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.