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.
A highly accurate interatomic potential for argon
NASA Astrophysics Data System (ADS)
Aziz, Ronald A.
1993-09-01
A modified potential based on the individually damped model of Douketis, Scoles, Marchetti, Zen, and Thakkar [J. Chem. Phys. 76, 3057 (1982)] is presented which fits, within experimental error, the accurate ultraviolet (UV) vibration-rotation spectrum of argon determined by UV laser absorption spectroscopy by Herman, LaRocque, and Stoicheff [J. Chem. Phys. 89, 4535 (1988)]. Other literature potentials fail to do so. The potential also is shown to predict a large number of other properties and is probably the most accurate characterization of the argon interaction constructed to date.
Sutton, Christopher; Gray, Matthew T.; Brunsfeld, Max; Parrish, Robert M.; Sherrill, C. David; Sears, John S.; Brédas, Jean-Luc E-mail: thomas.koerzdoerfer@uni-potsdam.de; Körzdörfer, Thomas E-mail: thomas.koerzdoerfer@uni-potsdam.de
2014-02-07
We investigate the torsion potentials in two prototypical π-conjugated polymers, polyacetylene and polydiacetylene, as a function of chain length using different flavors of density functional theory. Our study provides a quantitative analysis of the delocalization error in standard semilocal and hybrid density functionals and demonstrates how it can influence structural and thermodynamic properties. The delocalization error is quantified by evaluating the many-electron self-interaction error (MESIE) for fractional electron numbers, which allows us to establish a direct connection between the MESIE and the error in the torsion barriers. The use of non-empirically tuned long-range corrected hybrid functionals results in a very significant reduction of the MESIE and leads to an improved description of torsion barrier heights. In addition, we demonstrate how our analysis allows the determination of the effective conjugation length in polyacetylene and polydiacetylene chains.
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.
An accurate analytic representation of the water pair potential.
Cencek, Wojciech; Szalewicz, Krzysztof; Leforestier, Claude; van Harrevelt, Rob; van der Avoird, Ad
2008-08-28
The ab initio water dimer interaction energies obtained from coupled cluster calculations and used in the CC-pol water pair potential (Bukowski et al., Science, 2007, 315, 1249) have been refitted to a site-site form containing eight symmetry-independent sites in each monomer and denoted as CC-pol-8s. Initially, the site-site functions were assumed in a B-spline form, which allowed a precise optimization of the positions of the sites. Next, these functions were assumed in the standard exponential plus inverse powers form. The root mean square error of the CC-pol-8s fit with respect to the 2510 ab initio points is 0.10 kcal mol(-1), compared to 0.42 kcal mol(-1) of the CC-pol fit (0.010 kcal mol(-1) compared to 0.089 kcal mol(-1) for points with negative interaction energies). The energies of the stationary points in the CC-pol-8s potential are considerably more accurate than in the case of CC-pol. The water dimer vibration-rotation-tunneling spectrum predicted by the CC-pol-8s potential agrees substantially and systematically better with experiment than the already very accurate spectrum predicted by CC-pol, while specific features that could not be accurately predicted previously now agree very well with experiment. This shows that the uncertainties of the fit were the largest source of error in the previous predictions and that the present potential sets a new standard of accuracy in investigations of the water dimer. PMID:18688514
Accurate momentum transfer cross section for the attractive Yukawa potential
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.
An accurate model potential for alkali neon systems.
Zanuttini, D; Jacquet, E; Giglio, E; Douady, J; Gervais, B
2009-12-01
We present a detailed investigation of the ground and lowest excited states of M-Ne dimers, for M=Li, Na, and K. We show that the potential energy curves of these Van der Waals dimers can be obtained accurately by considering the alkali neon systems as one-electron systems. Following previous authors, the model describes the evolution of the alkali valence electron in the combined potentials of the alkali and neon cores by means of core polarization pseudopotentials. The key parameter for an accurate model is the M(+)-Ne potential energy curve, which was obtained by means of ab initio CCSD(T) calculation using a large basis set. For each MNe dimer, a systematic comparison with ab initio computation of the potential energy curve for the X, A, and B states shows the remarkable accuracy of the model. The vibrational analysis and the comparison with existing experimental data strengthens this conclusion and allows for a precise assignment of the vibrational levels. PMID:19968334
Accurate nuclear radii and binding energies from a chiral interaction
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
Accurate nuclear radii and binding energies from a chiral interaction
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 NNLO_{sat}, yield accurate binding energies and radii of nuclei up to ^{40}Ca, and are consistent with the empirical saturation point of symmetric nuclear matter. In addition, the low-lying collective J^{π}=3^{-} states in ^{16}O and ^{40}Ca are described accurately, while spectra for selected p- and sd-shell nuclei are in reasonable agreement with experiment.
A general, accurate procedure for calculating molecular interaction force.
Yang, Pinghai; Qian, Xiaoping
2009-09-15
The determination of molecular interaction forces, e.g., van der Waals force, between macroscopic bodies is of fundamental importance for understanding sintering, adhesion and fracture processes. In this paper, we develop an accurate, general procedure for van der Waals force calculation. This approach extends a surface formulation that converts a six-dimensional (6D) volume integral into a 4D surface integral for the force calculation. It uses non-uniform rational B-spline (NURBS) surfaces to represent object surfaces. Surface integrals are then done on the parametric domain of the NURBS surfaces. It has combined advantages of NURBS surface representation and surface formulation, including (1) molecular interactions between arbitrary-shaped objects can be represented and evaluated by the NURBS model further common geometries such as spheres, cones, planes can be represented exactly and interaction forces are thus calculated accurately; (2) calculation efficiency is improved by converting the volume integral to the surface integral. This approach is implemented and validated via its comparison with analytical solutions for simple geometries. Calculation of van der Waals force between complex geometries with surface roughness is also demonstrated. A tutorial on the NURBS approach is given in Appendix A. PMID:19596335
Accurate complex scaling of three dimensional numerical potentials
Cerioni, Alessandro; Genovese, Luigi; Duchemin, Ivan; Deutsch, Thierry
2013-05-28
The complex scaling method, which consists in continuing spatial coordinates into the complex plane, is a well-established method that allows to compute resonant eigenfunctions of the time-independent Schroedinger operator. Whenever it is desirable to apply the complex scaling to investigate resonances in physical systems defined on numerical discrete grids, the most direct approach relies on the application of a similarity transformation to the original, unscaled Hamiltonian. We show that such an approach can be conveniently implemented in the Daubechies wavelet basis set, featuring a very promising level of generality, high accuracy, and no need for artificial convergence parameters. Complex scaling of three dimensional numerical potentials can be efficiently and accurately performed. By carrying out an illustrative resonant state computation in the case of a one-dimensional model potential, we then show that our wavelet-based approach may disclose new exciting opportunities in the field of computational non-Hermitian quantum mechanics.
Interactive Isogeometric Volume Visualization with Pixel-Accurate Geometry.
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
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.
Highly accurate potential energy surface for the He-H2 dimer.
Bakr, Brandon W; Smith, Daniel G A; Patkowski, Konrad
2013-10-14
A new highly accurate interaction potential is constructed for the He-H2 van der Waals complex. This potential is fitted to 1900 ab initio energies computed at the very large-basis coupled-cluster level and augmented by corrections for higher-order excitations (up to full configuration interaction level) and the diagonal Born-Oppenheimer correction. At the vibrationally averaged H-H bond length of 1.448736 bohrs, the well depth of our potential, 15.870 ± 0.065 K, is nearly 1 K larger than the most accurate previous studies have indicated. In addition to constructing our own three-dimensional potential in the van der Waals region, we present a reparameterization of the Boothroyd-Martin-Peterson potential surface [A. I. Boothroyd, P. G. Martin, and M. R. Peterson, J. Chem. Phys. 119, 3187 (2003)] that is suitable for all configurations of the triatomic system. Finally, we use the newly developed potentials to compute the properties of the lone bound states of (4)He-H2 and (3)He-H2 and the interaction second virial coefficient of the hydrogen-helium mixture. PMID:24116617
Fullerton, G D; Keener, C R; Cameron, I L
1994-12-01
The authors describe empirical corrections to ideally dilute expressions for freezing point depression of aqueous solutions to arrive at new expressions accurate up to three molal concentration. The method assumes non-ideality is due primarily to solute/solvent interactions such that the correct free water mass Mwc is the mass of water in solution Mw minus I.M(s) where M(s) is the mass of solute and I an empirical solute/solvent interaction coefficient. The interaction coefficient is easily derived from the constant in the linear regression fit to the experimental plot of Mw/M(s) as a function of 1/delta T (inverse freezing point depression). The I-value, when substituted into the new thermodynamic expressions derived from the assumption of equivalent activity of water in solution and ice, provides accurate predictions of freezing point depression (+/- 0.05 degrees C) up to 2.5 molal concentration for all the test molecules evaluated; glucose, sucrose, glycerol and ethylene glycol. The concentration limit is the approximate monolayer water coverage limit for the solutes which suggests that direct solute/solute interactions are negligible below this limit. This is contrary to the view of many authors due to the common practice of including hydration forces (a soft potential added to the hard core atomic potential) in the interaction potential between solute particles. When this is recognized the two viewpoints are in fundamental agreement. PMID:7699200
Golibrzuch, Kai; Shirhatti, Pranav R.; Kandratsenka, Alexander; Wodtke, Alec M.; Bartels, Christof; Max Planck Institute for Biophysical Chemistry, Göttingen 37077 ; Rahinov, Igor; Auerbach, Daniel J.; Max Planck Institute for Biophysical Chemistry, Göttingen 37077; Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106
2014-01-28
We present a combined experimental and theoretical study of NO(v = 3 → 3, 2, 1) scattering from a Au(111) surface at incidence translational energies ranging from 0.1 to 1.2 eV. Experimentally, molecular beam–surface scattering is combined with vibrational overtone pumping and quantum-state selective detection of the recoiling molecules. Theoretically, we employ a recently developed first-principles approach, which employs an Independent Electron Surface Hopping (IESH) algorithm to model the nonadiabatic dynamics on a Newns-Anderson Hamiltonian derived from density functional theory. This approach has been successful when compared to previously reported NO/Au scattering data. The experiments presented here show that vibrational relaxation probabilities increase with incidence energy of translation. The theoretical simulations incorrectly predict high relaxation probabilities at low incidence translational energy. We show that this behavior originates from trajectories exhibiting multiple bounces at the surface, associated with deeper penetration and favored (N-down) molecular orientation, resulting in a higher average number of electronic hops and thus stronger vibrational relaxation. The experimentally observed narrow angular distributions suggest that mainly single-bounce collisions are important. Restricting the simulations by selecting only single-bounce trajectories improves agreement with experiment. The multiple bounce artifacts discovered in this work are also present in simulations employing electronic friction and even for electronically adiabatic simulations, meaning they are not a direct result of the IESH algorithm. This work demonstrates how even subtle errors in the adiabatic interaction potential, especially those that influence the interaction time of the molecule with the surface, can lead to an incorrect description of electronically nonadiabatic vibrational energy transfer in molecule-surface collisions.
Highly accurate eigenvalues for the distorted Coulomb potential
NASA Astrophysics Data System (ADS)
Ixaru, L. Gr.; de Meyer, H.; vanden Berghe, G.
2000-03-01
We consider the eigenvalue problem for the radial Schrödinger equation with potentials of the form V(r)=S(r)/r+R(r) where S(r) and R(r) are well behaved functions which tend to some (not necessarily equal) constants when r-->0 and r-->∞. Formulas (14.4.5)-(14.4.8) of Abramowitz and Stegun [Handbook of Mathematical Functions, 8th ed. (Dover, New York, 1972)], corresponding to the pure Coulomb case, are here generalized for this distorted case. We also present a complete procedure for the numerical solution of the problem. Our procedure is robust, very economic and particularly suited for very large n. Numerical illustrations for n up to 2000 are given.
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.
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
Towards accurate porosity descriptors based on guest-host interactions.
Paik, Dooam; Haranczyk, Maciej; Kim, Jihan
2016-05-01
For nanoporous materials at the characterization level, geometry-based approaches have become the methods of choice to provide information, often encoded in numerical descriptors, about the pores and the channels of a porous material. Examples of most common descriptors of the latter are pore limiting diameters, accessible surface area and accessible volume. The geometry-based methods exploit hard-sphere approximation for atoms, which (1) reduces costly computations of the interatomic interactions between the probe guest molecule and the porous material framework atoms, (2) effectively exploit applied mathematics methods such as Voronoi decomposition to represent and characterize porosity. In this work, we revisit and quantify the shortcoming of the geometry-based approaches. To do so, we have developed a series of algorithms to calculate pore descriptors such as void fraction, accessible surface area, pore limiting diameters (largest included sphere, and largest free sphere) based on a classical force field model of interactions between the guest and the framework atoms. Our resulting energy-based methods are tested on diverse sets of metal-organic frameworks and zeolite structures and comparisons against results obtained from geometric-based method indicate deviations in the cases for structures with small pore sizes. The method provides both high accuracy and performance making it suitable when screening a large database of materials. PMID:27054971
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.
Toward Hamiltonian Adaptive QM/MM: Accurate Solvent Structures Using Many-Body Potentials.
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
NASA Astrophysics Data System (ADS)
Heidari, M.; Cortes-Huerto, R.; Donadio, D.; Potestio, R.
2016-07-01
In adaptive resolution simulations the same system is concurrently modeled with different resolution in different subdomains of the simulation box, thereby enabling an accurate description in a small but relevant region, while the rest is treated with a computationally parsimonious model. In this framework, electrostatic interaction, whose accurate treatment is a crucial aspect in the realistic modeling of soft matter and biological systems, represents a particularly acute problem due to the intrinsic long-range nature of Coulomb potential. In the present work we propose and validate the usage of a short-range modification of Coulomb potential, the Damped shifted force (DSF) model, in the context of the Hamiltonian adaptive resolution simulation (H-AdResS) scheme. This approach, which is here validated on bulk water, ensures a reliable reproduction of the structural and dynamical properties of the liquid, and enables a seamless embedding in the H-AdResS framework. The resulting dual-resolution setup is implemented in the LAMMPS simulation package, and its customized version employed in the present work is made publicly available.
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.
Communication: An accurate global potential energy surface for the ground electronic state of ozone
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.
Accurate prediction of protein–protein interactions from sequence alignments using a Bayesian method
Burger, Lukas; van Nimwegen, Erik
2008-01-01
Accurate and large-scale prediction of protein–protein interactions directly from amino-acid sequences is one of the great challenges in computational biology. Here we present a new Bayesian network method that predicts interaction partners using only multiple alignments of amino-acid sequences of interacting protein domains, without tunable parameters, and without the need for any training examples. We first apply the method to bacterial two-component systems and comprehensively reconstruct two-component signaling networks across all sequenced bacteria. Comparisons of our predictions with known interactions show that our method infers interaction partners genome-wide with high accuracy. To demonstrate the general applicability of our method we show that it also accurately predicts interaction partners in a recent dataset of polyketide synthases. Analysis of the predicted genome-wide two-component signaling networks shows that cognates (interacting kinase/regulator pairs, which lie adjacent on the genome) and orphans (which lie isolated) form two relatively independent components of the signaling network in each genome. In addition, while most genes are predicted to have only a small number of interaction partners, we find that 10% of orphans form a separate class of ‘hub' nodes that distribute and integrate signals to and from up to tens of different interaction partners. PMID:18277381
Potential drug interactions with melatonin.
Papagiannidou, Eleni; Skene, Debra J; Ioannides, Costas
2014-05-28
Possible interactions of melatonin with concurrently administered drugs were investigated in in vitro studies utilising human hepatic post-mitochondrial preparations; similar studies were conducted with rat preparations to ascertain whether rat is a suitable surrogate for human. Drugs were selected based not only on the knowledge that the 6-hydroxylation of exogenous melatonin, its principal pathway of metabolism, is mainly mediated by hepatic CYP1A2, but also on the likelihood of the drug being concurrently administered with melatonin. Hepatic preparations were incubated with either melatonin or 6-hydroxymelatonin in the presence and absence of a range of concentrations of interacting drug, and the production of 6-sulphatoxymelatonin monitored using a radioimmunoassay procedure. Of the drugs screened, only the potent CYP1A2 inhibitor 5-methoxypsoralen impaired the 6-melatonin hydroxylation at pharmacologically relevant concentrations, and is likely to lead to clinical interactions; diazepam, tamoxifen and acetaminophen (paracetamol) did not impair the metabolic conversion of melatonin to 6-sulphatoxymelatonin at concentrations attained following therapeutic administration. 17-Ethinhyloestradiol appeared not to suppress the 6-hydroxylation of melatonin but inhibited the sulphation of 6-hydroxymelatonin, but this is unlikely to result in an interaction following therapeutic intake of the steroid. Species differences in the inhibition of melatonin metabolism in human and rat hepatic post-mitochondrial preparations were evident implying that the rat may not be an appropriate surrogate of human in such studies. PMID:24732412
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.
Chemically accurate description of aromatic rings interaction using quantum Monte Carlo
NASA Astrophysics Data System (ADS)
Azadi, Sam
We present an accurate study of interactions between benzene molecules using wave function based quantum Monte Carlo (QMC) methods. We compare our QMC results with density functional theory (DFT) using various van der Waals (vdW) functionals. This comparison enables us to tune vdW functionals. We show that highly optimizing the wave function and introducing more dynamical correlation into the wave function are crucial to calculate the weak chemical binding energy between benzene molecules. The good agreement among our results, experiments and quantum chemistry methods, is an important sign of the capability of the wave function based QMC methods to provide accurate description of very weak intermolecular interactions based on vdW dispersive forces.
Accurate control of a Bose-Einstein condensate by managing the atomic interaction
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.
Dixon, Andrew S; Schwinn, Marie K; Hall, Mary P; Zimmerman, Kris; Otto, Paul; Lubben, Thomas H; Butler, Braeden L; Binkowski, Brock F; Machleidt, Thomas; Kirkland, Thomas A; Wood, Monika G; Eggers, Christopher T; Encell, Lance P; Wood, Keith V
2016-02-19
Protein-fragment complementation assays (PCAs) are widely used for investigating protein interactions. However, the fragments used are structurally compromised and have not been optimized nor thoroughly characterized for accurately assessing these interactions. We took advantage of the small size and bright luminescence of NanoLuc to engineer a new complementation reporter (NanoBiT). By design, the NanoBiT subunits (i.e., 1.3 kDa peptide, 18 kDa polypeptide) weakly associate so that their assembly into a luminescent complex is dictated by the interaction characteristics of the target proteins onto which they are appended. To ascertain their general suitability for measuring interaction affinities and kinetics, we determined that their intrinsic affinity (KD = 190 μM) and association constants (kon = 500 M(-1) s(-1), koff = 0.2 s(-1)) are outside of the ranges typical for protein interactions. The accuracy of NanoBiT was verified under defined biochemical conditions using the previously characterized interaction between SME-1 β-lactamase and a set of inhibitor binding proteins. In cells, NanoBiT fusions to FRB/FKBP produced luminescence consistent with the linear characteristics of NanoLuc. Response dynamics, evaluated using both protein kinase A and β-arrestin-2, were rapid, reversible, and robust to temperature (21-37 °C). Finally, NanoBiT provided a means to measure pharmacology of kinase inhibitors known to induce the interaction between BRAF and CRAF. Our results demonstrate that the intrinsic properties of NanoBiT allow accurate representation of protein interactions and that the reporter responds reliably and dynamically in cells. PMID:26569370
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.
Vehicle bridge interaction dynamics and potential applications
NASA Astrophysics Data System (ADS)
Yang, Y. B.; Lin, C. W.
2005-06-01
The dynamic interaction between a moving vehicle and the sustaining bridge is studied. By the method of modal superposition, closed-form solutions are obtained for the vertical responses of both the bridge and moving vehicle, assuming the vehicle/bridge mass ratio to be small. For both the bridge and vehicle responses, it is confirmed that rather accurate solutions can be obtained by considering only the first mode. The displacement, velocity, and acceleration of the bridge are governed at different extents by two sets of frequencies, i.e., the driving frequency of the vehicle and natural frequencies of the bridge. From the spectrum for the bridge displacement, the vehicle speeds can be shown to be associated with some low-frequency pikes. On the other hand, the vehicle responses are governed by five distinct frequencies that appear as driving frequencies, vehicle frequency, and bridge frequencies with shift. From the vehicle's acceleration spectrum, the first bridge frequency (with shift) is shown to have rather high visibility and can be easily identified. The effects of damping of the vehicle and bridge are evaluated in the numerical studies. Potential applications of the present results, as well as further researches required, are also indicated in the paper.
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).
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.
Developing a general interaction potential for hydrophobic and hydrophilic interactions.
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. PMID:25072835
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.
Kieslich, Chris A.; Tamamis, Phanourios; Guzman, Yannis A.; Onel, Melis; Floudas, Christodoulos A.
2016-01-01
HIV-1 entry into host cells is mediated by interactions between the V3-loop of viral glycoprotein gp120 and chemokine receptor CCR5 or CXCR4, collectively known as HIV-1 coreceptors. Accurate genotypic prediction of coreceptor usage is of significant clinical interest and determination of the factors driving tropism has been the focus of extensive study. We have developed a method based on nonlinear support vector machines to elucidate the interacting residue pairs driving coreceptor usage and provide highly accurate coreceptor usage predictions. Our models utilize centroid-centroid interaction energies from computationally derived structures of the V3-loop:coreceptor complexes as primary features, while additional features based on established rules regarding V3-loop sequences are also investigated. We tested our method on 2455 V3-loop sequences of various lengths and subtypes, and produce a median area under the receiver operator curve of 0.977 based on 500 runs of 10-fold cross validation. Our study is the first to elucidate a small set of specific interacting residue pairs between the V3-loop and coreceptors capable of predicting coreceptor usage with high accuracy across major HIV-1 subtypes. The developed method has been implemented as a web tool named CRUSH, CoReceptor USage prediction for HIV-1, which is available at http://ares.tamu.edu/CRUSH/. PMID:26859389
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).
NASA Astrophysics Data System (ADS)
Stwalley, W. C.; Verma, K. K.; Rajaei-Rizi, A.; Bahns, J. T.; Harding, D. R.
This paper illustrates (using the molecules LiH, Li2 and Na2) how laser-induced fluorescence can be used to greatly expand the range of observed vibrational levels in ground electronic states. This expanded vibrational range leads to the determination of virtually the full well of the potential energy curve. This also leads to improved determination of the dissociation limit and serves as a severe test for highly accurate ab initio calculations now available for many small molecules.
NASA Technical Reports Server (NTRS)
Stwalley, W. C.; Verma, K. K.; Rajaei-Rizi, A.; Bahns, J. T.; Harding, D. R.
1982-01-01
This paper illustrates (using the molecules LiH, Li2 and Na2) how laser-induced fluorescence can be used to greatly expand the range of observed vibrational levels in ground electronic states. This expanded vibrational range leads to the determination of virtually the full well of the potential energy curve. This also leads to improved determination of the dissociation limit and serves as a severe test for highly accurate ab initio calculations now available for many small molecules.
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
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.
Potential interactions between alternative therapies and warfarin.
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
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.
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. PMID:25669533
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.
Nielsen, Jens; D’Avezac, Mayeul; Hetherington, James; Stamatakis, Michail
2013-12-14
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.
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
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.
Accurate potential drop sheet resistance measurements of laser-doped areas in semiconductors
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.
Intermolecular potentials and the accurate prediction of the thermodynamic properties of water.
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(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. PMID:24320337
Intermolecular potentials and the accurate prediction of the thermodynamic properties of water
NASA Astrophysics Data System (ADS)
Shvab, I.; Sadus, Richard J.
2013-11-01
The ability of intermolecular potentials to correctly predict the thermodynamic properties of liquid water at a density of 0.998 g/cm3 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.
Intermolecular potentials and the accurate prediction of the thermodynamic properties of water
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.
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. PMID:27357413
Fedorov, Dmitry A.; Varganov, Sergey A.; Derevianko, Andrei
2014-05-14
We calculate the potential energy curves, the permanent dipole moment curves, and the lifetimes of the ground and excited vibrational states of the heteronuclear alkali dimers XY (X, Y = Li, Na, K, Rb, Cs) in the X{sup 1}Σ{sup +} electronic state using the coupled cluster with singles doubles and triples method. All-electron quadruple-ζ basis sets with additional core functions are used for Li and Na, and small-core relativistic effective core potentials with quadruple-ζ quality basis sets are used for K, Rb, and Cs. The inclusion of the coupled cluster non-perturbative triple excitations is shown to be crucial for obtaining the accurate potential energy curves. A large one-electron basis set with additional core functions is needed for the accurate prediction of permanent dipole moments. The dissociation energies are overestimated by only 14 cm{sup −1} for LiNa and by no more than 114 cm{sup −1} for the other molecules. The discrepancies between the experimental and calculated harmonic vibrational frequencies are less than 1.7 cm{sup −1}, and the discrepancies for the anharmonic correction are less than 0.1 cm{sup −1}. We show that correlation between atomic electronegativity differences and permanent dipole moment of heteronuclear alkali dimers is not perfect. To obtain the vibrational energies and wave functions the vibrational Schrödinger equation is solved with the B-spline basis set method. The transition dipole moments between all vibrational states, the Einstein coefficients, and the lifetimes of the vibrational states are calculated. We analyze the decay rates of the vibrational states in terms of spontaneous emission, and stimulated emission and absorption induced by black body radiation. In all studied heteronuclear alkali dimers the ground vibrational states have much longer lifetimes than any excited states.
NASA Astrophysics Data System (ADS)
Fedorov, Dmitry A.; Derevianko, Andrei; Varganov, Sergey A.
2014-05-01
We calculate the potential energy curves, the permanent dipole moment curves, and the lifetimes of the ground and excited vibrational states of the heteronuclear alkali dimers XY (X, Y = Li, Na, K, Rb, Cs) in the X1Σ+ electronic state using the coupled cluster with singles doubles and triples method. All-electron quadruple-ζ basis sets with additional core functions are used for Li and Na, and small-core relativistic effective core potentials with quadruple-ζ quality basis sets are used for K, Rb, and Cs. The inclusion of the coupled cluster non-perturbative triple excitations is shown to be crucial for obtaining the accurate potential energy curves. A large one-electron basis set with additional core functions is needed for the accurate prediction of permanent dipole moments. The dissociation energies are overestimated by only 14 cm-1 for LiNa and by no more than 114 cm-1 for the other molecules. The discrepancies between the experimental and calculated harmonic vibrational frequencies are less than 1.7 cm-1, and the discrepancies for the anharmonic correction are less than 0.1 cm-1. We show that correlation between atomic electronegativity differences and permanent dipole moment of heteronuclear alkali dimers is not perfect. To obtain the vibrational energies and wave functions the vibrational Schrödinger equation is solved with the B-spline basis set method. The transition dipole moments between all vibrational states, the Einstein coefficients, and the lifetimes of the vibrational states are calculated. We analyze the decay rates of the vibrational states in terms of spontaneous emission, and stimulated emission and absorption induced by black body radiation. In all studied heteronuclear alkali dimers the ground vibrational states have much longer lifetimes than any excited states.
Accurate double many-body expansion potential energy surface for the 2(1)A' state of N2O.
Li, Jing; Varandas, António J C
2014-08-28
An accurate double many-body expansion potential energy surface is reported for the 2(1)A' state of N2O. The new double many-body expansion (DMBE) form has been fitted to a wealth of ab initio points that have been calculated at the multi-reference configuration interaction level using the full-valence-complete-active-space wave function as reference and the cc-pVQZ basis set, and subsequently corrected semiempirically via double many-body expansion-scaled external correlation method to extrapolate the calculated energies to the limit of a complete basis set and, most importantly, the limit of an infinite configuration interaction expansion. The topographical features of the novel potential energy surface are then examined in detail and compared with corresponding attributes of other potential functions available in the literature. Exploratory trajectories have also been run on this DMBE form with the quasiclassical trajectory method, with the thermal rate constant so determined at room temperature significantly enhancing agreement with experimental data. PMID:25173014
Accurate double many-body expansion potential energy surface for the 21A' state of N_2O
NASA Astrophysics Data System (ADS)
Li, Jing; Varandas, António J. C.
2014-08-01
An accurate double many-body expansion potential energy surface is reported for the 21A' state of N_2O. The new double many-body expansion (DMBE) form has been fitted to a wealth of ab initio points that have been calculated at the multi-reference configuration interaction level using the full-valence-complete-active-space wave function as reference and the cc-pVQZ basis set, and subsequently corrected semiempirically via double many-body expansion-scaled external correlation method to extrapolate the calculated energies to the limit of a complete basis set and, most importantly, the limit of an infinite configuration interaction expansion. The topographical features of the novel potential energy surface are then examined in detail and compared with corresponding attributes of other potential functions available in the literature. Exploratory trajectories have also been run on this DMBE form with the quasiclassical trajectory method, with the thermal rate constant so determined at room temperature significantly enhancing agreement with experimental data.
Tung, Wei-Cheng; Adamowicz, Ludwik
2014-03-28
Very accurate calculations of the ground-state potential energy curve (PEC) of the LiH(+) 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. PMID:24697449
NASA Astrophysics Data System (ADS)
Tung, Wei-Cheng; Adamowicz, Ludwik
2014-03-01
Very accurate calculations of the ground-state potential energy curve (PEC) of the LiH+ 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.
Quigley, A; Heng, J Y Y; Liddell, J M; Williams, D R
2013-11-01
Measurement of B22, the second virial coefficient, is an important technique for describing the solution behaviour of proteins, especially as it relates to precipitation, aggregation and crystallisation phenomena. This paper describes the best practise for calculating B22 values from self-interaction chromatograms (SIC) for aqueous protein solutions. Detailed analysis of SIC peak shapes for lysozyme shows that non-Gaussian peaks are commonly encountered for SIC, with typical peak asymmetries of 10%. This asymmetry reflects a non-linear chromatographic retention process, in this case heterogeneity of the protein-protein interactions. Therefore, it is important to use the centre of mass calculations for determining accurate retention volumes and thus B22 values. Empirical peak maximum chromatogram analysis, often reported in the literature, can result in errors of up to 50% in B22 values. A methodology is reported here for determining both the mean and the variance in B22 from SIC experiments, includes a correction for normal longitudinal peak broadening. The variance in B22 due to chemical effects is quantified statistically and is a measure of the heterogeneity of protein-protein interactions in solution. In the case of lysozyme, a wide range of B22 values are measured which can vary significantly from the average B22 values. PMID:23623796
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).
Skokov, S.; Peterson, K.A.; Bowman, J.M.
1998-08-01
Accurate {ital ab initio} multireference configuration interaction (CI) calculations with large correlation-consistent basis sets are performed for HOCl. After extrapolation to the complete basis set limit, the {ital ab initio} data are precisely fit to give a semiglobal three-dimensional potential energy surface to describe HOCl{r_arrow}Cl+OH from high overtone excitation of the OH-stretch. The average absolute deviation between the {ital ab initio} and fitted energies is 4.2thinspcm{sup {minus}1} for energies up to 60 kcal/mol relative to the HOCl minimum. Vibrational energies of HOCl including the six overtones of the OH-stretch are computed using a vibrational-Cl method on the fitted potential and also on a slightly adjusted potential. Near-spectroscopic accuracy is obtained using the adjusted potential; the average absolute deviation between theory and experiment for 19 experimentally reported states is 4.8thinspcm{sup {minus}1}. Very good agreement with experiment is also obtained for numerous rotational energies for the ground vibrational state, the ClO-stretch fundamental, and the fifth overtone of the OH-stretch. {copyright} {ital 1998 American Institute of Physics.}
Exact kinetic energy enables accurate evaluation of weak interactions by the FDE-vdW method
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.
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.
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
Accurate prediction of helix interactions and residue contacts in membrane proteins.
Hönigschmid, Peter; Frishman, Dmitrij
2016-04-01
Accurate prediction of intra-molecular interactions from amino acid sequence is an important pre-requisite for obtaining high-quality protein models. Over the recent years, remarkable progress in this area has been achieved through the application of novel co-variation algorithms, which eliminate transitive evolutionary connections between residues. In this work we present a new contact prediction method for α-helical transmembrane proteins, MemConP, in which evolutionary couplings are combined with a machine learning approach. MemConP achieves a substantially improved accuracy (precision: 56.0%, recall: 17.5%, MCC: 0.288) compared to the use of either machine learning or co-evolution methods alone. The method also achieves 91.4% precision, 42.1% recall and a MCC of 0.490 in predicting helix-helix interactions based on predicted contacts. The approach was trained and rigorously benchmarked by cross-validation and independent testing on up-to-date non-redundant datasets of 90 and 30 experimental three dimensional structures, respectively. MemConP is a standalone tool that can be downloaded together with the associated training data from http://webclu.bio.wzw.tum.de/MemConP. PMID:26851352
Santolini, Marc; Mora, Thierry; Hakim, Vincent
2014-01-01
The identification of transcription factor binding sites (TFBSs) on genomic DNA is of crucial importance for understanding and predicting regulatory elements in gene networks. TFBS motifs are commonly described by Position Weight Matrices (PWMs), in which each DNA base pair contributes independently to the transcription factor (TF) binding. However, this description ignores correlations between nucleotides at different positions, and is generally inaccurate: analysing fly and mouse in vivo ChIPseq data, we show that in most cases the PWM model fails to reproduce the observed statistics of TFBSs. To overcome this issue, we introduce the pairwise interaction model (PIM), a generalization of the PWM model. The model is based on the principle of maximum entropy and explicitly describes pairwise correlations between nucleotides at different positions, while being otherwise as unconstrained as possible. It is mathematically equivalent to considering a TF-DNA binding energy that depends additively on each nucleotide identity at all positions in the TFBS, like the PWM model, but also additively on pairs of nucleotides. We find that the PIM significantly improves over the PWM model, and even provides an optimal description of TFBS statistics within statistical noise. The PIM generalizes previous approaches to interdependent positions: it accounts for co-variation of two or more base pairs, and predicts secondary motifs, while outperforming multiple-motif models consisting of mixtures of PWMs. We analyse the structure of pairwise interactions between nucleotides, and find that they are sparse and dominantly located between consecutive base pairs in the flanking region of TFBS. Nonetheless, interactions between pairs of non-consecutive nucleotides are found to play a significant role in the obtained accurate description of TFBS statistics. The PIM is computationally tractable, and provides a general framework that should be useful for describing and predicting TFBSs beyond
An accurate nucleon-nucleon potential with charge-independence breaking
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.
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.
Knight, Joseph W; Wang, Xiaopeng; Gallandi, Lukas; Dolgounitcheva, Olga; Ren, Xinguo; Ortiz, J Vincent; Rinke, Patrick; Körzdörfer, Thomas; Marom, Noa
2016-02-01
The performance of different GW methods is assessed for a set of 24 organic acceptors. Errors are evaluated with respect to coupled cluster singles, doubles, and perturbative triples [CCSD(T)] reference data for the vertical ionization potentials (IPs) and electron affinities (EAs), extrapolated to the complete basis set limit. Additional comparisons are made to experimental data, where available. We consider fully self-consistent GW (scGW), partial self-consistency in the Green's function (scGW0), non-self-consistent G0W0 based on several mean-field starting points, and a "beyond GW" second-order screened exchange (SOSEX) correction to G0W0. We also describe the implementation of the self-consistent Coulomb hole with screened exchange method (COHSEX), which serves as one of the mean-field starting points. The best performers overall are G0W0+SOSEX and G0W0 based on an IP-tuned long-range corrected hybrid functional with the former being more accurate for EAs and the latter for IPs. Both provide a balanced treatment of localized vs delocalized states and valence spectra in good agreement with photoemission spectroscopy (PES) experiments. PMID:26731609
Measuring three-dimensional interaction potentials using optical interference.
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
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.
Statistical systems with nonintegrable interaction potentials.
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
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.
Kottmann, Jakob S; Höfener, Sebastian; Bischoff, Florian A
2015-12-21
In the present work, we report an efficient implementation of configuration interaction singles (CIS) excitation energies and oscillator strengths using the multi-resolution analysis (MRA) framework to address the basis-set convergence of excited state computations. In MRA (ground-state) orbitals, excited states are constructed adaptively guaranteeing an overall precision. Thus not only valence but also, in particular, low-lying Rydberg states can be computed with consistent quality at the basis set limit a priori, or without special treatments, which is demonstrated using a small test set of organic molecules, basis sets, and states. We find that the new implementation of MRA-CIS excitation energy calculations is competitive with conventional LCAO calculations when the basis-set limit of medium-sized molecules is sought, which requires large, diffuse basis sets. This becomes particularly important if accurate calculations of molecular electronic absorption spectra with respect to basis-set incompleteness are required, in which both valence as well as Rydberg excitations can contribute to the molecule's UV/VIS fingerprint. PMID:25913482
Nanoparticle interaction potentials constructed by multiscale computation
NASA Astrophysics Data System (ADS)
Lee, Cheng K.; Hua, Chi C.
2010-06-01
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 (SiO2)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 Si6O12 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 2α-α potential (α 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 polymer chains and
Very accurate potential energy curve of the LiH molecule
NASA Astrophysics Data System (ADS)
Tung, Wei-Cheng; Pavanello, Michele; Adamowicz, Ludwik
2011-02-01
We present very accurate calculations of the ground-state potential energy curve (PEC) of the LiH molecule performed with all-electron explicitly correlated Gaussian functions with shifted centers. The PEC is generated with the variational method involving simultaneous optimization of all Gaussians with an approach employing the analytical first derivatives of the energy with respect to the Gaussian nonlinear parameters (i.e., the exponents and the coordinates of the shifts). The LiH internuclear distance is varied between 1.8 and 40 bohrs. The absolute accuracy of the generated PEC is estimated as not exceeding 0.3 cm-1. The adiabatic corrections for the four LiH isotopologues, i.e., 7LiH, 6LiH, 7LiD, and 6LiD, are also calculated and added to the LiH PEC. The aforementioned PECs are then used to calculate the vibrational energies for these systems. The maximum difference between the computed and the experimental vibrational transitions is smaller than 0.9 cm-1. The contribution of the adiabatic correction to the dissociation energy of 7LiH molecule is 10.7 cm-1. The magnitude of this correction shows its importance in calculating the LiH spectroscopic constants. As the estimated contribution of the nonadiabatic and relativistic effects to the ground state dissociation energy is around 0.3 cm-1, their inclusion in the LiH PEC calculation seems to be the next most important contribution to evaluate in order to improve the accuracy achieved in this work.
Very accurate potential energy curve of the LiH molecule.
Tung, Wei-Cheng; Pavanello, Michele; Adamowicz, Ludwik
2011-02-14
We present very accurate calculations of the ground-state potential energy curve (PEC) of the LiH molecule performed with all-electron explicitly correlated Gaussian functions with shifted centers. The PEC is generated with the variational method involving simultaneous optimization of all Gaussians with an approach employing the analytical first derivatives of the energy with respect to the Gaussian nonlinear parameters (i.e., the exponents and the coordinates of the shifts). The LiH internuclear distance is varied between 1.8 and 40 bohrs. The absolute accuracy of the generated PEC is estimated as not exceeding 0.3 cm(-1). The adiabatic corrections for the four LiH isotopologues, i.e., (7)LiH, (6)LiH, (7)LiD, and (6)LiD, are also calculated and added to the LiH PEC. The aforementioned PECs are then used to calculate the vibrational energies for these systems. The maximum difference between the computed and the experimental vibrational transitions is smaller than 0.9 cm(-1). The contribution of the adiabatic correction to the dissociation energy of (7)LiH molecule is 10.7 cm(-1). The magnitude of this correction shows its importance in calculating the LiH spectroscopic constants. As the estimated contribution of the nonadiabatic and relativistic effects to the ground state dissociation energy is around 0.3 cm(-1), their inclusion in the LiH PEC calculation seems to be the next most important contribution to evaluate in order to improve the accuracy achieved in this work. PMID:21322671
Capturing the Interaction Potential of Amyloidogenic Proteins
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.
Hermann, Max; Schunke, Anja C; Schultz, Thomas; Klein, Reinhard
2016-01-01
Large image deformations pose a challenging problem for the visualization and statistical analysis of 3D image ensembles which have a multitude of applications in biology and medicine. Simple linear interpolation in the tangent space of the ensemble introduces artifactual anatomical structures that hamper the application of targeted visual shape analysis techniques. In this work we make use of the theory of stationary velocity fields to facilitate interactive non-linear image interpolation and plausible extrapolation for high quality rendering of large deformations and devise an efficient image warping method on the GPU. This does not only improve quality of existing visualization techniques, but opens up a field of novel interactive methods for shape ensemble analysis. Taking advantage of the efficient non-linear 3D image warping, we showcase four visualizations: 1) browsing on-the-fly computed group mean shapes to learn about shape differences between specific classes, 2) interactive reformation to investigate complex morphologies in a single view, 3) likelihood volumes to gain a concise overview of variability and 4) streamline visualization to show variation in detail, specifically uncovering its component tangential to a reference surface. Evaluation on a real world dataset shows that the presented method outperforms the state-of-the-art in terms of visual quality while retaining interactive frame rates. A case study with a domain expert was performed in which the novel analysis and visualization methods are applied on standard model structures, namely skull and mandible of different rodents, to investigate and compare influence of phylogeny, diet and geography on shape. The visualizations enable for instance to distinguish (population-)normal and pathological morphology, assist in uncovering correlation to extrinsic factors and potentially support assessment of model quality. PMID:26390470
Tissue resonance interaction accurately detects colon lesions: A double-blind pilot study
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
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.
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
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.
Potential drug interaction between paclitaxel and clopidogrel
SHINODA, YASUTAKA; KIMURA, MICHIO; USAMI, EISEKI; ASANO, HIROKI; YOSHIMURA, TOMOAKI
2016-01-01
Paclitaxel is mainly inactivated in vivo by cytochrome P5402C8 (CYP2C8). In recent years, the clopidogrel metabolite has been reported to potently inhibit CYP2C8. However, clinical information regarding the interaction between these two drugs is limited. To the best of our knowledge, this is the first retrospective study investigating the potential for the drug interaction between paclitaxel and clopidogrel. A total of 8 cases in which clopidogrel and paclitaxel were used in combination were examined. The incidence of adverse events and discontinuation rate in these cases were assessed. Neutrophil counts were compared in patients prior and subsequent to the combined administration of clopidogrel and paclitaxel. Grade 3 neutropenia occurred in all cases of combination therapy and grade 4 occurred in 7 cases (88%). In addition, 4 cases (50%) showed febrile neutropenia. Four cases (50%) involved a severe adverse event requiring discontinuation of drug administration. In 1 case involving 6 courses of paclitaxel and nedaplatin therapy prior and subsequent to clopidogrel, there was a significant reduction in the average neutrophil count after 8 days of combination treatment (1,240±395 counts/mm3 without clopidogrel; 370±148 counts/mm3 with clopidogrel; mean ± standard deviation, P<0.01). Drug interactions during co-administration of clopidogrel and paclitaxel may cause severe neutropenia. To avoid these interactions, alternative medications should be considered. If these two drugs are used in combination, it may be necessary to monitor for adverse events more carefully. PMID:27347418
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
Toward Accurate Modeling of the Effect of Ion-Pair Formation on Solute Redox Potential.
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
Bose-condensed atomic systems with nonlocal interaction potentials
NASA Astrophysics Data System (ADS)
Yukalov, V. I.; Yukalova, E. P.
2016-04-01
The general approach for describing systems with a Bose-Einstein condensate, where atoms interact through nonlocal pair potentials, is presented. Special attention is paid to nonintegrable potentials, such as the dipolar interaction potential. The potentials that are not absolutely integrable can have not well-defined Fourier transforms. Using formally these not defined Fourier transforms leads to unphysical conclusions. To make the Fourier transform well defined, the interaction potential has to be regularised. This is illustrated by the example of dipolar interactions.
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
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.
Peterson, Kirk A
2000-09-15
A global, analytical potential energy surface for the ground electronic state of HOBr has been determined using highly correlated multireference configuration interaction wave functions and explicit basis set extrapolations of large correlation consistent basis sets. The ab initio data have been fit to an analytical functional form that accurately includes both the HOBr and HBrO minima, as well as all dissociation asymptotes. Small adjustments to this surface are made based on the limited experimental data available and by indirectly taking into account the effects of spin-orbit coupling on the OH+Br dissociation channel. Vibrational energy levels are calculated variationally for both HOBr and HBrO up to the OH+Br dissociation limit using a truncation/recoupling method. The HOBr isomer is calculated to contain 708 bound vibrational energy levels, while the HBrO minimum lies above the OH+Br dissociation limit but is calculated to have 74 ''quasibound,'' localized eigenstates. Infrared intensities for all of these vibrational transitions are also calculated using MRCI dipole moment functions. The assignment of the HOBr states is complicated by strong stretch-bend resonances even at relatively low energies. In contrast to the HOCl case, these state mixings made it particularly difficult to assign the relatively intense OH overtone bands above v{sub 1}=2. The vibrational density of states of HOBr at the OH+Br dissociation limit is determined to be 0.16 states/cm-1. Comparisons to recent work on HOCl using similar methods are made throughout. (c) 2000 American Institute of Physics.
An Accurate Global Ab Initio Potential Energy Surface for the X(1)A' Electronic State of HOBr
Peterson, Kirk A.
1999-12-01
A global, analytical potential energy surface for the ground electronic state of HOBr has been determined using highly correlated multireference configuration interaction wave functions and explicit basis set extrapolations of large correlation consistent basis sets. The ab initio data have been fit to an analytical functional form that accurately includes both the HOBr and HBrO minima, as well as all dissociation asymptotes. Small adjustments to this surface are made based on the limited experimental data available and by indirectly taking into account the effects of spin-orbit coupling on the OH+Br dissociation channel. Vibrational energy levels are calculated variationally for both HOBr and HBrO up to the OH+Br dissociation limit using a truncation-recoupling method. The HOBr isomer is calculated to contain 708 bound vibrational energy levels, while the HBrO minimum lies above the OH+Br dissociation limit but is calculated to have 74 quasibound, localized eigenstates. Infrared intensities for all of these vibrational transitions are also calculated using MRCI dipole moment functions. The assignment of the HOBr states is complicated by strong stretch-bend resonances even at relatively low energies. In contrast to the HOCl case, these state mixings made it particularly difficult to assign the relatively intense OH overtone bands above v1=2. The vibrational density of states of HOBr at the OH+Br dissociation limit is determined to be 0.16 states/cm-1. Comparisons to recent work on HOCl using similar methods are made throughout.
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.
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.
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
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
NASA Astrophysics Data System (ADS)
Song, Yu-Zhi; Li, Yong-Qing; Gao, Shou-Bao; Meng, Qing-Tian
2014-01-01
A globally accurate potential energy surface is reported for the electronic ground-state HLi2 by fitting ab initio energies to double many-body expansion formalism. The total 3726 ab initio energies used to map the HLi2 potential energy surface are calculated using the multi-reference configuration interaction method, with their dynamical correlation being semiempirically corrected by the double many-body expansion-scaled external correlation method. The current potential energy surface generates an excellent fit of the ab initio energies, showing a small root-mean squared derivation of 0.636 kcal mol-1. The topographical features of the HLi2 potential energy surface are examined in detail, which concludes that the H + Li2(X 1Σg) → Li + LiH(X 1Σ) reaction is essentially barrierless and the exothermicity is calculated to be 33.668 kcal mol-1, thus corroborates the available experimental and theoretical results.
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.
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.
Apparatus for use in rapid and accurate controlled-potential coulometric analysis
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.
Finite domain simulations with adaptive boundaries: accurate potentials and nonequilibrium movesets.
Wagoner, Jason A; Pande, Vijay S
2013-12-21
We extend the theory of hybrid explicit/implicit solvent models to include an explicit domain that grows and shrinks in response to a solute's evolving configuration. The goal of this model is to provide an appropriate but not excessive amount of solvent detail, and the inclusion of an adjustable boundary provides a significant computational advantage for solutes that explore a range of configurations. In addition to the theoretical development, a successful implementation of this method requires (1) an efficient moveset that propagates the boundary as a new coordinate of the system, and (2) an accurate continuum solvent model with parameters that are transferable to an explicit domain of any size. We address these challenges and develop boundary updates using Monte Carlo moves biased by nonequilibrium paths. We obtain the desired level of accuracy using a "decoupling interface" that we have previously shown to remove boundary artifacts common to hybrid solvent models. Using an uncharged, coarse-grained solvent model, we then study the efficiency of nonequilibrium paths that a simulation takes by quantifying the dissipation. In the spirit of optimization, we study this quantity over a range of simulation parameters. PMID:24359359
Schütt, Heiko H; Harmeling, Stefan; Macke, Jakob H; Wichmann, Felix A
2016-05-01
The psychometric function describes how an experimental variable, such as stimulus strength, influences the behaviour of an observer. Estimation of psychometric functions from experimental data plays a central role in fields such as psychophysics, experimental psychology and in the behavioural neurosciences. Experimental data may exhibit substantial overdispersion, which may result from non-stationarity in the behaviour of observers. Here we extend the standard binomial model which is typically used for psychometric function estimation to a beta-binomial model. We show that the use of the beta-binomial model makes it possible to determine accurate credible intervals even in data which exhibit substantial overdispersion. This goes beyond classical measures for overdispersion-goodness-of-fit-which can detect overdispersion but provide no method to do correct inference for overdispersed data. We use Bayesian inference methods for estimating the posterior distribution of the parameters of the psychometric function. Unlike previous Bayesian psychometric inference methods our software implementation-psignifit 4-performs numerical integration of the posterior within automatically determined bounds. This avoids the use of Markov chain Monte Carlo (MCMC) methods typically requiring expert knowledge. Extensive numerical tests show the validity of the approach and we discuss implications of overdispersion for experimental design. A comprehensive MATLAB toolbox implementing the method is freely available; a python implementation providing the basic capabilities is also available. PMID:27013261
Matsui, Toru; Kitagawa, Yasutaka; Okumura, Mitsutaka; Shigeta, Yasuteru
2015-01-15
We computationally evaluated the standard hydrogen electrode (SHE) potential in aqueous phase and the Gibbs energy of a proton from the experimental pKa values of alcohol molecules. From the "golden standard" CCSD(T)/aug-cc-pVTZ level calculation, we estimated the SHE potential as 4.48 V, which is very close to the IUPAC-recommended experimental value of 4.44 V. As applications to the Gaussian-3 (G3) methods, which also reproduce the "golden standard" level calculations, we computed various pKa values and redox potentials for a vitamin series. For vitamin C, we support the experimental result of +0.35 V and predict the pKa value of d-ascorbic acid to be 3.7-3.9. Using a model molecule for nicotinamide adenine dinucleotide (NAD), we reproduced the redox potential and determined the order of the proton/electron addition, based on both the proton affinity and redox potential. PMID:25514626
Dolgounitcheva, O; Díaz-Tinoco, Manuel; Zakrzewski, V G; Richard, Ryan M; Marom, Noa; Sherrill, C David; Ortiz, J V
2016-02-01
Comparison of ab initio electron-propagator predictions of vertical ionization potentials and electron affinities of organic, acceptor molecules with benchmark calculations based on the basis set-extrapolated, coupled cluster single, double, and perturbative triple substitution method has enabled identification of self-energy approximations with mean, unsigned errors between 0.1 and 0.2 eV. Among the self-energy approximations that neglect off-diagonal elements in the canonical, Hartree-Fock orbital basis, the P3 method for electron affinities, and the P3+ method for ionization potentials provide the best combination of accuracy and computational efficiency. For approximations that consider the full self-energy matrix, the NR2 methods offer the best performance. The P3+ and NR2 methods successfully identify the correct symmetry label of the lowest cationic state in two cases, naphthalenedione and benzoquinone, where some other methods fail. PMID:26730459
Accurate solutions, parameter studies and comparisons for the Euler and potential flow equations
NASA Technical Reports Server (NTRS)
Anderson, W. Kyle; Batina, John T.
1988-01-01
Parameter studies are conducted using the Euler and potential flow equation models for steady and unsteady flows in both two and three dimensions. The Euler code is an implicit, upwind, finite volume code which uses the Van Leer method of flux vector splitting which has been recently extended for use on dynamic meshes and maintain all the properties of the original splitting. The potential flow code is an implicit, finite difference method for solving the transonic small disturbance equations and incorporates both entropy and vorticity corrections into the solution procedures thereby extending its applicability into regimes where shock strength normally precludes its use. Parameter studies resulting in benchmark type calculations include the effects of spatial and temporal refinement, spatial order of accuracy, far field boundary conditions for steady flow, frequency of oscillation, and the use of subiterations at each time step to reduce linearization and factorization errors. Comparisons between Euler and potential flow results are made, as well as with experimental data where available.
Accurate solutions, parameter studies and comparisons for the Euler and potential flow equations
NASA Technical Reports Server (NTRS)
Anderson, W. Kyle; Batina, John T.
1988-01-01
Parameter studies are conducted using the Euler and potential flow equation models for unsteady and steady flows in both two and three dimensions. The Euler code is an implicit, upwind, finite volume code which uses the Van Leer method of flux-vector-splitting which has been recently extended for use on dynamic meshes and maintain all the properties of the original splitting. The potential flow code is an implicit, finite difference method for solving the transonic small disturbance equations and incorporates both entropy and vorticity corrections into the solution procedures thereby extending its applicability into regimes where shock strength normally precludes its use. Parameter studies resulting in benchmark type calculations include the effects of spatial and temporal refinement, spatial order of accuracy, far field boundary conditions for steady flow, frequency of oscillation, and the use of subiterations at each time step to reduce linearization and factorization errors. Comparisons between Euler and potential flows results are made as well as with experimental data where available.
Amacher, David E
2016-07-01
Context The silencing or activation of cancer-associated genes by epigenetic mechanisms can ultimately lead to the clonal expansion of cancer cells. Objective The aim of this review is to summarize all relevant epigenetic biomarkers that have been proposed to date for the diagnosis of some prevalent human cancers. Methods A Medline search for the terms epigenetic biomarkers, human cancers, DNA methylation, histone modifications and microRNAs was performed. Results One hundred fifty-seven relevant publications were found and reviewed. Conclusion To date, a significant number of potential epigenetic cancer biomarkers of human cancer have been investigated, and some have advanced to clinical implementation. PMID:26983778
Accurate formula for dissipative interaction in frequency modulation atomic force microscopy
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.
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.
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
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
PLIF: A rapid, accurate method to detect and quantitatively assess protein-lipid interactions.
Ceccato, Laurie; Chicanne, Gaëtan; Nahoum, Virginie; Pons, Véronique; Payrastre, Bernard; Gaits-Iacovoni, Frédérique; Viaud, Julien
2016-01-01
Phosphoinositides are a type of cellular phospholipid that regulate signaling in a wide range of cellular and physiological processes through the interaction between their phosphorylated inositol head group and specific domains in various cytosolic proteins. These lipids also influence the activity of transmembrane proteins. Aberrant phosphoinositide signaling is associated with numerous diseases, including cancer, obesity, and diabetes. Thus, identifying phosphoinositide-binding partners and the aspects that define their specificity can direct drug development. However, current methods are costly, time-consuming, or technically challenging and inaccessible to many laboratories. We developed a method called PLIF (for "protein-lipid interaction by fluorescence") that uses fluorescently labeled liposomes and tethered, tagged proteins or peptides to enable fast and reliable determination of protein domain specificity for given phosphoinositides in a membrane environment. We validated PLIF against previously known phosphoinositide-binding partners for various proteins and obtained relative affinity profiles. Moreover, PLIF analysis of the sorting nexin (SNX) family revealed not only that SNXs bound most strongly to phosphatidylinositol 3-phosphate (PtdIns3P or PI3P), which is known from analysis with other methods, but also that they interacted with other phosphoinositides, which had not previously been detected using other techniques. Different phosphoinositide partners, even those with relatively weak binding affinity, could account for the diverse functions of SNXs in vesicular trafficking and protein sorting. Because PLIF is sensitive, semiquantitative, and performed in a high-throughput manner, it may be used to screen for highly specific protein-lipid interaction inhibitors. PMID:27025878
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.
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.
Argudo, David; Bethel, Neville P; Marcoline, Frank V; Grabe, Michael
2016-07-01
Biological membranes deform in response to resident proteins leading to a coupling between membrane shape and protein localization. Additionally, the membrane influences the function of membrane proteins. Here we review contributions to this field from continuum elastic membrane models focusing on the class of models that couple the protein to the membrane. While it has been argued that continuum models cannot reproduce the distortions observed in fully-atomistic molecular dynamics simulations, we suggest that this failure can be overcome by using chemically accurate representations of the protein. We outline our recent advances along these lines with our hybrid continuum-atomistic model, and we show the model is in excellent agreement with fully-atomistic simulations of the nhTMEM16 lipid scramblase. We believe that the speed and accuracy of continuum-atomistic methodologies will make it possible to simulate large scale, slow biological processes, such as membrane morphological changes, that are currently beyond the scope of other computational approaches. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov. PMID:26853937
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).
iTagPlot: an accurate computation and interactive drawing tool for tag density plot
Kim, Sung-Hwan; Ezenwoye, Onyeka; Cho, Hwan-Gue; Robertson, Keith D.; Choi, Jeong-Hyeon
2015-01-01
Motivation: Tag density plots are very important to intuitively reveal biological phenomena from capture-based sequencing data by visualizing the normalized read depth in a region. Results: We have developed iTagPlot to compute tag density across functional features in parallel using multicores and a grid engine and to interactively explore it in a graphical user interface. It allows us to stratify features by defining groups based on biological function and measurement, summary statistics and unsupervised clustering. Availability and implementation: http://sourceforge.net/projects/itagplot/. Contact: jechoi@gru.edu and jeochoi@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25792550
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.
Li, Sicheng; Smith, Daniel G A; Patkowski, Konrad
2015-07-01
We assessed the performance of a large variety of modern density functional theory approaches for the adsorption of carbon dioxide on molecular models of pyridinic N-doped graphene. Specifically, we selected eight polyheterocyclic aromatic compounds ranging from pyridine and pyrazine to 1,6-diazacoronene and investigated their complexes with CO2 for a large range of intermolecular distances and including both in-plane and stacked orientations. The benchmark interaction energies were computed at the complete-basis-set limit MP2 level plus a CCSD(T) coupled-cluster correction in a moderate but carefully selected basis set. Using a set of 96 benchmark CCSD(T)-level interaction energies as a reference, we investigated the accuracy of DFT-based approaches as a function of the density functional, the dispersion correction, the basis set, and the counterpoise correction or lack thereof. While virtually all DFT variants exhibit some deterioration of accuracy for distances slightly shorter than the van der Waals minima, we were able to identify several schemes such as B2PLYP-D3 and M05-2X-D3 whose average errors on the entire benchmark data set are in the 5-10% range. The top DFT performers were subsequently used to investigate the energy profile for a carbon dioxide transition through model N-doped graphene pores. All investigated methods confirmed that the largest, N4H4 pore allows for a barrierless CO2 transition to the other side of a graphene sheet. PMID:26055458
Relativistic point interactions: Approximation by smooth potentials
NASA Astrophysics Data System (ADS)
Hughes, Rhonda J.
1997-06-01
We show that the four-parameter family of one-dimensional relativistic point interactions studied by Benvegnu and Dąbrowski may be approximated in the strong resolvent sense by smooth, local, short-range perturbations of the Dirac Hamiltonian. In addition, we prove that the nonrelativistic limits correspond to the Schrödinger point interactions studied extensively by the author and Paul Chernoff.
NASA Astrophysics Data System (ADS)
Lonardoni, D.; Pederiva, F.; Gandolfi, S.
2014-01-01
Background: An accurate assessment of the hyperon-nucleon interaction is of great interest in view of recent observations of very massive neutron stars. The challenge is to build a realistic interaction that can be used over a wide range of masses and in infinite matter starting from the available experimental data on the binding energy of light hypernuclei. To this end, accurate calculations of the hyperon binding energy in a hypernucleus are necessary. Purpose: We present a quantum Monte Carlo study of Λ and ΛΛ hypernuclei up to A =91. We investigate the contribution of two- and three-body Λ-nucleon forces to the Λ binding energy. Method: Ground state energies are computed solving the Schrödinger equation for nonrelativistic baryons by means of the auxiliary field diffusion Monte Carlo algorithm extended to the hypernuclear sector. Results: We show that a simple adjustment of the parameters of the ΛNN three-body force yields a very good agreement with available experimental data over a wide range of hypernuclear masses. In some cases no experiments have been performed yet, and we give new predictions. Conclusions: The newly fitted ΛNN force properly describes the physics of medium-heavy Λ hypernuclei, correctly reproducing the saturation property of the hyperon separation energy.
Hughes, Timothy J; Kandathil, Shaun M; Popelier, Paul L A
2015-02-01
As intermolecular interactions such as the hydrogen bond are electrostatic in origin, rigorous treatment of this term within force field methodologies should be mandatory. We present a method able of accurately reproducing such interactions for seven van der Waals complexes. It uses atomic multipole moments up to hexadecupole moment mapped to the positions of the nuclear coordinates by the machine learning method kriging. Models were built at three levels of theory: HF/6-31G(**), B3LYP/aug-cc-pVDZ and M06-2X/aug-cc-pVDZ. The quality of the kriging models was measured by their ability to predict the electrostatic interaction energy between atoms in external test examples for which the true energies are known. At all levels of theory, >90% of test cases for small van der Waals complexes were predicted within 1 kJ mol(-1), decreasing to 60-70% of test cases for larger base pair complexes. Models built on moments obtained at B3LYP and M06-2X level generally outperformed those at HF level. For all systems the individual interactions were predicted with a mean unsigned error of less than 1 kJ mol(-1). PMID:24274986
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.
Zou, Lindong; Li, Jun; Wang, Hui; Ma, Jianyi; Guo, Hua
2015-07-16
Full-dimensional quantum dynamics studies of the photodetachment of HCO2(-) and DCO2(-) are reported using a wave-packet method on an accurate global potential energy surface of the neutral HOCO/HCO2 system. The calculated photoelectron spectra reproduced both the positions and widths of the main HCO2 and DCO2 peaks observed in experiment. Specifically, both the (2)A1 and (2)B2 resonance peaks of the neutral radicals were identified in our simulations thanks to the adiabatic PES that captures both the (2)A1 and (2)B2 minima. The narrow widths and isotope effect of the lowest resonances are indicative of tunneling-facilitated predissociation. Furthermore, the dissociation product CO2 was found to be excited in both its symmetric stretching and bending modes, which are coupled via a strong Fermi resonance, but rotationally cold, in good agreement with the recent photoelectron-photodetachment coincidence experiments. PMID:25607218
Peterson, K.A.; Skokov, S.; Bowman, J.M.
1999-10-01
A new, global analytical potential energy surface is constructed for the X&hthinsp;{sup 1}A{sup {prime}} electronic ground state of HOCl that accurately includes the HClO isomer. The potential is obtained by using accurate {ital ab initio} data from a previously published surface [Skokov {ital et al.}, J. Chem. Phys. {bold 109}, 2662 (1998)], as well as a significant number of new data for the HClO region of the surface at the same multireference configuration interaction, complete basis set limit level of theory. Vibrational energy levels and intensities are computed for both HOCl and HClO up to the OH+Cl dissociation limit and above the isomerization barrier. After making only minor adjustments to the {ital ab initio} surface, the errors with respect to experiment for HOCl are generally within a few cm{sup {minus}1} for 22 vibrational levels with the largest error being 26 cm{sup {minus}1}. A total of 813 bound vibrational states are calculated for HOCl. The HClO potential well supports 57 localized states, of which only the first 3 are bound. The strongest dipole transitions for HClO were computed for the fundamentals{emdash}33, 2.9, and 25 km/mol for {nu}{sub 1}, {nu}{sub 2}, and {nu}{sub 3}, respectively. From exact J=1 ro-vibrational calculations, state dependent rotational constants have been calculated for HClO. Lastly, resonance calculations with the new potential demonstrate that the presence of the HClO minimum has a negligible effect on the resonance states of HOCl near the dissociation threshold due to the relatively high and wide isomerization barrier. {copyright} {ital 1999 American Institute of Physics.}
Oyeyemi, Victor B.; Pavone, Michele; Carter, Emily A.
2011-11-03
Quantum chemistry has become one of the most reliable tools for characterizing the thermochemical underpinnings of reactions, such as bond dissociation energies (BDEs). The accurate prediction of these particular properties (BDEs) are challenging for ab initio methods based on perturbative corrections or coupled cluster expansions of the single-determinant Hartree-Fock wave function: the processes of bond breaking and forming are inherently multi-configurational and require an accurate description of non-dynamical electron correlation. To this end, we present a systematic ab initio approach for computing BDEs that is based on three components: (1) multi-reference single and double excitation configuration interaction (MRSDCI) for the electronic energies; (2) a two-parameter scheme for extrapolating MRSDCI energies to the complete basis set limit; and (3) DFT-B3LYP calculations of minimumenergy structures and vibrational frequencies to account for zero point energy and thermal corrections. We validated our methodology against a set of reliable experimental BDE values of C*C and C*H bonds of hydrocarbons. The goal of chemical accuracy is achieved, on average, without applying any empirical corrections to the MRSDCI electronic energies. We then use this composite scheme to make predictions of BDEs in a large number of hydrocarbon molecules for which there are no experimental data, so as to provide needed thermochemical estimates for fuel molecules.
Wake potentials of the ILC Interaction Region
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.
NASA Astrophysics Data System (ADS)
Li, Yong-Qing; Song, Yu-Zhi; Joaquim de Campos Varandas, António
2015-01-01
An accurate single-sheeted double many-body expansion potential energy surface is reported for the title system. It is obtained by using the aug-cc-pVTZ and aug-cc-pVQZ basis sets with extrapolation of the electron correlation energy to the complete basis set limit, plus extrapolation to the complete basis set limit of the complete-active-space self-consistent field energy. The collinear and bending barrier heights of the new global potential energy surface is 2.301 and 1.768 kcal mol-1, in very good agreement with the values of 2.222 and 1.770 kcal mol-1 from the current best potential energy surface. In particular, the new potential energy surface describes well the important van der Waals interactions which is very useful for investigating the dynamics of the title system. Thus, the new potential energy surface can both be recommended for dynamics studies of the F + H2 reaction and as building block for constructing the potential energy surfaces of larger fluorine/hydrogen containing systems. Based on the new potential energy surface, a preliminary theoretical study of the reaction F(2P) + H2 (X1 Σg+) → FH(X1Σ+) + H(2S) has been carried out with the methods of quasi-classical trajectory and quantum mechanical. The results have shown that the new PES is suitable for any kind of dynamics studies. Supplementary material in the form of one pdf file available from the Journal web page at http://dx.doi.org/10.1140/epjd/e2014-50445-3
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.
Xia, Peng; Wang, Zhikai; Liu, Xing; Wu, Bing; Wang, Juncheng; Ward, Tarsha; Zhang, Liangyu; Ding, Xia; Gibbons, Gary; Shi, Yunyu; Yao, Xuebiao
2012-10-01
In eukaryotes, microtubules are essential for cellular plasticity and dynamics. Here we show that P300/CBP-associated factor (PCAF), a kinetochore-associated acetyltransferase, acts as a negative modulator of microtubule stability through acetylation of EB1, a protein that controls the plus ends of microtubules. PCAF acetylates EB1 on K220 and disrupts the stability of a hydrophobic cavity on the dimerized EB1 C terminus, which was previously reported to interact with plus-end tracking proteins (TIPs) containing the SxIP motif. As determined with an EB1 acetyl-K220-specific antibody, K220 acetylation is dramatically increased in mitosis and localized to the spindle microtubule plus ends. Surprisingly, persistent acetylation of EB1 delays metaphase alignment, resulting in impaired checkpoint silencing. Consequently, suppression of Mad2 overrides mitotic arrest induced by persistent EB1 acetylation. Thus, our findings identify dynamic acetylation of EB1 as a molecular mechanism to orchestrate accurate kinetochore-microtubule interactions in mitosis. These results establish a previously uncharacterized regulatory mechanism governing localization of microtubule plus-end tracking proteins and thereby the plasticity and dynamics of cells. PMID:23001180
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.
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.
Song, Y Z; Varandas, A J C
2009-04-01
A single-sheeted potential energy surface is reported for the electronic ground-state of H(2)S by fitting accurate multireference configuration interaction energies calculated using aug-cc-pVTZ and aug-cc-pVQZ basis sets with extrapolation of the electron correlation energy to the complete basis set limit, plus extrapolation to the complete basis set limit of the complete-active-space self-consistent field energy. A switching function formalism has been used to warrant the correct behavior at the H(2)(X (1)Sigma(g) (+))+S((1)D) and SH(X (2)Pi)+H((2)S) dissociation limits. The topographical features of the novel global potential energy surface are examined in detail, with the former being used for exploratory quasiclassical trajectory calculations of the thermal rate constant for the S((1)D)+H(2), S((1)D)+D(2), and S((1)D)+HD reactions at room temperature. A comparison with other available potential energy surfaces as well as kinetics data is also provided. PMID:19355742
NASA Astrophysics Data System (ADS)
Shi, De-Heng; Liu, Yu-Fang; Sun, Jin-Feng; Zhu, Zun-Lue; Yang, Xiang-Dong
2006-12-01
The reasonable dissociation limit of the second excited singlet state B1Π of 7LiH molecule is obtained. The accurate dissociation energy and equilibrium geometry of the B1Π state are calculated using a symmetry-adapted-cluster configuration-interaction method in full active space. The whole potential energy curve for the B1Π state is obtained over the internuclear distance ranging from about 0.10 nm to 0.54 nm, and has a least-square fit to the analytic Murrell-Sorbie function form. The vertical excitation energy is calculated from the ground state to the B1Π state and compared with previous theoretical results. The equilibrium internuclear distance obtained by geometry optimization is found to be quite different from that obtained by single-point energy scanning under the same calculation condition. Based on the analytic potential energy function, the harmonic frequency value of the B1Π state is estimated. A comparison of the theoretical calculations of dissociation energies, equilibrium interatomic distances and the analytic potential energy function with those obtained by previous theoretical results clearly shows that the present work is more comprehensive and in better agreement with experiments than previous theories, thus it is an improvement on previous theories.
Chappelow, Jonathan; Tomaszewski, John E.; Feldman, Michael; Shih, Natalie; Madabhushi, Anant
2011-01-01
We present an interactive program called HistoStitcher© for accurate and rapid reassembly of histology fragments into a pseudo-whole digitized histological section. HistoStitcher© provides both an intuitive graphical interface to assist the operator in performing the stitch of adjacent histology fragments by selecting pairs of anatomical landmarks, and a set of computational routines for determining and applying an optimal linear transformation to generate the stitched image. Reconstruction of whole histological sections from images of slides containing smaller fragments is required in applications where preparation of whole sections of large tissue specimens is not feasible or efficient, and such whole mounts are required to facilitate (a) disease annotation and (b) image registration with radiological images. Unlike manual reassembly of image fragments in a general purpose image editing program (such as Photoshop), HistoStitcher© provides memory efficient operation on high resolution digitized histology images and a highly flexible stitching process capable of producing more accurate results in less time. Further, by parameterizing the series of transformations determined by the stitching process, the stitching parameters can be saved, loaded at a later time, refined, or reapplied to multi-resolution scans, or quickly transmitted to another site. In this paper, we describe in detail the design of HistoStitcher© and the mathematical routines used for calculating the optimal image transformation, and demonstrate its operation for stitching high resolution histology quadrants of a prostate specimen to form a digitally reassembled whole histology section, for 8 different patient studies. To evaluate stitching quality, a 6 point scoring scheme, which assesses the alignment and continuity of anatomical structures important for disease annotation, is employed by three independent expert pathologists. For 6 studies compared with this scheme, reconstructed sections
Multipole expansion in plasmas: Effective interaction potentials between compound particles
NASA Astrophysics Data System (ADS)
Ramazanov, T. S.; Moldabekov, Zh. A.; Gabdullin, M. T.
2016-05-01
In this paper, the multipole expansion method is used to determine effective interaction potentials between particles in both classical dusty plasma and dense quantum plasma. In particular, formulas for interactions of dipole-dipole and charge-dipole pairs in a classical nondegenerate plasma as well as in degenerate quantum and semiclassical plasmas were derived. The potentials describe interactions between atoms, atoms and charged particles, dust particles in the complex plasma, atoms and electrons in the degenerate plasma, and metals. Correctness of the results obtained from the multipole expansion is confirmed by their agreement with the results based on other methods of statistical physics and dielectric response function. It is shown that the method of multipole expansion can be used to derive effective interaction potentials of compound particles, if the effect of the medium on the potential of individual particles comprising compound particles is known.
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.
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
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.
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.
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)
Incidence of potential drug-drug interactions with antidiabetic drugs.
Samardzic, I; Bacic-Vrca, V
2015-06-01
In an effort to achieve normoglycemia more than one antidiabetic agent is usually needed. Diabetes is associated with several comorbidities and patients with diabetes are often treated with multiple medications. Therefore, patients with diabetes are especially exposed to drug-drug interactions (DDIs). The aim of this study was to analyse the incidence and type of potential DDIs of antidiabetic drugs in patients with diabetes. This retrospective study analyzed pharmacy record data of 225 patients with diabetes mellitus. Both type 1 and type 2 diabetic patients who were taking at least one antidiabetic agent during the period of six months were included. We investigated associated therapy in that period in order to identify potential DDIs with antidiabetic therapy. Potential interactions were identified by Lexicomp Lexi-Interat Online (Lexi-Comp, Inc., Hudson, USA) software which categorizes potential DDIs according to clinical significance in five types (A, B, C, D and X). Categories C, D and X are of clinical concern and always require medical attention (therapy monitoring, therapy modification or avoiding combination). We found that 80.9% of patients had at least one potential category C interaction while there were no D and X interactions. Most frequently encountered potential DDI (n = 176) included antidiabetic drugs and thiazide or thiazide like diuretics. Patients with diabetes are exposed to a large number of potential clinically significant DDIs that may require appropriate monitoring. Using databases of DDIs could be helpful in reducing the risk of potential clinically significant DDIs. PMID:26189304
Dense neuron system interacting with the gravitational potential.
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. PMID:26187097
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
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.
Potential drug interactions in an ambulatory geriatric population.
Costa, A J
1991-09-01
Drug interactions are a common cause of iatrogenic disease in geriatric patients. Computer programs now exist which allow one to analyse groups of drugs for potential interactions. In an audit of charts of 100 geriatric patients seen in the Family Practice Center at Barberton Citizens Hospital, a computer printout was obtained, listing all patients aged 60 years and over who were seen at the Center during 1989. Names were selected randomly from this list by the head nurse and their charts were obtained for review, generating information on patient identification number, age, sex, diagnoses, medications, and allergies. The medications were analysed using the Hansten Drug Interaction Knowledge Base Program, which identified 27 patients as being on a combination of medications which had one or more potential drug interactions. A total of 37 potential drug interactions were identified in this group of 27 patients. Relative risk ratios were determined using the computer program, 'Epi Info,' for sex (female versus male), age (greater than or equal to 75 vs. 60-75 years), number of diagnoses greater than or equal to 3 vs. 0-2), and number of medications (greater than or equal to 4 vs. 0-3). The five medications, or groups of medications, which were most likely to be involved in potential drug interactions were digoxin, beta-blockers, oestrogen, oral hypoglycaemic agents, and diuretics. PMID:1822974
Interaction potential between discrete solitons in waveguide arrays.
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
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. PMID:27146097
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^{-}(H_{2}O), X = F, Cl, Br, I, and alkali metal-water, M^{+}(H_{2}O), 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 χ^{2} 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.
Scattering with absorptive interaction: Energy-dependent potentials
NASA Astrophysics Data System (ADS)
Cassing, W.; Stingl, M.; Weiguny, A.
1983-05-01
The energy dependence and analytic structure of the effective interaction for elastic scattering of composite particles are investigated using Feshbach's projection technique. A generalized Levinson theorem is established for complex, nonlocal, and energy-dependent interactions. The analytical results are illustrated by means of Argand diagrams for a solvable model and the effect of energy averaging is discussed. NUCLEAR REACTIONS Scattering theory, S matrix for absorptive, energy-dependent potentials, Levinson theorem.
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
Localization of weakly interacting Bose gas in quasiperiodic potential
NASA Astrophysics Data System (ADS)
Ray, Sayak; Pandey, Mohit; Ghosh, Anandamohan; Sinha, Subhasis
2016-01-01
We study the localization properties of weakly interacting Bose gas in a quasiperiodic potential. The Hamiltonian of the non-interacting system reduces to the well known ‘Aubry-André model’, which shows the localization transition at a critical strength of the potential. In the presence of repulsive interaction we observe multi-site localization and obtain a phase diagram of the dilute Bose gas by computing the superfluid fraction and the inverse participation ratio. We construct a low-dimensional classical Hamiltonian map and show that the onset of localization is manifested by the chaotic phase space dynamics. The level spacing statistics also identify the transition to localized states resembling a Poisson distribution that are ubiquitous for both non-interacting and interacting systems. We also study the quantum fluctuations within the Bogoliubov approximation and compute the quasiparticle energy spectrum. Enhanced quantum fluctuation and multi-site localization phenomenon of non-condensate density are observed above the critical coupling of the potential. We briefly discuss the effect of the trapping potential on the localization of matter wave.
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).
OBSERVATIONAL EVIDENCE FOR DARK MATTER INTERACTING THROUGH A YUKAWA POTENTIAL
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.
NASA Astrophysics Data System (ADS)
Shi, De-Heng; Liu, Yu-Fang; Sun, Jin-Feng; Yang, Xiang-Dong; Zhu, Zun-Lue
2006-05-01
The reasonable dissociation limit of the A1Σ+ state 7LiH molecule is obtained. The accurate dissociation energy and the equilibrium geometry of this state are calculated using a symmetry-adapted-cluster configuration-interaction method in complete active space for the first time. The whole potential energy curve and the dipole moment function for the A1Σ+ state are calculated over a wide internuclear separation range from about 0.1 to 1.4 nm. The calculated equilibrium geometry and dissociation energy of this potential energy curve are of Re=0.2487 nm and De=1.064 eV, respectively. The unusual negative values of the anharmonicity constant and the vibration-rotational coupling constant are of ωeχe=-4.7158cm-1 and αe=-0.08649cm-1, respectively. The vertical excitation energy from the ground to the A1Σ+ state is calculated and the value is of 3.613 eV at 0.15875 nm (the equilibrium position of the ground state). The highly anomalous shape of this potential energy curve, which is exceptionally flat over a wide radial range around the equilibrium position, is discussed in detail. The harmonic frequency value of 502.47cm-1 about this state is approximately estimated. Careful comparison of the theoretical determinations with those obtained by previous theories about the A1Σ+ state dissociation energy clearly shows that the present calculations are much closer to the experiments than previous theories, thus represents an improvement.
Analytical first derivatives of the RE-squared interaction potential
NASA Astrophysics Data System (ADS)
Babadi, M.; Ejtehadi, M. R.; Everaers, R.
2006-12-01
We derive exact expressions for the forces and torques between biaxial molecules interacting via the RE-squared potential, a recent variant of the Gay-Berne potential. Moreover, efficient routines have been provided for rigid body MD simulations, resulting in 1.6 times speedup compared to the two-point finite difference approach. It has also been shown that the time cost of a MD simulation will be almost equal to a similar MC simulation, making use of the provided routines.
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.
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.
Accurate potential energy functions, non-adiabatic and spin-orbit couplings in the ZnH(+) system.
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. PMID:26637984
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.
Effective Electromagnetic Interaction Potential in Flat and Curved Spacetimes
Caicedo, Jose Alexander; Urrutia, Luis F.
2010-07-12
We present a summary of the main steps in the construction of the effective relativistic interaction potential between two charged Dirac particles in the presence of a background weak gravitational field, by extending a procedure previously used for electrodynamics in Minkowski space. We consider the full two-body problem and apply the method to the hydrogen atom.
The Generic Disc: Realizing the Potential of Adaptive, Interactive Videodiscs.
ERIC Educational Resources Information Center
Jonassen, David H.
1984-01-01
Discusses conflict between instructional potential of interactive videodiscs and interests of educational publishers and proposes a generic videodisc as a solution. Generic disc design preferences, equipment needed by teachers to program various learning options to adapt materials to local needs, and a list of videodisc authoring systems are…
Optimizing Interacting Potentials to Form Targeted Materials Structures
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.
Critical temperature of interacting Bose gases in periodic potentials.
Nguyen, T T; Herrmann, A J; Troyer, M; Pilati, S
2014-05-01
The superfluid transition of a repulsive Bose gas in the presence of a sinusoidal potential which represents a simple-cubic optical lattice is investigated using quantum Monte Carlo simulations. At the average filling of one particle per well the critical temperature has a nonmonotonic dependence on the interaction strength, with an initial sharp increase and a rapid suppression at strong interactions in the vicinity of the Mott transition. In an optical lattice the positive shift of the transition is strongly enhanced compared to the homogenous gas. By varying the lattice filling we find a crossover from a regime where the optical lattice has the dominant effect to a regime where interactions dominate and the presence of the lattice potential becomes almost irrelevant. PMID:24836222
Potential social interactions are important to social attention
Laidlaw, Kaitlin E. W.; Foulsham, Tom; Kuhn, Gustav; Kingstone, Alan
2011-01-01
Social attention, or how spatial attention is allocated to biologically relevant stimuli, has typically been studied using simplistic paradigms that do not provide any opportunity for social interaction. To study social attention in a complex setting that affords social interaction, we measured participants’ looking behavior as they were sitting in a waiting room, either in the presence of a confederate posing as another research participant, or in the presence of a videotape of the same confederate. Thus, the potential for social interaction existed only when the confederate was physically present. Although participants frequently looked at the videotaped confederate, they seldom turned toward or looked at the live confederate. Ratings of participants’ social skills correlated with head turns to the live, but not videotaped, confederate. Our results demonstrate the importance of studying social attention within a social context, and suggest that the mere opportunity for social interaction can alter social attention. PMID:21436052
Potential disruption of protein-protein interactions by graphene oxide.
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. PMID:27306022
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.
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}.
Finite-range model potentials for resonant interactions
NASA Astrophysics Data System (ADS)
Deb, Bimalendu
2016-03-01
We show that it is possible to model two-body resonant interactions at low energy with a class of finite-range potentials based on the methods of Jost and Kohn. These potentials are expressed in terms of the effective range r0 and the s-wave scattering length as. We derive continuum solutions of these potentials. By writing V±(r) = V0(r) + V±ɛ(r), where the sign + (‑) refers to positive(negative) scattering length, V0(r) is of the form of Pöschl-Teller potential and V±ɛ is expressed as a power series of the small parameter ɛ = (1 ‑ 2r0 /as)‑1 ‑ 1 when as is large, we derive Green’s function of V0(r). Using the Green’s function, solutions of V±(r) for |as|≫ r0 can be obtained numerically by treating V±ɛ(r) as a perturbation. We describe the threshold behavior of scattering phase shift for V0(r). This study may be important for developing a better understanding of physics of strongly interacting ultracold atomic gases with tunable interactions.
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.
Krause, Pascal; Sonk, Jason A.; Schlegel, H. Bernhard
2014-05-07
Ionization rates of molecules have been modeled with time-dependent configuration interaction simulations using atom centered basis sets and a complex absorbing potential. The simulations agree with accurate grid-based calculations for the ionization of hydrogen atom as a function of field strength and for charge resonance enhanced ionization of H{sub 2}{sup +} as the bond is elongated. Unlike grid-based methods, the present approach can be applied to simulate electron dynamics and ionization in multi-electron polyatomic molecules. Calculations on HCl{sup +} and HCO{sup +} demonstrate that these systems also show charge resonance enhanced ionization as the bonds are stretched.
Interaction potentials and thermodynamic properties of two component semiclassical plasma
Ramazanov, T. S.; Moldabekov, Zh. A.; Ismagambetova, T. N.; Gabdullin, M. T.
2014-01-15
In this paper, the effective interaction potential in two component semiclassical plasma, taking into account the long-range screening and the quantum-mechanical diffraction effects at short distances, is obtained on the basis of dielectric response function method. The structural properties of the semiclassical plasma are considered. The thermodynamic characteristics (the internal energy and the equation of state) are calculated using two methods: the method of effective potentials and the method of micropotentials with screening effect taken into account by the Ornstein-Zernike equation in the HNC approximation.
Effective Interaction Potentials and Physical Properties of Complex Plasmas
Ramazanov, T. S.; Dzhumagulova, K. N.; Gabdullin, M. T.; Omarbakiyeva, Y. A.
2009-11-10
Microscopic, thermodynamic and transport properties of complex plasmas are investigated on the basis of effective potentials of interparticle interaction. These potentials take into account correlation effects and quantum-mechanical diffraction. Plasma composition, thermodynamic functions of hydrogen and helium plasmas are obtained for a wide region of coupling parameter. Collision processes in partially ionized plasma are considered; some kinetic characteristics such as phase shift, scattering cross section, bremsstrahlung cross section and absorption coefficient are investigated. Dynamic and transport properties of dusty plasma are studied by computer simulation method of the Langevin dynamics.
Topological condensate in an interaction-induced gauge potential
NASA Astrophysics Data System (ADS)
Zheng, Jun-hui; Xiong, Bo; JuzeliÅ«nas, Gediminas; Wang, Daw-Wei
2015-07-01
We systematically investigate the ground-state and elementary excitations of a Bose-Einstein condensate within a synthetic vector potential, which is induced by the many-body effects and atom-light coupling. For a sufficiently strong spin-dependent interaction, we find the condensate undergoes a Stoner-type ferromagnetic transition through the self-consistent coupling with the vector potential. For a weak interaction, the critical velocity of a supercurrent is anisotropic due to the density fluctuations affecting the gauge field. We further analytically demonstrate the topological ground state with a coreless vortex ring in a three-dimensional (3D) harmonic trap and a coreless vortex-antivortex pair in a two-dimensional (2D) trap. The circulating persistent current is measurable in the time-of-flight experiment or in the dipolar oscillation through the violation of the Kohn theorem.
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
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
Studying bubble-particle interactions by zeta potential distribution analysis.
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. PMID:25731913
Dybeck, Eric C; Schieber, Natalie P; Shirts, Michael R
2016-08-01
We examine the free energies of three benzene polymorphs as a function of temperature in the point-charge OPLS-AA and GROMOS54A7 potentials as well as the polarizable AMOEBA09 potential. For this system, using a polarizable Hamiltonian instead of the cheaper point-charge potentials is shown to have a significantly smaller effect on the stability at 250 K than on the lattice energy at 0 K. The benzene I polymorph is found to be the most stable crystal structure in all three potentials examined and at all temperatures examined. For each potential, we report the free energies over a range of temperatures and discuss the added value of using full free energy methods over the minimized lattice energy to determine the relative crystal stability at finite temperatures. The free energies in the polarizable Hamiltonian are efficiently calculated using samples collected in a cheaper point-charge potential. The polarizable free energies are estimated from the point-charge trajectories using Boltzmann reweighting with MBAR. The high configuration-space overlap necessary for efficient Boltzmann reweighting is achieved by designing point-charge potentials with intramolecular parameters matching those in the expensive polarizable Hamiltonian. Finally, we compare the computational cost of this indirect reweighted free energy estimate to the cost of simulating directly in the expensive polarizable Hamiltonian. PMID:27341280
A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions
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
Coarse-grained interaction potentials for anisotropic molecules.
Babadi, M; Everaers, R; Ejtehadi, M R
2006-05-01
We have proposed an efficient parametrization method for a recent variant of the Gay Berne potential for dissimilar and biaxial particles [Phys. Rev. E 67, 041710 (2003)] and demonstrated it for a set of small organic molecules. Compared with the previously proposed coarse-grained models, the new potential exhibits a superior performance in close contact and large distant interactions. The repercussions of thermal vibrations and elasticity have been studied through a statistical method. The study justifies that the potential of mean force is representable with the same functional form, extending the application of this coarse-grained description to a broader range of molecules. Moreover, the advantage of employing coarse-grained models over truncated atomistic summations with large distance cutoffs has been briefly studied. PMID:16689591
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.
Modeling interactions of soliton trains. Effects of external potentials
NASA Astrophysics Data System (ADS)
Todorov, M. D.; Gerdjikov, V. S.; Kyuldjiev, A. V.
2014-11-01
The effects of several types of external potentials on the Manakov soliton interactions using the perturbed complex Toda chain (PCTC) model are analyzed. We use three classes of potentials: i) harmonic ii) periodic and iii) combinations of well-type potentials with small depth. In doing this we demonstrate how the potentials can change the asymptotic regimes of the soliton trains. Wide-well external potentials are easier to implement in experiments on Bose-Einstein condensates and can be used to control the soliton motion in a given direction and to achieve a predicted motion of the optical pulse. A general feature of the conducted numerical experiments is that the predictions of both CTC and PCTC match very well with the Manakov model numerics for long-time evolution, often much longer than expected. This means that PCTC is reliable dynamical model for predicting the evolution of the multisoliton solutions of Manakov model in adiabatic approximation. We also compare scalar soliton trains with the Manakov trains with compatible initial parameters.
Yildiz, Dilan; Bozkaya, Uğur
2016-01-30
The extended Koopmans' theorem (EKT) provides a straightforward way to compute ionization potentials and electron affinities from any level of theory. Although it is widely applied to ionization potentials, the EKT approach has not been applied to evaluation of the chemical reactivity. We present the first benchmarking study to investigate the performance of the EKT methods for predictions of chemical potentials (μ) (hence electronegativities), chemical hardnesses (η), and electrophilicity indices (ω). We assess the performance of the EKT approaches for post-Hartree-Fock methods, such as Møller-Plesset perturbation theory, the coupled-electron pair theory, and their orbital-optimized counterparts for the evaluation of the chemical reactivity. Especially, results of the orbital-optimized coupled-electron pair theory method (with the aug-cc-pVQZ basis set) for predictions of the chemical reactivity are very promising; the corresponding mean absolute errors are 0.16, 0.28, and 0.09 eV for μ, η, and ω, respectively. PMID:26458329
Potential food-drug interactions in patients with rheumatoid arthritis.
Masuko, Kayo; Tohma, Shigeto; Matsui, Toshihiro
2013-04-01
Various medications are used for the treatment of rheumatoid arthritis (RA). Food-drug interactions may occur with concomitant ingestion of particular food. For example, methotrexate (MTX), the anchor drug in the therapeutic strategy against RA, is an antifolate agent. Excessive presence or absence of dietary folic acid may regulate MTX metabolism, possibly leading to unexpected adverse reactions. In this review, we focus on MTX, isoniazide and calcineurin inhibitors, and the implications of potential food-drug reactions in rheumatology, suggesting the important role of nutritional evaluations in RA patients. PMID:23773634
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.
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
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}.
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.
Positive fitness consequences of interspecific interaction with a potential competitor.
Forsman, J T; Seppänen, J -T; Mönkkönen, M
2002-01-01
The coexistence of species sharing mutual resources is usually thought to be limited by negative processes such as interspecific competition. This is because an overlap in resource use leads to negative fitness consequences, and traits favouring avoidance of potential competitors, for example in habitat selection, are therefore selected for. However, species interactions are acknowledged to vary from negative (competition) to mutualism, although empirical evidence for positive interspecific interactions from natural communities of other than plants and sessile animals is scarce. Here, we experimentally examined the habitat selection and its fitness consequences of a migrant bird, the pied flycatcher (Ficedula hypoleuca), in relation to the presence of competitively superior birds, resident titmice (Parus spp.). Experiments were conducted on two spatial scales: landscape and nest-site scale. We demonstrate that pied flycatchers were attracted to and accrued fitness benefits from the presence of titmice. Flycatchers breeding in tight association with titmice initiated breeding earlier, had larger broods and heavier young than solitarily breeding flycatchers. This paradoxical result indicates that species interactions may switch from negative to positive and that the coexistence of species is not always restricted by negative costs caused by other species. PMID:12184832
Gallandi, Lukas; Marom, Noa; Rinke, Patrick; Körzdörfer, Thomas
2016-02-01
The performance of non-empirically tuned long-range corrected hybrid functionals for the prediction of vertical ionization potentials (IPs) and electron affinities (EAs) is assessed for a set of 24 organic acceptor molecules. Basis set-extrapolated coupled cluster singles, doubles, and perturbative triples [CCSD(T)] calculations serve as a reference for this study. Compared to standard exchange-correlation functionals, tuned long-range corrected hybrid functionals produce highly reliable results for vertical IPs and EAs, yielding mean absolute errors on par with computationally more demanding GW calculations. In particular, it is demonstrated that long-range corrected hybrid functionals serve as ideal starting points for non-self-consistent GW calculations. PMID:26731340
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.
NASA Astrophysics Data System (ADS)
van de Bovenkamp, J.; van Mourik, T.; van Duijneveldt, F. B.
A multi-reference configuration interaction (MRCI) method is described, which is devised for the calculation of interaction energies of van der Waals complexes and applied to calculating the HeNe potential energy curve. The MRCI calculations make use of a generalized Poplecorrection in order to account for the lack of size consistency. The orbital space is partitioned into three subspaces: the first active space (AS1), which contains the strongly occupied orbitals; the second active space (AS2), which contains the main intra-correlating orbitals; and the external space (ES). It is shown that, to keep the error below 0.2K in the excitation scheme and the active orbital space it is sufficient to include only sigma-orbitals in AS2 and to use an excitation scheme (labelled Qq-MRCI) that encompasses only up to quadruply excited configurations. The final active orbital space (AS2) turned out to be 2s(He), 2psigma(He), 3s(Ne), 3psigma(Ne) and 3dsigma(Ne). Other MRCI variants, in which most or all quadruply excited configurations were deleted from the CI expansion (Qt- and Tt-MRCI), were found to be inadequate. Using the Qq-MRCI scheme together with a 197-orbital 'interaction optimized' basis set (IO197), the MRCI interaction energy at R = 5.7 a0 was calculated to be-21.12K. The corresponding values at the MP4 and CCSD(T) levels of theory are-20.06K and-20.99K, respectively, indicating that the MP4 method is inappropriate for highly accurate calculations on this system. Fitting the calculated data using a generalized Morse function, including an additional C6/R6 term to account for a correct long-range behaviour of the potential, the MRCI well depth was calculated to be-21.16K at Req = 5.73 a0. The MRCI and CCSD(T) potentials have the same quality and are found to be in good agreement with the HartreeFock dispersion (HFD-B) potential of Keil, M., Danielson, L. J., and Dunlop, P. J., 1991, J. Chem. Phys., 94, 296. It is concluded that, for basis IO197, the CCSD(T) method is
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.
Tanzer, Dylan; Smith, Karen; Tanzer, Michael
2015-07-01
The American Academy of Orthopaedic Surgeons (AAOS) disclosure policy is designed to ensure that members involved in education or policy development remain free of outside influence. Although mandatory for these members, it is voluntary for the rest of the AAOS membership. To determine surgeon compliance with disclosure policy, we conducted a study in which we compared surgeon-consultants' disclosures as posted on 6 major orthopedic companies' websites in 2011 with those surgeons' disclosures as listed in AAOS disclosure program records. We found that 549 AAOS members were identified by at least 1 company as having received consulting payments. Overall, 44% of AAOS members did not comply with disclosure policy, or their information was not available on the AAOS website (range, 37%-61%). This study demonstrated that AAOS's policy of mandatory disclosure for select members and voluntary disclosure for all other members is ineffective. The AAOS disclosure program and the potential consequences of noncompliance need to be reevaluated by the organization if it wants its program to succeed. PMID:26161764
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.
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.
Liu, Tianhui; Zhang, Zhaojun; Fu, Bina; Yang, Xueming; Zhang, Dong H
2016-03-16
The mode-specific dynamics for the dissociative chemisorption of H2O on Cu(111) is first investigated by seven-dimensional quantum dynamics calculations, based on an accurately fitted potential energy surface (PES) recently developed by neural network fitting to DFT energy points. It is indicated that excitations in all three vibrational modes have a significant impact on reactivity, which are more efficacious than increasing the translational energy in promoting the reaction, with the largest enhancement for the excitation in the asymmetric stretching mode. There is large discrepancy between the six-dimensional reactivities with fixed azimuthal angles and seven-dimensional results, revealing that the 6D "flat surface" model cannot accurately characterize the reaction dynamics. The azimuthal angle-averaging approach is validated for vibrational excited states of the reactant, where the 7D mode-specific probability can be well reproduced by averaging the 6D azimuthal angle-fixed probabilities over 18 angles. PMID:26941197
NASA Astrophysics Data System (ADS)
Kosemura, Daisuke; Yamamoto, Shotaro; Takeuchi, Kazuma; Usuda, Koji; Ogura, Atsushi
2016-02-01
The phonon deformation potentials (PDPs), p and q, of Si1-xGex with the whole range of the Ge concentration x were examined in detail in pursuit of accurate strain measurements by Raman spectroscopy. An oil-immersion Raman technique was adopted to extract the PDPs of Si1-xGex, in which a complex sample preparation process or a stress-introduction device is not necessary. The strain-shift coefficients bLO and bTO, which can be calculated using the obtained PDPs, were compared with the values in the literature, and we suggested which values were best for application to accurate strain measurements. Ab initio calculation was also performed to understand the behavior of the PDPs throughout the whole range of x in Si1-xGex.
Mineral-microbe interactions: biotechnological potential of bioweathering.
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
Potential interactions among linguistic, autonomic, and motor factors in speech.
Kleinow, Jennifer; Smith, Anne
2006-05-01
Though anecdotal reports link certain speech disorders to increases in autonomic arousal, few studies have described the relationship between arousal and speech processes. Additionally, it is unclear how increases in arousal may interact with other cognitive-linguistic processes to affect speech motor control. In this experiment we examine potential interactions between autonomic arousal, linguistic processing, and speech motor coordination in adults and children. Autonomic responses (heart rate, finger pulse volume, tonic skin conductance, and phasic skin conductance) were recorded simultaneously with upper and lower lip movements during speech. The lip aperture variability (LA variability index) across multiple repetitions of sentences that varied in length and syntactic complexity was calculated under low- and high-arousal conditions. High arousal conditions were elicited by performance of the Stroop color word task. Children had significantly higher lip aperture variability index values across all speaking tasks, indicating more variable speech motor coordination. Increases in syntactic complexity and utterance length were associated with increases in speech motor coordination variability in both speaker groups. There was a significant effect of Stroop task, which produced increases in autonomic arousal and increased speech motor variability in both adults and children. These results provide novel evidence that high arousal levels can influence speech motor control in both adults and children. PMID:16617462
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
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.
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.
Isolating the non-polar contributions to the intermolecular potential for water-alkane interactions
NASA Astrophysics Data System (ADS)
Ballal, Deepti; Venkataraman, Pradeep; Fouad, Wael A.; Cox, Kenneth R.; Chapman, Walter G.
2014-08-01
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 ɛW/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—ɛW/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.
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.
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 IP_{3} through IP_{6}.
Polarizable intermolecular potentials for water and benzene interacting with halide and metal ions
Archambault, Fabien; Soteras, Ignacio; Luque, F. Javier; Schulten, Klaus
2010-01-01
A complete derivation of polarizable intermolecular potentials based on high-level, gas-phase quantum-mechanical calculations is proposed. The importance of appreciable accuracy together with inherent simplicity represents a significant endeavor when enhancement of existing force fields for biological systems is sought. Toward this end, symmetry-adapted perturbation theory (SAPT) can provide an expansion of the total interaction energy into physically meaningful e.g. electrostatic, induction and van der Waals terms. Each contribution can be readily compared with its counterpart in classical force fields. Since the complexity of the different intermolecular terms cannot be fully embraced using a minimalist description, it is necessary to resort to polyvalent expressions capable of encapsulating overlooked contributions from the quantum-mechanical expansion. This choice results in consistent force field components that reflect the underlying physical principles of the phenomena. This simplified potential energy function is detailed and definitive guidelines are drawn. As a proof of concept, the methodology is illustrated through a series of test cases that include the interaction of water and benzene with halide and metal ions. In each case considered, the total energy is reproduced accurately over a range of biologically relevant distances. PMID:21113276
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
An enhanced Immersed Structural Potential Method for fluid-structure interaction
NASA Astrophysics Data System (ADS)
Gil, A. J.; Arranz Carreño, A.; Bonet, J.; Hassan, O.
2013-10-01
Within the group of immersed boundary methods employed for the numerical simulation of fluid-structure interaction problems, the Immersed Structural Potential Method (ISPM) was recently introduced (Gil et al., 2010) [1] in order to overcome some of the shortcomings of existing immersed methodologies. In the ISPM, an incompressible immersed solid is modelled as a deviatoric strain energy functional whose spatial gradient defines a fluid-structure interaction force field in the Navier-Stokes equations used to resolve the underlying incompressible Newtonian viscous fluid. In this paper, two enhancements of the methodology are presented. First, the introduction of a new family of spline-based kernel functions for the transfer of information between both physics. In contrast to classical IBM kernels, these new kernels are shown not to introduce spurious oscillations in the solution. Second, the use of tensorised Gaussian quadrature rules that allow for accurate and efficient numerical integration of the immersed structural potential. A series of numerical examples will be presented in order to demonstrate the capabilities of the enhanced methodology and to draw some key comparisons against other existing immersed methodologies in terms of accuracy, preservation of the incompressibility constraint and computational speed.
Commercially available interactive video games in burn rehabilitation: therapeutic potential.
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. PMID:22385641
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.
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
Li, Jun; Guo, Hua
2015-12-14
A globally accurate full-dimensional potential energy surface (PES) for the OH + CH4 → H2O + CH3 reaction is developed using the permutation invariant polynomial-neural network approach based on ∼135,000 points at the level of correlated coupled cluster singles, doubles, and perturbative triples level with the augmented correlation consistent polarized valence triple-zeta basis set. The total root mean square fitting error is only 3.9 meV or 0.09 kcal/mol. This PES is shown to reproduce energies, geometries, and harmonic frequencies of stationary points along the reaction path. Kinetic and dynamical calculations on the PES indicated a good agreement with the available experimental data. PMID:26671351
NASA Astrophysics Data System (ADS)
Li, Jun; Guo, Hua
2015-12-01
A globally accurate full-dimensional potential energy surface (PES) for the OH + CH4 → H2O + CH3 reaction is developed using the permutation invariant polynomial-neural network approach based on ˜135 000 points at the level of correlated coupled cluster singles, doubles, and perturbative triples level with the augmented correlation consistent polarized valence triple-zeta basis set. The total root mean square fitting error is only 3.9 meV or 0.09 kcal/mol. This PES is shown to reproduce energies, geometries, and harmonic frequencies of stationary points along the reaction path. Kinetic and dynamical calculations on the PES indicated a good agreement with the available experimental data.
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((2)D) + H2 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((2)D)+H2(X(1)Σg (+))(ν=0,j=0)→NH(a(1)Δ)+H((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. PMID:24160511
NASA Astrophysics Data System (ADS)
Li, Y. Q.; Ma, F. C.; Sun, M. T.
2013-10-01
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(2D) + H2 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(^2D)+H_2(X^1Σ _g^+)(ν =0,j=0)rArr NH(a^1Δ )+H(^2S) 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.
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.
Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions.
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
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.
Li, Yongqing; Yuan, Jiuchuang; Chen, Maodu; Ma, Fengcai; Sun, Mengtao
2013-07-15
An accurate single-sheeted double many-body expansion potential energy surface is reported for the title system. A switching function formalism has been used to warrant the correct behavior at the H2(X1Σg+)+N(2D) and NH (X3Σ-)+H(2S) dissociation channels involving nitrogen in the ground N(4S) and first excited N(2D) states. The topographical features of the novel 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. The novel surface can be using to treat well the Renner-Teller degeneracy of the 12A″ and 12A' states of NH 2. Such a work can both be recommended for dynamics studies of the N(2D)+H2 reaction and as building blocks for constructing the double many-body expansion potential energy surface of larger nitrogen/hydrogen-containing systems. In turn, a test theoretical study of the reaction N(2D)+H2(X1Σg+)(ν=0,j=0)→NH (X3Σ-)+H(2S) has been carried out with the method of quantum wave packet on the new potential energy surface. Reaction probabilities, integral cross sections, and differential cross sections have been calculated. Threshold exists because of the energy barrier (68.5 meV) along the minimum energy path. On the curve of reaction probability for total angular momentum J = 0, there are two sharp peaks just above threshold. The value of integral cross section increases quickly from zero to maximum with the increase of collision energy, and then stays stable with small oscillations. The differential cross section result shows that the reaction is a typical forward and backward scatter in agreement with experimental measurement result. PMID:23666848
Jiang, Bin; Hu, Xixi; Lin, Sen; Xie, Daiqian; Guo, Hua
2015-09-28
Cobalt is a widely used catalyst for many heterogeneous reactions, including the Fischer-Tropsch (FT) process, which converts syngas (H2 and CO) to higher hydrocarbons. As a result, a better understanding of the key chemical steps on the Co surface, such as the dissociative chemisorption of H2 as an initial step of the FT process, is of fundamental importance. Here, we report an accurate full-dimensional global potential energy surface for the dissociative chemisorption of H2 on the rigid Co(0001) surface constructed from more than 3000 density functional theory points. The high-fidelity potential energy surface was obtained using the permutation invariant polynomial-neural network method, which preserves both the permutation symmetry of H2 and translational symmetry of the Co(0001) surface. The reaction path features a very low barrier on the top site. Full-dimensional quantum dynamical calculations provide insights into the dissociation dynamics and influence of the initial vibrational, rotational, and orientational degrees of freedom. PMID:26286861
Bytautas, Laimutis; Matsunaga, Nikita; Ruedenberg, Klaus
2010-02-21
In the first paper of this series, a very accurate ab initio potential energy curve of the (3)Sigma(g)(-) ground state of O(2) has been determined in the approximation that all valence shell electron correlations were calculated at the complete basis set limit. In the present study, the corrections arising from core electron correlations and relativity effects, viz., spin-orbit coupling and scalar relativity, are determined and added to the potential energy curve. From the 24 points calculated on this curve, an analytical expression in terms of even-tempered Gaussian functions is determined and, from it, the vibrational and rotational energy levels are calculated by means of the discrete variable representation. We find 42 vibrational levels. Experimental data (from the Schumann-Runge band system) only yield the lowest 36 levels due to significant reduction in the transition intensities of higher levels. For the 35 term values G(v), the mean absolute deviation between theoretical and experimental data is 12.8 cm(-1). The dissociation energy with respect to the lowest vibrational energy is calculated within 25 cm(-1) of the experimental value of 41,268.2+/-3 cm(-1). The theoretical crossing between the (3)Sigma(g)(-) state and the (1)Sigma(g)(+) state is found to occur at 2.22 A and the spin-orbit coupling in this region is analyzed. PMID:20170227
Exploring the potential of algae/bacteria interactions.
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. PMID:25744715
Cardoen, Wim; Gdanitz, Robert J
2005-07-01
We compute the potential-energy curve of the hydrogen fluoride molecule (HF) using a novel variant of the explicitly correlated multireference averaged coupled-pair functional method with a carefully selected basis set and reference space. After correcting for scalar relativistic effects and spin-orbit coupling, the potential is used to compute the dissociation energy, the equilibrium bond distance, the harmonic frequency, the anharmonicity, and the vibrational levels up to the dissociation limit. The errors in the equilibrium geometry constants compare favorably with the most elaborate (single reference) calculations of the literature. Starting at the region of RA/angstroms approximately 2,...,3, where the covalent HF bond begins to break and where single-reference methods become impractical, our potential begins to slightly underestimate the atomic interaction, which is reflected in an estimated error in the well depth of -0.2 kcal/mol. PMID:16050742
NASA Astrophysics Data System (ADS)
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 collision energy
NASA Astrophysics Data System (ADS)
Bartolomei, Massimiliano; Carmona-Novillo, Estela; Hernández, Marta I.; Campos-Martínez, José; Hernandez-Lamoneda, Ramón
2008-06-01
A new potential energy surface (PES) for the quintet state of rigid O2(3Σg-)+O2(3Σg-) has been obtained using restricted coupled-cluster theory with singles, doubles, and perturbative triple excitations [RCCSD(T)]. A large number of relative orientations of the monomers (65) and intermolecular distances (17) have been considered. A spherical harmonic expansion of the interaction potential has been built from the ab initio data. It involves 29 terms, as a consequence of the large anisotropy of the interaction. The spherically averaged term agrees quite well with the one obtained from analysis of total integral cross sections. The absolute minimum of the PES corresponds to the crossed (D2d) structure (X shape) with an intermolecular distance of 6.224 bohrs and a well depth of 16.27 meV. Interestingly, the PES presents another (local) minimum close in energy (15.66 meV) at 6.50 bohrs and within a planar skewed geometry (S shape). We find that the origin of this second structure is due to the orientational dependence of the spin-exchange interactions which break the spin degeneracy and leads to three distinct intermolecular PESs with singlet, triplet, and quintet multiplicities. The lowest vibrational bound states of the O2-O2 dimer have been obtained and it is found that they reflect the above mentioned topological features of the PES: The first allowed bound state for the 16O isotope has an X structure but the next state is just 0.12 meV higher in energy and exhibits an S shape.
McLaughlin, Keith; Cioce, Christian R; Belof, Jonathan L; Space, Brian; Space, Brian B
2012-05-21
A highly accurate aniostropic intermolecular potential for diatomic hydrogen has been developed that is transferable for molecular modeling in heterogeneous systems. The potential surface is designed to be efficacious in modeling mixed sorbates in metal-organic materials that include sorption interactions with charged interfaces and open metal sites. The potential parameters are compatible for mixed simulations but still maintain high accuracy while deriving dispersion parameters from a proven polarizability model. The potential includes essential physical interactions including: short-range repulsions, dispersion, and permanent and induced electrostatics. Many-body polarization is introduced via a point-atomic polarizability model that is also extended to account for many-body van der Waals interactions in a consistent fashion. Permanent electrostatics are incorporated using point partial charges on atomic sites. However, contrary to expectation, the best potentials are obtained by permitting the charges to take on values that do not reproduce the first non-vanishing moment of the electrostatic potential surface, i.e., the quadrupole moment. Potential parameters are fit to match ab initio energies for a representative range of dimer geometries. The resulting potential is shown to be highly effective by comparing to electronic structure calculations for a thermal distribution of trimer geometries, and by reproducing experimental bulk pressure-density isotherms. The surface is shown to be superior to other similarly portable potential choices even in tests on homogeneous systems without strong polarizing fields. The present streamlined approach to developing such potentials allows for a simple adaptation to other molecules amenable to investigation by high-level electronic structure methods. PMID:22612090
Woon, D.E. )
1994-02-15
Dimer interactions of helium, neon, and argon have been studied using the augmented correlation consistent basis sets of Dunning and co-workers. Two correlation methods have been employed throughout; Moller--Plesset perturbation theory through fourth-order (MP4) and single and double excitation coupled-cluster theory with perturbative treatment of triple excitations [CCSD(T)]. Full configuration interaction (FCI) calculations were performed on He[sub 2] for some basis sets. In general, only valence electrons were correlated, although some calculations which also correlated the [ital n]=2 shell of Ar[sub 2] were performed. Dimer potential energy curves were determined using the supermolecule method with and without the counterpoise correction. A series of additional basis sets beyond the augmented correlation consistent sets were explored in which the diffuse region of the radial function space has been systematically saturated. In combination with the systematic expansion across angular function space which is inherent to the correlation consistent prescription, this approach guarantees very accurate atomic polarizabilities and hyperpolarizabilities and should lead to an accurate description of dispersion forces. The best counterpoise-corrected MP4 values for the well depths of the three dimers are (in microhartrees, empirical values in parentheses) He[sub 2], 31.9 (34.6); Ne[sub 2], 123 (134); and Ar[sub 2], 430 (454). The corresponding CCSD(T) values are He[sub 2], 33.1; Ne[sub 2], 128; and Ar[sub 2], 417. Although these values are very good, the nearly exponential convergence of well depth as a function of basis quality afforded by using the various series of correlation consistent basis sets allows estimation of complete basis set (CBS) limiting values. The MP4 estimated CBS limits are He[sub 2], 32.2; Ne[sub 2], 126; and Ar[sub 2], 447.
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…
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...
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
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.
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
Effective Semi-empirical Interaction Potential for Dusty Particles
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.
Solubility of methane in water: the significance of the methane-water interaction potential.
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
Confining Potential from Interacting Magnetic and Torsion Fields
NASA Astrophysics Data System (ADS)
Gaete, Patricio; Helaÿel-Neto, José A.
Adopting the gauge-invariant but path-dependent variables formalism, we study the coupling of torsion fields with photons in the presence of an external background electromagnetic. We explicitly show that, in the case of a constant electric field strength expectation value, the static potential remains Coulombic, while in the case of a constant magnetic field strength expectation value a confining potential is obtained. This result displays a marked qualitative departure from the usual coupling of axionlike particles with photons in the presence of an external magnetic field.
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. PMID:26560189
Calculation of interaction-induced spectra using complex absorbing potentials
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.
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.
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.
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.
Copper interaction on the long-term potentiation.
Leiva, J; Gaete, P; Palestini, M
2003-10-01
The role of copper on the CA1 piramidal neurons and their sinaptic connections to the Schaffer's collateral was investigated using the field excitatory post-sinaptic potential (fEPSP). The same fEPSP was used to study copper effects on Long-term potentiation (LTP). We have found that copper 10 microM has an inhibitory action on the fEPSP. Similar effects were demonstrated with 10 microM of GABA. Moreover, copper showed a strong inhibitory action on the consolidated LTP. However, copper washout left a significant and persistent excitatory response. In our opinion, copper shows a dual sinaptic effect depending on the sinaptic experience. PMID:14502829
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.
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.
Renormalized interaction of relativistic bosons with delta function potentials
Dogan, Caglar; Turgut, O. Teoman
2010-08-15
We study the interaction of mutually noninteracting Klein-Gordon particles with localized sources on stochastically complete Riemannian surfaces. This asymptotically free theory requires regularization and coupling constant renormalization. Renormalization is performed nonperturbatively using the orthofermion algebra technique and the principal operator {Phi} is found. The principal operator is then used to obtain the bound state spectrum, in terms of binding energies to single Dirac-delta function centers. The heat kernel method allows us to generalize this procedure to compact and Cartan-Hadamard type Riemannian manifolds. We make use of upper and lower bounds on the heat kernel to constrain the ground state energy from below, thus confirming that our neglect of pair creation is justified for certain ranges of parameters in the problem.
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
Réal, Florent; Trumm, Michael; Schimmelpfennig, Bernd; Masella, Michel; Vallet, Valérie
2013-04-01
Pursuing our efforts on the development of accurate classical models to simulate radionuclides in complex environments (Réal et al., J. Phys. Chem. A 2010, 114, 15913; Trumm et al. J. Chem. Phys. 2012, 136, 044509), this article places a large emphasis on the discussion of the influence of models/parameters uncertainties on the computed structural, dynamical, and temporal properties. Two actinide test cases, trivalent curium and tetravalent thorium, have been studied with three different potential energy functions, which allow us to account for the polarization and charge-transfer effects occurring in hydrated actinide ion systems. The first type of models considers only an additive energy term for modeling ion/water charge-transfer effects, whereas the other two treat cooperative charge-transfer interactions with two different analytical expressions. Model parameters are assigned to reproduce high-level ab initio data concerning only hydrated ion species in gas phase. For the two types of cooperative charge-transfer models, we define two sets of parameters allowing or not to cancel out possible errors inherent to the force field used to model water/water interactions at the ion vicinity. We define thus five different models to characterize the solvation of each ion. For both ions, our cooperative charge-transfer models lead to close results in terms of structure in solution: the coordination number is included within 8 and 9, and the mean ion/water oxygen distances are 2.45 and 2.49 Å, respectively, for Th(IV) and Cm(III). PMID:23233426
Quasielastic nucleon transfer and the heavy-ion interaction potential
van den Berg, A.M.; Henning, W.; Lee L.L. Jr.; Lesko, K.T.; Rehm, K.E.; Schiffer, J.P.; Stephans, G.S.F.; Wolfs, F.L.H.; Freeman, W.S.
1986-02-10
Quasielastic nucleon-transfer cross sections have been mea- sured at energies roughly-equal35% above the Coulomb barrier for /sup 58,64/Ni + /sup 112,116,120,124/Sn. The systematic trends were studied over the range of systems, which span a factor of 2 in neutron excess N-Z. The observed magnitude of the cross sections and their surface localization suggest that quasielastic processes play an important role in the average nucleus-nucleus potential, a quantity of considerable recent interest in near-barrier collisions of heavy systems.
Carra, Claudio; Cucinotta, Francis A
2012-06-01
The eukaryotic replication protein A (RPA) has several pivotal functions in the cell metabolism, such as chromosomal replication, prevention of hairpin formation, DNA repair and recombination, and signaling after DNA damage. Moreover, RPA seems to have a crucial role in organizing the sequential assembly of DNA processing proteins along single stranded DNA (ssDNA). The strong RPA affinity for ssDNA, K(A) between 10(-9)-10(-10) M, is characterized by a low cooperativity with minor variation for changes on the nucleotide sequence. Recently, new data on RPA interactions was reported, including the binding free energy of the complex RPA70AB with dC(8) and dC(5), which has been estimated to be -10 ± 0.4 kcal mol(-1) and -7 ± 1 kcal mol(-1), respectively. In view of these results we performed a study based on molecular dynamics aimed to reproduce the absolute binding free energy of RPA70AB with the dC(5) and dC(8) oligonucleotides. We used several tools to analyze the binding free energy, rigidity, and time evolution of the complex. The results obtained by MM-PBSA method, with the use of ligand free geometry as a reference for the receptor in the separate trajectory approach, are in excellent agreement with the experimental data, with ±4 kcal mol(-1) error. This result shows that the MM-PB(GB)SA methods can provide accurate quantitative estimates of the binding free energy for interacting complexes when appropriate geometries are used for the receptor, ligand and complex. The decomposition of the MM-GBSA energy for each residue in the receptor allowed us to correlate the change of the affinity of the mutated protein with the ΔG(gas+sol) contribution of the residue considered in the mutation. The agreement with experiment is optimal and a strong change in the binding free energy can be considered as the dominant factor in the loss for the binding affinity resulting from mutation. PMID:22116609
Correlations between potentials and observables in the NN interaction
NASA Astrophysics Data System (ADS)
Pauss, F.; Mathelitsch, L.; Côté, J.; Lacombe, M.; Loiseau, B.; Vinh Mau, R.
1981-08-01
We study the effects of the components of the soft-core and velocity-dependent Paris nucleon-nucleon potential on the scattering observables for laboratory energies, TL, between 10 and 350 MeV. Knowledge of these correlations is useful to indicate constraints on components of the nucléon-nucléon force. The velocity-dependent component, attractive at low energy and repulsive at high energy, plays a role at all energies. The polarisation P, the depolarisation D and the parameters Dt, A, R, CKP and CNN are good tests for the tensor, spin-orbit and, to a smaller extent, quadratic spin-orbit forces. The isovector tensor force contribution is important at low energy and that of the isovector spin-orbit at high energy. The isoscalar tensor force effect is large at all energies and that of the isoscalar spin-orbit force rather small. The potential without quadratic spin-orbit term reproduces well the experimental data for TL < 150 MeV.
Pharmacological potential of biogenic amine–polyamine interactions beyond neurotransmission
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
Severe potential drug-drug interactions in older adults with dementia and associated factors
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
Dactinomycin potentiation of radiation pneumonitis: A forgotten interaction
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.
Evaluation of a potential clinical interaction between ceftriaxone and calcium.
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
2010-04-01
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
Orchid–pollinator interactions and potential vulnerability to biological invasion
Chupp, Adam D.; Battaglia, Loretta L.; Schauber, Eric M.; Sipes, Sedonia D.
2015-01-01
an indirect threat to plant–pollinator interactions. PMID:26286221
Orchid-pollinator interactions and potential vulnerability to biological invasion.
Chupp, Adam D; Battaglia, Loretta L; Schauber, Eric M; Sipes, Sedonia D
2015-01-01
an indirect threat to plant-pollinator interactions. PMID:26286221
Evaluation of a Potential Clinical Interaction between Ceftriaxone and Calcium▿
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
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.
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.
NASA Astrophysics Data System (ADS)
B. Araujo, Rafael; S. de Almeida, J.; Ferreira da Silva, A.; Ahuja, Rajeev
2015-09-01
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 LiFePO4 and FePO4 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 LiFePO4 and FePO4. However, it does not appear to have the same efficiency for evaluating the redox reaction energies for the investigated system.
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
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
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
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
On the theory of interaction potentials in ionic crystals
NASA Astrophysics Data System (ADS)
Acevedo, Roberto; Soto-Bubert, Andrés
2008-11-01
The aim of this research work is to report a more comprehensive and detailed study of both, the intermolecular and intramolecular potencial functions with reference to the various families of the elpasolite type crystals. The cohesive energy has been thought as a sum of three terms; the long range (Coulombic), the Born and the van der Waals contributions to the total energy. The Born-Mayer-Buckingham potential1 has been employed in all of these current studies and a number of convergence tests are analyzed from a formal viewpoint. Our work has been focused to the following systems: Cs2NaLnF6, Cs2NaLnCl6, Cs2NaLnBr6, Rb2NaLnF6 and Cs2KLnF6 in the Fm3m space group. A substantial amount of theoretical models have been analyzed and several computing simulations have been undertaken to estimate the reticular energies and the corresponding heat of formation for these crystals. To achieve this goal, a Born-Haber thermodynamic cycle has been introduced in our model. It is shown that the calculated energy values are reasonable and follow the expected trend along the lanthanide series in the periodic chart. We also discuss the advantages and disadvantages of the current and proposed generalized model. The most likely sources for improvement are discussed in detail. New convergence tests as well as some master equations have been introduced to study the various diagonal contributions to the total energy.
Effective potentials in concentrated colloid-polymer mixtures with competing interactions
NASA Astrophysics Data System (ADS)
Laurati, Marco; Valadez Perez, Nestor; Capellmann, Ronja; Egelhaaf, Stefan; Castañeda-Priego, Ramon
We determine the effective potentials describing the interactions between colloidal particles in concentrated colloid-polymer mixtures in which depletion attraction competes with electrostatic repulsion. To obtain the potentials, the method of Monte-Carlo inversion is applied to experimental pair distribution functions obtained by confocal microscopy. Both fluid and gel states are investigated. We compare the results of the inversion method with those obtained by describing the interactions using a combination of a square well potential for the attractive component and a Yukawa potential for the repulsive component. This allows us to test the validity range of the one-component pair-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.
Comment on determination of the interaction potential between Ar and HCl
NASA Technical Reports Server (NTRS)
Green, S.
1974-01-01
To test the accuracy of the Gordon-Kim theory of intermolecular forces, predicted and experimental values are compared for Ar-HCl. The method appears to accurately predict the short-range repulsive forces and also the position (but possibly not the depth) of the potential well.
Pigment Spectra and Intermolecular Interaction Potentials in Glasses and Proteins
Renge, I.; van Grondelle, R.; Dekker, J. P.
2007-01-01
A model is proposed for chromophore optical spectra in solids over a wide range of temperatures and pressures. Inhomogeneous band shapes and their pressure dependence, as well as baric shift coefficients of spectral lines, selected by the frequency, were derived using Lennard-Jones potentials of the ground and excited states. Quadratic electron-phonon coupling constants, describing the thermal shift and broadening of zero-phonon lines, were also calculated. Experimentally, thermal shift and broadening of spectral holes were studied between 5 and 40 K for a synthetic pigment, chlorin, embedded in polymer hosts. The baric effects on holes were determined by applying hydrostatic He gas pressure up to 200 bar, at 6 K. Absorption spectra of pheophytin a, chlorophyll a, and β-carotene in polymers and plant photosystem II CP47 complex were measured between 5 (or 77) and 300 K, and subject to Voigtian deconvolution. A narrowing of inhomogeneous bandwidth with increasing temperature, predicted on the basis of hole behavior, was observed as the shrinking of Gaussian spectral component. The Lorentzian broadening was ascribed to optical dephasing up to 300 K in transitions with weak to moderate linear electron-phonon coupling strength. The thermal broadening is purely Gaussian in multiphonon transitions (S2 band of β-carotene, Soret bands of tetrapyrrolic pigments), and the Lorentz process appears to be suppressed, indicating a lack of exponential dephasing. Density, polarity, polarizability, compressibility, and other local parameters of the pigment binding sites in biologically relevant systems can be deduced from spectroscopic data, provided that sufficient background information is available. PMID:17557783
Shi, Deheng; Liu, Qionglan; Sun, Jinfeng; Zhu, Zunlue
2014-03-25
The potential energy curves (PECs) of 28 Ω states generated from the 12 states (X(4)Σ(-), 1(2)Π, 1(2)Σ(-), 1(2)Δ, 1(2)Σ(+), 2(2)Π, A(4)Π, B(4)Σ(-), 3(2)Π, 1(6)Σ(-), 2(2)Σ(-) and 1(6)Π) of the BN(+) cation are studied for the first time for internuclear separations from about 0.1 to 1.0 nm using an ab initio quantum chemical method. All the Λ-S states correlate to the first four dissociation channels. The 1(6)Σ(-), 3(2)Π and A(4)Π states are found to be the inverted ones. The 1(2)Σ(+), 2(2)Π, 3(2)Π and 2(2)Σ(-) states are found to possess the double well. The PECs are calculated by the complete active space self-consistent field method, which is followed by the internally contracted multireference configuration interaction approach with the Davidson correction. Core-valence correlation correction is included by a cc-pCV5Z basis set. Scalar relativistic correction is calculated by the third-order Douglas-Kroll Hamiltonian approximation at the level of a cc-pV5Z basis set. The convergent behavior of present calculations is discussed with respect to the basis set and level of theory. The spin-orbit coupling is accounted for by the state interaction approach with the Breit-Pauli Hamiltonian using the all-electron cc-pCV5Z basis set. All the PECs are extrapolated to the complete basis set limit. The spectroscopic parameters are obtained, and the vibrational properties of 1(2)Σ(+), 2(2)Π, 3(2)Π and 2(2)Σ(-) states are evaluated. Analyses demonstrate that the spectroscopic parameters reported here can be expected to be reliably predicted ones. The conclusion is gained that the effect of spin-orbit coupling on the spectroscopic parameters are not obvious almost for all the Λ-S states involved in the present paper. PMID:24334021
Shi, Deheng; Li, Peiling; Sun, Jinfeng; Zhu, Zunlue
2014-01-01
The potential energy curves (PECs) of 28 Ω states generated from 9 Λ-S states (X(2)Π, 1(4)Π, 1(6)Π, 1(2)Σ(+), 1(4)Σ(+), 1(6)Σ(+), 1(4)Σ(-), 2(4)Π and 1(4)Δ) are studied for the first time using an ab initio quantum chemical method. All the 9 Λ-S states correlate to the first two dissociation limits, N((4)Su)+Se((3)Pg) and N((4)Su)+Se((3)Dg), of NSe radical. Of these Λ-S states, the 1(6)Σ(+), 1(4)Σ(+), 1(6)Π, 2(4)Π and 1(4)Δ are found to be rather weakly bound states. The 1(2)Σ(+) is found to be unstable and has double wells. And the 1(6)Σ(+), 1(4)Σ(+), 1(4)Π and 1(6)Π are found to be the inverted ones with the SO coupling included. The PEC calculations are made by the complete active space self-consistent field method, which is followed by the internally contracted multireference configuration interaction approach with the Davidson modification. The spin-orbit coupling is accounted for by the state interaction approach with the Breit-Pauli Hamiltonian. The convergence of the present calculations is discussed with respect to the basis set and the level of theory. Core-valence correlation corrections are included with a cc-pCVTZ basis set. Scalar relativistic corrections are calculated by the third-order Douglas-Kroll Hamiltonian approximation at the level of a cc-pV5Z basis set. All the PECs are extrapolated to the complete basis set limit. The variation with internuclear separation of spin-orbit coupling constants is discussed in brief for some Λ-S states with one shallow well on each PEC. The spectroscopic parameters of 9 Λ-S and 28 Ω states are determined by fitting the first ten vibrational levels whenever available, which are calculated by solving the rovibrational Schrödinger equation with Numerov's method. The splitting energy in the X(2)Π Λ-S state is determined to be about 864.92 cm(-1), which agrees favorably with the measurements of 891.80 cm(-1). Moreover, other spectroscopic parameters of Λ-S and Ω states involved here are
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.
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. PMID:26429033
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.
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…
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
ERIC Educational Resources Information Center
Proctor, Michael D.; Gubler, Justin C.
2001-01-01
This research reports findings from field observations of debriefing sessions following organizational operations in interactive simulation systems. Focuses on the relationship of different debriefing session techniques to identification of potential organizational learning opportunities to improve performance. (Author/LRW)
Potential of the neutron lloyd's mirror interferometer for the search for new interactions
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.
Guidez, Emilie B; Xu, Peng; Gordon, Mark S
2016-02-01
The dispersion interaction energy may be expressed as a sum over R(-n) terms, with n ≥ 6. Most implementations of the dispersion interaction in model potentials are terminated at n = 6. Those implementations that do include higher order contributions commonly only include even power terms, despite the fact that odd power terms can be important. Because the effective fragment potential (EFP) method contains no empirically fitted parameters, the EFP method provides a useful vehicle for examining the importance of the leading R(-7) odd power term in the dispersion expansion. To fully evaluate the importance of the R(-7) contribution to the dispersion energy, it is important to have analytic energy first derivatives for all terms. In the present work, the gradients of the term E7 ∼ R(-7) are derived analytically, implemented in the GAMESS software package, and evaluated relative to other terms in the dispersion expansion and relative to the total EFP interaction energy. Periodic boundary conditions in the minimum image convention are also implemented. A more accurate dispersion energy contribution can now be obtained during molecular dynamics simulations. PMID:26745447
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.
NASA Astrophysics Data System (ADS)
Akpan, N. Ikot; Hassan, Hassanabadi; Tamunoimi, M. Abbey
2015-12-01
The Dirac equation with Hellmann potential is presented in the presence of Coulomb-like tensor (CLT), Yukawa-like tensor (YLT), and Hulthen-type tensor (HLT) interactions by using Nikiforov-Uvarov method. The bound state energy spectra and the radial wave functions are obtained approximately within the framework of spin and pseudospin symmetries limit. We have also reported some numerical results and figures to show the effects of the tensor interactions. Special cases of the potential are also discussed.
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...
Dzhumagulova, K. N.; Shalenov, E. O.; Gabdullina, G. L.
2013-04-15
The dynamic model of the charged particles interaction in non-ideal semiclassical plasma is presented. This model takes into account the quantum mechanical diffraction effect and the dynamic screening effect. On the basis of the dynamic interaction potential, the electron scattering cross sections are investigated. Comparison with the results obtained on the basis of other models and conclusions were made.
Liu, Hui; Shi, Deheng; Sun, Jinfeng; Zhu, Zunlue; Shulin, Zhang
2014-04-24
The potential energy curves (PECs) of 54 spin-orbit states generated from the 22 electronic states of O2 molecule are investigated for the first time for internuclear separations from about 0.1 to 1.0nm. Of the 22 electronic states, the X(3)Σg(-), A(')(3)Δu, A(3)Σu(+), B(3)Σu(-), C(3)Πg, a(1)Δg, b(1)Σg(+), c(1)Σu(-), d(1)Πg, f(1)Σu(+), 1(5)Πg, 1(3)Πu, 2(3)Σg(-), 1(5)Σu(-), 2(1)Σu(-) and 2(1)Δg are found to be bound, whereas the 1(5)Σg(+), 2(5)Σg(+), 1(1)Πu, 1(5)Δg, 1(5)Πu and 2(1)Πu are found to be repulsive ones. The B(3)Σu(-) and d(1)Πg states possess the double well. And the 1(3)Πu, C(3)Πg, A'(3)Δu, 1(5)Δg and 2(5)Σg(+) states are the inverted ones when the spin-orbit coupling is included. The PEC calculations are done by the complete active space self-consistent field (CASSCF) method, which is followed by the internally contracted multireference configuration interaction (icMRCI) approach with the Davidson correction. Core-valence correlation and scalar relativistic corrections are taken into account. The convergence of present calculations is evaluated with respect to the basis set and level of theory. The vibrational properties are discussed for the 1(5)Πg, 1(3)Πu, d(1)Πg and 1(5)Σu(-) states and for the second well of the B(3)Σu(-) state. The spin-orbit coupling effect is accounted for by the state interaction method with the Breit-Pauli Hamiltonian. The PECs of all the electronic states and spin-orbit states are extrapolated to the complete basis set limit. The spectroscopic parameters are obtained, and compared with available experimental and other theoretical results. Analyses demonstrate that the spectroscopic parameters reported here can be expected to be reliably predicted ones. The conclusion is obtained that the effect of spin-orbit coupling on the spectroscopic parameters are small almost for all the electronic states involved in this paper except for the 1(5)Σu(-), 1(5)Πg and 1(3)Πu. PMID:24486866
NASA Astrophysics Data System (ADS)
Shi, De-Heng; Liu, Qionglan; Yu, Wei; Sun, Jinfeng; Zhu, Zunlue
2014-05-01
The potential energy curves (PECs) of 23 Ω states generated from the 12 electronic states (X1 Σ +, 21 Σ +, 11 Σ -, 11 Π, 21 Π, 11 Δ, 13 Σ +, 23 Σ +, 13 Σ -, a3 Π, 23 Π and 13 Δ) are studied for the first time. All the states correlate to the first dissociation channel of the SiBr+ cation. Of these electronic states, the 23 Σ + is the repulsive one without the spin-orbit coupling, whereas it becomes the bound one with the spin-orbit coupling added. On the one hand, without the spin-orbit coupling, the 11 Π, 21 Π and 23 Π are the rather weakly bound states, and only the 11 Π state possesses the double well; on the other hand, with the spin-orbit coupling included, the a3 Π and 11 Π states possess the double well, and the 13 Σ + and 13 Σ - are the inverted states. The PECs are calculated by the CASSCF method, which is followed by the internally contracted MRCI approach with the Davidson modification. Scalar relativistic correction is calculated by the third-order Douglas-Kroll Hamiltonian approximation with a cc-pVTZ-DK basis set. Core-valence correlation correction is included with a cc-pCVTZ basis set. The spin-orbit coupling is accounted for by the state interaction method with the Breit-Pauli Hamiltonian using the all-electron aug-cc-pCVTZ basis set. All the PECs are extrapolated to the complete basis set limit. The variation with internuclear separation of the spin-orbit coupling constant is discussed in brief. The spectroscopic parameters are evaluated for the 11 bound electronic states and the 23 bound Ω states, and are compared with available measurements. Excellent agreement has been found between the present results and the experimental data. It demonstrates that the spectroscopic parameters reported here can be expected to be reliably predicted ones. The Franck-Condon factors and radiative lifetimes of the transitions from the a3 Π 0 + and a3 Π 1 states to the X1 Σ + 0+ state are calculated for several low vibrational levels, and
Rikala, Maria; Hauta-Aho, Milka; Helin-Salmivaara, Arja; Lassila, Riitta; Korhonen, Maarit Jaana; Huupponen, Risto
2015-08-01
We analysed the occurrence of co-prescribing of potentially interacting drugs during warfarin therapy in the community-dwelling population of Finland. We identified drugs having interaction potential with warfarin using the Swedish Finnish INteraction X-referencing drug-drug interaction database (SFINX) and obtained data on drug purchases from the nationwide Prescription Register. We defined warfarin users as persons purchasing warfarin in 2010 (n = 148,536) and followed them from their first prescription in 2010 until the end of the calendar year. Co-prescribing was defined as at least 1-day overlap between warfarin and interacting drug episodes. In addition, we identified persons who initiated warfarin therapy between 1 January 2007 and 30 September 2010 (n = 110,299) and followed these incident users for a 3-month period since warfarin initiation. Overall, 74.4% of warfarin users were co-prescribed interacting drugs. Co-prescribing covered 46.4% of the total person-years of warfarin exposure. Interacting drugs that should be avoided with warfarin were co-prescribed for 13.4% of warfarin users. The majority of the co-prescriptions were for drugs that are not contraindicated during warfarin therapy but require special consideration. Among incident users, 57.1% purchased potentially interacting drugs during the 3-month period after initiation, while 9.0% purchased interacting drugs that should be avoided with warfarin. To conclude, the occurrence of co-prescribing of potentially interacting drugs was high during warfarin therapy. Our findings highlight the importance of close monitoring of warfarin therapy and the need for further studies on the clinical consequences of co-prescribing of interacting drugs with warfarin. PMID:25537751
A note on the binary interaction potential in complex (dusty) plasmas
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.
NASA Astrophysics Data System (ADS)
Zhang, Xiao-Fei; Hu, Xing-Hua; Liu, Xun-Xu; Liu, W. M.
2009-03-01
We present a family of exact vector-soliton solutions for the coupled nonlinear Schrödinger equations with tunable interactions and harmonic potential, and then apply the model to investigate the dynamics of solitons and collisions between two orthogonal solitons in the case with equal interaction parameters. Our results show that the exact vector-soliton solutions can be obtained with arbitrary tunable interactions as long as a proper harmonic potential is applied. The dynamics of solitons can be controlled by the Feshbach resonance and the collisions are essentially elastic and do not depend on the initial conditions.
Potential Drug-drug Interactions in Post-CCU of a Teaching Hospital.
Haji Aghajani, Mohammad; Sistanizad, Mohammad; Abbasinazari, Mohammad; Abiar Ghamsari, Mahdieh; Ayazkhoo, Ladan; Safi, Olia; Kazemi, Katayoon; Kouchek, Mehran
2013-01-01
Drug-drug interactions (DDIs) can lead to increased toxicity or reduction in therapeutic efficacy. This study was designed to assess the incidence of potential drug interactions (PDI) and rank their clinical value in post coronary care unit (Post-CCU) of a teaching hospital in Tehran, Iran. In this prospective study, three pharmacists with supervision of a clinical pharmacist actively gathered necessary information for detection of DDIs. Data were tabulated according to the combinations of drugs in treatment chart. Verification of potential drug interactions was carried out using the online Lexi-Interact™ 2011. A total of 203 patients (113 males and 90 females) were enrolled in the study. The mean age of patients was 61 ± 12.55 years (range = 26-93). A total of 90 drugs were prescribed to 203 patients and most prescribed drugs were atorvastatin, clopidogrel and metoprolol. Mean of drugs was 11.22 per patient. A total of 3166 potential drug interactions have been identified by Lexi- Interact™, 149 (4.71%) and 55 (1.73%) of which were categorized as D and X, respectively. The most serious interactions were clopidogrel+omeprazole and metoprolol+salbutamol. Drug interactions leading to serious adverse effects are to be cautiously watched for when multiple drugs are used simultaneously. In settings with multiple drug use attendance of a pharmacist or clinical pharmacist, taking the responsibility for monitoring drug interactions and notifying the physician about potential problems could decrease the harm in patient and increase the patient safety. PMID:24250596
Potential drug interaction between Rho(D) immune globulin and live virus vaccine.
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
Prevalence of potential drug–drug interactions in cancer patients treated with oral anticancer drugs
van Leeuwen, R W F; Brundel, D H S; Neef, C; van Gelder, T; Mathijssen, R H J; Burger, D M; Jansman, F G A
2013-01-01
Background: Potential drug–drug interactions (PDDIs) in patients with cancer are common, but have not previously been quantified for oral anticancer treatment. We assessed the prevalence and seriousness of potential PDDIs among ambulatory cancer patients on oral anticancer treatment. Methods: A search was conducted in a computer-based medication prescription system for dispensing oral anticancer drugs to outpatients in three Dutch centres. Potential drug–drug interactions were identified using electronic (Drug Interaction Fact software) and manual screening methods (peer-reviewed reports). Results: In the 898 patients included in the study, 1359 PDDIs were identified in 426 patients (46%, 95% confidence interval (CI)=42–50%). In 143 patients (16%), a major PDDI was identified. The drug classes most frequently involved in a major PDDI were coumarins and opioids. The majority of cases concerned central nervous system interactions, PDDIs that can cause gastrointestinal toxicity and prolongation of QT intervals. In multivariate analysis, concomitant use of more drugs (odds ratio (OR)=1.66, 95% CI=1.54–1.78, P<0001) and genito-urinary cancer (OR=0.25, 95% CI=0.12–0.52, P<0001) were risk factors. Conclusion: Potential drug–drug interactions are very common among cancer patients on oral cancer therapy. Physicians and pharmacists should be more aware of these potential interactions. PMID:23412102
Andrić, Jelena M; Misini-Ignjatović, Majda Z; Murray, Jane S; Politzer, Peter; Zarić, Snežana D
2016-07-01
The hydrogen bonding of noncoordinated water molecules to each other and to water molecules that are coordinated to metal-ion complexes has been investigated by means of a search of the Cambridge Structural Database (CSD) and through quantum chemical calculations. Tetrahedral and octahedral complexes that were both charged and neutral were studied. A general conclusion is that hydrogen bonds between noncoordinated water and coordinated water are much stronger than those between noncoordinated waters, whereas hydrogen bonds of water molecule in tetrahedral complexes are stronger than in octahedral complexes. We examined the possibility of correlating the computed interaction energies with the most positive electrostatic potentials on the interacting hydrogen atoms prior to interaction and obtained very good correlation. This study illustrates the fact that electrostatic potentials computed for ground-state molecules, prior to interaction, can provide considerable insight into the interactions. PMID:26989883
Collisional effects on interaction potential in complex plasma in presence of magnetic field
NASA Astrophysics Data System (ADS)
Bezbaruah, Pratikshya; Das, Nilakshi
2016-04-01
Interaction potential in complex plasma with streaming ions is derived analytically in presence of ion-neutral collision and magnetic field. The linear dielectric response function obtained describes the behavior of charged micron sized dust particles in strong collisional limit. A new type of repulsive potential is found to be operative among the dust grains apart from the normal Debye-Hückel potential. The amplitude and shielding length involved in the potential are substantially affected by the parameters describing ion cyclotron frequency, collision frequency among ions and neutrals, and ion streaming. It is also observed that the usual mechanism of ion focusing surrounding the grain is inhibited due to collision. As a result, the attractive wake potential structure is destroyed in the ion flow direction. The horizontal interaction involves only Debye-Hückel potential.
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
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
Flewelling, R F; Hubbell, W L
1986-01-01
The total potential energy profile for hydrophobic ion interactions with lipid bilayers can be written as the sum of four terms: the electrical Born, image and dipole contributions, and a neutral energy term. We introduce a specific model for the membrane dipole potential, treating it as a two-dimensional array of point dipoles located near each membrane-water interface. Together with specific theoretical models for the other energy terms, a total potential profile is developed that successfully describes the complete set of thermodynamic parameters for binding and translocation for the two hydrophobic ion structural analogues, tetraphenylphosphonium (TPP+) and tetraphenylboron (TPB-). A reasonable fit to the data is possible if the dipole potential energy has a magnitude of 5.5 + 0.5 kcal/mol (240 + 20 mV), positive inside, and if the neutral energy contribution for TPP+ and TPB- is -7.0 + 1.0 kcal/mol. These results may also have important implications for small ion interactions with membranes and the energetics of charged groups in membrane proteins. PMID:3955184
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
Farzanegan, Behrooz; Alehashem, Maryam; Bastani, Marjan; Baniasadi, Shadi
2015-02-01
Little is known about clinically significant drug-drug interactions (DDIs) in respiratory settings. DDIs are more likely to occur in critically ill patients due to complex pharmacotherapy regimens and organ dysfunctions. The aim of this study was to identify the pattern of potential DDIs (pDDIs) occurring in cardiothoracic intensive care unit (ICU) of a pulmonary hospital. A prospective observational study was conducted for 6 months. All pDDIs for admitted patients in cardiothoracic ICU were identified with Lexi-Interact program and assessed by a clinical pharmacologist. The interacting drugs, reliability, mechanisms, potential outcomes, and clinical management were evaluated for severe and contraindicated interactions. The study included 195 patients. Lung cancer (14.9%) was the most common diagnosis followed by tracheal stenosis (14.3%). The rate of pDDIs was 720.5/100 patients. Interactions were more commonly observed in transplant patients. 17.7% of pDDIs were considered as severe and contraindicated interactions. Metabolism (54.8%) and additive (24.2%) interactions were the most frequent mechanisms leading to pDDIs, and azole antifungals and fluoroquinolones were the main drug classes involved. The pattern of pDDIs in cardiothoracic ICU differs from other ICU settings. Specialized epidemiological knowledge of drug interactions may help clinical practitioners to reduce the risk of adverse drug events. PMID:25369984
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.
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.
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.
NASA Astrophysics Data System (ADS)
Seo, Dong-Hwa; Urban, Alexander; Ceder, Gerbrand
2015-09-01
Transition-metal (TM) oxides play an increasingly important role in technology today, including applications such as catalysis, solar energy harvesting, and energy storage. In many of these applications, the details of their electronic structure near the Fermi level are critically important for their properties. We propose a first-principles-based computational methodology for the accurate prediction of oxygen charge transfer in TM oxides and lithium TM (Li-TM) oxides. To obtain accurate electronic structures, the Heyd-Scuseria-Ernzerhof (HSE06) hybrid functional is adopted, and the amount of exact Hartree-Fock exchange (mixing parameter) is adjusted to reproduce reference band gaps. We show that the HSE06 functional with optimal mixing parameter yields not only improved electronic densities of states, but also better energetics (Li-intercalation voltages) for LiCo O2 and LiNi O2 as compared to the generalized gradient approximation (GGA), Hubbard U corrected GGA (GGA +U ), and standard HSE06. We find that the optimal mixing parameters for TM oxides are system specific and correlate with the covalency (ionicity) of the TM species. The strong covalent (ionic) nature of TM-O bonding leads to lower (higher) optimal mixing parameters. We find that optimized HSE06 functionals predict stronger hybridization of the Co 3 d and O 2 p orbitals as compared to GGA, resulting in a greater contribution from oxygen states to charge compensation upon delithiation in LiCo O2 . We also find that the band gaps of Li-TM oxides increase linearly with the mixing parameter, enabling the straightforward determination of optimal mixing parameters based on GGA (α =0.0 ) and HSE06 (α =0.25 ) calculations. Our results also show that G0W0@GGA +U band gaps of TM oxides (M O ,M =Mn ,Co ,Ni ) and LiCo O2 agree well with experimental references, suggesting that G0W0 calculations can be used as a reference for the calibration of the mixing parameter in cases when no experimental band gap has been
NASA Astrophysics Data System (ADS)
Itano, Wayne M.; Ramsey, Norman F.
1993-07-01
The paper discusses current methods for accurate measurements of time by conventional atomic clocks, with particular attention given to the principles of operation of atomic-beam frequency standards, atomic hydrogen masers, and atomic fountain and to the potential use of strings of trapped mercury ions as a time device more stable than conventional atomic clocks. The areas of application of the ultraprecise and ultrastable time-measuring devices that tax the capacity of modern atomic clocks include radio astronomy and tests of relativity. The paper also discusses practical applications of ultraprecise clocks, such as navigation of space vehicles and pinpointing the exact position of ships and other objects on earth using the GPS.
NASA Astrophysics Data System (ADS)
Mandt, Stephan; Rapp, Akos; Rosch, Achim
2011-06-01
We consider a cloud of fermionic atoms in an optical lattice described by a Hubbard model with an additional linear potential. While homogeneous interacting systems mainly show damped Bloch oscillations and heating, a finite cloud behaves differently: It expands symmetrically such that gains of potential energy at the top are compensated by losses at the bottom. Interactions stabilize the necessary heat currents by inducing gradients of the inverse temperature 1/T, with T<0 at the bottom of the cloud. An analytic solution of hydrodynamic equations shows that the width of the cloud increases with t1/3 for long times consistent with results from our Boltzmann simulations.
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.
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.
Signal type and signal-to-noise ratio interact to affect cortical auditory evoked potentials.
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
Nonlinear pressure dependence of the interaction potential of dense protein solutions.
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
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.
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.
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
Baranowska-Łączkowska, Angelika; Fernández, Berta
2014-01-30
In order to obtain efficient basis sets for the evaluation of van der Waals complex intermolecular potentials, we carry out systematic basis set studies. For this, interaction energies at representative geometries on the potential energy surfaces are evaluated using the CCSD(T) correlation method and large polarized LPol-n and augmented polarization-consistent aug-pc-2 basis sets extended with different sets of midbond functions. On the basis of the root mean square errors calculated with respect to the values for the most accurate potentials available, basis sets are selected for fitting the corresponding interaction energies and getting analytical potentials. In this work, we study the Ne-N2 van der Waals complex and after the above procedure, the aug-pc-2-3321 and the LPol-ds-33221 basis set results are fitted. The obtained potentials are characterized by T-shaped global minima at distances between the Ne atom and the N2 center of mass of 3.39 Å, with interaction energies of -49.36 cm(-1) for the aug-pc-2-3321 surface and -50.28 cm(-1) for the LPol-ds-33221 surface. Both sets of results are in excellent agreement with the reference surface. To check the potentials further microwave transition frequencies are calculated that agree well with the experimental and the aV5Z-33221 values. The success of this study suggests that it is feasible to carry out similar accurate calculations of interaction energies and ro-vibrational spectra at reduced cost for larger complexes than has been possible hitherto. PMID:24375320
Intrapartum Magnesium Sulfate and the Potential for Cardiopulmonary Drug-Drug Interactions
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
Zhang, Chi; Liu, Song; Zhou, Yaoqi
2006-04-01
Molecular networks in cells are organized into functional modules, where genes in the same module interact densely with each other and participate in the same biological process. Thus, identification of modules from molecular networks is an important step toward a better understanding of how cells function through the molecular networks. Here, we propose a simple, automatic method, called MC(2), to identify functional modules by enumerating and merging cliques in the protein-interaction data from large-scale experiments. Application of MC(2) to the S. cerevisiae protein-interaction data produces 84 modules, whose sizes range from 4 to 69 genes. The majority of the discovered modules are significantly enriched with a highly specific process term (at least 4 levels below root) and a specific cellular component in Gene Ontology (GO) tree. The average fraction of genes with the most enriched GO term for all modules is 82% for specific biological processes and 78% for specific cellular components. In addition, the predicted modules are enriched with coexpressed proteins. These modules are found to be useful for annotating unknown genes and uncovering novel functions of known genes. MC(2) is efficient, and takes only about 5 min to identify modules from the current yeast gene interaction network with a typical PC (Intel Xeon 2.5 GHz CPU and 512 MB memory). The CPU time of MC(2) is affordable (12 h) even when the number of interactions is increased by a factor of 10. MC(2) and its results are publicly available on http://theory.med.buffalo.edu/MC2. PMID:16602686
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
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.
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
Folch, Benjamin; Rooman, Marianne; Dehouck, Yves
2008-01-01
The temperature dependence of the interactions that stabilize protein structures is a long-standing issue, the elucidation of which would enable the prediction and the rational modification of the thermostability of a target protein. It is tackled here by deriving distance-dependent amino acid pair potentials from four datasets of proteins with increasing melting temperatures (Tm). The temperature dependence of the interactions is determined from the differences in the shape of the potentials derived from the four datasets. Note that, here, we use an unusual dataset definition, which is based on the Tm values, rather than on the living temperature of the host organisms. Our results show that the stabilizing weight of hydrophobic interactions (between Ile, Leu, and Val) remains constant as the temperature increases, compared to the other interactions. In contrast, the two minima of the Arg--Glu and Arg--Asp salt bridge potentials show a significant Tm dependence. These two minima correspond to two geometries: the fork--fork geometry, where the side chains point toward each other, and the fork--stick geometry, which involves the N(epsilon) side chain atom of Arg. These two types of salt bridges were determined to be significantly more stabilizing at high temperature. Moreover, a preference for more-compact salt bridges is noticeable in heat-resistant proteins, especially for the fork--fork geometry. The Tm-dependent potentials that have been defined here should be useful for predicting thermal stability changes upon mutation. PMID:18161956
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
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…
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.
The potential of protein-nanomaterial interaction for advanced drug delivery.
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. PMID:26812004
Strong Rashba Spin-Orbit Interaction Intensity in Low-Potential-Barrier Quantum Dots
NASA Astrophysics Data System (ADS)
Huang, Shiu-Ming; Olegovich Badrutdinov, Alexander; Kono, Kimitoshi; Ono, Keiji
2013-04-01
We study the spin splitting energies of different orbital states of quantum dots with a low-potential barrier. The experimental results show that the splitting energies are orbital state dependent. The theoretical analysis is done with a generalization of the Fock-Darwin states in the presence of spin-orbit interactions. The theoretical predictions match well with the experimental observations and exhibits that the Rashba interaction strength in vertical In0.05Ga0.95As/GaAs quantum dots is in the range 80≤λR≤120 meV Å. This enhanced Rashba spin-orbit interaction intensity can be understood from the high penetration of the electron wavefunction into the quantum well with a low-potential barrier.
Clore, G Marius; Kuszewski, John
2002-03-27
The equilibrium angles and distributions of chi(1) rotamers for mobile surface side chains of the small, 63-residue, B1 domain of protein L have been calculated from the static crystal structure by rigid body/torsion angle simulated annealing using a torsion angle database potential of mean force and compared to those deduced by Monte Carlo analysis of side chain residual dipolar couplings measured in solution. Good agreement between theory and experiment is observed, indicating that for side chains undergoing rotamer averaging that is fast on the chemical shift time scale, the equilibrium angles and distribution of chi(1) rotamers are largely determined by the backbone phi/psi torsion angles. PMID:11902865
NASA Astrophysics Data System (ADS)
Takeuchi, Wataru
2013-10-01
Since in impact-collision ion scattering spectroscopy (ICISS) data analysis the interaction potential represented by the screening length as the screening effect is not satisfactorily established up to the present, we introduce commonly the correction factor in the screening length. Previously, Yamamura, Takeuchi and Kawamura (YTK) have suggested the theory taking the shell effect of electron distributions into account for the correction factor to Firsov screening length in the Moliere potential. The application of YTK theory to the evaluation of screening length corrections for the interaction potentials in ICISS manifested that the screening length corrections calculated by the YTK theory agree almost with those determined by simulations or numerical calculations in ICISS and its variants data analyses, being superior to the evaluation of screening length corrections with the O'Connor and Biersack (OB) formula.
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.
Interaction potentials of lithium and potassium ions with argon, krypton, and xenon atoms
Palyukh, B.M.; Rykalyuk, R.E.; Chigin', V.I.
1981-11-01
Based on experimental measurements of the collision energy dependence obtained for the total cross sections of elastic scattering of ions of alkali metals Li/sup +/ and K/sup +/ on atoms of inert gases Ar, Kr, and Xe, as well as of the quantum glory oscillations, first discovered for ionic-atomic collisions, the interaction potentials are determined for these particles in a wide region of internuclear distances, including repulsion, the potential minimum, and long-range polarization atttraction. A method is described for obtaining the five free parameters of the potential, assumed to have the form of a piecewise-continuous function, making it possible, regardless of the variation of the potential at large and small distances, to form the potential minimum using three quantities: the depth epsilon-c of the well, the equilibrium distance R/sub m/, and the curvature k/sub epsilon-c/.
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
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
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. PMID:25833860
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
Kinetic and interaction components of the exact time-dependent correlation potential
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.
Greene, Meredith; Steinman, Michael A.; McNicholl, Ian R.; Valcour, Victor
2014-01-01
Objectives To describe the frequency of medication-related problems in older HIV-infected adults Design Retrospective chart review Setting And Participants Community dwelling HIV-infected adults age 60 and older and age and sex-matched HIV-uninfected adults Measurements Total number of medications, potentially inappropriate medications as defined by the modified Beers criteria, anticholinergic drug burden as defined by the Anticholinergic Risk Scale, and drug-drug interactions using Lexi-Interact online drug interactions database. Results Of 89 HIV-infected participants, most were Caucasian (91%) and male (94%) with a median age of 64 (range 60-82). Common comorbidities included hyperlipidemia, hypertension, and depression. Participants were taking a median of 13 medications (range 2-38), of which only a median of 4 were antiretrovirals. At least one potentially inappropriate medication was prescribed in 46 participants (52%). Sixty-two (70%) participants had at least one Category D (consider therapy modification) drug-drug interaction and 10 (11%) had a Category X (avoid combination) interaction. One-third of these interactions were between two non-antiretroviral medications. We identified 15 participants (17%) with an anticholinergic risk scale score ≥3. In contrast, HIV-uninfected participants were taking a median of 6 medications, 29% had at least one potentially inappropriate medication, and 4% had an anticholinergic risk scale score ≥ 3 (p-value <0.05 for each comparison except p=0.07 for anticholinergic burden). Conclusion HIV-infected older adults have a high frequency of medication-related problems, of which a large portion is due to medications used to treat comorbid diseases. These medication issues were substantially higher than HIV-uninfected participants. Attention to the principles of geriatric prescribing is needed as this population ages in order to minimize complications from multiple medication use. PMID:24576251
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).
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.
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.
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
NASA Astrophysics Data System (ADS)
Yigit, Cemil; Heyda, Jan; Dzubiella, Joachim
2015-08-01
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.
Pogodin, Sergey; López, Núria
2014-07-01
The theoretical study of catalysis would substantialy benefit from the use of atomistic simulations that can provide information beyond mean-field approaches. To date, the nanoscale understanding of surface reactions has been only qualitatively achieved by means of kinetic Monte Carlo coupled to density functional theory, KMC-DFT. Here, we examine a widely employed model for oxygen interaction with the RuO2(110) surface, a highly anisotropic system. Our analysis reveals several covert problems that render as questionable the model's predictions. We suggest an advanced approach that considers all the relevant elementary steps and configurations while smoothing the intrinsic errors in the DFT description of oxygen. Under these conditions, KMC provides quantitative agreement to temperature-programmed desorption experiments. These results illustrate how KMC-based simulations can be pushed forward so that they evolve toward being the standard methodology to study complex chemistry at the nanoscale. PMID:25061545
2014-01-01
The theoretical study of catalysis would substantialy benefit from the use of atomistic simulations that can provide information beyond mean-field approaches. To date, the nanoscale understanding of surface reactions has been only qualitatively achieved by means of kinetic Monte Carlo coupled to density functional theory, KMC-DFT. Here, we examine a widely employed model for oxygen interaction with the RuO2(110) surface, a highly anisotropic system. Our analysis reveals several covert problems that render as questionable the model’s predictions. We suggest an advanced approach that considers all the relevant elementary steps and configurations while smoothing the intrinsic errors in the DFT description of oxygen. Under these conditions, KMC provides quantitative agreement to temperature-programmed desorption experiments. These results illustrate how KMC-based simulations can be pushed forward so that they evolve toward being the standard methodology to study complex chemistry at the nanoscale. PMID:25061545
Concomitant therapy in people with epilepsy: potential drug-drug interactions and patient awareness.
Eyal, Sara; Rasaby, Sivan; Ekstein, Dana
2014-02-01
People with epilepsy (PWE) may use prescription and over-the-counter (OTC) drugs for the treatment of concomitant diseases. Combinations of these drugs, as well as dietary supplements, with antiepileptic drugs (AEDs) may lead to reduced control of seizures and of coexisting medical conditions and increased risk of adverse drug reactions (ADRs). The aims of this study were to obtain comprehensive lists of medications, dietary supplements, botanicals, and specific food components used by adult PWE and to evaluate the potential for interactions involving AEDs and patients' awareness of such potential interactions. We conducted a prospective, questionnaire-based study of PWE attending the Hadassah-Hebrew University Epilepsy Clinic over a period of 7months. The questionnaire interview included the listing of medications, medicinal herbs, dietary supplements, and specific food components consumed and the knowledge of potential drug-drug interactions (DDIs), and it was conducted by a pharmacist. Drug-drug interactions were analyzed via the Micromedex online database. Out of 179 patients who attended the clinic over the study period, we interviewed 73 PWE, of which 71 were included in our final analysis. The mean number of AEDs consumed per subject was 1.7 (SD: 0.8, range: 1-4). Forty (56%) subjects were also treated with other prescription and/or OTC medications, and thirty-four (48%) took dietary supplements. Drug families most prone to DDIs involving AEDs included antipsychotic agents, selective serotonin reuptake inhibitors, and statins. Two-thirds of study participants (67%) knew that DDIs may lead to ADRs, but only half (56%) were aware of the potential for reduced seizure control. Only 44% always reported treatment with AEDs to medical professionals. This study provides for the first time a comprehensive picture of prescription and OTC drugs and food supplements used by PWE. Despite a considerable potential for DDIs involving AEDs, patient awareness is limited
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.
Fukuda, Ikuo; Kamiya, Narutoshi; Yonezawa, Yasushige; Nakamura, Haruki
2012-08-01
The zero-dipole summation method was extended to general molecular systems, and then applied to molecular dynamics simulations of an isotropic water system. In our previous paper [I. Fukuda, Y. Yonezawa, and H. Nakamura, J. Chem. Phys. 134, 164107 (2011)], for evaluating the electrostatic energy of a classical particle system, we proposed the zero-dipole summation method, which conceptually prevents the nonzero-charge and nonzero-dipole states artificially generated by a simple cutoff truncation. Here, we consider the application of this scheme to molecular systems, as well as some fundamental aspects of general cutoff truncation protocols. Introducing an idea to harmonize the bonding interactions and the electrostatic interactions in the scheme, we develop a specific algorithm. As in the previous study, the resulting energy formula is represented by a simple pairwise function sum, enabling facile applications to high-performance computation. The accuracy of the electrostatic energies calculated by the zero-dipole summation method with the atom-based cutoff was numerically investigated, by comparison with those generated by the Ewald method. We obtained an electrostatic energy error of less than 0.01% at a cutoff length longer than 13 Å for a TIP3P isotropic water system, and the errors were quite small, as compared to those obtained by conventional truncation methods. The static property and the stability in an MD simulation were also satisfactory. In addition, the dielectric constants and the distance-dependent Kirkwood factors were measured, and their coincidences with those calculated by the particle mesh Ewald method were confirmed, although such coincidences are not easily attained by truncation methods. We found that the zero damping-factor gave the best results in a practical cutoff distance region. In fact, in contrast to the zero-charge scheme, the damping effect was insensitive in the zero-charge and zero-dipole scheme, in the molecular system we
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.
Smith, Paul E
2006-08-01
New expressions for chemical potential derivatives and preferential interaction parameters for ternary mixtures are derived for open, semiopen, and closed ensembles in terms of Kirkwood-Buff integrals, where all three components are present at finite concentrations. This is achieved using a simple approach that avoids the use of the general matrix formulation of Kirkwood-Buff theory. The resulting expressions provide a rigorous foundation for the analysis of experimental and simulation data. Using the results, a simple model is developed and used to investigate the possible effects of finite protein concentrations on the corresponding cosolvent dependent chemical potential and denaturation thermodynamics. PMID:16679363
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.
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.
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%.
Potential of lateral interactions of CO on Pt (111) fitted to recent STM images
NASA Astrophysics Data System (ADS)
Myshlyavtsev, Alexander V.; Stishenko, Pavel V.
2015-12-01
Monolayers of carbon monoxide (CO) on Pt(111) surfaces are one of the most studied adsorption systems. However, molecular models of this system still do not take into account the reliable potential of lateral interactions between adsorbed CO molecules. Recent advances in experimental technique have brought high-resolution real-space images of CO/Pt(111) monolayers. For example, Yang et al. (J. Phys. Chem. C 117 (2013) 16429-16437) found island structures for coverages from 0.11 to 0.25 ML. In this study we have shown that these island structures can be explained with long-range oscillating lateral interactions. Parameters of the proposed potential were fitted to experimental scanning tunneling microscopy images with a series of Monte Carlo simulations.
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
Life history determines genetic structure and evolutionary potential of host–parasite interactions
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
Herbal medicines in Brazil: pharmacokinetic profile and potential herb-drug interactions
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
Specific anion effects on the pressure dependence of the protein-protein interaction potential.
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
Potential drug–drug interactions in Alzheimer patients with behavioral symptoms
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
Formation of chain structures in systems of charged grains interacting via isotropic pair potentials
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.
Multi-time Schrödinger equations cannot contain interaction potentials
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.
Effect of taurine and potential interactions with caffeine on cardiovascular function.
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. PMID:24615238
Potential Interaction of Green Tea Extract with Hydrochlorothiazide on Diuretic Activity in Rats
Chakraborty, Manodeep; Kamath, Jagadish V.; Bhattacharjee, Ananya
2014-01-01
Treatment of ischemic hypertensive patients with hydrochlorothiazide can precipitate cardiac arrhythmias. The present study was undertaken to evaluate the diuretic potential of green tea alone and its effects on hydrochlorothiazide in interactive groups. Rats were treated with high (500 mg/kg, p.o.) and low (100 mg/kg, p.o.) dose of green tea extract in alone and interactive groups for 30 days. Standard, high, and low dose interactive groups received hydrochlorothiazide (10 mg/kg, p.o.) on the day of experiment. Effect of different treatments was that assessed by evaluating diuretic action, diuretic activity, percentage of saline load excreted, and sodium and potassium levels in urine. Green tea in both high and low doses showed significant diuretic potential and when it is combined with hydrochlorothiazide resulted in significant improvement in the activity compared to hydrochlorothiazide alone treated group. It can be concluded that green tea extract when combined with hydrochlorothiazide showed significant increase in diuretic activity. Most important observation of the present study is even though the combination increases the diuretic potential, it is responsible for decrease in urinary potassium loss. PMID:27355016
An effective interaction potential model for the shape memory alloy AuCd
NASA Astrophysics Data System (ADS)
Guthikonda, Venkata Suresh; Elliott, Ryan S.
2009-09-01
The unusual properties of shape memory alloys (SMAs) result from a lattice level martensitic transformation (MT) corresponding to an instability of the SMAs crystal structure. Currently, there exists a shortage of material models that can capture the details of lattice level MTs occurring in SMAs and that can be used for efficient computational investigations of the interaction between MTs and larger-scale features found in typical materials. These larger-scale features could include precipitates, dislocation networks, voids, and even cracks. In this article, one such model is developed for the SMA AuCd. The model is based on effective interaction potentials (EIPs). These are atomic interaction potentials that are explicit functions of temperature. In particular, the Morse pair potential is used and its adjustable coefficients are taken to be temperature dependent. An extensive exploration of the Morse pair potential is performed to identify an appropriate functional form for the temperature dependence of the potential parameters. A fitting procedure is developed for the EIPs that matches, at suitable temperatures, the stress-free equilibrium lattice parameters, instantaneous bulk moduli, cohesive energies, thermal expansion coefficients, and heat capacities of FCC Au, HCP Cd, and the B2 cubic austenite phase of the Au-47.5at%Cd alloy. The resulting model is explored using branch-following and bifurcation techniques. A hysteretic temperature-induced MT between the B2 cubic and B19 orthorhombic crystal structures is predicted. This is the behavior that is observed in the real material. In addition to reproducing the important properties mentioned above, the model predicts, to reasonable accuracy, the transformation strain tensor and captures the latent heat and thermal hysteresis to within an order of magnitude.
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. PMID:25721922
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
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.
Towards an accurate dissociative potential for water
NASA Astrophysics Data System (ADS)
Akin-Ojo, Omololu
2014-03-01
Most models of water describe the molecule as rigid, i.e., with fixed bond angles and bond lengths, or as flexible in which the bond angles and bond lengths vary but the chemical bonds cannot be broken. In this work we present our progress in the development of a water model which allows for the breaking and formation of chemical bonds. The force field was obtained by fitting ab initio (not DFT) energies, forces, and molecular properties. The ability of the model to predict properties of water at ambient and extreme conditions will be presented. We will also report on the modeling of small clusters of water using the dissociative force field.
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
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.
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.
Kostal, Jakub; Voutchkova-Kostal, Adelina
2016-01-19
Using computer models to accurately predict toxicity outcomes is considered to be a major challenge. However, state-of-the-art computational chemistry techniques can now be incorporated in predictive models, supported by advances in mechanistic toxicology and the exponential growth of computing resources witnessed over the past decade. The CADRE (Computer-Aided Discovery and REdesign) platform relies on quantum-mechanical modeling of molecular interactions that represent key biochemical triggers in toxicity pathways. Here, we present an external validation exercise for CADRE-SS, a variant developed to predict the skin sensitization potential of commercial chemicals. CADRE-SS is a hybrid model that evaluates skin permeability using Monte Carlo simulations, assigns reactive centers in a molecule and possible biotransformations via expert rules, and determines reactivity with skin proteins via quantum-mechanical modeling. The results were promising with an overall very good concordance of 93% between experimental and predicted values. Comparison to performance metrics yielded by other tools available for this endpoint suggests that CADRE-SS offers distinct advantages for first-round screenings of chemicals and could be used as an in silico alternative to animal tests where permissible by legislative programs. PMID:26650775
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
Interaction grand potential between calcium-silicate-hydrate nanoparticles at the molecular level.
Bonnaud, Patrick A; Labbez, Christophe; Miura, Ryuji; Suzuki, Ai; Miyamoto, Naoto; Hatakeyama, Nozomu; Miyamoto, Akira; Van Vliet, Krystyn J
2016-02-21
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. PMID:26866999
Potential Regulatory Interactions of Escherichia coli RraA Protein with DEAD-box Helicases*
Pietras, Zbigniew; Hardwick, Steven W.; Swiezewski, Szymon; Luisi, Ben F.
2013-01-01
Members of the DEAD-box family of RNA helicases contribute to virtually every aspect of RNA metabolism, in organisms from all domains of life. Many of these helicases are constituents of multicomponent assemblies, and their interactions with partner proteins within the complexes underpin their activities and biological function. In Escherichia coli the DEAD-box helicase RhlB is a component of the multienzyme RNA degradosome assembly, and its interaction with the core ribonuclease RNase E boosts the ATP-dependent activity of the helicase. Earlier studies have identified the regulator of ribonuclease activity A (RraA) as a potential interaction partner of both RNase E and RhlB. We present structural and biochemical evidence showing how RraA can bind to, and modulate the activity of RhlB and another E. coli DEAD-box enzyme, SrmB. Crystallographic structures are presented of RraA in complex with a portion of the natively unstructured C-terminal tail of RhlB at 2.8-Å resolution, and in complex with the C-terminal RecA-like domain of SrmB at 2.9 Å. The models suggest two distinct mechanisms by which RraA might modulate the activity of these and potentially other helicases. PMID:24045937
Murtaza, Ghulam; Khan, Muhammad Yasir Ghani; Azhar, Saira; Khan, Shujaat Ali; Khan, Tahir M
2016-03-01
Drug-drug interactions (DDIs) may result in the alteration of therapeutic response. Sometimes they may increase the untoward effects of many drugs. Hospitalized cardiac patients need more attention regarding drug-drug interactions due to complexity of their disease and therapeutic regimen. This research was performed to find out types, prevalence and association between various predictors of potential drug-drug interactions (pDDIs) in the Department of Cardiology and to report common interactions. This study was performed in the hospitalized cardiac patients at Ayub Teaching Hospital, Abbottabad, Pakistan. Patient charts of 2342 patients were assessed for pDDIs using Micromedex® Drug Information. Logistic regression was applied to find predictors of pDDIs. The main outcome measure in the study was the association of the potential drug-drug interactions with various factors such as age, gender, polypharmacy, and hospital stay of the patients. We identified 53 interacting-combinations that were present in total 5109 pDDIs with median number of 02 pDDIs per patient. Overall, 91.6% patients had at least one pDDI; 86.3% were having at least one major pDDI, and 84.5% patients had at least one moderate pDDI. Among 5109 identified pDDIs, most were of moderate (55%) or major severity (45%); established (24.2%), theoretical (18.8%) or probable (57%) type of scientific evidence. Top 10 common pDDIs included 3 major and 7 moderate interactions. Results obtained by multivariate logistic regression revealed a significant association of the occurrence of pDDIs in patient with age of 60 years or more (p < 0.001), hospital stay of 7 days or longer (p < 0.001) and taking 7 or more drugs (p < 0.001). We found a high prevalence for pDDIs in the Department of Cardiology, most of which were of moderate severity. Older patients, patients with longer hospital stay and with elevated number of prescribed drugs were at higher risk of pDDIs. PMID:27013915
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.
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.
Assessment of Potential Herb-Drug Interactions among Nigerian Adults with Type-2 Diabetes.
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
Assessment of Potential Herb-Drug Interactions among Nigerian Adults with Type-2 Diabetes
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
Mechanisms of radiation interaction with DNA: Potential implications for radiation protection
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.
Iacob, Roxana E.; Krystek, Stanley R.; Huang, Richard Y.-C.; Wei, Hui; Tao, Li; Lin, Zheng; Morin, Paul E.; Doyle, Michael L.; Tymiak, Adrienne A.; Engen, John R.
2015-01-01
Interleukin-23 (IL-23) is an important therapeutic target for the treatment of inflammatory diseases. Adnectins are targeted protein therapeutics that are derived from domain III of human fibronectin, and have similar protein scaffold to antibodies. A specific adnectin (Adnectin 2) was identified to bind to IL-23 and compete with IL-23/IL-23R interaction, being a potential protein therapeutic. Hydrogen/deuterium exchange mass spectrometry (HDX MS) and computational methods were applied to probe the binding interactions between IL-23 and Adnectin2 and to determine the correlation between the two orthogonal methods. This review article summarizes the current structural knowledge about Il-23 and it focuses on the applicability of HDX MS to investigate the higher order structure of proteins, which plays an important role for the discovery of new and improved biotherapeutics. PMID:25711416
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.
Tong, Lianming; Miljković, Vladimir D; Johansson, Peter; Käll, Mikael
2011-11-01
The understanding of interaction forces between nanoparticles in colloidal suspension is central to a wide range of novel applications and processes in science and industry. However, few methods are available for actual characterization of such forces at the single particle level. Here we demonstrate the first measurements of colloidal interactions between two individual diffusing nanoparticles using a colorimetric assay based on plasmon hybridization, that is, strong near-field coupling between localized surface plasmon resonances. The measurements are possible because individual gold nanoparticle pairs can be loosely confined in an optical potential well created by a laser tweezers. We quantify the degree of plasmon hybridization for a large number of individual particle pairs as a function of increasing salt concentration. The data reveal a considerable heterogeneity at the single particle level but the estimated average surface separations are in excellent agreements with predictions based on the classical theory of Derjaguin, Landau, Verwey, and Overbeek. PMID:21142200
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.
NASA Astrophysics Data System (ADS)
Becquart, C. S.; Souidi, A.; Hou, M.
2002-10-01
The binary collision approximation (BCA) grounded on molecular dynamics results is used to investigate the influence of the range and stiffness of interatomic potentials on the replacement collision sequence (RCS) length and frequency distributions as well as on the displacement cascade expansion and density. Different screened Coulomb potential functions are used in the Marlowe BCA program with suitably adjusted screening lengths. We show in this paper that for screened Coulomb potentials, the shorter the range, the lower the focusing threshold and the more important the RCS production. The cascade expansion and density is quite sensitive to the potential range at high interaction energies. The overall cascade expansion is found to be governed by the 10% highest-energy recoils. Their energy is above the RCS focusing energy threshold. The cascade density, i.e., the number of transient defects produced per unit volume, is suggested sufficient to interfere significantly with RCS propagation and thus with the spatial distribution of Frenkel pairs. Primary damage production thus involves the combined effect of high-energy collisions and RCS production. A careful choice of the short range potential has thus to be made when simulating displacement cascades.
Solid phase stability of a double-minimum interaction potential system
Suematsu, Ayumi; Yoshimori, Akira Saiki, Masafumi; Matsui, Jun; Odagaki, Takashi
2014-06-28
We study phase stability of a system with double-minimum interaction potential in a wide range of parameters by a thermodynamic perturbation theory. The present double-minimum potential is the Lennard-Jones-Gauss potential, which has a Gaussian pocket as well as a standard Lennard-Jones minimum. As a function of the depth and position of the Gaussian pocket in the potential, we determine the coexistence pressure of crystals (fcc and bcc). We show that the fcc crystallizes even at zero pressure when the position of the Gaussian pocket is coincident with the first or third nearest neighbor site of the fcc crystal. The bcc crystal is more stable than the fcc crystal when the position of the Gaussian pocket is coincident with the second nearest neighbor sites of the bcc crystal. The stable crystal structure is determined by the position of the Gaussian pocket. These results show that we can control the stability of the solid phase by tuning the potential function.
In vitro and in vivo Evaluation of CYP1A Interaction Potential of Terminalia Arjuna Bark
Varghese, Alice; Pandita, Nancy; Gaud, R. S.
2014-01-01
Terminalia arjuna Wight and Arn. (Combretaceae) is a tree having an extensive medicinal potential in cardiovascular disorders. Triterpenoids are mainly responsible for cardiovascular properties. Aqueous, hydroalcoholic and alcoholic extract of T. arjuna, arjunic acid and arjungenin were examined for their potential to inhibit CYP1A enzyme in rat and human liver microsomes. IC50 values of aqueous, hydroalcoholic and alcoholic extract of T. arjuna was found to be 11.4, 28.9 and 44.6 μg/ml in rat liver microsomes while 30.0, 29.7 and 39.0 μg/ml in human liver microsomes, respectively for CYP1A. However IC50 values of arjunic acid and arjungenin for both rat liver microsomes and human liver microsomes were found to be >50 μM. Arjunic acid and arjungenin did not show inhibition of CYP1A enzyme up to concentrations of 50 μM. These in vitro data indicate that Terminalia arjuna extracts contain constituents that can potently inhibit the activity of CYP1A, which could in turn lead to undesirable pharmacokinetic drug–herb interactions in vivo. Based on the in vitro data, interaction potential of the aqueous extract of Terminalia arjuna orally in rats was investigated. A probe substrate, phenacetin, was used to index the activity of CYP1A. In vivo pharmacokinetic study of coadministration of aqueous extract of Terminalia arjuna and phenacetin, revealed that the aqueous extract did not lead to any significant change in the pharmacokinetic parameters of phenacetin as compared with control group. Though there was no in vivo–in vitro correlation, drug interactions could arise with drugs having a narrow therapeutic range and extensively cleared by CYP1A enzyme, which could lead to undesirable side effects. PMID:24843187
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
Huhtamaeki, J. A. M.; Virtanen, S. M. M.; Moettoenen, M.; Ankerhold, J.
2007-09-15
We investigate theoretically the tunneling of a dilute Bose-Einstein condensate through a potential barrier. This scenario is closely related to recent experimental studies of condensates trapped in one-dimensional optical lattices. We derive analytical results for the tunneling rate of the condensate with emphasis on the effects of atom-atom interactions. Furthermore, we consider the effect of fluctuating barrier height to the tunneling rate. We have computed the tunneling rate as a function of the characteristic frequency of the noise. The result is seen to be closely related to the excitation spectrum of the condensate. These observations should be experimentally verifiable.
NASA Technical Reports Server (NTRS)
Van Dalsem, W. R.; Steger, J. L.
1983-01-01
A new, fast, direct-inverse, finite-difference boundary-layer code has been developed and coupled with a full-potential transonic airfoil analysis code via new inviscid-viscous interaction algorithms. The resulting code has been used to calculate transonic separated flows. The results are in good agreement with Navier-Stokes calculations and experimental data. Solutions are obtained in considerably less computer time than Navier-Stokes solutions of equal resolution. Because efficient inviscid and viscous algorithms are used, it is expected this code will also compare favorably with other codes of its type as they become available.
A systematic formulation of the virial expansion for nonadditive interaction potentials.
Hellmann, Robert; Bich, Eckard
2011-08-28
A new formulation of the virial expansion for a classical gas is derived without the restriction to pairwise-additive interaction potentials. Explicit expressions up to the eighth virial coefficient, suitable for numerical evaluation, are given in the form of integrals over sums of cluster diagrams. Compared with previous approaches, the number of cluster diagrams increases more moderately with increasing order of the virial coefficient. Thus, the new formulation should be particularly useful for the computation of high-order virial coefficients. PMID:21895169
Potential Role of Elicitins in the Interaction between Phytophthora Species and Tobacco
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
Effective Mass and Pseudoscalar Interaction in the Dirac Equation with Woods-Saxon Potential
NASA Astrophysics Data System (ADS)
Chargui, Yassine
2016-04-01
We consider the one-dimensional Dirac equation with the Woods-Saxon potential in the Framework of position dependent mass and pseudoscalar interaction. By imposing appropriate constraints on the mass function and the pseudoscalar term new exact solvable models are obtained. A detailed study of the scattering and bound-states problems for these models is presented. Meanwhile, we work out the exact expressions for the transmission and reflection probabilities of scattered states and obtain the exact equation for the energy eigenvalues associated to bound states. In particular, transmission resonance at zero-momentum is observed for supercritical states.
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. PMID:26070840
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
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.
NASA Astrophysics Data System (ADS)
Campos, L. Q. Costa; Apolinario, S. W. S.
2015-01-01
We implement Brownian dynamics to investigate the static properties of colloidal particles confined anisotropically and interacting via a potential which can be tailored in a repulsive-attractive-respulsive fashion as the interparticle distance increases. A diverse number of structural phases are self-assembled, which were classified according to two aspects, that is, their macroscopic and microscopic patterns. Concerning the microscopic phases we found the quasicrystalline, triangular, square, and mixed orderings, where this latter is a combination of square and triangular cells in a 3 ×2 proportion, i.e., the so-called (33,42) Archimedian lattice. On the macroscopic level the system could self-organize in a compact or perforated single cluster surrounded or not by fringes. All the structural phases are summarized in detailed phases diagrams, which clearly show that the different phases are extended as the confinement potential becomes more anisotropic.
NASA Astrophysics Data System (ADS)
Babatunde, J. Falaye; Sameer, M. Ikhdair
2013-06-01
The Dirac equation is solved to obtain its approximate bound states for a spin-1/2 particle in the presence of trigonometric Pöschl—Teller (tPT) potential including a Coulomb-like tensor interaction with arbitrary spin—orbit quantum number κ using an approximation scheme to substitute the centrifugal terms κ(κ ± 1)r-2. In view of spin and pseudo-spin (p-spin) symmetries, the relativistic energy eigenvalues and the corresponding two-component wave functions of a particle moving in the field of attractive and repulsive tPT potentials are obtained using the asymptotic iteration method (AIM). We present numerical results in the absence and presence of tensor coupling A and for various values of spin and p-spin constants and quantum numbers n and κ. The non-relativistic limit is also obtained.
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
Hb lepore/β0-thalassaemia with α+-thalassaemia interactions, a potential diagnostic pitfall.
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
Callegari, Carlo; Ancilotto, Francesco
2011-06-30
A method is proposed for the calculation of potential energy curves and related electronic excitation spectra of dopant atoms captured in/on He nanodroplets and is applied to alkali metal atoms. The method requires knowledge of the droplet density distribution at equilibrium (here calculated within a bosonic-He density functional approach) and of a set of valence electron orbitals of the bare dopant atom (here calculated by numeric solution of the Schrödinger equation in a suitably parametrized model potential). The electron-helium interaction is added as a perturbation, and potential energy curves are obtained by numeric diagonalization of the resulting Hamiltonian as a function of an effective coordinate z(A) (here the distance between the dopant atom and center of mass of the droplet, resulting in a pseudodiatomic potential). Excitation spectra are calculated for Na in the companion paper as the Franck-Condon factors between the v = 0 vibrational state in the ground electronic state and excited states of the pseudodiatomic molecule. They agree well with available experimental data, even for highly excited states where a more traditional approach fails. PMID:21434657
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
Structure and Raman spectra in cryolitic melts: simulations with an ab initio interaction potential.
Cikit, Serpil; Akdeniz, Zehra; Madden, Paul A
2014-01-30
The Raman spectra of cryolitic melts have been calculated from molecular dynamics computer simulations using a polarizable ionic potential obtained by force-fitting to ab initio electronic structure calculations. Simulations which made use of this ab initio derived polarizable interaction potential reproduced the structure and dynamical properties of crystalline cryolite, Na3AlF6, rather well. The transferability of the potential model from solid state to the molten state is tested by comparing results for the Raman spectra of melts of various compositions with those previously obtained with empirically developed potentials and with experimental data. The shapes of the spectra and their evolution with composition in the mixtures conform quite well to those seen experimentally, and we discuss the relationship between the bands seen in the spectra and the vibrational modes of the AlFn((3–n)) coordination complexes which are found in the NaF/AlF3 mixtures. The simulations thus enable a link between the structure of the melt as derived through Raman spectroscopy and through diffraction experiments. We report results for quantities which relate to the degree of cross-linking between these coordination complexes and the diffusive properties of ions. PMID:24432905
NASA Astrophysics Data System (ADS)
Zarghami, Ahad; Looije, Niels; Van den Akker, Harry
2015-08-01
The pseudopotential lattice Boltzmann model (PP-LBM) is a very popular model for simulating multiphase systems. In this model, phase separation occurs via a short-range attraction between different phases when the interaction potential term is properly chosen. Therefore, the potential term is expected to play a significant role in the model and to affect the accuracy and the stability of the computations. The original PP-LBM suffers from some drawbacks such as being capable of dealing with low density ratios only, thermodynamic inconsistency, and spurious velocities. In this paper, we aim to analyze the PP-LBM with the view to simulate single-component (non-)isothermal multiphase systems at large density ratios and in spite of the presence of spurious velocities. For this purpose, the performance of two popular potential terms and of various implementation schemes for these potential terms is examined. Furthermore, the effects of different parameters (i.e., equation of state, viscosity, etc.) on the simulations are evaluated, and, finally, recommendations for a proper simulation of (non-)isothermal multiphase systems are presented.
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.
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
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
Cubic-quintic long-range interactions with double well potentials
NASA Astrophysics Data System (ADS)
Tsilifis, Panagiotis A.; Kevrekidis, Panayotis G.; Rothos, Vassilis M.
2014-01-01
In the present work, we examine the combined effects of cubic and quintic terms of the long-range type in the dynamics of a double well potential. Employing a two-mode approximation, we systematically develop two cubic-quintic ordinary differential equations and assess the contributions of the long-range interactions in each of the relevant prefactors, gauging how to simplify the ensuing dynamical system. Finally, we obtain a reduced canonical description for the conjugate variables of relative population imbalance and relative phase between the two wells and proceed to a dynamical systems analysis of the resulting pair of ordinary differential equations. While in the case of cubic and quintic interactions of the same kind (e.g. both attractive or both repulsive), only a symmetry-breaking bifurcation can be identified, a remarkable effect that emerges e.g. in the setting of repulsive cubic but attractive quintic interactions is a ‘symmetry-restoring’ bifurcation. Namely, in addition to the supercritical pitchfork that leads to a spontaneous symmetry breaking of the antisymmetric state, there is a subcritical pitchfork that eventually reunites the asymmetric daughter branch with the antisymmetric parent one. The relevant bifurcations, the stability of the branches and their dynamical implications are examined both in the reduced (ODE) and in the full (PDE) setting. The model is argued to be of physical relevance, especially so in the context of optical thermal media.
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
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.
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
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
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.
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. PMID:26809959
Hostaš, Jiří; Jakubec, Dávid; Laskowski, Roman A; Gnanasekaran, Ramachandran; Řezáč, Jan; Vondrášek, Jiří; Hobza, Pavel
2015-09-01
Representative pairs of amino acid side chains and nucleic acid bases extracted from available high-quality structures of protein-DNA complexes were analyzed using a range of computational methods. CCSD(T)/CBS interaction energies were calculated for the chosen 272 pairs. These reference interaction energies were used to test the MP2.5/CBS, MP2.X/CBS, MP2-F12, DFT-D3, PM6, and Amber force field methods. Method MP2.5 provided excellent agreement with reference data (root-mean-square error (RMSE) of 0.11 kcal/mol), which is more than 1 order of magnitude faster than the CCSD(T) method. When MP2-F12 and MP2.5 were combined, the results were within reasonable accuracy (0.20 kcal/mol), with a computational savings of almost 2 orders of magnitude. Therefore, this method is a promising tool for accurate calculations of interaction energies in protein-DNA motifs of up to ∼100 atoms, for which CCSD(T)/CBS benchmark calculations are not feasible. B3-LYP-D3 calculated with def2-TZVPP and def2-QZVP basis sets yielded sufficiently good results with a reasonably small RMSE. This method provided better results for neutral systems, whereas positively charged species exhibited the worst agreement with the benchmark data. The Amber force field yielded unbalanced results-performing well for systems containing nonpolar amino acids but severely underestimating interaction energies for charged complexes. The semiempirical PM6 method with corrections for hydrogen bonding and dispersion energy (PM6-D3H4) exhibited considerably smaller error than the Amber force field, which makes it an effective tool for modeling extended protein-ligand complexes (of up to 10,000 atoms). PMID:26575904
Specific Targeting of Caspase-9/PP2A Interaction as Potential New Anti-Cancer Therapy
Arrouss, Issam; Nemati, Fariba; Roncal, Fernando; Wislez, Marie; Dorgham, Karim; Vallerand, David; Rabbe, Nathalie; Karboul, Narjesse; Carlotti, Françoise; Bravo, Jeronimo; Mazier, Dominique
2013-01-01
Purpose PP2A is a serine/threonine phosphatase critical to physiological processes, including apoptosis. Cell penetrating peptides are molecules that can translocate into cells without causing membrane damage. Our goal was to develop cell-penetrating fusion peptides specifically designed to disrupt the caspase-9/PP2A interaction and evaluate their therapeutic potential in vitro and in vivo. Experimental Design We generated a peptide containing a penetrating sequence associated to the interaction motif between human caspase-9 and PP2A (DPT-C9h), in order to target their association. Using tumour cell lines, primary human cells and primary human breast cancer (BC) xenografts, we investigated the capacity of DPT-C9h to provoke apoptosis in vitro and inhibition of tumour growth (TGI) in vivo. DPT-C9h was intraperitonealy administered at doses from 1 to 25 mg/kg/day for 5 weeks. Relative Tumour Volume (RTV) was calculated. Results We demonstrated that DPT-C9h specifically target caspase-9/PP2A interaction in vitro and in vivo and induced caspase-9-dependent apoptosis in cancer cell lines. DPT-C9h also induced significant TGI in BC xenografts models. The mouse-specific peptide DPT-C9 also induced TGI in lung (K-Ras model) and breast cancer (PyMT) models. DPT-C9h has a specific effect on transformed B cells isolated from chronic lymphocytic leukemia patients without any effect on primary healthy cells. Finally, neither toxicity nor immunogenic responses were observed. Conclusion Using the cell-penetrating peptides blocking caspase-9/PP2A interactions, we have demonstrated that DPT-C9h had a strong therapeutic effect in vitro and in vivo in mouse models of tumour progression. PMID:23637769
ERIC Educational Resources Information Center
Rom, Mark Carl
2011-01-01
Grades matter. College grading systems, however, are often ad hoc and prone to mistakes. This essay focuses on one factor that contributes to high-quality grading systems: grading accuracy (or "efficiency"). I proceed in several steps. First, I discuss the elements of "efficient" (i.e., accurate) grading. Next, I present analytical results…
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
Dissipative self-assembly of particles interacting through time-oscillatory potentials.
Tagliazucchi, Mario; Weiss, Emily A; Szleifer, Igal
2014-07-01
Dissipative self-assembly is the emergence of order within a system due to the continuous input of energy. This form of nonequilibrium self-organization allows the creation of structures that are inaccessible in equilibrium self-assembly. However, design strategies for dissipative self-assembly are limited by a lack of fundamental understanding of the process. This work proposes a novel route for dissipative self-assembly via the oscillation of interparticle potentials. It is demonstrated that in the limit of fast potential oscillations the structure of the system is exactly described by an effective potential that is the time average of the oscillatory potential. This effective potential depends on the shape of the oscillations and can lead to effective interactions that are physically inaccessible in equilibrium. As a proof of concept, Brownian dynamics simulations were performed on a binary mixture of particles coated by weak acids and weak bases under externally controlled oscillations of pH. Dissipative steady-state structures were formed when the period of the pH oscillations was smaller than the diffusional timescale of the particles, whereas disordered oscillating structures were observed for longer oscillation periods. Some of the dissipative structures (dimers, fibers, and honeycombs) cannot be obtained in equilibrium (fixed pH) simulations for the same system of particles. The transition from dissipative self-assembled structures for fast oscillations to disordered oscillating structures for slow oscillations is characterized by a maximum in the energy dissipated per oscillation cycle. The generality of the concept is demonstrated in a second system with oscillating particle sizes. PMID:24958868
Dissipative self-assembly of particles interacting through time-oscillatory potentials
Tagliazucchi, Mario; Weiss, Emily A.; Szleifer, Igal
2014-01-01
Dissipative self-assembly is the emergence of order within a system due to the continuous input of energy. This form of nonequilibrium self-organization allows the creation of structures that are inaccessible in equilibrium self-assembly. However, design strategies for dissipative self-assembly are limited by a lack of fundamental understanding of the process. This work proposes a novel route for dissipative self-assembly via the oscillation of interparticle potentials. It is demonstrated that in the limit of fast potential oscillations the structure of the system is exactly described by an effective potential that is the time average of the oscillatory potential. This effective potential depends on the shape of the oscillations and can lead to effective interactions that are physically inaccessible in equilibrium. As a proof of concept, Brownian dynamics simulations were performed on a binary mixture of particles coated by weak acids and weak bases under externally controlled oscillations of pH. Dissipative steady-state structures were formed when the period of the pH oscillations was smaller than the diffusional timescale of the particles, whereas disordered oscillating structures were observed for longer oscillation periods. Some of the dissipative structures (dimers, fibers, and honeycombs) cannot be obtained in equilibrium (fixed pH) simulations for the same system of particles. The transition from dissipative self-assembled structures for fast oscillations to disordered oscillating structures for slow oscillations is characterized by a maximum in the energy dissipated per oscillation cycle. The generality of the concept is demonstrated in a second system with oscillating particle sizes. PMID:24958868
A C-code for the double folding interaction potential for reactions involving deformed target nuclei
NASA Astrophysics Data System (ADS)
Gontchar, I. I.; Chushnyakova, M. V.
2013-01-01
We present a C-code designed to obtain the interaction potential between a spherical projectile nucleus and an axial-symmetrical deformed target nucleus and in particular to find the Coulomb barrier, by using the double folding model (DFM). The program calculates the nucleus-nucleus potential as a function of the distance between the centers of mass of colliding nuclei as well as of the angle between the axis of symmetry of the target nucleus and the beam direction. The most important output parameters are the Coulomb barrier energy and the radius. Since many researchers use a Woods-Saxon profile for the nuclear term of the potential we provide an option in our code for fitting the DFM potential by such a profile near the barrier. Program summaryProgram title: DFMDEF Catalogue identifier: AENI_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENI_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 2245 No. of bytes in distributed program, including test data, etc.: 215442 Distribution format: tar.gz Programming language: C. Computer: PC, Mac. Operating system: Windows XP (with the GCC-compiler version 2), MacOS, Linux. RAM: 100 MB with average parameters set Classification: 17.9. Nature of problem: The code calculates in a semimicroscopic way the bare interaction potential between a spherical projectile nucleus and a deformed but axially symmetric target nucleus as a function of the center of mass distance as well as of the angle between the axis of symmetry of the target nucleus and the beam direction. The height and the position of the Coulomb barrier are found. The calculated potential is approximated by a conventional Woods-Saxon profile near the barrier. Dependence of the barrier parameters upon the characteristics of the effective NN forces (like, e
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
Namazi, Soha; Pourhatami, Shiva; Borhani-Haghighi, Afshin; Roosta, Sareh
2014-01-01
Background: Reciprocal drug interactions are among the most common causes of adverse drug reactions. We investigated the incidence and related risk factors associated with mutual drug interactions in relation to prescriptions written in the neurology wards of two major teaching hospitals in Shiraz, southern Iran. Methods: Data was collected from hand-written prescriptions on a daily basis. Mutual drug interactions were identified using Lexi-Comp 2012 version 1.9.1. Type D and X drug interactions were considered as potential drug-drug interactions. The potential risk factors associated with drug-drug interactions included the patient’s age and gender, number of medications and orders, length of hospitalization and the type of neurological disorder. To determine potential drug-drug interactions, relevant interventions were suggested to the physicians or nurses and the outcome of the interventions were documented. Results: The study comprised 589 patients, of which 53% were males and 47% females, with a mean age of 56.65±18.19 SD years. A total of 4942 drug orders and 3784 medications were prescribed among which 4539 drug-drug interactions were detected, including 4118 type C, 403 type D, and 18 type X. Using a logistic regression model, the number of medications, length of hospitalization and non-vascular type of the neurological disorder were found to be significantly associated with potential drug-drug interactions. From the total interventions, 74.24% were accepted by physicians and nurses. Conclusion: Potentially hazardous reciprocal drug interactions are common among patients in neurology wards. Clinical pharmacists can play a critical role in the prevention of drug-drug interactions in hospitalized patients. PMID:25429173
NASA Astrophysics Data System (ADS)
Garrett, Bruce C.; Truhlar, Donald G.
1980-03-01
Rate constants are calculated for the reactions D+H2→DH+H and H+D2→HD+D and compared to measured values. An accurate potential energy surface, based on the ab initio calculations of Liu and Siegbahn, was used. Rates were calculated using both conventional transition state theory and canonical variational theory. In the former, the generalized transition state dividing surface is located at the saddle point; in the latter it is located to maximize the generalized free energy of activation. We show that, in the absence of tunneling corrections, locating the generalized-transition-state dividing surface variationally has an important quantitative effect on the predicted rate constants for these systems and that, when tunneling is included, most of the effect of using a better dividing surface can be included in conventional transition state theory for these systems by using a consistent transmission coefficient for quantal scattering by the vibrationally adiabatic potential energy curve. Tunneling effects are important for these reactions even for temperatures larger than 400 K. We show how to separate classical recrossing effects from quantal corrections on reaction-coordinate motion in both the transmission coefficients and the kinetic isotope effects. Our most complete calculations are in excellent agreement with most of the measured rate constants and kinetic isotope effects.
Cation Interactions and Membrane Potential Induce Conformational Changes in NaPi-IIb.
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
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
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.
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.
Teng, Yue; Zou, Luyi; Huang, Ming; Zong, Wansong
2014-12-01
2-Mercaptobenzimidazole (MBI) is widely utilized as a corrosion inhibitor, copper-plating brightener and rubber accelerator. The residue of MBI in the environment possesses a potential risk to human health. In this work, the toxic interaction of MBI with the important antioxidant enzyme catalase (CAT) was investigated using spectroscopic and molecular docking methods under physiological conditions. MBI can spontaneously bind with CAT with one binding site through hydrogen bonds and van der Waals forces to form MBI-CAT complex. The molecular docking study revealed that MBI bound into the CAT interface of chains B and C, which led to some conformational and microenvironmental changes of CAT and further resulted in the inhibition of CAT activity. This present study provides direct evidence at a molecular level to show that exposure to MBI could induce changes in the structure and function of the enzyme CAT. PMID:25463673
Olive, Michael Foster
2014-01-01
Throughout the 20th century a body of literature concerning the long lasting effects of early environment was produced. Adverse experiences in early life, or early life stress (ELS), is associated with a higher risk for 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. PMID:25003947
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
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.
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.
Paglia, Gianluca; Rohl, Andrew L.; Gale, Julian D.; Buckley, Craig E.
2005-06-01
We have performed an extensive computational study of {gamma}-Al{sub 2}O{sub 3}, beginning with the geometric analysis of approximately 1.47 billion spinel-based structural candidates, followed by derivative method energy minimization calculations of approximately 122 000 structures. Optimization of the spinel-based structural models demonstrated that structures exhibiting nonspinel site occupancy after simulation were more energetically favorable, as suggested in other computational studies. More importantly, none of the spinel structures exhibited simulated diffraction patterns that were characteristic of {gamma}-Al{sub 2}O{sub 3}. This suggests that cations of {gamma}-Al{sub 2}O{sub 3} are not exclusively held in spinel positions, that the spinel model of {gamma}-Al{sub 2}O{sub 3} does not accurately reflect its structure, and that a representative structure cannot be achieved from molecular modeling when the spinel representation is used as the starting structure. The latter two of these three findings are extremely important when trying to accurately model the structure. A second set of starting models were generated with a large number of cations occupying c symmetry positions, based on the findings from recent experiments. Optimization of the new c symmetry-based structural models resulted in simulated diffraction patterns that were characteristic of {gamma}-Al{sub 2}O{sub 3}. The modeling, conducted using supercells, yields a more accurate and complete determination of the defect structure of {gamma}-Al{sub 2}O{sub 3} than can be achieved with current experimental techniques. The results show that on average over 40% of the cations in the structure occupy nonspinel positions, and approximately two-thirds of these occupy c symmetry positions. The structures exhibit variable occupancy in the site positions that follow local symmetry exclusion rules. This variation was predominantly represented by a migration of cations away from a symmetry positions to other
NASA Astrophysics Data System (ADS)
Paglia, Gianluca; Rohl, Andrew L.; Buckley, Craig E.; Gale, Julian D.
2005-06-01
We have performed an extensive computational study of γ-Al2O3 , beginning with the geometric analysis of approximately 1.47 billion spinel-based structural candidates, followed by derivative method energy minimization calculations of approximately 122 000 structures. Optimization of the spinel-based structural models demonstrated that structures exhibiting nonspinel site occupancy after simulation were more energetically favorable, as suggested in other computational studies. More importantly, none of the spinel structures exhibited simulated diffraction patterns that were characteristic of γ-Al2O3 . This suggests that cations of γ-Al2O3 are not exclusively held in spinel positions, that the spinel model of γ-Al2O3 does not accurately reflect its structure, and that a representative structure cannot be achieved from molecular modeling when the spinel representation is used as the starting structure. The latter two of these three findings are extremely important when trying to accurately model the structure. A second set of starting models were generated with a large number of cations occupying c symmetry positions, based on the findings from recent experiments. Optimization of the new c symmetry-based structural models resulted in simulated diffraction patterns that were characteristic of γ-Al2O3 . The modeling, conducted using supercells, yields a more accurate and complete determination of the defect structure of γ-Al2O3 than can be achieved with current experimental techniques. The results show that on average over 40% of the cations in the structure occupy nonspinel positions, and approximately two-thirds of these occupy c symmetry positions. The structures exhibit variable occupancy in the site positions that follow local symmetry exclusion rules. This variation was predominantly represented by a migration of cations away from a symmetry positions to other tetrahedral site positions during optimization which were found not to affect the diffraction
Evaluation of drug interaction potential of Labisia pumila (Kacip Fatimah) and its constituents.
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
Final Report - Assessment of Potential Phosphate Ion-Cementitious Materials Interactions
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.
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
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
Evaluation of drug interaction potential of Labisia pumila (Kacip Fatimah) and its constituents
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
The emotion potential of simple sentences: additive or interactive effects of nouns and adjectives?
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
Baskerville, Tracey A; Douglas, Alison J
2010-06-01
Dopamine is an important neuromodulator that exerts widespread effects on the central nervous system (CNS) function. Disruption in dopaminergic neurotransmission can have profound effects on mood and behavior and as such is known to be implicated in various neuropsychiatric behavioral disorders including autism and depression. The subsequent effects on other neurocircuitries due to dysregulated dopamine function have yet to be fully explored. Due to the marked social deficits observed in psychiatric patients, the neuropeptide, oxytocin is emerging as one particular neural substrate that may be influenced by the altered dopamine levels subserving neuropathologic-related behavioral diseases. Oxytocin has a substantial role in social attachment, affiliation and sexual behavior. More recently, it has emerged that disturbances in peripheral and central oxytocin levels have been detected in some patients with dopamine-dependent disorders. Thus, oxytocin is proposed to be a key neural substrate that interacts with central dopamine systems. In addition to psychosocial improvement, oxytocin has recently been implicated in mediating mesolimbic dopamine pathways during drug addiction and withdrawal. This bi-directional role of dopamine has also been implicated during some components of sexual behavior. This review will discuss evidence for the existence dopamine/oxytocin positive interaction in social behavioral paradigms and associated disorders such as sexual dysfunction, autism, addiction, anorexia/bulimia, and depression. Preliminary findings suggest that whilst further rigorous testing has to be conducted to establish a dopamine/oxytocin link in human disorders, animal models seem to indicate the existence of broad and integrated brain circuits where dopamine and oxytocin interactions at least in part mediate socio-affiliative behaviors. A profound disruption to these pathways is likely to underpin associated behavioral disorders. Central oxytocin pathways may serve as a
Chakraborty, Manodeep; Kamath, Jagadish V.; Bhattacharjee, Ananya
2015-01-01
Background: Treatment of ischemic hypertensive patients with hydrochlorothiazide can precipitate cardiac arrhythmias. Green tea, by virtue of its antioxidant potential, is responsible for cardio-protective activity. Objective: The present study was under taken to evaluate the pharmacodynamic interaction of green tea extract with hydrochlorothiazide (HCTZ) against doxorubicin (DOX)-induced myocardial toxicity. Materials and Methods: Rats were treated with high (500 mg/kg, p.o.) and low (100 mg/kg, p.o.) dose of green tea extract in alone and interactive groups for 28 days. Standard, high and low dose of interactive groups received hydrochlorothiazide (10 mg/kg, p.o.) for the last 7 days. Apart from normal controls, all other groups were subjected to DOX (3 mg/kg, i.p.) toxicity on Days 1, 7, 14, 21 and 28, and the effect of different treatments was evaluated by changes in electrocardiographic parameters, serum biomarkers and tissue antioxidant levels. Apart from that, lipid profile and histological studies were also carried out. Results: Compared with the DOX control group, both high and low dose of green tea exhibited a significant decrease in serum biomarkers and increase in tissue antioxidant levels. Green tea treatment was also responsible for significant improvement in ECG parameter, lipid profile and histological score. Incorporation of high and low dose of green tea with HCTZ exhibited significant protection compared with the HCTZ alone treated group. Conclusion: The present findings clearly suggest that the green tea extract dose-dependently reduces DOX-induced myocardial toxicity. Green tea when combined with HCTZ can reduce the associated side-effects and exhibits myocardial protection. PMID:26604554
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.
Visuo-tactile interactions in the congenitally deaf: a behavioral and event-related potential study.
Hauthal, Nadine; Debener, Stefan; Rach, Stefan; Sandmann, Pascale; Thorne, Jeremy D
2014-01-01
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
Therapeutic potential of mitotic interaction between the nucleoporin Tpr and aurora kinase A
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. PMID:25789545
New directly acting antivirals for hepatitis C: potential for interaction with antiretrovirals.
Seden, Kay; Back, David; Khoo, Saye
2010-06-01
Recent advances in the development of agents that act specifically to inhibit hepatitis C virus (HCV) are set to fundamentally change the way that patients will be treated. New directly acting anti-HCV agents such as protease and polymerase inhibitors will initially be added to standard of care with pegylated interferon-alpha and ribavirin. However, future therapy is likely to constitute combinations of agents which act at distinct stages of viral replication and have differing resistance profiles. While directly acting anti-HCV agents will undoubtedly improve treatment outcomes, the introduction of combination therapy may not be without complications in some patient groups. HIV-positive patients who are receiving antiretrovirals (ARVs) are relatively highly represented among those with HCV infection, and are at high risk of drug-drug interactions (DDIs). As combination anti-HCV treatment gradually evolves to resemble anti-HIV therapy, it is essential to consider the increased potential for DDIs in patients receiving combination anti-HCV therapy, and particularly in HCV/HIV-co-infected individuals. Therapeutic drug monitoring is likely to play a role in the clinical management of such interactions. PMID:20335191
Visuo-tactile interactions in the congenitally deaf: a behavioral and event-related potential study
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
NASA Astrophysics Data System (ADS)
Tong, X. M.; Chu, S. I.
1998-05-01
We introduce a self-interaction-free relativistic density functional theory (DFT) for the treatment of both the static and dynamical properties of many-electron atoms (X.M. Tong and S.I. Chu, Phys. Rev. A57), 855 (1998).. The theory is based on the extension of our recent development of non-relativistic DFT treatment (X.M. Tong and S.I. Chu, Phys. Rev. A55), 3406 (1997). with optimized effective potential (OEP) and self-interaction-corrction (SIC) to the relativistic domain. The relativistic OEP/SIC procedure yields orbital-independent single- particle local potential with proper long-range Coulombic (-1/r) behavior and is capable of providing accurate description of the ground, excited, and autoionizing states. The method is applied to the atomic structure calculations of atoms with Z = 2 to 106. Good agreement with the experimental data for both the ionization potentials (obtained from the highest occupied orbital energies) and individual orbital binding energies is obtained across the periodic table. To our knowledage, this is the first DFT calculation that has achieved such a quantitative accuracy. Detailed results will be presented.
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
Direct interaction of a CFTR potentiator and a CFTR corrector with phospholipid bilayers.
Baroni, Debora; Zegarra-Moran, Olga; Svensson, Agneta; Moran, Oscar
2014-07-01
Cystic fibrosis transmembrane conductance regulator (CFTR) potentiators and correctors are new drugs that target the basic CFTR protein defect and are expected to benefit cystic fibrosis patients. To optimize the substances so far proposed for human use, and to minimise unwanted side effects, it is essential to investigate possible interactions between the drugs and cell components. We used small-angle X-ray scattering with synchrotron radiation to analyse the effects of two representative drugs, the potentiator VX-770 (Ivacaftor), approved for human use, and the corrector VX-809 (Lumacaftor), on a model phospholipid membrane. By reconstruction of the electron density profile of unilamellar vesicles treated with VX-770 or VX-809 we found that these drugs penetrate the phospholipid bilayer. VX-809 becomes homogeneously distributed throughout the bilayer whereas VX-770 accumulates predominantly in the internal leaflet, behaviour probably favoured by the asymmetry of the bilayer, because of vesicle curvature. Penetration of the bilayer by these drugs, probably as part of the mechanisms of permeation, causes destabilization of the membrane; this must be taken into account during future drug development. PMID:24771136
Structure and freezing of fluids interacting via the Gay-Berne (n-6) potentials.
Singh, Ram C; Ram, Jokhan; Singh, Yashwant
2002-03-01
We have calculated the pair-correlation functions of a fluid interacting via the Gay-Berne (n-6) pair potentials using the Percus-Yevick integral equation theory and have shown how these correlations depend on the value of n that measures the sharpness of the repulsive core of the pair potential. These results have been used in the density-functional theory to locate the freezing transitions of these fluids. We have used two different versions of the theory known as the second order and the modified weighted-density-functional theory and examined the freezing of these fluids for 8< or =n< or =30 and in the reduced temperature range lying between 0.65 and 1.25 into the nematic and the smectic A phases. For none of these cases smectic A phase was found to be stabilized though in some range of temperature for a given n it appeared as a metastable state. We have examined the variation of freezing parameters for the isotropic-nematic transition with temperature and n. We have also compared our results with simulation results wherever they are available. While we find that the density-functional theory is good to study the freezing transitions in such fluids the structural parameters found from the Percus-Yevick theory need to be improved particularly at high temperatures and lower values of n. PMID:11909085
Structure and freezing of fluids interacting via the Gay-Berne (n-6) potentials
NASA Astrophysics Data System (ADS)
Singh, Ram C.; Ram, Jokhan; Singh, Yashwant
2002-03-01
We have calculated the pair-correlation functions of a fluid interacting via the Gay-Berne (n-6) pair potentials using the Percus-Yevick integral equation theory and have shown how these correlations depend on the value of n that measures the sharpness of the repulsive core of the pair potential. These results have been used in the density-functional theory to locate the freezing transitions of these fluids. We have used two different versions of the theory known as the second order and the modified weighted-density-functional theory and examined the freezing of these fluids for 8<=n<=30 and in the reduced temperature range lying between 0.65 and 1.25 into the nematic and the smectic A phases. For none of these cases smectic A phase was found to be stabilized though in some range of temperature for a given n it appeared as a metastable state. We have examined the variation of freezing parameters for the isotropic-nematic transition with temperature and n. We have also compared our results with simulation results wherever they are available. While we find that the density-functional theory is good to study the freezing transitions in such fluids the structural parameters found from the Percus-Yevick theory need to be improved particularly at high temperatures and lower values of n.
Dham, Ashok K; McBane, George C; McCourt, Frederick R W; Meath, William J
2010-01-14
results that agree similarly well for all but one of the properties considered. When the present comparisons are combined with the ability to give accurate spectroscopic transition frequencies for the Ne-CO van der Waals complex, only the XC potential energy surfaces give results that agree well with all extant experimental data for the Ne-CO interaction. PMID:20095675
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.
Kennedy-Dixon, Tracia-Gay; Gossell-Williams, Maxine; Hall, Jannel; Anglin-Brown, Blossom
2015-01-01
Objective: To identify major potential drug-drug interactions (DDIs) on prescriptions filled at the University Health Centre Pharmacy, Mona Campus, Jamaica. Methods: This investigation utilised a cross-sectional analysis on all prescriptions with more than one drug that were filled at the Health Centre Pharmacy between November 2012 and February 2013. Potential DDIs were identified using the online Drug Interactions Checker database of Drugs.com. Results: During the period of the study, a total of 2814 prescriptions were analysed for potential DDIs. The prevalence of potential DDIs found during the study period was 49.82%. Major potential DDIs accounted for 4.7 % of the total number of interactions detected, while moderate potential DDIs and minor potential DDIs were 80.8 % and 14.5 % respectively. The three most frequently occurring major potential DDIs were amlodipine and simvastatin (n=46), amiloride and losartan (n=27) and amiloride and lisinopril (n=16). Conclusion: This study has highlighted the need for educational initiatives to ensure that physicians and pharmacists collaborate in an effort to minimise the risks to the patients. These interactions are avoidable for the most part, as the use of online tools can facilitate the selection of therapeutic alternatives or guide decisions for closer patient monitoring and thus reduce the risks of adverse events. PMID:26759615
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
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
Application of the pair torque interaction potential to simulate the elastic behavior of SLMoS2
NASA Astrophysics Data System (ADS)
Berinskii, I. E.; Panchenko, A. Yu; Podolskaya, E. A.
2016-05-01
This paper is devoted to the application of the pair torque interaction potential for the simulation of the elastic behavior of a promising two-dimensional material: single layer molybdenium disulphide (SLMoS2). It is demonstrated that both Mo-Mo and S-S interactions can be regarded as pair force interactions with sufficient accuracy. Using both experimental and calculated numerically elastic moduli, and also the phonon spectrum available in the literature, the parameters of the Morse potential are determined for Mo-Mo and S-S bonds, and the parameters of the pair torque potential are obtained for the Mo-S bond. As a result, a combination of force and torque pair potentials is proposed, which allows for the correct modelling of SLMoS2 mechanical behavior.
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
Matsumoto, Celso Soiti; Nakagomi, Ryota; Matsumoto, Harue; Minoda, Haruka; Shinoda, Kei; Iwata, Takeshi; Mizota, Atsushi
2014-01-01
To analyze the interaction of cortical potentials elicited by dichoptic stimulation of the dominant and fellow eyes at different frequencies, a pair of programmed power supply units were used to drive a light emitting diode (LED) mounted in the right and left eyes of light-proof goggles to elicit the visually evoked cortical responses (VECPs). The right eye was stimulated at 11.5 Hz and the left eye at 11.0 Hz. Then the stimulation was repeated with the frequency of stimulation switched to the other eyes. The stimulus duration was 5 ms. The sampling rate was 1.0 Hz, and the duration of collection was 200 ms. The VECP of each eye was extracted separately. Individual VECPs could be recorded separately after simultaneous dichoptic stimulation of each eye. The amplitudes of the VECPs were not significantly different after stimulating the dominant eye and the fellow eye separately. The implicit times of negative peak (N-2) and the second positive peak (P-2) were shorter after stimulation of the dominant eye than after stimulation of the fellow eye, but the difference was not significant. However, the implicit time of N-2 elicited by stimulating the dominant eye was significantly shorter when the stimulation rate was 11.5 Hz. The VECPs elicited by stimulating the two eyes can be recorded separately by simultaneous dichoptic stimulation. Dichoptic simultaneous stimulation required a shorter time and may be a more sensitive method of analyzing binocular interactions compared to the classic VECPs using monocular stimulation. PMID:25194016
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
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.
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.
Interaction of spirochetes with the host fibrinolytic system and potential roles in pathogenesis.
Vieira, Mônica Larucci; Nascimento, Ana Lucia T O
2016-08-01
The pathogenic spirochetes Borrelia burgdorferi, B. hermsii, B. recurrentis, Treponema denticola and Leptospira spp. are the etiologic agents of Lyme disease, relapsing fever, periodontitis and leptospirosis, respectively. Lyme borreliosis is a multi-systemic disorder and the most prevalent tick-borne disease in the northern hemisphere. Tick-borne relapsing fever is persistent in endemic areas worldwide, representing a significant burden in some African regions. Periodontal disease, a chronic inflammatory disorder that often leads to tooth loss, is caused by several potential pathogens found in the oral cavity including T. denticola. Leptospirosis is considered the most widespread zoonosis, and the predominant human disease in tropical, undeveloped regions. What these diseases have in common is that they are a significant burden to healthcare costs in the absence of prophylactic measures. This review addresses the interaction of these spirochetes with the fibrinolytic system, plasminogen (Plg) binding to the surface of bacteria and the generation of plasmin (Pla) on their surface. The consequences on host-pathogen interactions when the spirochetes are endowed with this proteolytic activity are discussed on the basis of the results reported in the literature. Spirochetes equipped with Pla activity have been shown to degrade extracellular matrix (ECM) components, in addition to digesting fibrin, facilitating bacterial invasion and dissemination. Pla generation triggers the induction of matrix metalloproteases (MMPs) in a cascade of events that enhances the proteolytic capacity of the spirochetes. These activities in concert with the interference exerted by the Plg/Pla on the complement system - helping the bacteria to evade the immune system - should illuminate our understanding of the mechanisms involved in host infection. PMID:25914944
NASA Astrophysics Data System (ADS)
Czakó, Gábor; Bowman, Joel M.
2012-01-01
We report a high-quality, ab initio, full-dimensional global potential energy surface (PES) for the Cl(2P, 2P3/2) + CH4 reaction, which describes both the abstraction (HCl + CH3) and substitution (H + CH3Cl) channels. The analytical PES is a least-squares fit, using a basis of permutationally invariant polynomials, to roughly 16 000 ab initio energy points, obtained by an efficient composite method, including counterpoise and spin-orbit corrections for the entrance channel. This composite method is shown to provide accuracy almost equal to all-electron CCSD(T)/aug-cc-pCVQZ results, but at much lower computational cost. Details of the PES, as well as additional high-level benchmark characterization of structures and energetics are reported. The PES has classical barrier heights of 2650 and 15 060 cm-1 (relative to Cl(2P3/2) + CH4(eq)), respectively, for the abstraction and substitution reactions, in good agreement with the corresponding new computed benchmark values, 2670 and 14 720 cm-1. The PES also accurately describes the potential wells in the entrance and exit channels for the abstraction reaction. Quasiclassical trajectory calculations using the PES show that (a) the inclusion of the spin-orbit corrections in the PES decreases the cross sections by a factor of 1.5-2.5 at low collision energies (Ecoll); (b) at Ecoll ≈ 13 000 cm-1 the substitution channel opens and the H/HCl ratio increases rapidly with Ecoll; (c) the maximum impact parameter (bmax) for the abstraction reaction is ˜6 bohr; whereas bmax is only ˜2 bohr for the substitution; (d) the HCl and CH3 products are mainly in the vibrational ground state even at very high Ecoll; and (e) the HCl rotational distributions are cold, in excellent agreement with experiment at Ecoll = 1280 cm-1.
Interspecies interactions and potential Influenza A virus risk in small swine farms in Peru
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
NASA Astrophysics Data System (ADS)
Bewerunge, Jörg; Sengupta, Ankush; Capellmann, Ronja F.; Platten, Florian; Sengupta, Surajit; Egelhaaf, Stefan U.
2016-07-01
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.
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. PMID:27475395
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.
Alvim, Mariana Macedo; da Silva, Lidiane Ayres; Leite, Isabel Cristina Gonçalves; Silvério, Marcelo Silva
2015-01-01
Objective To evaluate the incidence of potential drug-drug interactions in an intensive care unit of a hospital, focusing on antimicrobial drugs. Methods This cross-sectional study analyzed electronic prescriptions of patients admitted to the intensive care unit of a teaching hospital between January 1 and March 31, 2014 and assessed potential drug-drug interactions associated with antimicrobial drugs. Antimicrobial drug consumption levels were expressed in daily doses per 100 patient-days. The search and classification of the interactions were based on the Micromedex® system. Results The daily prescriptions of 82 patients were analyzed, totaling 656 prescriptions. Antimicrobial drugs represented 25% of all prescription drugs, with meropenem, vancomycin and ceftriaxone being the most prescribed medications. According to the approach of daily dose per 100 patient-days, the most commonly used antimicrobial drugs were cefepime, meropenem, sulfamethoxazole + trimethoprim and ciprofloxacin. The mean number of interactions per patient was 2.6. Among the interactions, 51% were classified as contraindicated or significantly severe. Highly significant interactions (clinical value 1 and 2) were observed with a prevalence of 98%. Conclusion The current study demonstrated that antimicrobial drugs are frequently prescribed in intensive care units and present a very high number of potential drug-drug interactions, with most of them being considered highly significant. PMID:26761473
Vashishta, Priya; Kalia, Rajiv K.; Nakano, Aiichiro; Rino, Jose Pedro
2011-01-01
An effective interatomic interaction potential for AlN is proposed. The potential consists of two-body and three-body covalent interactions. The two-body potential includes steric repulsions due to atomic sizes, Coulomb interactions resulting from charge transfer between atoms, charge-induced dipole-interactions due to the electronic polarizability of ions, and induced dipole–dipole (van der Waals) interactions. The covalent characters of the Al–N–Al and N–Al–N bonds are described by the three-body potential. The proposed three-body interaction potential is a modification of the Stillinger–Weber form proposed to describe Si. Using the molecular dynamics method, the interaction potential is used to study structural, elastic, and dynamical properties of crystalline and amorphous states of AlN for several densities and temperatures. The structural energy for wurtzite (2H) structure has the lowest energy, followed zinc-blende and rock-salt (RS) structures. The pressure for the structural transformation from wurtzite-to-RS from the common tangent is found to be 24 GPa. For AlN in the wurtzite phase, our computed elastic constants ( C{sub 11} , C{sub 12} , C{sub 13} , C{sub 33} , C{sub 44} , and C{sub 66} ), melting temperature, vibrational density-of-states, and specific heat agree well with the experiments. Predictions are made for the elastic constant as a function of density for the crystalline and amorphous phase. Structural correlations, such as pair distribution function and neutron and x-ray static structure factors are calculated for the amorphous and liquid state.
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.
The two-body interaction potential in the STF tensor formalism: an application to binary asteroids
NASA Astrophysics Data System (ADS)
Compère, A.; Lemaître, A.
2014-08-01
The symmetric trace free (STF) tensor formalism, developed by Hartmann et al. (Celest Mech Dyn Astron 60:139-159. doi: 10.1007/BF00693097, 1994), is a nice tool, not much used in Celestial Mechanics. It is fully equivalent to the usual spherical harmonics but permits more elegant and compact formulations. The coupling between the gravitational fields of extended bodies with this formalism has been used in Mathis and Le Poncin-Lafitte (Astron Astrophys 497:889-910. doi: 10.1051/0004-6361/20079054, 2009) for binary stars or planetary systems, but not yet applied to binary asteroids. However, binary asteroids are common in the Solar System and usually their study requires a full two rigid body approach. The formulation of the two-body interaction potential in the STF formalism in the full two rigid body problem is detailed and completed in this article. An application to the binary asteroid (66391) 1999 KW4 is presented with a comparison of our results with other results of the literature for validation.
Mechanisms of radiation interaction with DNA: Potential implications for radiation protection
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.
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
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.
MOLECULAR INTERACTION POTENTIALS FOR THE DEVELOPMENT OF STRUCTURE-ACTIVITY RELATIONSHIPS
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...
Piculell, Bridget J; Hoeksema, Jason D; Thompson, John N
2008-01-01
Background Geographic selection mosaics, in which species exert different evolutionary impacts on each other in different environments, may drive diversification in coevolving species. We studied the potential for geographic selection mosaics in plant-mycorrhizal interactions by testing whether the interaction between bishop pine (Pinus muricata D. Don) and one of its common ectomycorrhizal fungi (Rhizopogon occidentalis Zeller and Dodge) varies in outcome, when different combinations of plant and fungal genotypes are tested under a range of different abiotic and biotic conditions. Results We used a 2 × 2 × 2 × 2 factorial experiment to test the main and interactive effects of plant lineage (two maternal seed families), fungal lineage (two spore collections), soil type (lab mix or field soil), and non-mycorrhizal microbes (with or without) on the performance of plants and fungi. Ecological outcomes, as assessed by plant and fungal performance, varied widely across experimental environments, including interactions between plant or fungal lineages and soil environmental factors. Conclusion These results show the potential for selection mosaics in plant-mycorrhizal interactions, and indicate that these interactions are likely to coevolve in different ways in different environments, even when initially the genotypes of the interacting species are the same across all environments. Hence, selection mosaics may be equally as effective as genetic differences among populations in driving divergent coevolution among populations of interacting species. PMID:18507825
Grenier, Romain; To, Quy-Dong; de Lara-Castells, María Pilar; Léonard, Céline
2015-07-01
Global potentials for the interaction between the Ar atom and gold surfaces are investigated and Ar-Au pair potentials suitable for molecular dynamics simulations are derived. Using a periodic plane-wave representation of the electronic wave function, the nonlocal van-der-Waals vdW-DF2 and vdW-OptB86 approaches have been proved to describe better the interaction. These global interaction potentials have been decomposed to produce pair potentials. Then, the pair potentials have been compared with those derived by combining the dispersionless density functional dlDF for the repulsive part with an effective pairwise dispersion interaction. These repulsive potentials have been obtained from the decomposition of the repulsive interaction between the Ar atom and the Au2 and Au4 clusters and the dispersion coefficients have been evaluated by means of ab initio calculations on the Ar+Au2 complex using symmetry adapted perturbation theory. The pair potentials agree very well with those evaluated through periodic vdW-DF2 calculations. For benchmarking purposes, CCSD(T) calculations have also been performed for the ArAu and Ar+Au2 systems using large basis sets and extrapolations to the complete basis set limit. This work highlights that ab initio calculations using very small surface clusters can be used either as an independent cross-check to compare the performance of state-of-the-art vdW-corrected periodic DFT approaches or, directly, to calculate the pair potentials necessary in further molecular dynamics calculations. PMID:26046588
The potential use of SUISEKI as a protein interaction discovery tool.
Blaschke, C; Valencia, A
2001-01-01
Relevant information about protein interactions is stored in textual sources. This sources are commonly used not only as archives of what is already known but also as information for generating new knowledge, particularly to pose hypothesis about new possible interactions that can be inferred from the existing ones. This task is the more creative part of scientific work in experimental systems. We present a large-scale analysis for the prediction of new interactions based on the interaction network for the ones already known and detected automatically in the literature. During the last few years it has became clear that part of the information about protein interactions could be extracted with automatic tools, even if these tools are still far from perfect and key problems such as detection of protein names are not completely solved. We have developed a integrated automatic approach, called SUISEKI (System for Information Extraction on Interactions), able to extract protein interactions from collections of Medline abstracts. Previous experiments with the system have shown that it is able to extract almost 70% of the interactions present in relatively large text corpus, with an accuracy of approximately 80% (for the best defined interactions) that makes the system usable in real scenarios, both at the level of extraction of protein names and at the level of extracting interaction between them. With the analysis of the interaction map of Saccharomyces cerevisiae we show that interactions published in the years 2000/2001 frequently correspond to proteins or genes that were already very close in the interaction network deduced from the literature published before these years and that they are often connected to the same proteins. That is, discoveries are commonly done among highly connected entities. Some biologically relevant examples illustrate how interactions described in the year 2000 could have been proposed as reasonable working hypothesis with the information
Bowman, Joel M.; Xantheas, Sotiris S.
2004-01-01
We present anharmonic vibrational calculations for the Cl-(H2O) cluster and their convergence with the n-mode representation of the interaction potential. Extension of this representation up to 4-mode couplings produces results that are converged to within 10 cm-1 or less relative to the exact 6-mode representation for this system. This methodology, in conjunction with the ''morphing'' technique, which is based on the scaling of the internal coordinates, provides for an effective means of fitting intermolecular potentials to measured vibrational spectra. Application of this approach to the chloride-water interaction produces a revision of a previously developed empirical interaction potential that reproduces the measured fundamental and first overtone frequencies to within an average absolute deviation of 1.75 cm-1 in the 4-mode coupling representation.
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.
NASA Astrophysics Data System (ADS)
Maniero, Angelo M.; Acioli, Paulo H.
A full configuration interaction (CI) with a norm-conserving pseudopotential procedure to determine potential energy surfaces is proposed. Analysis of the potentiality and the possible sources of inaccuracies of the methodology is given in terms of its application to the generation of the ground-state potential energy curves of the LiH and Li2 molecules. The vibrational energy levels were obtained using the discrete variable representation. The agreement between our results and those from Rydberg-Klein-Ress-derived potentials is very good. The extension of this procedure to larger systems is straightforward.
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
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
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.
NASA Astrophysics Data System (ADS)
Garza, Jorge; Nichols, Jeffrey A.; Dixon, David A.
2000-05-01
The Krieger, Li, and Iafrate approximation to the optimized effective potential including the self-interaction correction for density functional theory has been implemented in a molecular code, NWChem, that uses Gaussian functions to represent the Kohn and Sham spin-orbitals. The differences between the implementation of the self-interaction correction in codes where planewaves are used with an optimized effective potential are discussed. The importance of the localization of the spin-orbitals to maximize the exchange-correlation of the self-interaction correction is discussed. We carried out exchange-only calculations to compare the results obtained with these approximations, and those obtained with the local spin density approximation, the generalized gradient approximation and Hartree-Fock theory. Interesting results for the energy difference (GAP) between the highest occupied molecular orbital, HOMO, and the lowest unoccupied molecular orbital, LUMO, (spin-orbital energies of closed shell atoms and molecules) using the optimized effective potential and the self-interaction correction have been obtained. The effect of the diffuse character of the basis set on the HOMO and LUMO eigenvalues at the various levels is discussed. Total energies obtained with the optimized effective potential and the self-interaction correction show that the exchange energy with these approximations is overestimated and this will be an important topic for future work.
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
Interaction potentials of LiH, NaH, KH, RbH, and CsH
NASA Astrophysics Data System (ADS)
Geum, N.; Jeung, G.-H.; Derevianko, A.; Côté, R.; Dalgarno, A.
2001-10-01
Quantum-mechanical calculations of the potential energy curves of the singlet and triplet states of LiH, NaH, KH, RbH, and CsH formed by the approach of ground state alkali-metal atoms and hydrogen atoms are presented. Precise values are determined for the coefficients of the van der Waals interaction and estimates are made of the contribution of the exchange interaction at large distances. Together with empirical data, they are used to assess and improve the accuracy of the ab initio potentials.
The Coulomb interaction in Helium-3: Interplay of strong short-range and weak long-range potentials
NASA Astrophysics Data System (ADS)
Kirscher, J.; Gazit, D.
2016-04-01
Quantum chromodynamics and the electroweak theory at low energies are prominent instances of the combination of a short-range and a long-range interaction. For the description of light nuclei, the large nucleon-nucleon scattering lengths produced by the strong interaction, and the reduction of the weak interaction to the Coulomb potential, play a crucial role. Helium-3 is the first bound nucleus comprised of more than one proton in which this combination of forces can be studied. We demonstrate a proper renormalization of Helium-3 using the pionless effective field theory as the formal representation of the nuclear regime as strongly interacting fermions. The theory is found consistent at leading and next-to-leading order without isospin-symmetry-breaking 3-nucleon interactions and a non-perturbative treatment of the Coulomb interaction. The conclusion highlights the significance of the regularization method since a comparison to previous work is contradictory if the difference in those methods is not considered. With a perturbative Coulomb interaction, as suggested by dimensional analysis, we find the Helium-3 system properly renormalized, too. For both treatments, renormalization-scheme independence of the effective field theory is demonstrated by regulating the potential and a variation of the associated cutoff.
Interaction potential of Carmegliptin with P-glycoprotein (Pgp) transporter in healthy volunteers
Kuhlmann, Olaf; Carlile, David; Noe, Johannes; Bentley, Darren
2014-01-01
Objective The primary objective of this study was to investigate the interaction potential of carmegliptin with P-glycoprotein transporter in vitro and in vivo. A secondary objective was to investigate the safety and tolerability of carmegliptin alone or co-administered with verapamil. Research design and methods The inhibition potential of carmegliptin was tested in vitro and in a non-randomized open-label study in 16 healthy male volunteers. On day 1 a single dose of carmegliptin (150 mg) was given, followed by a single dose of verapamil (80 mg) on day 7, on day 10 a single dose of carmegliptin (150 mg) together with verapamil (80 mg t.i.d.), and verapamil (80 mg t.i.d.) on days 11–14. Finally, on day 15 a single dose of 150 mg carmegliptin together with 80 mg t.i.d. verapamil was administered. Pharmacokinetic and safety parameters were assessed. Results Carmegliptin showed in vitro a low cell permeability and was a good substrate for human MDR1 cells. When carmegliptin was taken with verapamil, the mean exposure and Cmax to carmegliptin increased by 29% and 53%, respectively. Increases in exposure were slightly greater on the sixth day of verapamil dosing than on the first day. Verapamil Cmax was 17% lower on average when given with carmegliptin than when verapamil was taken alone, and similar trends were apparent in corresponding norverapamil pharmacokinetics. All reported adverse events (n = 28) were mild in intensity, and verapamil had no apparent effect on the pattern or incidence of events. Conclusions In vitro, carmegliptin is a substrate but not an inhibitor of human Pgp. Consistently, the co-administration of carmegliptin with verapamil altered the pharmacokinetics of carmegliptin slightly and moderately increased the exposure. Peak exposure of verapamil and its metabolite norverapamil tended to be lower when co-administered with carmegliptin. The combination of carmegliptin and verapamil was generally well tolerated. Although the
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.
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
Vazquez-Mayagoitia, Alvaro; Sherrill, David; Apra, Edoardo; Sumpter, Bobby G
2010-01-01
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.
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…
Becker, Matthijs L.; Caspers, Peter W. J.; Kallewaard, Marjon; Bruinink, Riekert J.; Kylstra, Nico B.; Heisterkamp, Siem; de Valk, Vincent; van der Veen, André A.
2006-01-01
Objective: There are many drug–drug interactions (D–DI) of which some may cause severe adverse patient outcomes. Dispensing interacting drug combinations should be avoided when the risks are higher than the benefits. The objective of this study was to identify determinants of dispensing undesirable interacting drug combinations by community pharmacies in the Netherlands. Methods: A total of 256 Dutch community pharmacies were selected, based on the dispensing of 11 undesirable interacting drug combinations between January 1st, 2001 and October 31st, 2002. These pharmacies were sent a questionnaire by the Inspectorate for Health Care (IHC) concerning their process and structure characteristics. Main outcome measure: The number of times the 11 undesirable interacting drug combinations were dispensed. Results: Two hundred and forty-six questionnaires (response rate 96.1%) were completed. Dispensing determinants were only found for the D–DI between macrolide antibiotics and digoxin but not for the other 10 D–DIs. Pharmacies using different medication surveillance systems differed in the dispensing of this interacting drug combination, and pharmacies, which were part of a health care centre dispensed this interacting drug combination more often. Conclusion: Medication surveillance in Dutch community pharmacies seems to be effective. Although for most D–DIs no determinants were found, process and structure characteristics may have consequences for the dispensing of undesirable interacting drug combinations. PMID:17187223
Lopes, Juliana Fedoce; Rocha, Willian R; Dos Santos, Hélio F; De Almeida, Wagner B
2008-04-28
In this work, a systematic study of the interaction of neutral cisplatin ([Pt(NH(3))(2)Cl(2)]) and their charged aquated species ([Pt(NH(3))(2)Cl(H(2)O)](+) and [Pt(NH(3))(2)(H(2)O)(2)](2+)) with water was carried out. The potential energy surface (PES) was analyzed by considering 35 spatial orientations for the interacting species. The calculations were performed at various levels of theory including Moller-Plesset fourth order perturbation theory and density functional theory (DFT-B3LYP) using extended basis sets. Lennard-Jones (12-6) plus Coulomb classical potential was also used to assess the repulsion-dispersion and electrostatic contributions. The effect of atomic charges on the interaction energies is discussed using Mulliken, charges from electrostatic potential grid method and natural bond orbital schemes. The outcomes show that the electrostatic term plays a primary role on the calculation of interaction energies, with the absolute values of atomic charges from different approaches significantly affecting the overall interaction. Unusual results were revealed by basis set superposition error calculations for the structures located on the platinum-water PES. PMID:18447507
Lin, Iris Y; Kwantes, Catherine T
2015-01-01
This study looked at the extent to which personality and cultural factors predicted participants' perceptions of the importance private interactions played in the workplace. The 134 participants read a vignette (where a new employee socially interacted at low or high levels with co-workers) and completed the Big Five Inventory, Social Axioms Survey, and questions concerning expected workplace experiences. Results indicated employees who engaged in high levels of private interaction with co-workers were expected to be better liked, to receive better performance evaluations, were more likely to receive co-worker assistance, and were thought to be more likely chosen for future projects. However, the personality and social axiom variables studied did not significantly interact with social interaction to influence expectations of workplace outcomes. PMID:25590341
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 scatteri