultures. Results 1) Three-week-old cultured dorsal root ganglion neurons highly expressed transient TRPV1, synaptic vesicle 2A (SV2A) and synaptosomal-associated protein 25 (SNAP-25). SV2A and SNAP-25 are the binding receptor and target protein, respectively, of BoNT⁄A. 2) TRPV1 colocalized with both BoNT⁄A and cleaved SNAP-25 when BoNT⁄A was added to dorsal root ganglia neuronal cultures. 3) After 24 hours of BoNT⁄A treatment (1 nmol⁄l), both TRPV1 and BoNT⁄A positive bands were detected in western blots of immunoprecipitated pellets. 4) Blocking TRPV1 with a specific antibody decreased the cleavage of SNAP-25 by BoNT⁄A. Conclusion BoNT/A interacts with TRPV1 both structurally and functionally in cultured mouse embryonic dorsal root ganglion neurons. These results suggest that an alternative mechanism is used by BoNT⁄A to mediate pain relief. PMID:26745805

  18. Hydrodynamic interactions of two nearly touching Brownian spheres in a stiff potential: Effect of fluid inertia

    NASA Astrophysics Data System (ADS)

    Radiom, Milad; Robbins, Brian; Paul, Mark; Ducker, William

    2015-02-01

    The hydrodynamic interaction of two closely spaced micron-scale spheres undergoing Brownian motion was measured as a function of their separation. Each sphere was attached to the distal end of a different atomic force microscopy cantilever, placing each sphere in a stiff one-dimensional potential (0.08 Nm-1) with a high frequency of thermal oscillations (resonance at 4 kHz). As a result, the sphere's inertial and restoring forces were significant when compared to the force due to viscous drag. We explored interparticle gap regions where there was overlap between the two Stokes layers surrounding each sphere. Our experimental measurements are the first of their kind in this parameter regime. The high frequency of oscillation of the spheres means that an analysis of the fluid dynamics would include the effects of fluid inertia, as described by the unsteady Stokes equation. However, we find that, for interparticle separations less than twice the thickness of the wake of the unsteady viscous boundary layer (the Stokes layer), the hydrodynamic interaction between the Brownian particles is well-approximated by analytical expressions that neglect the inertia of the fluid. This is because elevated frictional forces at narrow gaps dominate fluid inertial effects. The significance is that interparticle collisions and concentrated suspensions at this condition can be modeled without the need to incorporate fluid inertia. We suggest a way to predict when fluid inertial effects can be ignored by including the gap-width dependence into the frequency number. We also show that low frequency number analysis can be used to determine the microrheology of mixtures at interfaces.

  19. Hydrodynamic interactions of two nearly touching Brownian spheres in a stiff potential: Effect of fluid inertia

    SciTech Connect

    Radiom, Milad Ducker, William; Robbins, Brian; Paul, Mark

    2015-02-15

    The hydrodynamic interaction of two closely spaced micron-scale spheres undergoing Brownian motion was measured as a function of their separation. Each sphere was attached to the distal end of a different atomic force microscopy cantilever, placing each sphere in a stiff one-dimensional potential (0.08 Nm{sup −1}) with a high frequency of thermal oscillations (resonance at 4 kHz). As a result, the sphere’s inertial and restoring forces were significant when compared to the force due to viscous drag. We explored interparticle gap regions where there was overlap between the two Stokes layers surrounding each sphere. Our experimental measurements are the first of their kind in this parameter regime. The high frequency of oscillation of the spheres means that an analysis of the fluid dynamics would include the effects of fluid inertia, as described by the unsteady Stokes equation. However, we find that, for interparticle separations less than twice the thickness of the wake of the unsteady viscous boundary layer (the Stokes layer), the hydrodynamic interaction between the Brownian particles is well-approximated by analytical expressions that neglect the inertia of the fluid. This is because elevated frictional forces at narrow gaps dominate fluid inertial effects. The significance is that interparticle collisions and concentrated suspensions at this condition can be modeled without the need to incorporate fluid inertia. We suggest a way to predict when fluid inertial effects can be ignored by including the gap-width dependence into the frequency number. We also show that low frequency number analysis can be used to determine the microrheology of mixtures at interfaces.

  20. Interspecies interactions and potential Influenza A virus risk in small swine farms in Peru

    PubMed Central

    2012-01-01

    Background The recent avian influenza epidemic in Asia and the H1N1 pandemic demonstrated that influenza A viruses pose a threat to global public health. The animal origins of the viruses confirmed the potential for interspecies transmission. Swine are hypothesized to be prime "mixing vessels" due to the dual receptivity of their trachea to human and avian strains. Additionally, avian and human influenza viruses have previously been isolated in swine. Therefore, understanding interspecies contact on smallholder swine farms and its potential role in the transmission of pathogens such as influenza virus is very important. Methods This qualitative study aimed to determine swine-associated interspecies contacts in two coastal areas of Peru. Direct observations were conducted at both small-scale confined and low-investment swine farms (n = 36) and in open areas where swine freely range during the day (n = 4). Interviews were also conducted with key stakeholders in swine farming. Results In both locations, the intermingling of swine and domestic birds was common. An unexpected contact with avian species was that swine were fed poultry mortality in 6/20 of the farms in Chancay. Human-swine contacts were common, with a higher frequency on the confined farms. Mixed farming of swine with chickens or ducks was observed in 36% of all farms. Human-avian interactions were less frequent overall. Use of adequate biosecurity and hygiene practices by farmers was suboptimal at both locations. Conclusions Close human-animal interaction, frequent interspecies contacts and suboptimal biosecurity and hygiene practices pose significant risks of interspecies influenza virus transmission. Farmers in small-scale swine production systems constitute a high-risk population and need to be recognized as key in preventing interspecies pathogen transfer. A two-pronged prevention approach, which offers educational activities for swine farmers about sound hygiene and biosecurity practices and

  1. Colloids exposed to random potential energy landscapes: From particle number density to particle-potential and particle-particle interactions.

    PubMed

    Bewerunge, Jörg; Sengupta, Ankush; Capellmann, Ronja F; Platten, Florian; Sengupta, Surajit; Egelhaaf, Stefan U

    2016-07-28

    Colloidal particles were exposed to a random potential energy landscape that has been created optically via a speckle pattern. The mean particle density as well as the potential roughness, i.e., the disorder strength, were varied. The local probability density of the particles as well as its main characteristics were determined. For the first time, the disorder-averaged pair density correlation function g((1))(r) and an analogue of the Edwards-Anderson order parameter g((2))(r), which quantifies the correlation of the mean local density among disorder realisations, were measured experimentally and shown to be consistent with replica liquid state theory results.

  2. Mesoscale properties of clay aggregates from potential of mean force representation of interactions between nanoplatelets

    NASA Astrophysics Data System (ADS)

    Ebrahimi, Davoud; Whittle, Andrew J.; Pellenq, Roland J.-M.

    2014-04-01

    Face-to-face and edge-to-edge free energy interactions of Wyoming Na-montmorillonite platelets were studied by calculating potential of mean force along their center to center reaction coordinate using explicit solvent (i.e., water) molecular dynamics and free energy perturbation methods. Using a series of configurations, the Gay-Berne potential was parametrized and used to examine the meso-scale aggregation and properties of platelets that are initially random oriented under isothermal-isobaric conditions. Aggregates of clay were defined by geometrical analysis of face-to-face proximity of platelets with size distribution described by a log-normal function. The isotropy of the microstructure was assessed by computing a scalar order parameter. The number of platelets per aggregate and anisotropy of the microstructure both increases with platelet plan area. The system becomes more ordered and aggregate size increases with increasing pressure until maximum ordered state at confining pressure of 50 atm. Further increase of pressure slides platelets relative to each other leading to smaller aggregate size. The results show aggregate size of (3-8) platelets for sodium-smectite in agreement with experiments (3-10). The geometrical arrangement of aggregates affects mechanical properties of the system. The elastic properties of the meso-scale aggregate assembly are reported and compared with nanoindentation experiments. It is found that the elastic properties at this scale are close to the cubic systems. The elastic stiffness and anisotropy of the assembly increases with the size of the platelets and the level of external pressure.

  3. Vortices in a rotating two-component Bose–Einstein condensate with tunable interactions and harmonic potential

    SciTech Connect

    Zhang, Xiao-Fei; Du, Zhi-Jing; Tan, Ren-Bing; Dong, Rui-Fang; Chang, Hong; Zhang, Shou-Gang

    2014-07-15

    We consider a pair of coupled nonlinear Schrödinger equations modeling a rotating two-component Bose–Einstein condensate with tunable interactions and harmonic potential, with emphasis on the structure of vortex states by varying the strength of inter-component interaction, rotational frequency, and the aspect ratio of the harmonic potential. Our results show that the inter-component interaction greatly enhances the effect of rotation. For the case of isotropic harmonic potential and small inter-component interaction, the initial vortex structure remains unchanged. As the ratio of inter- to intra-component interactions increases, each component undergoes a transition from a vortex lattice (vortex line) in an isotropic (anisotropic) harmonic potential to an alternatively arranged stripe pattern, and eventually to the interwoven “serpentine” vortex sheets. Moreover, in the case of anisotropic harmonic potential the system can develop to a rotating droplet structure. -- Highlights: •Different vortex structures are obtained within the full parameter space. •Effects of system parameters on the ground state structure are discussed. •Phase transition between different vortex structures is also examined. •Present one possible way to obtain the rotating droplet structure. •Provide many possibilities to manipulate vortex in two-component BEC.

  4. MOLECULAR INTERACTION POTENTIALS FOR THE DEVELOPMENT OF STRUCTURE-ACTIVITY RELATIONSHIPS

    EPA Science Inventory

    Abstract
    One reasonable approach to the analysis of the relationships between molecular structure and toxic activity is through the investigation of the forces and intermolecular interactions responsible for chemical toxicity. The interaction between the xenobiotic and the bio...

  5. Formalizing the potential of stereoscopic 3D user experience in interactive entertainment

    NASA Astrophysics Data System (ADS)

    Schild, Jonas; Masuch, Maic

    2015-03-01

    The use of stereoscopic 3D vision affects how interactive entertainment has to be developed as well as how it is experienced by the audience. The large amount of possibly impacting factors and variety as well as a certain subtlety of measured effects on user experience make it difficult to grasp the overall potential of using S3D vision. In a comprehensive approach, we (a) present a development framework which summarizes possible variables in display technology, content creation and human factors, and (b) list a scheme of S3D user experience effects concerning initial fascination, emotions, performance, and behavior as well as negative feelings of discomfort and complexity. As a major contribution we propose a qualitative formalization which derives dependencies between development factors and user effects. The argumentation is based on several previously published user studies. We further show how to apply this formula to identify possible opportunities and threats in content creation as well as how to pursue future steps for a possible quantification.

  6. Potential Interactions between the Autonomic Nervous System and Higher Level Functions in Neurological and Neuropsychiatric Conditions

    PubMed Central

    Bassi, Andrea; Bozzali, Marco

    2015-01-01

    The autonomic nervous system (ANS) maintains the internal homeostasis by continuously interacting with other brain structures. Its failure is commonly observed in many neurological and neuropsychiatric disorders, including neurodegenerative and vascular brain diseases, spinal cord injury, and peripheral neuropathies. Despite the different underlying pathophysiological mechanisms, ANS failure associates with various forms of higher level dysfunctions, and may also negatively impact on patients’ clinical outcome. In this review, we will discuss potential relationships between ANS and higher level dysfunctions in a selection of neurological and neuropsychiatric disorders. In particular, we will focus on the effect of a documented fall in blood pressure fulfilling the criteria for orthostatic hypotension and/or autonomic-reflex impairment on cognitive performances. Some evidence supports the hypothesis that cardiovascular autonomic failure may play a negative prognostic role in most neurological disorders. Despite a clear causal relationship between ANS involvement and higher level dysfunctions that is still controversial, this might have implications for neuro-rehabilitation strategies aimed at improving patients’ clinical outcome. PMID:26388831

  7. Potentiating toxicological interaction of single-walled carbon nanotubes with dissolved metals.

    PubMed

    Al-Shaeri, Majed; Ahmed, Dina; McCluskey, Fiona; Turner, Gavin; Paterson, Lynn; Dyrynda, Elisabeth A; Hartl, Mark G J

    2013-12-01

    The present study explored the ecotoxicology of single-walled carbon nanotubes (SWCNTs) and their likely interaction with dissolved metals, with a focus on the effect of in vivo exposure in marine mussels. Any nano-scale effects were negated by the tendency of uncoated SWCNTs to agglomerate in water, particularly with high ionic strength as is the case in estuarine and full-strength seawater. However, SWCNTs, in combination with natural organic matter, remained suspended in seawater for long enough to become available to filter-feeding mussels, leading to their concentration on and increased contact with gill epithelia during exposure. For the first time, the authors describe a potentiating toxicological effect, expressed as DNA strand breaks obtained using the comet assay, on divalent metals afforded by negatively charged SWCNT agglomerates in seawater at concentrations as low as 5 µg L⁻¹. This is supported by the observation that SWCNTs alone were only toxic at concentrations ≥100 µg L⁻¹ and that the SWCNT-induced DNA damage was correlated with oxidative stress only in the absence of metals. If these laboratory experiments are confirmed in the natural environment, the present results will have implications for the understanding of the role of carbon nanotubes in environmental metal dynamics, toxicology, and consequently, regulatory requirements.

  8. Mechanisms of radiation interaction with DNA: Potential implications for radiation protection

    SciTech Connect

    Not Available

    1988-01-01

    The Office of Health and Environmental Research (OHER) of the US Department of Energy conducts a broad multidisciplinary research program which includes basic biophysics, biophysical chemistry, molecular and cellular biology as well as experimental animal studies and opportunistic human studies. This research is directed at understanding how low levels of radiation of various qualities produce the spectrum of biological effects that are seen for such exposures. This workshop was entitled ''Mechanisms of Radiation Interaction with DNA: Potential Implications for Radiation Protection.'' It ws jointly sponsored by the Department of Energy and the Commission of European Communities. The aim of the workshop was to review the base of knowledge in the area of mechanisms of radiation action at the DNA level, and to explore ways in which this information can be applied to the development of scientifically sound concepts and procedures for use in the field of radiation protection. The overview of research provided by this multidisciplinary group will be helpful to the Office in program planning. This report includes a summary of the presentations, extended abstracts, the meeting agenda, research recommendations, and a list of participants. Individual papers are processed separately for the data base.

  9. Error-related EEG potentials generated during simulated brain-computer interaction.

    PubMed

    Ferrez, Pierre W; del R Millan, José

    2008-03-01

    Brain-computer interfaces (BCIs) are prone to errors in the recognition of subject's intent. An elegant approach to improve the accuracy of BCIs consists in a verification procedure directly based on the presence of error-related potentials (ErrP) in the electroencephalogram (EEG) recorded right after the occurrence of an error. Several studies show the presence of ErrP in typical choice reaction tasks. However, in the context of a BCI, the central question is: "Are ErrP also elicited when the error is made by the interface during the recognition of the subject's intent?"; We have thus explored whether ErrP also follow a feedback indicating incorrect responses of the simulated BCI interface. Five healthy volunteer subjects participated in a new human-robot interaction experiment, which seem to confirm the previously reported presence of a new kind of ErrP. However, in order to exploit these ErrP, we need to detect them in each single trial using a short window following the feedback associated to the response of the BCI. We have achieved an average recognition rate of correct and erroneous single trials of 83.5% and 79.2%, respectively, using a classifier built with data recorded up to three months earlier.

  10. Interactions of dietary carotenoids with activated (singlet) oxygen and free radicals: potential effects for human health.

    PubMed

    Böhm, Fritz; Edge, Ruth; Truscott, George

    2012-02-01

    Molecular mechanisms associated with the anti-/pro-oxidative properties of carotenoids (CARs) are described in organic solvents, micro-heterogeneous environments and model lipid membranes and in cellular suspensions. Singlet oxygen is important in the skin and eye and CARs are efficient singlet oxygen (SO) quenchers with corresponding rate constants near diffusion controlled (typically app. 10¹⁰ M⁻¹ s⁻¹) with lycopene (LYC) exhibiting the most efficient quenching in organic solvents. However, in membrane environments there is little or no difference in the quenching efficiency between the dietary CARs. Furthermore, aggregation of CARs, particularly those in the macula (lutein and zeaxanthin), markedly reduces SO quenching efficiency. Free radical interactions with CARs leads to at least three processes, electron and hydrogen atom transfer and adduct formation. The most studied is electron transfer where the CAR loses an electron to become a radical cation. The reactivity/lifetime of such CAR radicals may lead to a switch from anti- to pro-oxidant behaviour of CARs. These reactions are related to CAR redox potentials with LYC being the lowest (most easily oxidised) allowing LYC to reduce/repair all other CAR radical cations and LYC 'sacrificed' where mixtures of CARs are present in oxidative environments. Such redox-controlled reactions may lead to deleterious as well as beneficial health effects.

  11. Approximate bound-state solutions of the Dirac equation for the generalized yukawa potential plus the generalized tensor interaction

    NASA Astrophysics Data System (ADS)

    Ikot, Akpan N.; Maghsoodi, Elham; Hassanabadi, Hassan; Obu, Joseph A.

    2014-05-01

    In this paper, we obtain the approximate analytical bound-state solutions of the Dirac particle with the generalized Yukawa potential within the framework of spin and pseudospin symmetries for the arbitrary к state with a generalized tensor interaction. The generalized parametric Nikiforov-Uvarov method is used to obtain the energy eigenvalues and the corresponding wave functions in closed form. We also report some numerical results and present figures to show the effect of the tensor interaction.

  12. Ab initio potential energy surfaces describing the interaction of CH(X2Π) with H2

    NASA Astrophysics Data System (ADS)

    Dagdigian, Paul J.

    2016-09-01

    We have determined four-dimensional ab initio quasi-diabatic potential energy surfaces describing the interaction of CH(X2Π) with H2, under the assumption of fixed CH and H2 internuclear separations. These calculations employed the multi-reference configuration interaction method [MRCISD+Q(Davidson)]. The computed points were fit to an analytical form suitable for time-independent quantum scattering calculations of rotationally inelastic cross sections and rate constants.

  13. 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}

    SciTech Connect

    Huang, Xinchuan E-mail: Timothy.J.Lee@nasa.gov; Schwenke, David W.; Lee, Timothy J. 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, 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.

  14. MONITORING POTENTIAL DRUG INTERACTIONS AND REACTIONS VIA NETWORK ANALYSIS OF INSTAGRAM USER TIMELINES.

    PubMed

    Correia, Rion Brattig; Li, Lang; Rocha, Luis M

    2016-01-01

    Much recent research aims to identify evidence for Drug-Drug Interactions (DDI) and Adverse Drug reactions (ADR) from the biomedical scientific literature. In addition to this "Bibliome", the universe of social media provides a very promising source of large-scale data that can help identify DDI and ADR in ways that have not been hitherto possible. Given the large number of users, analysis of social media data may be useful to identify under-reported, population-level pathology associated with DDI, thus further contributing to improvements in population health. Moreover, tapping into this data allows us to infer drug interactions with natural products-including cannabis-which constitute an array of DDI very poorly explored by biomedical research thus far. Our goal is to determine the potential of Instagram for public health monitoring and surveillance for DDI, ADR, and behavioral pathology at large. Most social media analysis focuses on Twitter and Facebook, but Instagram is an increasingly important platform, especially among teens, with unrestricted access of public posts, high availability of posts with geolocation coordinates, and images to supplement textual analysis. Using drug, symptom, and natural product dictionaries for identification of the various types of DDI and ADR evidence, we have collected close to 7000 user timelines spanning from October 2010 to June 2015.We report on 1) the development of a monitoring tool to easily observe user-level timelines associated with drug and symptom terms of interest, and 2) population-level behavior via the analysis of co-occurrence networks computed from user timelines at three different scales: monthly, weekly, and daily occurrences. Analysis of these networks further reveals 3) drug and symptom direct and indirect associations with greater support in user timelines, as well as 4) clusters of symptoms and drugs revealed by the collective behavior of the observed population. This demonstrates that Instagram

  15. MONITORING POTENTIAL DRUG INTERACTIONS AND REACTIONS VIA NETWORK ANALYSIS OF INSTAGRAM USER TIMELINES.

    PubMed

    Correia, Rion Brattig; Li, Lang; Rocha, Luis M

    2016-01-01

    Much recent research aims to identify evidence for Drug-Drug Interactions (DDI) and Adverse Drug reactions (ADR) from the biomedical scientific literature. In addition to this "Bibliome", the universe of social media provides a very promising source of large-scale data that can help identify DDI and ADR in ways that have not been hitherto possible. Given the large number of users, analysis of social media data may be useful to identify under-reported, population-level pathology associated with DDI, thus further contributing to improvements in population health. Moreover, tapping into this data allows us to infer drug interactions with natural products-including cannabis-which constitute an array of DDI very poorly explored by biomedical research thus far. Our goal is to determine the potential of Instagram for public health monitoring and surveillance for DDI, ADR, and behavioral pathology at large. Most social media analysis focuses on Twitter and Facebook, but Instagram is an increasingly important platform, especially among teens, with unrestricted access of public posts, high availability of posts with geolocation coordinates, and images to supplement textual analysis. Using drug, symptom, and natural product dictionaries for identification of the various types of DDI and ADR evidence, we have collected close to 7000 user timelines spanning from October 2010 to June 2015.We report on 1) the development of a monitoring tool to easily observe user-level timelines associated with drug and symptom terms of interest, and 2) population-level behavior via the analysis of co-occurrence networks computed from user timelines at three different scales: monthly, weekly, and daily occurrences. Analysis of these networks further reveals 3) drug and symptom direct and indirect associations with greater support in user timelines, as well as 4) clusters of symptoms and drugs revealed by the collective behavior of the observed population. This demonstrates that Instagram

  16. MONITORING POTENTIAL DRUG INTERACTIONS AND REACTIONS VIA NETWORK ANALYSIS OF INSTAGRAM USER TIMELINES

    PubMed Central

    CORREIA, RION BRATTIG; LI, LANG; ROCHA, LUIS M.

    2015-01-01

    Much recent research aims to identify evidence for Drug-Drug Interactions (DDI) and Adverse Drug reactions (ADR) from the biomedical scientific literature. In addition to this “Bibliome”, the universe of social media provides a very promising source of large-scale data that can help identify DDI and ADR in ways that have not been hitherto possible. Given the large number of users, analysis of social media data may be useful to identify under-reported, population-level pathology associated with DDI, thus further contributing to improvements in population health. Moreover, tapping into this data allows us to infer drug interactions with natural products—including cannabis—which constitute an array of DDI very poorly explored by biomedical research thus far. Our goal is to determine the potential of Instagram for public health monitoring and surveillance for DDI, ADR, and behavioral pathology at large. Most social media analysis focuses on Twitter and Facebook, but Instagram is an increasingly important platform, especially among teens, with unrestricted access of public posts, high availability of posts with geolocation coordinates, and images to supplement textual analysis. Using drug, symptom, and natural product dictionaries for identification of the various types of DDI and ADR evidence, we have collected close to 7000 user timelines spanning from October 2010 to June 2015. We report on 1) the development of a monitoring tool to easily observe user-level timelines associated with drug and symptom terms of interest, and 2) population-level behavior via the analysis of co-occurrence networks computed from user timelines at three different scales: monthly, weekly, and daily occurrences. Analysis of these networks further reveals 3) drug and symptom direct and indirect associations with greater support in user timelines, as well as 4) clusters of symptoms and drugs revealed by the collective behavior of the observed population. This demonstrates that

  17. Accurate Optical Reference Catalogs

    NASA Astrophysics Data System (ADS)

    Zacharias, N.

    2006-08-01

    Current and near future all-sky astrometric catalogs on the ICRF are reviewed with the emphasis on reference star data at optical wavelengths for user applications. The standard error of a Hipparcos Catalogue star position is now about 15 mas per coordinate. For the Tycho-2 data it is typically 20 to 100 mas, depending on magnitude. The USNO CCD Astrograph Catalog (UCAC) observing program was completed in 2004 and reductions toward the final UCAC3 release are in progress. This all-sky reference catalogue will have positional errors of 15 to 70 mas for stars in the 10 to 16 mag range, with a high degree of completeness. Proper motions for the about 60 million UCAC stars will be derived by combining UCAC astrometry with available early epoch data, including yet unpublished scans of the complete set of AGK2, Hamburg Zone astrograph and USNO Black Birch programs. Accurate positional and proper motion data are combined in the Naval Observatory Merged Astrometric Dataset (NOMAD) which includes Hipparcos, Tycho-2, UCAC2, USNO-B1, NPM+SPM plate scan data for astrometry, and is supplemented by multi-band optical photometry as well as 2MASS near infrared photometry. The Milli-Arcsecond Pathfinder Survey (MAPS) mission is currently being planned at USNO. This is a micro-satellite to obtain 1 mas positions, parallaxes, and 1 mas/yr proper motions for all bright stars down to about 15th magnitude. This program will be supplemented by a ground-based program to reach 18th magnitude on the 5 mas level.

  18. Validation of an interactive map assessing the potential spread of Galba truncatula as intermediate host of Fasciola hepatica in Switzerland.

    PubMed

    Baggenstos, Rhea; Dahinden, Tobias; Torgerson, Paul R; Bär, Hansruedi; Rapsch, Christina; Knubben-Schweizer, Gabriela

    2016-01-01

    Bovine fasciolosis, caused by Fasciola hepatica, is widespread in Switzerland. The risk regions were modelled in 2008 by an interactive map, showing the monthly potential risk of transmission of F. hepatica in Switzerland. As this map is based on a mathematical model, the aim of the present study was to evaluate the interactive map by means of a field survey taking different data sources into account. It was found that the interactive map has a sensitivity of 40.7-88.9%, a specificity of 11.4-18.8%, a positive predictive value of 26.7-51.4%, and a negative predictive value of 13.1-83.6%, depending on the source of the data. In conclusion, the grid of the interactive map (100 x 100 m) does not reflect enough detail and the underlying model of the interactive map is lacking transmission data. PMID:27245800

  19. Drug-Drug Interaction Potentials of Tyrosine Kinase Inhibitors via Inhibition of UDP-Glucuronosyltransferases

    PubMed Central

    Zhang, Nan; Liu, Yong; Jeong, Hyunyoung

    2015-01-01

    Tyrosine kinase inhibitors (TKIs) are anticancer drugs that may be co-administered with other drugs. The aims of this study are to investigate the inhibitory effects of TKIs on UDP-glucuronosyltransferase (UGT) activities, and to quantitatively evaluate their potential to cause drug-drug interactions (DDIs). Inhibition kinetic profiles of a panel of UGT enzymes (UGT1A1, 1A3, 1A4, 1A6, 1A7, 1A8, 1A9, 1A10, 2B4, 2B7, 2B15, and 2B17) by four TKIs (axitinib, imatinib, lapatinib and vandetanib) were characterized by using hepatic microsomes and recombinant proteins. Lapatinib exhibited potent competitive inhibition against UGT1A1 activity with a Ki of 0.5 μM. Imatinib was found to exhibit broad inhibition on several UGTs, particularly potent competitive inhibition against UGT2B17 with a Ki of 0.4 μM. The TKIs also exerted intermediate inhibition against several UGTs (i.e., UGT1A7 by lapatinib; UGT1A1 by imatinib; UGT1A4, 1A7 and 1A9 by axitinib; and UGT1A9 by vandetanib). Results from modeling for the quantitative prediction of DDI risk indicated that the coadministration of lapatinib or imatinib at clinical doses could result in a significant increase in AUC of drugs primarily cleared by UGT1A1 or 2B17. Lapatinib and imatinib may cause clinically significant DDIs when co-administered UGT1A1 or 2B17 substrates. PMID:26642944

  20. Uptake of munitions materiels (TNT, RDX) by crop plants and potential interactions of nitrogen nutrition

    SciTech Connect

    Fellows, R.J.; Harvey, S.D.; Cataldo, D.A.; Mitchell, W.

    1995-12-31

    Munitions materiel such as trinitrotoluene (TNT) and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and their combustion/decomposition products can accumulate/cycle in terrestrial environs. High soil organic matter and fertility have been previously shown to negatively correlate with both TNT or RDX uptake in plants such as grass, wheat, and bean. The present study was therefore conducted using low fertility soil to assess uptake and distribution patterns of C-radiolabelled TNT and RDX (15 and 30 {micro}g/g) within corn (Zea mays), spinach (Spinacea oleraceae), carrot (Daucus carota), and alfalfa (Medicago sativa) grown to maturity in growth chambers. Uptake by the plants at maturity (90- to 120-days) ranged from 1.8 to 2.7% of total amended {sup 14}C-TNT for carrots and corn respectively and 17 to 33% of total amended {sup 14}C-RDX for corn and carrots respectively. Distribution patterns of total radiolabel indicate that the TNT-derived label was primarily retained within the roots (60 to 85%) while the RDX-derived label was distributed to the shoots (85 to 97%). Less than 0.01 {micro}g/g dry wt. TNT was found in all analyzed shoot tissues with > 90% of the TNT-derived radiolabel in the form of polar metabolites. Concentrations of RDX in shoot tissues of corn exceeded 180 {micro}g/g dry wt. Alfalfa grown in unfertilized, fertilized (NO{sub 3}), or unfertilized-inoculated (Rhizobia) soil exhibited a 70 to 100% increase in dry wt. after 45 days in the TNT-amended (15 {micro}g/g) fertilized and unfertilized-inoculated plants versus the controls. A potential TNT/nitrogen interaction will be discussed.

  1. Potential for electropositive metal to reduce the interactions of Atlantic sturgeon with fishing gear.

    PubMed

    Bouyoucos, Ian; Bushnell, Peter; Brill, Richard

    2014-02-01

    Atlantic sturgeon (Acipenser oxyrhynchus) populations have been declared either endangered or threatened under the U.S. Endangered Species Act. Effective measures to repel sturgeon from fishing gear would be beneficial to both fish and fishers because they could reduce both fishery-associated mortality and the need for seasonal and area closures of specific fisheries. Some chondrostean fishes (e.g., sturgeons and paddlefishes) can detect weak electric field gradients (possibly as low as 5 Μv/cm) due to arrays of electroreceptors (ampullae of Lorenzini) on their snout and gill covers. Weak electric fields, such as those produced by electropositive metals (typically mixtures of the lanthanide elements), could therefore potentially be used as a deterrent. To test this idea, we recorded the behavioral responses of juvenile Atlantic sturgeon (31-43 cm fork length) to electropositive metal (primarily a mixture of the lanthanide elements neodymium and praseodymium) both in the presence and absence of food stimuli. Trials were conducted in an approximately 2.5 m diameter × 0.3 m deep tank, and fish behaviors were recorded with an overhead digital video camera. Video records were subsequently digitized (x, y coordinate system), the distance between the fish and the electropositive metal calculated, and data summarized by compiling frequency distributions with 5-cm bins. Juvenile sturgeon showed clear avoidance of electropositive metal but only when food was present. On the basis of our results, we conclude that the electropositive metals, or other sources of weak electric fields, may eventually be used to reduce the interactions of Atlantic sturgeon with fishing gear, but further investigation is needed.

  2. Potential interaction between zinc ions and a cyclodextrin-based diclofenac formulation.

    PubMed

    Hamdan, Imad I; El-Sabawi, Dina; Abdel Jalil, Mariam

    2016-01-01

    Complexes of diclofenac sodium (DF-Na) with hydroxypropyl betacyclodextrin (HPβCD) were prepared by co-evaporation in a 1:1 ratio and characterized in light of previously reported data. Phase solubility diagrams were obtained for DF-Na with HPβCD in the presence and absence of zinc ions. Dissolution profiles were obtained for DF-Na and its HPβCD complex at acidic (pH 1.2) as well as in phosphate buffer (pH 6.8), in the presence and absence of zinc. HPβCD, as expected, was shown to improve the dissolution of DF-Na in acidic medium but not in phosphate buffer (pH 6.8). The presence of zinc ions decreased the in vitro dissolution of DF-HPβCD complex in acidic medium (pH 1.2) but not in phosphate buffer (pH 6.8). It was confirmed that the precipitate that was formed by zinc ions in the presence of HPβCD and DF-Na contained no cyclodextrin and most likely it was a mixture of the complexes: DF2-Zn and DF-Zn with some molecules of water. In vivo experiments on rats have shown that HPβCD has no statistically significant effect on absorption or bioavailability of DF-Na in spite of the observed improvement of its in vitro dissolution by HPβCD. Moreover, zinc ions were shown to decrease the absorption rate of DF-Na in rats model but did neither significantly alter the absorption nor bioavailability of DF-HPβCD complex. The zinc induced precipitates of DF were shown to have significantly different crystalline properties when HPβCD was present. Therefore, the pharmaceutical details of a DF-Na preparation should be considered when designing the formulation and predicting possible interaction between DF-Na (or other potential NSAIDs) and zinc metal.

  3. Potential for electropositive metal to reduce the interactions of Atlantic sturgeon with fishing gear.

    PubMed

    Bouyoucos, Ian; Bushnell, Peter; Brill, Richard

    2014-02-01

    Atlantic sturgeon (Acipenser oxyrhynchus) populations have been declared either endangered or threatened under the U.S. Endangered Species Act. Effective measures to repel sturgeon from fishing gear would be beneficial to both fish and fishers because they could reduce both fishery-associated mortality and the need for seasonal and area closures of specific fisheries. Some chondrostean fishes (e.g., sturgeons and paddlefishes) can detect weak electric field gradients (possibly as low as 5 Μv/cm) due to arrays of electroreceptors (ampullae of Lorenzini) on their snout and gill covers. Weak electric fields, such as those produced by electropositive metals (typically mixtures of the lanthanide elements), could therefore potentially be used as a deterrent. To test this idea, we recorded the behavioral responses of juvenile Atlantic sturgeon (31-43 cm fork length) to electropositive metal (primarily a mixture of the lanthanide elements neodymium and praseodymium) both in the presence and absence of food stimuli. Trials were conducted in an approximately 2.5 m diameter × 0.3 m deep tank, and fish behaviors were recorded with an overhead digital video camera. Video records were subsequently digitized (x, y coordinate system), the distance between the fish and the electropositive metal calculated, and data summarized by compiling frequency distributions with 5-cm bins. Juvenile sturgeon showed clear avoidance of electropositive metal but only when food was present. On the basis of our results, we conclude that the electropositive metals, or other sources of weak electric fields, may eventually be used to reduce the interactions of Atlantic sturgeon with fishing gear, but further investigation is needed. PMID:24372943

  4. Development of Immune-Specific Interaction Potentials and Their Application in the Multi-Agent-System VaccImm

    PubMed Central

    Woelke, Anna Lena; von Eichborn, Joachim; Murgueitio, Manuela S.; Worth, Catherine L.; Castiglione, Filippo; Preissner, Robert

    2011-01-01

    Peptide vaccination in cancer therapy is a promising alternative to conventional methods. However, the parameters for this personalized treatment are difficult to access experimentally. In this respect, in silico models can help to narrow down the parameter space or to explain certain phenomena at a systems level. Herein, we develop two empirical interaction potentials specific to B-cell and T-cell receptor complexes and validate their applicability in comparison to a more general potential. The interaction potentials are applied to the model VaccImm which simulates the immune response against solid tumors under peptide vaccination therapy. This multi-agent system is derived from another immune system simulator (C-ImmSim) and now includes a module that enables the amino acid sequence of immune receptors and their ligands to be taken into account. The multi-agent approach is combined with approved methods for prediction of major histocompatibility complex (MHC)-binding peptides and the newly developed interaction potentials. In the analysis, we critically assess the impact of the different modules on the simulation with VaccImm and how they influence each other. In addition, we explore the reasons for failures in inducing an immune response by examining the activation states of the immune cell populations in detail. In summary, the present work introduces immune-specific interaction potentials and their application to the agent-based model VaccImm which simulates peptide vaccination in cancer therapy. PMID:21858048

  5. An Assessment of Density Functional Methods for Potential Energy Curves of Nonbonded Interactions: The XYG3 and B97-D Approximations.

    PubMed

    Vázquez-Mayagoitia, Álvaro; Sherrill, C David; Aprà, Edoardo; Sumpter, Bobby G

    2010-03-01

    A recently proposed double-hybrid functional called XYG3 and a semilocal GGA functional (B97-D) with a semiempirical correction for van der Waals interactions have been applied to study the potential energy curves along the dissociation coordinates of weakly bound pairs of molecules governed by London dispersion and induced dipole forces. Molecules treated in this work were the parallel sandwich, T-shaped, and parallel-displaced benzene dimer, (C6H6)2; hydrogen sulfide and benzene, H2S·C6H6; methane and benzene, CH4·C6H6; the methane dimer, (CH4)2; and the pyridine dimer, (C5H5N)2. We compared the potential energy curves of these functionals with previously published benchmarks at the coupled cluster singles, doubles, and perturbative triplets [CCSD(T)] complete-basis-set limit. Both functionals, XYG3 and B97-D, exhibited very good performance, reproducing accurate energies for equilibrium distances and a smooth behavior along the dissociation coordinate. Overall, we found an agreement within a few tenths of one kcal mol(-1) with the CCSD(T) results across the potential energy curves.

  6. Accurate thickness measurement of graphene

    NASA Astrophysics Data System (ADS)

    Shearer, Cameron J.; Slattery, Ashley D.; Stapleton, Andrew J.; Shapter, Joseph G.; Gibson, Christopher T.

    2016-03-01

    Graphene has emerged as a material with a vast variety of applications. The electronic, optical and mechanical properties of graphene are strongly influenced by the number of layers present in a sample. As a result, the dimensional characterization of graphene films is crucial, especially with the continued development of new synthesis methods and applications. A number of techniques exist to determine the thickness of graphene films including optical contrast, Raman scattering and scanning probe microscopy techniques. Atomic force microscopy (AFM), in particular, is used extensively since it provides three-dimensional images that enable the measurement of the lateral dimensions of graphene films as well as the thickness, and by extension the number of layers present. However, in the literature AFM has proven to be inaccurate with a wide range of measured values for single layer graphene thickness reported (between 0.4 and 1.7 nm). This discrepancy has been attributed to tip-surface interactions, image feedback settings and surface chemistry. In this work, we use standard and carbon nanotube modified AFM probes and a relatively new AFM imaging mode known as PeakForce tapping mode to establish a protocol that will allow users to accurately determine the thickness of graphene films. In particular, the error in measuring the first layer is reduced from 0.1-1.3 nm to 0.1-0.3 nm. Furthermore, in the process we establish that the graphene-substrate adsorbate layer and imaging force, in particular the pressure the tip exerts on the surface, are crucial components in the accurate measurement of graphene using AFM. These findings can be applied to other 2D materials.

  7. Accurate thickness measurement of graphene.

    PubMed

    Shearer, Cameron J; Slattery, Ashley D; Stapleton, Andrew J; Shapter, Joseph G; Gibson, Christopher T

    2016-03-29

    Graphene has emerged as a material with a vast variety of applications. The electronic, optical and mechanical properties of graphene are strongly influenced by the number of layers present in a sample. As a result, the dimensional characterization of graphene films is crucial, especially with the continued development of new synthesis methods and applications. A number of techniques exist to determine the thickness of graphene films including optical contrast, Raman scattering and scanning probe microscopy techniques. Atomic force microscopy (AFM), in particular, is used extensively since it provides three-dimensional images that enable the measurement of the lateral dimensions of graphene films as well as the thickness, and by extension the number of layers present. However, in the literature AFM has proven to be inaccurate with a wide range of measured values for single layer graphene thickness reported (between 0.4 and 1.7 nm). This discrepancy has been attributed to tip-surface interactions, image feedback settings and surface chemistry. In this work, we use standard and carbon nanotube modified AFM probes and a relatively new AFM imaging mode known as PeakForce tapping mode to establish a protocol that will allow users to accurately determine the thickness of graphene films. In particular, the error in measuring the first layer is reduced from 0.1-1.3 nm to 0.1-0.3 nm. Furthermore, in the process we establish that the graphene-substrate adsorbate layer and imaging force, in particular the pressure the tip exerts on the surface, are crucial components in the accurate measurement of graphene using AFM. These findings can be applied to other 2D materials.

  8. [Evaluation of potential drug interactions in primary health care prescriptions in Vitória da Conquista, Bahia (Brazil)].

    PubMed

    Leão, Danyllo Fábio Lessa; de Moura, Cristiano Soares; de Medeiros, Danielle Souto

    2014-01-01

    Drug interactions are risk factors for the occurrence of adverse drug reactions. The risk for drug interactions includes factors related to prescription that are intrinsic to the patient. This study sought to evaluate the potential drug interactions in primary care prescriptions in Vitória da Conquista in the state of Bahia to fill the knowledge gap on this topic in Brazil. Information about several variables derived from the primary health care prescriptions was collected and drug interactions were evaluated based on information from Medscape and Micromedex(R) databases. Polypharmacy frequency and its association with the occurrence of drug interactions were also evaluated. Results revealed a 48,9% frequency of drug interactions, 74,9% of moderate or greater severity, 8,6% of prescriptions in polypharmacy that in the chi-square test showed a positive association with the occurrence of drug interactions (p < 0,001). Prescriptions from primary care in Vitória da Conquista in the state of Bahia showed a high frequency of drug interactions, however it is necessary to analyze other risk factors for their occurrence at this level of health care.

  9. Interactions among Future Study Abroad Students: Exploring Potential Intercultural Learning Sequences

    ERIC Educational Resources Information Center

    Borghetti, C.; Beaven, A.; Pugliese, R.

    2015-01-01

    The study presented in this article aims to explore if and how intercultural learning may take place in students' class interaction. It is grounded in the assumption that interculturality is not a clear-cut feature inherent to interactions occurring when individuals with presumed different linguistic and cultural/national backgrounds talk to…

  10. Electrostatic potentials and electrostatic interaction energies of rat cytochrome b5 and a simulated anion-exchange adsorbent surface.

    PubMed Central

    Roush, D J; Gill, D S; Willson, R C

    1994-01-01

    Electrostatic potentials were determined for the soluble tryptic core of rat cytochrome b5 (using a structure derived from homology modeling) and a simulated anion-exchange surface through application of the linearized finite-difference Poisson-Boltzmann equation with the simulation code UHBD. Objectives of this work included determination of the contributions of the various charged groups on the protein surface to electrostatic interactions with a simulated anion-exchange surface as a function of orientation, separation distance, and ionic strength, as well as examining the potential existence of a preferred contact orientation. Electrostatic interaction free energies for the complex of the model protein and the simulated surface were computed using the electrostatics section of UHBD employing a 110(3) grid. An initial coarse grid spacing of 2.0 A was required to obtain correct boundary conditions. The boundary conditions of the coarse grid were used in subsequent focusing steps until the electrostatic interaction free energies were relatively independent of grid spacing (at approximately 0.5 A). Explicit error analyses were performed to determine the effects of grid spacing and other model assumptions on the electrostatic interaction free energies. The computational results reveal the presence of a preferred interaction orientation; the interaction energy between these two entities, of opposite net charge, is repulsive over a range of orientations. The electrostatic interaction free energies appear to be the summation of multiple fractional interactions between the protein and the anion-exchange surface. The simulation results are compared with those of ion-exchange adsorption experiments with site-directed mutants of the recombinant protein. Comparisons of the results from the computational and experimental studies should lead to a better understanding of electrostatic interactions of proteins and charged surfaces. Images FIGURE 4 FIGURE 5 FIGURE 6 PMID:8061185

  11. The APP-Interacting Protein FE65 is Required for Hippocampus-Dependent Learning and Long-Term Potentiation

    ERIC Educational Resources Information Center

    Wang, Yan; Zhang, Ming; Moon, Changjong; Hu, Qubai; Wang, Baiping; Martin, George; Sun, Zhongsheng; Wang, Hongbing

    2009-01-01

    FE65 is expressed predominantly in the brain and interacts with the C-terminal domain of [beta]-amyloid precursor protein (APP). We examined hippocampus-dependent memory and in vivo long-term potentiation (LTP) at the CA1 synapses with isoform-specific FE65 knockout (p97FE65[superscript -/-]) mice. When examined using the Morris water maze,…

  12. Two trapped particles interacting by a finite-range two-body potential in two spatial dimensions

    NASA Astrophysics Data System (ADS)

    Doganov, Rostislav A.; Klaiman, Shachar; Alon, Ofir E.; Streltsov, Alexej I.; Cederbaum, Lorenz S.

    2013-03-01

    We examine the problem of two particles confined in an isotropic harmonic trap, which interact via a finite-range Gaussian-shaped potential in two spatial dimensions. We derive an approximative transcendental equation for the energy and study the resulting spectrum as a function of the interparticle interaction strength. Both the attractive and repulsive systems are analyzed. We study the impact of the potential's range on the ground-state energy. We also explicitly verify by a variational treatment that in the zero-range limit the positive δ potential in two dimensions only reproduces the noninteracting results, if the Hilbert space in not truncated, and demonstrate that an extremely large Hilbert space is required to approach the ground state when one is to tackle the limit of zero-range interaction numerically. Finally, we establish and discuss the connection between our finite-range treatment and regularized zero-range results from the literature. The present results indicate that a finite-range interparticle potential is numerically amenable for treating the statics and the nonequilibrium dynamics of interacting many-particle systems (bosons) in two dimensions.

  13. Accurate adiabatic correction in the hydrogen molecule

    NASA Astrophysics Data System (ADS)

    Pachucki, Krzysztof; Komasa, Jacek

    2014-12-01

    A new formalism for the accurate treatment of adiabatic effects in the hydrogen molecule is presented, in which the electronic wave function is expanded in the James-Coolidge basis functions. Systematic increase in the size of the basis set permits estimation of the accuracy. Numerical results for the adiabatic correction to the Born-Oppenheimer interaction energy reveal a relative precision of 10-12 at an arbitrary internuclear distance. Such calculations have been performed for 88 internuclear distances in the range of 0 < R ⩽ 12 bohrs to construct the adiabatic correction potential and to solve the nuclear Schrödinger equation. Finally, the adiabatic correction to the dissociation energies of all rovibrational levels in H2, HD, HT, D2, DT, and T2 has been determined. For the ground state of H2 the estimated precision is 3 × 10-7 cm-1, which is almost three orders of magnitude higher than that of the best previous result. The achieved accuracy removes the adiabatic contribution from the overall error budget of the present day theoretical predictions for the rovibrational levels.

  14. Accurate adiabatic correction in the hydrogen molecule

    SciTech Connect

    Pachucki, Krzysztof; Komasa, Jacek

    2014-12-14

    A new formalism for the accurate treatment of adiabatic effects in the hydrogen molecule is presented, in which the electronic wave function is expanded in the James-Coolidge basis functions. Systematic increase in the size of the basis set permits estimation of the accuracy. Numerical results for the adiabatic correction to the Born-Oppenheimer interaction energy reveal a relative precision of 10{sup −12} at an arbitrary internuclear distance. Such calculations have been performed for 88 internuclear distances in the range of 0 < R ⩽ 12 bohrs to construct the adiabatic correction potential and to solve the nuclear Schrödinger equation. Finally, the adiabatic correction to the dissociation energies of all rovibrational levels in H{sub 2}, HD, HT, D{sub 2}, DT, and T{sub 2} has been determined. For the ground state of H{sub 2} the estimated precision is 3 × 10{sup −7} cm{sup −1}, which is almost three orders of magnitude higher than that of the best previous result. The achieved accuracy removes the adiabatic contribution from the overall error budget of the present day theoretical predictions for the rovibrational levels.

  15. Accurate adiabatic correction in the hydrogen molecule.

    PubMed

    Pachucki, Krzysztof; Komasa, Jacek

    2014-12-14

    A new formalism for the accurate treatment of adiabatic effects in the hydrogen molecule is presented, in which the electronic wave function is expanded in the James-Coolidge basis functions. Systematic increase in the size of the basis set permits estimation of the accuracy. Numerical results for the adiabatic correction to the Born-Oppenheimer interaction energy reveal a relative precision of 10(-12) at an arbitrary internuclear distance. Such calculations have been performed for 88 internuclear distances in the range of 0 < R ⩽ 12 bohrs to construct the adiabatic correction potential and to solve the nuclear Schrödinger equation. Finally, the adiabatic correction to the dissociation energies of all rovibrational levels in H2, HD, HT, D2, DT, and T2 has been determined. For the ground state of H2 the estimated precision is 3 × 10(-7) cm(-1), which is almost three orders of magnitude higher than that of the best previous result. The achieved accuracy removes the adiabatic contribution from the overall error budget of the present day theoretical predictions for the rovibrational levels. PMID:25494728

  16. Theory of Auger-electron and appearance-potential spectroscopy for interacting valence-band electrons

    NASA Astrophysics Data System (ADS)

    Nolting, W.; Geipel, G.; Ertl, K.

    1991-12-01

    A theory of Auger-electron spectroscopy (AES) and appearance-potential spectroscopy (APS) is presented for interacting electrons in a nondegenerate energy band, described within the framework of the Hubbard model. Both types of spectroscopy are based on the same two-particle spectral density. A diagrammatic vertex-correction method (Matsubara formalism) is used to express this function in terms of the one-particle spectral density. The latter is approximately determined for arbitrary temperature T, arbitrary coupling strength U/W (U, the intra-atomic Coulomb matrix element; W, the width of the ``free'' Bloch band), and arbitrary band occupations n (0<=n<=2 average number of band electrons per site) by a self-consistent moment method. In weakly coupled systems the electron correlations give rise to certain deformations of the quasiparticle density of states (QDOS) in relation to the Bloch density of states (BDOS), where, however, spontaneous magnetic order is excluded, irrespective of the band filling n. The AE (AP) spectra consist of only one structure a few eV wide (``bandlike'') which is strongly n dependent, but only slightly T dependent, being rather well approximated by a simple self-convolution of the occupied (unoccupied) QDOS. For strongly correlated electrons the Bloch band splits into two quasiparticle subbands. This leads for n<1 to one line in the AE spectrum and three lines in the AP spectrum, and vice versa for n>1. For sufficiently strong correlations U/W additional satellites appear that refer to situations where the two excited quasiparticles (quasiholes) propagate as tightly bound pairs through the lattice without being scattered by other charge carriers. As soon as the satellite splits off from the bandlike part of the spectrum, it takes almost the full spectral weight, conveying the impression of an ``atomiclike'' AE (AP) line shape. The satellite has almost exactly the structure of the free BDOS. If the particle density n as well as the hole

  17. Molecular dynamics simulation of crystalline UF6 using the pair interaction potentials of the uranium and fluorine particles

    NASA Astrophysics Data System (ADS)

    Shekunov, G. S.; Nekrasov, K. A.; Boyarchenkov, A. S.; Kupryazhkin, A. Ya.

    2016-09-01

    A model of uranium hexafluoride is suggested that is based on the empirical pair potentials of U-U, F-F, U-F used for both intra- and intermolecular interactions. The potentials for this model are obtained from the lattice parameters and the thermal expansion coefficient of UF6 crystal using the molecular dynamics simulation under the periodic boundary conditions with constant volume and temperature. Within the framework of the model, the thermal expansion and sublimation of crystalline UF6 are investigated. A set of potential parameters is identified that provides satisfactory simulation of both UF6 crystal and the dependence of the UF6 saturated vapor pressure on temperature.

  18. Universal scaling of potential energy functions describing intermolecular interactions. I. Foundations and scalable forms of new generalized Mie, Lennard-Jones, Morse, and Buckingham exponential-6 potentials

    SciTech Connect

    Xantheas, Sotiris S.; Werhahn, Jasper C.

    2014-08-14

    Based on the formulation of the analytical expression of the potential V(r) describing intermolecular interactions in terms of the dimensionless variables r*=r/rm and !*=V/!, where rm is the separation at the minimum and ! the well depth, we propose more generalized scalable forms for the commonly used Lennard-Jones, Mie, Morse and Buckingham exponential-6 potential energy functions (PEFs). These new generalized forms have an additional parameter from and revert to the original ones for some choice of that parameter. In this respect, the original forms can be considered as special cases of the more general forms that are introduced. We also propose a scalable, but nonrevertible to the original one, 4-parameter extended Morse potential.

  19. Influence of protein interactions on oxidation/reduction midpoint potentials of cofactors in natural and de novo metalloproteins.

    PubMed

    Olson, T L; Williams, J C; Allen, J P

    2013-01-01

    As discussed throughout this special issue, oxidation and reduction reactions play critical roles in the function of many organisms. In photosynthetic organisms, the conversion of light energy drives oxidation and reduction reactions through the transfer of electrons and protons in order to create energy-rich compounds. These reactions occur in proteins such as cytochrome c, a heme-containing water-soluble protein, the bacteriochlorophyll-containing reaction center, and photosystem II where water is oxidized at the manganese cluster. A critical measure describing the ability of cofactors in proteins to participate in such reactions is the oxidation/reduction midpoint potential. In this review, the basic concepts of oxidation/reduction reactions are reviewed with a summary of the experimental approaches used to measure the midpoint potential of metal cofactors. For cofactors in proteins, the midpoint potential not only depends upon the specific chemical characteristics of cofactors but also upon interactions with the surrounding protein, such as the nature of the coordinating ligands and protein environment. These interactions can be tailored to optimize an oxidation/reduction reaction carried out by the protein. As examples, the midpoint potentials of hemes in cytochromes, bacteriochlorophylls in reaction centers, and the manganese cluster of photosystem II are discussed with an emphasis on the influence that protein interactions have on these potentials. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.

  20. Non-Chemical Distant Cellular Interactions as a potential confounder of cell biology experiments.

    PubMed

    Farhadi, Ashkan

    2014-01-01

    Distant cells can communicate with each other through a variety of methods. Two such methods involve electrical and/or chemical mechanisms. Non-chemical, distant cellular interactions may be another method of communication that cells can use to modify the behavior of other cells that are mechanically separated. Moreover, non-chemical, distant cellular interactions may explain some cases of confounding effects in Cell Biology experiments. In this article, we review non-chemical, distant cellular interactions studies to try to shed light on the mechanisms in this highly unconventional field of cell biology. Despite the existence of several theories that try to explain the mechanism of non-chemical, distant cellular interactions, this phenomenon is still speculative. Among candidate mechanisms, electromagnetic waves appear to have the most experimental support. In this brief article, we try to answer a few key questions that may further clarify this mechanism.

  1. The Potential of CGI: Using Pre-Built CGI Scripts to Make Interactive Web Pages.

    ERIC Educational Resources Information Center

    Nackerud, Shane A.

    1998-01-01

    Describes CGI (Common Gateway Interface) scripts that are available on the Web and explains how librarians can use them to make Web pages more interactive. Topics include CGI security; Perl scripts; UNIX; and HTML. (LRW)

  2. Potential measurements of neutrino-deuterium interactions with the T2K near detectors

    NASA Astrophysics Data System (ADS)

    Mahn, Kendall; T2K Collaboration

    2015-04-01

    Uncertainties on neutrino interactions with matter are important for current and future generation neutrino long baseline experiments, which infer neutrino mixing parameters. Measurements of neutrinos on deuterium constrain neutrino-nucleon interaction models, such as axial form factors, and are relatively free of complicating nuclear effects. Existing measurements of neutrino interaction using deuterium bubble chambers suffer from low statistics and significant systematic uncertainty on neutrino flux production. This talk describes the possibility of modern neutrino-deuterium cross section measurements using modifications to the existing T2K experiment near detector complex. A comparison of data taken with deuterated water and normal water would provide a measurement of neutrino-deuteron interactions with high-intensity neutrino beam. T2K is supported by the Department of Energy.

  3. Comparing photophysiology of seagrasses in the Pacific Northwest: potential implications for species interactions

    EPA Science Inventory

    Physiological tolerances are a primary control on species interactions mediated through production and growth. We examined how the physiology of native eelgrass (Zostera marina L.) and introduced Japanese eelgrass (Z. japonica Aschers. & Graeb) responded to temperature in or...

  4. Comparing photophysiology of seagrasses in the Pacific Northwest: potential implications for species interactions - July 28, 2014

    EPA Science Inventory

    Physiological tolerances are a primary control on species interactions mediated through production and growth. We examined how the physiology of native eelgrass (Zostera marina L.) and introduced Japanese eelgrass (Z. japonica Aschers. & Graeb) responded to temperature in ord...

  5. Inelastic Neutron Scattering and Molecular Dynamics Determination of the Interaction Potential in Liquid CD{sub 4}

    SciTech Connect

    Guarini, E.; Barocchi, F.

    2007-10-19

    Anisotropic interactions of liquid CD{sub 4} are studied in detail by comparison of inelastic neutron Brillouin scattering data with molecular dynamics simulations using up to four different models of the methane site-site potential. We demonstrate that the experimental dynamic structure factor S(Q,{omega}) acts as a highly discriminating quantity for possible interaction schemes. In particular, the Q evolution of the spectra enables a selective probing of the short- and medium-range features of the anisotropic potentials. We show that the preferential configuration of methane dimers at liquid densities can thus be discerned by analyzing the orientation-dependent model potential curves, in light of the experimental and simulation results.

  6. Time-dependent wave packet quantum and quasi-classical trajectory study of He + H₂⁺, D₂⁺ → HeH⁺ + H, HeD⁺ + D reaction on an accurate FCI potential energy surface.

    PubMed

    Zhao, Juan; Luo, Yi

    2012-03-15

    The quantum scattering dynamics and quasi-classical trajectory (QCT) calculations have been carried out for the title reaction on an accurate potential energy surface (PES) computed using the full configuration interaction (FCI). On the basis of the PES, the integral cross-sections of He + H₂⁺ (v = 0-3, j = 1) → HeH⁺ + H reaction have been calculated, and the results are generally agreed with the experimental cross-sections obtained by Tang et al. [J. Chem. Phys. 2005, 122, 164301] after taking into account the experimental uncertainties, which proves the reliability of implementing dynamics calculations on the FCI PES. The reaction probability of He + D₂⁺ (v = 0-2, j = 0) → HeD⁺ + D reactions for total angular momentum J = 0 and the integral cross-section (ICS) have been calculated. The significant quantum effect has been explored by the comparison between the QCT reaction probabilities (or ICS) and the quantum mechanical (QM) reaction probabilities (or ICS), which may be attributed to the deep well in the PES of this light atoms system. Furthermore, the role of Coriolis coupling (CC) effects has also been found not important by the comparison between the CC calculation and the centrifugal sudden (CS) approximation calculation, except that the CC total cross-sections for the v = 1 and 2 states show the collision energy-dependent behaviors in the low-energy area, which are different from those based on the CS calculation.

  7. Surface plasmon resonance spectroscopy for characterisation of membrane protein-ligand interactions and its potential for drug discovery.

    PubMed

    Patching, Simon G

    2014-01-01

    Surface plasmon resonance (SPR) spectroscopy is a rapidly developing technique for the study of ligand binding interactions with membrane proteins, which are the major molecular targets for validated drugs and for current and foreseeable drug discovery. SPR is label-free and capable of measuring real-time quantitative binding affinities and kinetics for membrane proteins interacting with ligand molecules using relatively small quantities of materials and has potential to be medium-throughput. The conventional SPR technique requires one binding component to be immobilised on a sensor chip whilst the other binding component in solution is flowed over the sensor surface; a binding interaction is detected using an optical method that measures small changes in refractive index at the sensor surface. This review first describes the basic SPR experiment and the challenges that have to be considered for performing SPR experiments that measure membrane protein-ligand binding interactions, most importantly having the membrane protein in a lipid or detergent environment that retains its native structure and activity. It then describes a wide-range of membrane protein systems for which ligand binding interactions have been characterised using SPR, including the major drug targets G protein-coupled receptors, and how challenges have been overcome for achieving this. Finally it describes some recent advances in SPR-based technology and future potential of the technique to screen ligand binding in the discovery of drugs. This article is part of a Special Issue entitled: Structural and biophysical characterisation of membrane protein-ligand binding.

  8. Transitioning from Microbiome Composition to Microbial Community Interactions: The Potential of the Metaorganism Hydra as an Experimental Model

    PubMed Central

    Deines, Peter; Bosch, Thomas C. G.

    2016-01-01

    Animals are home to complex microbial communities, which are shaped through interactions within the community, interactions with the host, and through environmental factors. The advent of high-throughput sequencing methods has led to novel insights in changing patterns of community composition and structure. However, deciphering the different types of interactions among community members, with their hosts and their interplay with their environment is still a challenge of major proportion. The emerging fields of synthetic microbial ecology and community systems biology have the potential to decrypt these complex relationships. Studying host-associated microbiota across multiple spatial and temporal scales will bridge the gap between individual microorganism studies and large-scale whole community surveys. Here, we discuss the unique potential of Hydra as an emerging experimental model in microbiome research. Through in vivo, in vitro, and in silico approaches the interaction structure of host-associated microbial communities and the effects of the host on the microbiota and its interactions can be disentangled. Research in the model system Hydra can unify disciplines from molecular genetics to ecology, opening up the opportunity to discover fundamental rules that govern microbiome community stability. PMID:27790207

  9. Metabolism-mediated interaction potential of standardized extract of Tinospora cordifolia through rat and human liver microsomes

    PubMed Central

    Bahadur, Shiv; Mukherjee, Pulok K.; Milan Ahmmed, S. K.; Kar, Amit; Harwansh, Ranjit K.; Pandit, Subrata

    2016-01-01

    Objective: Tinospora cordifolia is used for treatment of several diseases in Indian system of medicine. In the present study, the inhibition potential of T. cordifolia extracts and its constituent tinosporaside to cause herb-drug interactions through rat and human liver cytochrome enzymes was evaluated. Materials and Methods: Bioactive compound was quantified through reverse phase high-performance liquid chromatography, to standardize the plant extracts and interaction potential of standardized extract. Interaction potential of the test sample was evaluated through cytochrome P450-carbon monoxide complex (CYP450-CO) assay with pooled rat liver microsome. Influence on individual recombinant human liver microsomes such as CYP3A4, CYP2D6, CYP2C9, and CYP1A2 isozymes was analyzed through fluorescence microplate assay, and respective IC50 values were determined. Results: The content of tinosporaside was found to be 1.64% (w/w) in T. cordifolia extract. Concentration-dependent inhibition was observed through T. cordifolia extract. Observed IC50 (μg/ml) value was 136.45 (CYP3A4), 144.37 (CYP2D6), 127.55 (CYP2C9), and 141.82 (CYP1A2). Tinosporaside and extract showed higher IC50 (μg/ml) value than the known inhibitors. T. cordifolia extract showed significantly less interaction potential and indicates that the selected plant has not significant herb-drug interactions relating to the inhibition of major CYP450 isozymes. Conclusions: Plant extract showed significantly higher IC50 value than respective positive inhibitors against CYP3A4, 2D6, 2C9, and 1A2 isozymes. Consumption of T. cordifolia may not cause any adverse effects when consumed along with other xenobiotics. PMID:27721546

  10. Older Age and Steroid Use Are Associated with Increasing Polypharmacy and Potential Medication Interactions Among Patients with Inflammatory Bowel Disease

    PubMed Central

    Parian, Alyssa

    2015-01-01

    Background: Comorbidity and polypharmacy, more prevalent among older persons, may impact the treatment of patients with inflammatory bowel disease (IBD). The aims of this study were to assess the frequency of polypharmacy and medication interactions within a cohort of older patients with IBD and describe IBD treatment patterns. Methods: Cohort study of 190 patients with IBD 65 years or older followed at a tertiary IBD referral center from 2006 to 2012. Data collected included demographics, IBD-specific characteristics including disease activity, and comorbidity. Medication histories were extracted from medical records, and data were used to classify polypharmacy, frequency, and severity of potential medication interactions and inappropriate medication use. Results: Older patients with IBD were prescribed an average of 9 routine medications. Severe polypharmacy (≥10 routine medications) was present in 43.2% of studied patients and associated with increasing age, greater comorbidity, and steroid use. Overall, 73.7% of patients had at least 1 potential medication interaction, including 40% of patients with potential IBD medication-associated interactions. Chronic steroids were prescribed to 40% of the older patients including 24% who were in remission or with mild disease activity. Only 39.5% of patients were on immunomodulators and 21.1% on biologics. Approximately, 35% of patients were given at least 1 Beers inappropriate medication and almost 10% were receiving chronic narcotics. Conclusions: Older patients with IBD are at increased risk for severe polypharmacy and potential major medication interactions especially with increasing comorbidity and chronic steroid use. Steroid-maintenance therapies are prevalent among the older patients with IBD with lower utilization of steroid-sparing regimens. PMID:25856768

  11. Monitoring potential molecular interactions of adenine with other amino acids using Raman spectroscopy and DFT modeling.

    PubMed

    Singh, Shweta; Donfack, P; Srivastava, Sunil K; Singh, Dheeraj K; Materny, A; Asthana, B P; Mishra, P C

    2015-01-01

    We report on the modes of inter-molecular interaction between adenine (Ade) and the amino acids: glycine (Gly), lysine (Lys) and arginine (Arg) using Raman spectroscopy of binary mixtures of adenine and each of the three amino acids at varying molar ratios in the spectral region 1550-550 cm(-1). We focused our attention on certain specific changes in the Raman bands of adenine arising due to its interaction with the amino acids. While the changes are less apparent in the Ade/Gly system, in the Ade/Lys or Ade/Arg systems, significant changes are observed, particularly in the Ade Raman bands that involve the amino group moiety and the N7 and N1 atoms of the purine ring. The ν(N1-C6), ν(N1-C2), δ(C8-H) and δ(N7-C8-N9) vibrations at 1486, 1332, 1253 and 948 cm(-1) show spectral changes on varying the Ade to amino acid molar ratio, the extent of variation being different for the three amino acids. This observation suggests a specific interaction mode between Ade and Lys or Arg, which is due to the hydrogen bonding. The measured spectral changes provide a clear indication that the interaction of Ade depends strongly on the structures of the amino acids, especially their side chains. Density functional theory (DFT) calculations were carried out to elucidate the most probable interaction modes of Ade with the different amino acids.

  12. Analytic ab initio-based molecular interaction potential for the BrO⋅H2O complex.

    PubMed

    Hoehn, Ross D; Yeole, Sachin D; Kais, Sabre; Francisco, Joseph S

    2016-05-28

    Radical halogen oxide species play important roles within atmospheric processes, specifically those responsible for the removal of O3. To facilitate future investigations on this family of compounds, RCCSD(T)/aug-cc-pVQZ-level electronic structure calculations were employed to generate individual-molecule optimized geometries, as well as to determine the global minimum energy structure for the BrO⋅H2O complex. This information facilitated the generation of several one-dimensional potential energy surface (PES) scans for the BrO⋅H2O complex. Scans were performed for both the ground state and the first excited state; this inclusion is due to a low-lying first electronic excited-state energy. These rigid-geometry PES scans were used both to generate a novel analytic interaction potential by modifying the existing Thole-type model used for water and to the fitted potential function. This interaction potential features anisotropic atomic polarizabilities facilitating appropriate modeling of the physics regarding the unpaired electron residing within the p-orbitals of the oxygen atom of the bromine oxide radical. The intention of this work is to facilitate future molecular dynamics simulations involving the interaction between the BrO radical and water clusters as a first step in devising possible novel chemistries taking place at the water interface of clouds within the atmosphere. PMID:27250293

  13. Analytic ab initio-based molecular interaction potential for the BrO⋅H2O complex.

    PubMed

    Hoehn, Ross D; Yeole, Sachin D; Kais, Sabre; Francisco, Joseph S

    2016-05-28

    Radical halogen oxide species play important roles within atmospheric processes, specifically those responsible for the removal of O3. To facilitate future investigations on this family of compounds, RCCSD(T)/aug-cc-pVQZ-level electronic structure calculations were employed to generate individual-molecule optimized geometries, as well as to determine the global minimum energy structure for the BrO⋅H2O complex. This information facilitated the generation of several one-dimensional potential energy surface (PES) scans for the BrO⋅H2O complex. Scans were performed for both the ground state and the first excited state; this inclusion is due to a low-lying first electronic excited-state energy. These rigid-geometry PES scans were used both to generate a novel analytic interaction potential by modifying the existing Thole-type model used for water and to the fitted potential function. This interaction potential features anisotropic atomic polarizabilities facilitating appropriate modeling of the physics regarding the unpaired electron residing within the p-orbitals of the oxygen atom of the bromine oxide radical. The intention of this work is to facilitate future molecular dynamics simulations involving the interaction between the BrO radical and water clusters as a first step in devising possible novel chemistries taking place at the water interface of clouds within the atmosphere.

  14. Coulomb interactions and fermion condensation

    SciTech Connect

    Capstick, S.; Cutkosky, R.E.; Joensen, M.A. ); Wang, K.C. )

    1990-08-15

    The influence of the Coulomb interaction in states containing massless and flavorless fermion-antifermion pairs is studied, using a continuum formulation within the finite volume {ital S}{sup 3}. Several different forms for the Coulomb interaction are examined, including confining potentials as well as nonconfining potentials. The calculations show that if the interaction is strong enough, the Coulomb interaction leads to condensation of pairs, and that this condensation has a chiral character. The condensation does not depend on whether the interaction is confining. It is found that simplified variational approximations are not accurate enough for an adequate description of the states.

  15. Accurate ab initio potential energy surface, thermochemistry, and dynamics of the F{sup −} + CH{sub 3}F S{sub N}2 and proton-abstraction reactions

    SciTech Connect

    Szabó, István; Telekes, Hajnalka; Czakó, Gábor

    2015-06-28

    We develop a full-dimensional global analytical potential energy surface (PES) for the F{sup −} + CH{sub 3}F reaction by fitting about 50 000 energy points obtained by an explicitly correlated composite method based on the second-order Møller–Plesset perturbation-F12 and coupled-cluster singles, doubles, and perturbative triples-F12a methods and the cc-pVnZ-F12 [n = D, T] basis sets. The PES accurately describes the (a) back-side attack Walden inversion mechanism involving the pre- and post-reaction (b) ion-dipole and (c) hydrogen-bonded complexes, the configuration-retaining (d) front-side attack and (e) double-inversion substitution pathways, as well as (f) the proton-abstraction channel. The benchmark quality relative energies of all the important stationary points are computed using the focal-point analysis (FPA) approach considering electron correlation up to coupled-cluster singles, doubles, triples, and perturbative quadruples method, extrapolation to the complete basis set limit, core-valence correlation, and scalar relativistic effects. The FPA classical(adiabatic) barrier heights of (a), (d), and (e) are −0.45(−0.61), 46.07(45.16), and 29.18(26.07) kcal mol{sup −1}, respectively, the dissociation energies of (b) and (c) are 13.81(13.56) and 13.73(13.52) kcal mol{sup −1}, respectively, and the endothermicity of (f) is 42.54(38.11) kcal mol{sup −1}. Quasiclassical trajectory computations of cross sections, scattering (θ) and initial attack (α) angle distributions, as well as translational and internal energy distributions are performed for the F{sup −} + CH{sub 3}F(v = 0) reaction using the new PES. Apart from low collision energies (E{sub coll}), the S{sub N}2 excitation function is nearly constant, the abstraction cross sections rapidly increase with E{sub coll} from a threshold of ∼40 kcal mol{sup −1}, and retention trajectories via double inversion are found above E{sub coll} = ∼ 30 kcal mol{sup −1}, and at E{sub coll} =

  16. New potential peptide therapeutics perturbing CK1δ/α-tubulin interaction.

    PubMed

    Krüger, Marc; Kalbacher, Hubert; Kastritis, Panagiotis L; Bischof, Joachim; Barth, Holger; Henne-Bruns, Doris; Vorgias, Constantinos; Sarno, Stefania; Pinna, Lorenzo A; Knippschild, Uwe

    2016-06-01

    Members of the CK1 family are highly conserved serine/threonine specific kinases being expressed in all eukaryotes. They are involved in many cellular processes and therefore tightly regulated. A central mechanism to modulate CK1 activity is via interaction with cellular proteins. CK1δ interacts with α-/β-tubulin and is involved in the regulation of microtubule dynamics. Therefore, it is important to identify the structural elements responsible for the interaction between these proteins. Using a peptide library covering the human CK1δ amino acid sequence in SPR and ELISA analyses, we identified peptide 39 (P39), encompassing aa361-aa375 of CK1δ, as a prominent binding partner of α-tubulin. P39 decreases α-tubulin phosphorylation by CK1δ and reduces the thermodynamic stability of α-tubulin in fluorescence thermal shift assays. Furthermore, P39 induces an inhibition of mitotic progression and a disruption of cells entering mitosis in CV-1 cells. Taken together our data provide valuable information regarding the interaction of CK1δ and α-tubulin and a novel approach for the development of pharmacological tools to inhibit proliferation of cancer cells.

  17. The Current and Potential Uses of Computer Assisted Interactive Videodisc in the Education of Social Workers.

    ERIC Educational Resources Information Center

    Lynett, Patricia

    1985-01-01

    Describes learning system that incorporates several technologies, including the videodisc, computer, and monitor, to accomplish interactive individualized learning in several audio and visual modes. Discusses experiences in the use of learning system courseware for new-hire training, and continuing education. Raises issues which will affect the…

  18. New potential peptide therapeutics perturbing CK1δ/α-tubulin interaction.

    PubMed

    Krüger, Marc; Kalbacher, Hubert; Kastritis, Panagiotis L; Bischof, Joachim; Barth, Holger; Henne-Bruns, Doris; Vorgias, Constantinos; Sarno, Stefania; Pinna, Lorenzo A; Knippschild, Uwe

    2016-06-01

    Members of the CK1 family are highly conserved serine/threonine specific kinases being expressed in all eukaryotes. They are involved in many cellular processes and therefore tightly regulated. A central mechanism to modulate CK1 activity is via interaction with cellular proteins. CK1δ interacts with α-/β-tubulin and is involved in the regulation of microtubule dynamics. Therefore, it is important to identify the structural elements responsible for the interaction between these proteins. Using a peptide library covering the human CK1δ amino acid sequence in SPR and ELISA analyses, we identified peptide 39 (P39), encompassing aa361-aa375 of CK1δ, as a prominent binding partner of α-tubulin. P39 decreases α-tubulin phosphorylation by CK1δ and reduces the thermodynamic stability of α-tubulin in fluorescence thermal shift assays. Furthermore, P39 induces an inhibition of mitotic progression and a disruption of cells entering mitosis in CV-1 cells. Taken together our data provide valuable information regarding the interaction of CK1δ and α-tubulin and a novel approach for the development of pharmacological tools to inhibit proliferation of cancer cells. PMID:26996302

  19. A Report on the Effectiveness and Potential of an Interactive Video Teaching Trial.

    ERIC Educational Resources Information Center

    Baker, Robert, Comp.; And Others

    An interactive video trial involved teaching two Year-7 lessons to elementary school students in Queensland (Australia). French was taught to one class through two-way video and audio so that students and teachers could see and hear each other, and Japanese was taught simultaneously to three classes through one-way video and two-way audio.…

  20. The Potential of Interactive Videodisc Technology for Defense Training and Education. Report to Congress.

    ERIC Educational Resources Information Center

    Fletcher, J. D.

    This study was performed in response to the 1989 Department of Defense Appropriations Bill, which directed the Department of Defense to conduct a study on the use of interactive videodisk technology in education and training as it pertains to effectiveness, cost effectiveness, time on task, retention, and overall applicability to current and…