Accurate first principles model potentials for intermolecular interactions.
Gordon, Mark S; Smith, Quentin A; Xu, Peng; Slipchenko, Lyudmila V
2013-01-01
The general effective fragment potential (EFP) method provides model potentials for any molecule that is derived from first principles, with no empirically fitted parameters. The EFP method has been interfaced with most currently used ab initio single-reference and multireference quantum mechanics (QM) methods, ranging from Hartree-Fock and coupled cluster theory to multireference perturbation theory. The most recent innovations in the EFP model have been to make the computationally expensive charge transfer term much more efficient and to interface the general EFP dispersion and exchange repulsion interactions with QM methods. Following a summary of the method and its implementation in generally available computer programs, these most recent new developments are discussed.
The importance of accurate interaction potentials in the melting of argon nanoclusters
NASA Astrophysics Data System (ADS)
Pahl, E.; Calvo, F.; Schwerdtfeger, P.
The melting temperatures of argon clusters ArN (N = 13, 55, 147, 309, 561, and 923) and of bulk argon have been obtained from exchange Monte Carlo simulations and are compared using different two-body interaction potentials, namely the standard Lennard-Jones (LJ), Aziz and extended Lennard-Jones (ELJ) potentials. The latter potential has many advantages: while maintaining the computational efficiency of the commonly used LJ potential, it is as accurate as the Aziz potential but the computer time scales more favorably with increasing cluster size. By applying the ELJ form and extrapolating the cluster data to the infinite system, we are able to extract the melting point of argon already in good agreement with experimental measurements. By considering the additional Axilrod-Teller three-body contribution as well, we calculate a melting temperature of T meltELJ = 84.7 K compared to the experimental value of T meltexp = 83.85 K, whereas the LJ potential underestimates the melting point by more than 7 K. Thus melting temperatures within 1 K accuracy are now feasible.
An accurate H2-H2 interaction potential from first principles
NASA Astrophysics Data System (ADS)
Diep, Phong; Johnson, J. Karl
2000-03-01
We have calculated the potential energy surface extrapolated to the complete basis set limit using coupled-cluster theory with singles, doubles, and perturbational triples excitations [CCSD(T)] for the rigid monomer model of (H2)2. There is significant anisotropy among the 37 unique angular configurations selected to represent the surface. A four term spherical harmonics expansion model was chosen to fit the surface. The calculated potential energy surface reproduces the quadrupole moment to within 0.58% and the experimental well depth to within 1%. The second virial coefficient has been computed from the fitted potential energy surface. The usual semiclassical treatment of quantum mechanical effects on the second virial coefficient was applied in the temperature range of 100-500 K. We have developed a new technique for computing the quantum second virial coefficient by combining Feynman's path integral formalism and Monte Carlo integration. The calculated virial coefficient compares very well with published experimental measurements. Integral elastic cross sections were calculated for the scattering of para-H2/para-H2 by use of the close-coupling method. The interaction potential model from this work is able to reproduce the experimental cross sections in the relative kinetic velocity range of 900-2300 m/s.
Sun, Y Y; Kim, Yong-Hyun; Lee, Kyuho; Zhang, S B
2008-10-21
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.
Cybulski, Hubert; Baranowska-Łączkowska, Angelika; Henriksen, Christian; Fernández, Berta
2014-11-06
By evaluating a representative set of CCSD(T) ground state interaction energies for van der Waals dimers formed by aromatic molecules and the argon atom, we test the performance of the polarized basis sets of Sadlej et al. (J. Comput. Chem. 2005, 26, 145; Collect. Czech. Chem. Commun. 1988, 53, 1995) and the augmented polarization-consistent bases of Jensen (J. Chem. Phys. 2002, 117, 9234) in providing accurate intermolecular potentials for the benzene-, naphthalene-, and anthracene-argon complexes. The basis sets are extended by addition of midbond functions. As reference we consider CCSD(T) results obtained with Dunning's bases. For the benzene complex a systematic basis set study resulted in the selection of the (Z)Pol-33211 and the aug-pc-1-33321 bases to obtain the intermolecular potential energy surface. The interaction energy values and the shape of the CCSD(T)/(Z)Pol-33211 calculated potential are very close to the best available CCSD(T)/aug-cc-pVTZ-33211 potential with the former basis set being considerably smaller. The corresponding differences for the CCSD(T)/aug-pc-1-33321 potential are larger. In the case of the naphthalene-argon complex, following a similar study, we selected the (Z)Pol-3322 and aug-pc-1-333221 bases. The potentials show four symmetric absolute minima with energies of -483.2 cm(-1) for the (Z)Pol-3322 and -486.7 cm(-1) for the aug-pc-1-333221 basis set. To further check the performance of the selected basis sets, we evaluate intermolecular bound states of the complexes. The differences between calculated vibrational levels using the CCSD(T)/(Z)Pol-33211 and CCSD(T)/aug-cc-pVTZ-33211 benzene-argon potentials are small and for the lowest energy levels do not exceed 0.70 cm(-1). Such differences are substantially larger for the CCSD(T)/aug-pc-1-33321 calculated potential. For naphthalene-argon, bound state calculations demonstrate that the (Z)Pol-3322 and aug-pc-1-333221 potentials are of similar quality. The results show that these
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.
Interacting with image hierarchies for fast and accurate object segmentation
NASA Astrophysics Data System (ADS)
Beard, David V.; Eberly, David H.; Hemminger, Bradley M.; Pizer, Stephen M.; Faith, R. E.; Kurak, Charles; Livingston, Mark
1994-05-01
Object definition is an increasingly important area of medical image research. Accurate and fairly rapid object definition is essential for measuring the size and, perhaps more importantly, the change in size of anatomical objects such as kidneys and tumors. Rapid and fairly accurate object definition is essential for 3D real-time visualization including both surgery planning and Radiation oncology treatment planning. One approach to object definition involves the use of 3D image hierarchies, such as Eberly's Ridge Flow. However, the image hierarchy segmentation approach requires user interaction in selecting regions and subtrees. Further, visualizing and comprehending the anatomy and the selected portions of the hierarchy can be problematic. In this paper we will describe the Magic Crayon tool which allows a user to define rapidly and accurately various anatomical objects by interacting with image hierarchies such as those generated with Eberly's Ridge Flow algorithm as well as other 3D image hierarchies. Preliminary results suggest that fairly complex anatomical objects can be segmented in under a minute with sufficient accuracy for 3D surgery planning, 3D radiation oncology treatment planning, and similar applications. Potential modifications to the approach for improved accuracy are summarized.
An accurate potential energy curve for helium based on ab initio calculations
NASA Astrophysics Data System (ADS)
Janzen, A. R.; Aziz, R. A.
1997-07-01
Korona, Williams, Bukowski, Jeziorski, and Szalewicz [J. Chem. Phys. 106, 1 (1997)] constructed a completely ab initio potential for He2 by fitting their calculations using infinite order symmetry adapted perturbation theory at intermediate range, existing Green's function Monte Carlo calculations at short range and accurate dispersion coefficients at long range to a modified Tang-Toennies potential form. The potential with retardation added to the dipole-dipole dispersion is found to predict accurately a large set of microscopic and macroscopic experimental data. The potential with a significantly larger well depth than other recent potentials is judged to be the most accurate characterization of the helium interaction yet proposed.
Accurate nuclear radii and binding energies from a chiral interaction
Ekstrom, Jan A.; Jansen, G. R.; Wendt, Kyle A.; ...
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.
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.
A highly accurate ab initio potential energy surface for methane
NASA Astrophysics Data System (ADS)
Owens, Alec; Yurchenko, Sergei N.; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter
2016-09-01
A new nine-dimensional potential energy surface (PES) for methane has been generated using state-of-the-art ab initio theory. The PES is based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set limit and incorporates a range of higher-level additive energy corrections. These include core-valence electron correlation, higher-order coupled cluster terms beyond perturbative triples, scalar relativistic effects, and the diagonal Born-Oppenheimer correction. Sub-wavenumber accuracy is achieved for the majority of experimentally known vibrational energy levels with the four fundamentals of 12CH4 reproduced with a root-mean-square error of 0.70 cm-1. The computed ab initio equilibrium C-H bond length is in excellent agreement with previous values despite pure rotational energies displaying minor systematic errors as J (rotational excitation) increases. It is shown that these errors can be significantly reduced by adjusting the equilibrium geometry. The PES represents the most accurate ab initio surface to date and will serve as a good starting point for empirical refinement.
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.
Manzi, Lucio; Barrow, Andrew S.; Scott, Daniel; Layfield, Robert; Wright, Timothy G.; Moses, John E.; Oldham, Neil J.
2016-01-01
Specific interactions between proteins and their binding partners are fundamental to life processes. The ability to detect protein complexes, and map their sites of binding, is crucial to understanding basic biology at the molecular level. Methods that employ sensitive analytical techniques such as mass spectrometry have the potential to provide valuable insights with very little material and on short time scales. Here we present a differential protein footprinting technique employing an efficient photo-activated probe for use with mass spectrometry. Using this methodology the location of a carbohydrate substrate was accurately mapped to the binding cleft of lysozyme, and in a more complex example, the interactions between a 100 kDa, multi-domain deubiquitinating enzyme, USP5 and a diubiquitin substrate were located to different functional domains. The much improved properties of this probe make carbene footprinting a viable method for rapid and accurate identification of protein binding sites utilizing benign, near-UV photoactivation. PMID:27848959
Manzi, Lucio; Barrow, Andrew S; Scott, Daniel; Layfield, Robert; Wright, Timothy G; Moses, John E; Oldham, Neil J
2016-11-16
Specific interactions between proteins and their binding partners are fundamental to life processes. The ability to detect protein complexes, and map their sites of binding, is crucial to understanding basic biology at the molecular level. Methods that employ sensitive analytical techniques such as mass spectrometry have the potential to provide valuable insights with very little material and on short time scales. Here we present a differential protein footprinting technique employing an efficient photo-activated probe for use with mass spectrometry. Using this methodology the location of a carbohydrate substrate was accurately mapped to the binding cleft of lysozyme, and in a more complex example, the interactions between a 100 kDa, multi-domain deubiquitinating enzyme, USP5 and a diubiquitin substrate were located to different functional domains. The much improved properties of this probe make carbene footprinting a viable method for rapid and accurate identification of protein binding sites utilizing benign, near-UV photoactivation.
NASA Astrophysics Data System (ADS)
Manzi, Lucio; Barrow, Andrew S.; Scott, Daniel; Layfield, Robert; Wright, Timothy G.; Moses, John E.; Oldham, Neil J.
2016-11-01
Specific interactions between proteins and their binding partners are fundamental to life processes. The ability to detect protein complexes, and map their sites of binding, is crucial to understanding basic biology at the molecular level. Methods that employ sensitive analytical techniques such as mass spectrometry have the potential to provide valuable insights with very little material and on short time scales. Here we present a differential protein footprinting technique employing an efficient photo-activated probe for use with mass spectrometry. Using this methodology the location of a carbohydrate substrate was accurately mapped to the binding cleft of lysozyme, and in a more complex example, the interactions between a 100 kDa, multi-domain deubiquitinating enzyme, USP5 and a diubiquitin substrate were located to different functional domains. The much improved properties of this probe make carbene footprinting a viable method for rapid and accurate identification of protein binding sites utilizing benign, near-UV photoactivation.
Can dielectric spheres accurately model atomic-scale interactions?
NASA Astrophysics Data System (ADS)
Obolensky, O. I.; Doerr, T. P.; Ogurtsov, A. Y.; Yu, Yi-Kuo
2016-10-01
We calculate the polarization portion of electrostatic interactions at the atomic scale using quantum-mechanical methods such as density functional theories (DFT) and the coupled cluster approach, and using classical methods such as a surface charge method and a polarizable force field. The agreement among various methods is investigated. Using the coupled clusters method CCSD(T) with large basis sets as the reference, we find that for systems comprising two to six atoms and ions in S-states the classical surface charge method performs much better than commonly used DFT methods with moderate basis sets such as B3LYP/6-31G(d,p). The remarkable performance of the classical approach comes as a surprise. The present results indicate that the use of a rigorous formalism of classical electrostatics can be better justified for determining molecular interactions at intermediate distances than some of the widely used methods of quantum chemistry.
Varandas, A J C
2009-09-28
Multireference configuration interaction calculations using large correlation consistent basis sets and full configuration interaction calculations with the smallest of such basis are utilized to describe the ionic-neutral curve crossing for the title system. The results of the former calculations have then been extrapolated to the complete basis set limit using the uniform singlet- and triplet-pair extrapolation scheme. A recent suggestion for locating the nonadiabatic matrix terms at the point where the dynamical correlation split vanishes has also been tested. Additionally, a consistent formalism is suggested to model the radial dependence of the nonadiabatic matrix terms that warrants an overlap dependence away from the crossing. When applied to LiF, the overall approach yields results in excellent agreement with the commonly accepted values for the geometric and energetic attributes at both the equilibrium and diabatic crossing regions.
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
How accurate are chronic wound assessments using interactive video technology?
Gardner, S E; Frantz, R A; Specht, J K; Johnson-Mekota, J L; Buresh, K A; Wakefield, B; Flanagan, J
2001-01-01
This project examined the accuracy of chronic wound assessments made using an interactive, video telecommunications system (Teledoc 5000, NEC America, Inc., Irving, TX) by comparing a nurse expert's in-person wound assessments with wound assessments made from taped Teledoc sessions. Wound assessments determined the absence or presence of nine wound characteristics instrumental in guiding treatment (e.g., tunneling, undermining, granulation tissue, necrotic tissue, epithelial tissue, purulent exudate, erythema, edema, induration). A sample of 13 paired wound observations was analyzed. The accuracy of the Teledoc technology was examined by calculating the amount of agreement between the in-person assessments and the taped Teledoc assessments for each of the nine characteristics. Agreement for eight of the nine wound characteristic exceeded 75%, suggesting this telehealth medium does not alter wound assessment data, which are essential in guiding treatment decisions. In addition to connecting the remotely based nurse with nursing expertise to improve patient care, telehealth technology seemed to increase the remotely-based nurses' knowledge of wound assessment and treatment as well.
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
2016-08-09
Adaptive quantum mechanical (QM)/molecular mechanical (MM) methods enable efficient molecular simulations of chemistry in solution. Reactive subregions are modeled with an accurate QM potential energy expression while the rest of the system is described in a more approximate manner (MM). As solvent molecules diffuse in and out of the reactive region, they are gradually included into (and excluded from) the QM expression. It would be desirable to model such a system with a single adaptive Hamiltonian, but thus far this has resulted in distorted structures at the boundary between the two regions. Solving this long outstanding problem will allow microcanonical adaptive QM/MM simulations that can be used to obtain vibrational spectra and dynamical properties. The difficulty lies in the complex QM potential energy expression, with a many-body expansion that contains higher order terms. Here, we outline a Hamiltonian adaptive multiscale scheme within the framework of many-body potentials. The adaptive expressions are entirely general, and complementary to all standard (nonadaptive) QM/MM embedding schemes available. We demonstrate the merit of our approach on a molecular system defined by two different MM potentials (MM/MM'). For the long-range interactions a numerical scheme is used (particle mesh Ewald), which yields energy expressions that are many-body in nature. Our Hamiltonian approach is the first to provide both energy conservation and the correct solvent structure everywhere in this system.
NASA Astrophysics Data System (ADS)
Heidari, M.; Cortes-Huerto, R.; Donadio, D.; Potestio, R.
2016-10-01
In adaptive resolution simulations the same system is concurrently modeled with different resolution in different subdomains of the simulation box, thereby enabling an accurate description in a small but relevant region, while the rest is treated with a computationally parsimonious model. In this framework, electrostatic interaction, whose accurate treatment is a crucial aspect in the realistic modeling of soft matter and biological systems, represents a particularly acute problem due to the intrinsic long-range nature of Coulomb potential. In the present work we propose and validate the usage of a short-range modification of Coulomb potential, the Damped shifted force (DSF) model, in the context of the Hamiltonian adaptive resolution simulation (H-AdResS) scheme. This approach, which is here validated on bulk water, ensures a reliable reproduction of the structural and dynamical properties of the liquid, and enables a seamless embedding in the H-AdResS framework. The resulting dual-resolution setup is implemented in the LAMMPS simulation package, and its customized version employed in the present work is made publicly available.
Mezei, Pál D; Csonka, Gábor I; Ruzsinszky, Adrienn; Sun, Jianwei
2015-01-13
A correct description of the anion-π interaction is essential for the design of selective anion receptors and channels and important for advances in the field of supramolecular chemistry. However, it is challenging to do accurate, precise, and efficient calculations of this interaction, which are lacking in the literature. In this article, by testing sets of 20 binary anion-π complexes of fluoride, chloride, bromide, nitrate, or carbonate ions with hexafluorobenzene, 1,3,5-trifluorobenzene, 2,4,6-trifluoro-1,3,5-triazine, or 1,3,5-triazine and 30 ternary π-anion-π' sandwich complexes composed from the same monomers, we suggest domain-based local-pair natural orbital coupled cluster energies extrapolated to the complete basis-set limit as reference values. We give a detailed explanation of the origin of anion-π interactions, using the permanent quadrupole moments, static dipole polarizabilities, and electrostatic potential maps. We use symmetry-adapted perturbation theory (SAPT) to calculate the components of the anion-π interaction energies. We examine the performance of the direct random phase approximation (dRPA), the second-order screened exchange (SOSEX), local-pair natural-orbital (LPNO) coupled electron pair approximation (CEPA), and several dispersion-corrected density functionals (including generalized gradient approximation (GGA), meta-GGA, and double hybrid density functional). The LPNO-CEPA/1 results show the best agreement with the reference results. The dRPA method is only slightly less accurate and precise than the LPNO-CEPA/1, but it is considerably more efficient (6-17 times faster) for the binary complexes studied in this paper. For 30 ternary π-anion-π' sandwich complexes, we give dRPA interaction energies as reference values. The double hybrid functionals are much more efficient but less accurate and precise than dRPA. The dispersion-corrected double hybrid PWPB95-D3(BJ) and B2PLYP-D3(BJ) functionals perform better than the GGA and meta
Low-energy structures of benzene clusters with a novel accurate potential surface.
Bartolomei, M; Pirani, F; Marques, J M C
2015-12-05
The benzene-benzene (Bz-Bz) interaction is present in several chemical systems and it is known to be crucial in understanding the specificity of important biological phenomena. In this work, we propose a novel Bz-Bz analytical potential energy surface which is fine-tuned on accurate ab initio calculations in order to improve its reliability. Once the Bz-Bz interaction is modeled, an analytical function for the energy of the Bzn clusters may be obtained by summing up over all pair potentials. We apply an evolutionary algorithm (EA) to discover the lowest-energy structures of Bzn clusters (for n=2-25), and the results are compared with previous global optimization studies where different potential functions were employed. Besides the global minimum, the EA also gives the structures of other low-lying isomers ranked by the corresponding energy. Additional ab initio calculations are carried out for the low-lying isomers of Bz3 and Bz4 clusters, and the global minimum is confirmed as the most stable structure for both sizes. Finally, a detailed analysis of the low-energy isomers of the n = 13 and 19 magic-number clusters is performed. The two lowest-energy Bz13 isomers show S6 and C3 symmetry, respectively, which is compatible with the experimental results available in the literature. The Bz19 structures reported here are all non-symmetric, showing two central Bz molecules surrounded by 12 nearest-neighbor monomers in the case of the five lowest-energy structures.
Using Interpolation for Fast and Accurate Calculation of Ion–Ion Interactions
2015-01-01
We perform extensive molecular dynamics (MD) simulations between pairs of ions of various diameters (2–5.5 Å in increments of 0.5 Å) and charge (+1 or −1) interacting in explicit water (TIP3P) under ambient conditions. We extract their potentials of mean force (PMFs). We develop an interpolation scheme, called i-PMF, that is capable of capturing the full set of PMFs for arbitrary combinations of ion sizes ranging from 2 to 5.5 Å. The advantage of the interpolation process is computational cost. Whereas it can take 100 h to simulate each PMF by MD, we can compute an equivalently accurate i-PMF in seconds. This process may be useful for rapid and accurate calculation of the strengths of salt bridges and the effects of bridging waters in biomolecular simulations. We also find that our data is consistent with Collins’ “law of matching affinities” of ion solubilities: small–small or large–large ion pairs are poorly soluble in water, whereas small–large are highly soluble. PMID:24625086
Accurate potential energy surfaces with a DFT+U(R) approach.
Kulik, Heather J; Marzari, Nicola
2011-11-21
We introduce an improvement to the Hubbard U augmented density functional approach known as DFT+U that incorporates variations in the value of self-consistently calculated, linear-response U with changes in geometry. This approach overcomes the one major shortcoming of previous DFT+U studies, i.e., the use of an averaged Hubbard U when comparing energies for different points along a potential energy surface is no longer required. While DFT+U is quite successful at providing accurate descriptions of localized electrons (e.g., d or f) by correcting self-interaction errors of standard exchange correlation functionals, we show several diatomic molecule examples where this position-dependent DFT+U(R) provides a significant two- to four-fold improvement over DFT+U predictions, when compared to accurate correlated quantum chemistry and experimental references. DFT+U(R) reduces errors in binding energies, frequencies, and equilibrium bond lengths by applying the linear-response, position-dependent U(R) at each configuration considered. This extension is most relevant where variations in U are large across the points being compared, as is the case with covalent diatomic molecules such as transition-metal oxides. We thus provide a tool for deciding whether a standard DFT+U approach is sufficient by determining the strength of the dependence of U on changes in coordinates. We also apply this approach to larger systems with greater degrees of freedom and demonstrate how DFT+U(R) may be applied automatically in relaxations, transition-state finding methods, and dynamics.
Boothroyd, A.I. ); Dove, J.E.; Keogh, W.J. ); Martin, P.G. ); Peterson, M.R. )
1991-09-15
The interaction potential energy surface (PES) of H{sub 4} is of great importance for quantum chemistry, as a test case for molecule--molecule interactions. It is also required for a detailed understanding of certain astrophysical processes, namely, collisional excitation and dissociation of H{sub 2} in molecular clouds, at densities too low to be accessible experimentally. Accurate {ital ab} {ital initio} energies were computed for 6046 conformations of H{sub 4}, using a multiple reference (single and) double excitation configuration interaction (MRD-CI) program. Both systematic and random'' errors were estimated to have an rms size of 0.6 mhartree, for a total rms error of about 0.9 mhartree (or 0.55 kcal/mol) in the final {ital ab} {ital initio} energy values. It proved possible to include in a self-consistent way {ital ab} {ital initio} energies calculated by Schwenke, bringing the number of H{sub 4} conformations to 6101. {ital Ab} {ital initio} energies were also computed for 404 conformations of H{sub 3}; adding {ital ab} {ital initio} energies calculated by other authors yielded a total of 772 conformations of H{sub 3}. (The H{sub 3} results, and an improved analytic PES for H{sub 3}, are reported elsewhere.) {ital Ab} {ital initio} energies are tabulated in this paper only for a sample of H{sub 4} conformations; a full list of all 6101 conformations of H{sub 4} (and 772 conformations of H{sub 3} ) is available from Physics Auxiliary Publication Service (PAPS), or from the authors.
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.
How to conduct and interpret ITC experiments accurately for cyclodextrin-guest interactions.
Bouchemal, Kawthar; Mazzaferro, Silvia
2012-06-01
Isothermal titration calorimetry (ITC) is one of the most interesting methods for the characterization of the interaction mechanisms of cyclodextrins (CDs) with drugs. In this review we explain how to conduct ITC experiments correctly for CD-guest interactions, how to choose an accurate fitting model for the titration curve and how to interpret carefully the ITC results. Finally, the use of ITC for the characterization of CD-containing nanoparticles is discussed.
Accurate oxidation potentials of 40 benzene and biphenyl derivatives with heteroatom substituents.
Luo, Pu; Feinberg, Adam M; Guirado, Gonzalo; Farid, Samir; Dinnocenzo, Joseph P
2014-10-03
The redox equilibrium method was used to determine accurate oxidation potentials in acetonitrile for 40 heteroatom-substituted compounds. These include methoxy-substituted benzenes and biphenyls, aromatic amines, and substituted acetanilides. The redox equilibrium method allowed oxidation potentials to be determined with high precision (≤ ±6 mV). Whereas most of the relative oxidation potentials follow well-established chemical trends, interestingly, the oxidation potentials of substituted N-methylacetanilides were found to be higher than those of the corresponding acetanilides. Density functional theory calculations provided insight into the origin of these surprising results in terms of the preferred conformations of the amides versus their cation radicals.
Mackie, Iain D; Dilabio, Gino A
2010-06-21
B971, PBE and PBE1 density functionals with 6-31G(d) basis sets are shown to accurately describe the binding in dispersion bound dimers. This is achieved through the use of dispersion-correcting potentials (DCPs) in conjunction with counterpoise corrections. DCPs resemble and are applied like conventional effective core potentials that can be used with most computational chemistry programs without code modification. Rather, DCPs are implemented by simple appendage to the input files for these types of programs. Binding energies are predicted to within ca. 11% and monomer separations to within ca. 0.06 A of high-level wavefunction data using B971/6-31G(d)-DCP. Similar results are obtained for PBE and PBE1 with the 6-31G(d) basis sets and DCPs. Although results found using the 3-21G(d) are not as impressive, they never-the-less show promise as a means of initial study for a wide variety of dimers, including those dominated by dispersion, hydrogen-bonding and a mixture of interactions. Notable improvement is found in comparison to M06-2X/6-31G(d) data, e.g., mean absolute deviations for the S22-set of dimers of ca. 13.6 and 16.5% for B971/6-31G(d)-DCP and M06-2X, respectively. However, it should be pointed out that the latter data were obtained using a larger integration grid size since a smaller grid results in different binding energies and geometries for simple dispersion-bound dimers such as methane and ethene.
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.
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.
Kistler, Melissa L; Patel, Komal G; Liu, Tianbo
2009-07-07
We report an approach of exploring the interaction between cationic surfactants and a type of structurally well-defined, spherical "Keplerate" polyoxometalate (POM) macroanionic molecular clusters, {Mo72V30}, in aqueous solution. The effectiveness of the interaction can be determined by monitoring the size change of the "blackberry" supramolecular structures formed by the self-assembly of {Mo72V30} macroions, which is determined by the effective charge density on the macroions. Long-chain surfactants (CTAB and CTAT) can interact with {Mo72V30} macroions stoichiometrically and lower their charge density. Consequently, the blackberry size decreases continuously with increasing surfactant concentration in solution. On the other hand, for short-chain surfactants (e.g., OTAB), a larger fraction of surfactants exist as discrete chains in solution and do not strongly interact with the macroions. This approach shows that a controllable amount of suitable surfactants can accurately tune the charge on large molecular clusters.
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).
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.
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.
NASA Astrophysics Data System (ADS)
Thompson, A. P.; Swiler, L. P.; Trott, C. R.; Foiles, S. M.; Tucker, G. J.
2015-03-01
We present a new interatomic potential for solids and liquids called Spectral Neighbor Analysis Potential (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected onto a basis of hyperspherical harmonics in four dimensions. The bispectrum components are the same bond-orientational order parameters employed by the GAP potential [1]. The SNAP potential, unlike GAP, assumes a linear relationship between atom energy and bispectrum components. The linear SNAP coefficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. We demonstrate that a previously unnoticed symmetry property can be exploited to reduce the computational cost of the force calculations by more than one order of magnitude. We present results for a SNAP potential for tantalum, showing that it accurately reproduces a range of commonly calculated properties of both the crystalline solid and the liquid phases. In addition, unlike simpler existing potentials, SNAP correctly predicts the energy barrier for screw dislocation migration in BCC tantalum.
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/.
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.
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).
Accurate and efficient computation of nonlocal potentials based on Gaussian-sum approximation
NASA Astrophysics Data System (ADS)
Exl, Lukas; Mauser, Norbert J.; Zhang, Yong
2016-12-01
We introduce an accurate and efficient method for the numerical evaluation of nonlocal potentials, including the 3D/2D Coulomb, 2D Poisson and 3D dipole-dipole potentials. Our method is based on a Gaussian-sum approximation of the singular convolution kernel combined with a Taylor expansion of the density. Starting from the convolution formulation of the nonlocal potential, for smooth and fast decaying densities, we make a full use of the Fourier pseudospectral (plane wave) approximation of the density and a separable Gaussian-sum approximation of the kernel in an interval where the singularity (the origin) is excluded. The potential is separated into a regular integral and a near-field singular correction integral. The first is computed with the Fourier pseudospectral method, while the latter is well resolved utilizing a low-order Taylor expansion of the density. Both parts are accelerated by fast Fourier transforms (FFT). The method is accurate (14-16 digits), efficient (O (Nlog N) complexity), low in storage, easily adaptable to other different kernels, applicable for anisotropic densities and highly parallelizable.
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.
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.
Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; Pronobis, Wiktor; von Lilienfeld, O Anatole; Müller, Klaus-Robert; Tkatchenko, Alexandre
2015-06-18
Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. In addition, the same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.
Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; ...
2015-06-04
Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstratemore » prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. The same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.« less
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.
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.
Neuberg, S L
1989-03-01
Investigated the idea that impression formation goals may regulate the impact that perceiver expectancies have on social interactions. In simulated interviews, interviewers Ss were given a negative expectancy about one applicant S and no expectancy about another. Half the interviewers were encouraged to form accurate impressions; the others were not. As predicted, no-goal interviewers exhibited a postinteraction impression bias against the negative-expectancy applicants, whereas the accuracy-goal interviewers did not. Moreover, the ability of the accuracy goal to reduce this bias was apparently mediated by more extensive and less biased interviewer information-gathering, which in turn elicited an improvement in negative-expectancy applicants' performances. These findings stress the theoretical and practical importance of considering the motivational context within which expectancy-tinged social interactions occur.
Electron-Vector Potential Interaction Hamiltonian
Ritchie, B
2003-03-27
The authors investigate an ambiguity inherent in the definition of the vector potential used in electron-electromagnetic field interactions. Two cases, Zeeman effect and Compton scattering, are studied.
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
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(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.
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.
Zaytsev, Anatoly V.; Sundin, Lynsie J.R.; DeLuca, Keith F.
2014-01-01
Accurate chromosome segregation relies on dynamic interactions between microtubules (MTs) and the NDC80 complex, a major kinetochore MT-binding component. Phosphorylation at multiple residues of its Hec1 subunit may tune kinetochore–MT binding affinity for diverse mitotic functions, but molecular details of such phosphoregulation remain elusive. Using quantitative analyses of mitotic progression in mammalian cells, we show that Hec1 phosphorylation provides graded control of kinetochore–MT affinity. In contrast, modeling the kinetochore interface with repetitive MT binding sites predicts a switchlike response. To reconcile these findings, we hypothesize that interactions between NDC80 complexes and MTs are not constrained, i.e., the NDC80 complexes can alternate their binding between adjacent kinetochore MTs. Experiments using cells with phosphomimetic Hec1 mutants corroborate predictions of such a model but not of the repetitive sites model. We propose that accurate regulation of kinetochore–MT affinity is driven by incremental phosphorylation of an NDC80 molecular “lawn,” in which the NDC80–MT bonds reorganize dynamically in response to the number and stability of MT attachments. PMID:24982430
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.
Fedorov, Dmitry A; Derevianko, Andrei; Varganov, Sergey A
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(1)Σ(+) 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.
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.
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).
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.
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.
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
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
Du, Qi-Shi; Wang, Cheng-Hua; Wang, Yu-Ting; Huang, Ri-Bo
2010-04-01
The electrostatic potential (ESP) is an important property of interactions within and between macromolecules, including those of importance in the life sciences. Semiempirical quantum chemical methods and classical Coulomb calculations fail to provide even qualitative ESP for many of these biomolecules. A new empirical ESP calculation method, namely, EM-ESP, is developed in this study, in which the traditional approach of point atomic charges and the classical Coulomb equation is discarded. In its place, the EM-ESP generates a three-dimensional electrostatic potential V(EM)(r) in molecular space that is the sum of contributions from all component atoms. The contribution of an atom k is formulated as a Gaussian function g(r(k);alpha(k),beta(k)) = alpha(k)/r(k)(betak) with two parameters (alpha(k) and beta(k)). The benchmark for the parameter optimization is the ESP obtained by using higher-level quantum chemical approaches (e.g., CCSD/TZVP). A set of atom-based parameters is optimized in a training set of common organic molecules. Calculated examples demonstrate that the EM-ESP approach is a vast improvement over the Coulombic approach in producing the molecular ESP contours that are comparable to the results obtained with higher-level quantum chemical methods. The atom-based parameters are shown to be transferrable between one part of closely related aromatic molecules. The atom-based ESP formulization and parametrization strategy can be extended to biological macromolecules, such as proteins, DNA, and RNA molecules. Since ESP is frequently used to rationalize and predict intermolecular interactions, we expect that the EM-ESP method will have important applications for studies of protein-ligand and protein-protein interactions in numerous areas of chemistry, molecular biology, and other life sciences.
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.
NASA Astrophysics Data System (ADS)
Marom, Noa; Knight, Joseph; Wang, Xiaopeng; Gallandi, Lukas; Dolgounitcheva, Olga; Ren, Xinguo; Ortiz, Vincent; Rinke, Patrick; Korzdorfer, Thomas
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, 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. 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.
Lao, Ka Un; Herbert, John M
2015-01-15
We present an overview of "XSAPT", a family of quantum chemistry methods for noncovalent interactions. These methods combine an efficient, iterative, monomer-based approach to computing many-body polarization interactions with a two-body version of symmetry-adapted perturbation theory (SAPT). The result is an efficient method for computing accurate intermolecular interaction energies in large noncovalent assemblies such as molecular and ionic clusters, molecular crystals, clathrates, or protein-ligand complexes. As in traditional SAPT, the XSAPT energy is decomposable into physically meaningful components. Dispersion interactions are problematic in traditional low-order SAPT, and two new approaches are introduced here in an attempt to improve this situation: (1) third-generation empirical atom-atom dispersion potentials, and (2) an empirically scaled version of second-order SAPT dispersion. Comparison to high-level ab initio benchmarks for dimers, water clusters, halide-water clusters, a methane clathrate hydrate, and a DNA intercalation complex illustrate both the accuracy of XSAPT-based methods as well as their limitations. The computational cost of XSAPT scales as O(N(3))-O(N(5)) with respect to monomer size, N, depending upon the particular version that is employed, but the accuracy is typically superior to alternative ab initio methods with similar scaling. Moreover, the monomer-based nature of XSAPT calculations makes them trivially parallelizable, such that wall times scale linearly with respect to the number of monomer units. XSAPT-based methods thus open the door to both qualitative and quantitative studies of noncovalent interactions in clusters, biomolecules, and condensed-phase systems.
Park, Sun Joo
2010-12-01
Huntingtin-interacting protein 1-related (HIP1r) is known to function in clathrin-mediated endocytosis and regulation of the actin cytoskeleton, which occurs continuously in non-dividing cells. This study reports a new function for HIP1r in mitosis. Green fluorescent protein-fused HIP1r localizes to the mitotic spindles. Depletion of HIP1r by RNA interference induces misalignment of chromosomes and prolonged mitosis, which is associated with decreased proliferation of HIP1r-deficeint cells. Chromosome misalignment leads to missegregation and ultimately production of multinucleated cells. Depletion of HIP1r causes persistent activation of the spindle checkpoint in misaligned chromosomes. These findings suggest that HIP1r plays an important role in regulating the attachment of spindle microtubules to chromosomes during mitosis, an event that is required for accurate congression and segregation of chromosomes. This finding may provide new insights that improve the understanding of various human diseases involving HIP1r as well as its fusion genes.
Nanoparticle interaction potentials constructed by multiscale computation.
Lee, Cheng K; Hua, Chi C
2010-06-14
The van der Waals (vdW) potentials governing macroscopic objects have long been formulated in the context of classical theories, such as Hamaker's microscopic theory and Lifshitz's continuum theory. This work addresses the possibility of constructing the vdW interaction potentials of nanoparticle species using multiscale simulation schemes. Amorphous silica nanoparticles were considered as a benchmark example for which a series of (SiO(2))(n) (n being an integer) has been systematically surveyed as the potential candidates of the packing units that reproduce known bulk material properties in atomistic molecular dynamics simulations. This strategy led to the identification of spherical Si(6)O(12) molecules, later utilized as the elementary coarse-grained (CG) particles to compute the pair interaction potentials of silica nanoparticles ranging from 0.62 to 100 nm in diameter. The model nanoparticles so built may, in turn, serve as the children CG particles to construct nanoparticles assuming arbitrary sizes and shapes. Major observations are as follows. The pair interaction potentials for all the investigated spherical silica nanoparticles can be cast into a semiempirical, generalized Lennard-Jones 2alpha-alpha potential (alpha being a size-dependent, large integral number). In its reduced form, we discuss the implied universalities for the vdW potentials governing a certain range of amorphous nanoparticle species as well as how thermodynamic transferability can be fulfilled automatically. In view of future applications with colloidal suspensions, we briefly evaluated the vdW potential in the presence of a "screening" medium mimicking the effects of electrical double layers or grafting materials atop the nanoparticle core. The general observations shed new light on strategies to attain a microscopic control over interparticle attractions. In future perspectives, the proposed multiscale computation scheme shall help bridge the current gap between the modeling of
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.
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.
Bozkaya, Uğur
2013-10-21
The extended Koopmans' theorem (EKT) provides a straightforward way to compute ionization potentials (IPs) from any level of theory, in principle. However, for non-variational methods, such as Møller-Plesset perturbation and coupled-cluster theories, the EKT computations can only be performed as by-products of analytic gradients as the relaxed generalized Fock matrix (GFM) and one- and two-particle density matrices (OPDM and TPDM, respectively) are required [J. Cioslowski, P. Piskorz, and G. Liu, J. Chem. Phys. 107, 6804 (1997)]. However, for the orbital-optimized methods both the GFM and OPDM are readily available and symmetric, as opposed to the standard post Hartree-Fock (HF) methods. Further, the orbital optimized methods solve the N-representability problem, which may arise when the relaxed particle density matrices are employed for the standard methods, by disregarding the orbital Z-vector contributions for the OPDM. Moreover, for challenging chemical systems, where spin or spatial symmetry-breaking problems are observed, the abnormal orbital response contributions arising from the numerical instabilities in the HF molecular orbital Hessian can be avoided by the orbital-optimization. Hence, it appears that the orbital-optimized methods are the most natural choice for the study of the EKT. In this research, the EKT for the orbital-optimized methods, such as orbital-optimized second- and third-order Møller-Plesset perturbation [U. Bozkaya, J. Chem. Phys. 135, 224103 (2011)] and coupled-electron pair theories [OCEPA(0)] [U. Bozkaya and C. D. Sherrill, J. Chem. Phys. 139, 054104 (2013)], are presented. The presented methods are applied to IPs of the second- and third-row atoms, and closed- and open-shell molecules. Performances of the orbital-optimized methods are compared with those of the counterpart standard methods. Especially, results of the OCEPA(0) method (with the aug-cc-pVTZ basis set) for the lowest IPs of the considered atoms and closed
Song, Yu-Zhi; Zhang, Lu-Lu; Gao, Shou-Bao; Meng, Qing-Tian
2016-01-01
A globally accurate many-body expansion potential energy surface is reported for HCS(X2A′) by fitting a wealth of accurate ab initio energies calculated at the multireference configuration interaction level using aug-cc-pVQZ and aug-cc-pV5Z basis sets via extrapolation to the complete basis set limit. The topographical features of the present potential energy surface are examined in detail and is in good agreement with the raw ab initio results, as well as other theoretical results available in literatures. By utilizing the potential energy surface of HCS(X2A′), the dynamic studies of the C(3P) + SH(X2Π) → H(2S) + CS(X1∑+) reaction has been carried out using quasi-classical trajectory method. PMID:27898106
NASA Technical Reports Server (NTRS)
Kiris, Cetin; Kwak, Dochan
2001-01-01
Two numerical procedures, one based on artificial compressibility method and the other pressure projection method, are outlined for obtaining time-accurate solutions of the incompressible Navier-Stokes equations. The performance of the two method are compared by obtaining unsteady solutions for the evolution of twin vortices behind a at plate. Calculated results are compared with experimental and other numerical results. For an un- steady ow which requires small physical time step, pressure projection method was found to be computationally efficient since it does not require any subiterations procedure. It was observed that the artificial compressibility method requires a fast convergence scheme at each physical time step in order to satisfy incompressibility condition. This was obtained by using a GMRES-ILU(0) solver in our computations. When a line-relaxation scheme was used, the time accuracy was degraded and time-accurate computations became very expensive.
NASA Astrophysics Data System (ADS)
Gibelli, François; Lombez, Laurent; Guillemoles, Jean-François
2017-02-01
In order to characterize hot carrier populations in semiconductors, photoluminescence measurement is a convenient tool, enabling us to probe the carrier thermodynamical properties in a contactless way. However, the analysis of the photoluminescence spectra is based on some assumptions which will be discussed in this work. We especially emphasize the importance of the variation of the material absorptivity that should be considered to access accurate thermodynamical properties of the carriers, especially by varying the excitation power. The proposed method enables us to obtain more accurate results of thermodynamical properties by taking into account a rigorous physical description and finds direct application in investigating hot carrier solar cells, which are an adequate concept for achieving high conversion efficiencies with a relatively simple device architecture.
Gibelli, François; Lombez, Laurent; Guillemoles, Jean-François
2017-02-15
In order to characterize hot carrier populations in semiconductors, photoluminescence measurement is a convenient tool, enabling us to probe the carrier thermodynamical properties in a contactless way. However, the analysis of the photoluminescence spectra is based on some assumptions which will be discussed in this work. We especially emphasize the importance of the variation of the material absorptivity that should be considered to access accurate thermodynamical properties of the carriers, especially by varying the excitation power. The proposed method enables us to obtain more accurate results of thermodynamical properties by taking into account a rigorous physical description and finds direct application in investigating hot carrier solar cells, which are an adequate concept for achieving high conversion efficiencies with a relatively simple device architecture.
Askalany, Ahmed A; Saha, Bidyut B
2017-03-15
Accurate estimation of the isosteric heat of adsorption is mandatory for a good modeling of adsorption processes. In this paper a thermodynamic formalism on adsorbed phase volume which is a function of adsorption pressure and temperature has been proposed for the precise estimation of the isosteric heat of adsorption. The estimated isosteric heat of adsorption using the new correlation has been compared with measured values of prudently selected several adsorbent-refrigerant pairs from open literature. Results showed that the proposed isosteric heat of adsorption correlation fits the experimentally measured values better than the Clausius-Clapeyron equation.
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.
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
Accurate calculation of second virial coefficient of the Exp-6 potential and its application
NASA Astrophysics Data System (ADS)
Mamedov, B. A.; Somuncu, E.
2015-02-01
In this study, a new approach to calculate the second virial coefficient of the Exp-6 potential is proposed. Over a wide temperature range, the calculated results of the second virial coefficient determined from Exp-6 potential are comparable with the calculations of second virial coefficient over Lennard-Jones (12-6) potential. As an example of application, the formulas obtained for second virial coefficient are calculated for molecules Kr,Xe,N2,Hg,CH4 and C2H6. The obtained results are in good agreement with the data available in the literature.
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
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.
Guo, Lifen; Han, Huixian; Ma, Jianyi; Guo, Hua
2015-08-06
Vinylidene is a high-energy isomer of acetylene, and the rearrangement of bonds in the two species serves as a prototype for isomerization reactions. Here, a full-dimensional quantum mechanical study of the vinylidene vibration is carried out on a recently developed global acetylene-vinylidene potential energy surface by simulating the photodetachment dynamics of the vinylidene anion. Several low-lying vibrational levels of the anion were first determined on a new ab initio based potential energy surface, and their photoelectron spectra were obtained within the Condon approximation. The vibrational features of the vinylidene isomer are found to agree well with the experiment in both positions and intensities, validating the global acetylene-vinylidene potential energy surface.
Accurate determination of the first ionization potential of actinides by laser spectroscopy
NASA Astrophysics Data System (ADS)
Trautmann, N.
1994-10-01
A new method is described for the precise determination of the first ionization potential of elements which are available only in small amounts such as the heavier actinides. It is based on resonance ionization mass spectroscopy (RIMS) in the presence of an external electric field. Extrapolation of the ionization thresholds obtained with different electric field strengths to field strength zero leads directly to the first ionization potential. With samples of 10(exp 12) atoms of Np-237 and Am-243 experimental values for the first ionization potential of neptunium of IP(sub Np) = 6.2655(2) eV and of americium of IP(sub Am) = 5.9738(2) eV were obtained. This technique was also applied to thorium yielding a value of IP(sub Th) = 6.3067(2) eV. In addition the precision of the method was confirmed by the convergences of Rydberg series of americium measured by means of RIMS.
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.
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.
The potential of more accurate InSAR covariance matrix estimation for land cover mapping
NASA Astrophysics Data System (ADS)
Jiang, Mi; Yong, Bin; Tian, Xin; Malhotra, Rakesh; Hu, Rui; Li, Zhiwei; Yu, Zhongbo; Zhang, Xinxin
2017-04-01
Synthetic aperture radar (SAR) and Interferometric SAR (InSAR) provide both structural and electromagnetic information for the ground surface and therefore have been widely used for land cover classification. However, relatively few studies have developed analyses that investigate SAR datasets over richly textured areas where heterogeneous land covers exist and intermingle over short distances. One of main difficulties is that the shapes of the structures in a SAR image cannot be represented in detail as mixed pixels are likely to occur when conventional InSAR parameter estimation methods are used. To solve this problem and further extend previous research into remote monitoring of urban environments, we address the use of accurate InSAR covariance matrix estimation to improve the accuracy of land cover mapping. The standard and updated methods were tested using the HH-polarization TerraSAR-X dataset and compared with each other using the random forest classifier. A detailed accuracy assessment complied for six types of surfaces shows that the updated method outperforms the standard approach by around 9%, with an overall accuracy of 82.46% over areas with rich texture in Zhuhai, China. This paper demonstrates that the accuracy of land cover mapping can benefit from the 3 enhancement of the quality of the observations in addition to classifiers selection and multi-source data ingratiation reported in previous studies.
Accurate high-pressure and high-temperature effective pair potentials for the systems N2-N and O2-O
NASA Astrophysics Data System (ADS)
van Thiel, M.; Ree, F. H.
1996-04-01
Statistical mechanical chemical equilibrium calculations of N2 and O2 show that these molecules dissociate behind strong shock waves. Our determination of accurate intermolecular potentials has required the consideration of the dissociation products N and O. Our previous theoretical efforts to predict the thermodynamic properties of these molecules relied in part on corresponding states theory and shock wave data of argon, without consideration of the dissociation products. Recent high-pressure Hugoniot measurements, however, allowed a more accurate determination of the potentials and the explicit inclusion of the dissociation products. The best fit to the data is obtained with the exponential-6 coefficients, for O2-O2: ɛ/k=125 K, r*=3.86 Å, α=13.2; for O-O: ɛ/k=700 K, r*=2.40 Å, α=11.0; for N2-N2: ɛ/k=293 K, r*=3.91 Å, α=11.5; and for N-N: ɛ/k=600 K, r*=2.47 Å, α=10.0. The unlike pair interactions are obtained from these like interactions with a modified Lorentz-Berthelot rule. The coefficients in the modified Lorentz-Berthelot equations are k/l/m=1/1/0.93 for O2-O- and k/l/m=1/1/0.90 for N2-N interactions.
Sharapa, Dmitry I; Margraf, Johannes T; Hesselmann, Andreas; Clark, Timothy
2017-01-10
The self-assembly of molecular building blocks is a promising route to low-cost nanoelectronic devices. It would be very appealing to use computer-aided design to identify suitable molecules. However, molecular self-assembly is guided by weak interactions, such as dispersion, which have long been notoriously difficult to describe with quantum chemical methods. In recent years, several viable techniques have emerged, ranging from empirical dispersion corrections for DFT to fast perturbation and coupled-cluster theories. In this work, we test these methods for the dimer of the prototypical building block for nanoelectronics, C60-fullerene. Benchmark quality data is obtained from DFT-based symmetry-adapted perturbation theory (SAPT), the adiabatic-connection fluctuation dissipation (ACFD) theorem using an adiabatic LDA kernel, and domain-based local pair natural orbital (DLPNO) coupled-pair and coupled-cluster methods. These benchmarks are used to evaluate economical dispersion-corrected DFT methods, double-hybrid DFT functionals, and second-order Møller-Plesset theory. Furthermore, we provide analytical fits to the benchmark interaction curves, which can be used for a coarse-grain description of fullerene self-assembly. These analytical expressions differ significantly from those reported previously based on bulk data.
NASA Astrophysics Data System (ADS)
Chaplin, D. H.; Hutchison, W. D.; Prandolini, M. J.; Bowden, G. J.
1998-01-01
The application of double and triple resonance techniques to enhance signals in quadrupole interaction — nuclear magnetic resonance on oriented nuclei spectroscopy, is illustrated for the antiferromagnet ( 54Mn)MnBr 2-4H 2O. Unusual shifts of the quadrupolar split, higher order, ν ±2, ±1 subresonance, comparable to the NMRON linewidth, are observed and explained.
Accurate method for including solid-fluid boundary interactions in mesoscopic model fluids
Berkenbos, A. Lowe, C.P.
2008-04-20
Particle models are attractive methods for simulating the dynamics of complex mesoscopic fluids. Many practical applications of this methodology involve flow through a solid geometry. As the system is modeled using particles whose positions move continuously in space, one might expect that implementing the correct stick boundary condition exactly at the solid-fluid interface is straightforward. After all, unlike discrete methods there is no mapping onto a grid to contend with. In this article we describe a method that, for axisymmetric flows, imposes both the no-slip condition and continuity of stress at the interface. We show that the new method then accurately reproduces correct hydrodynamic behavior right up to the location of the interface. As such, computed flow profiles are correct even using a relatively small number of particles to model the fluid.
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.
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.
Can a Global Model Accurately Simulate Land-Atmosphere Interactions under Climate Change Conditions?
NASA Astrophysics Data System (ADS)
Zhou, C., VI; Wang, K.
2015-12-01
Surface air temperature (Ta) is largely determined by surface net radiation (Rn) and its partitioning into latent (LE) and sensible heat fluxes (H). Existing model evaluations of the absolute values of these fluxes are less helpful because the evaluation results are a blending of inconsistent spatial scales, inaccurate model forcing data and inaccurate parameterizations. This study further evaluates the relationship of LE and H with Rn and environmental parameters, including Ta, relative humidity (RH) and wind speed (WS), using ERA-interim reanalysis data at a grid of 0.125°×0.125° with measurements at AmeriFlux sites from 1998 to 2012. The results demonstrate that ERA-Interim can reproduce the absolute values of environmental parameters, radiation and turbulent fluxes rather accurately. The model performs well in simulating the correlation of LE and H to Rn, except for the notable correlation overestimation of H against Rn over high-density vegetation (e.g., deciduous broadleaf forest (DBF), grassland (GRA) and cropland (CRO)). The sensitivity of LE to Rn in the model is similar to the observations, but that of H to Rn is overestimated by 24.2%. In regions with high-density vegetation, the correlation coefficient between H and Ta is overestimated by more than 0.2, whereas that between H and WS is underestimated by more than 0.43. The sensitivity of H to Ta is overestimated by 0.72 Wm-2 °C-1, whereas that of H to WS in the model is underestimated by 16.15 Wm-2/(ms-1) over all of the sites. Considering both LE and H, the model cannot accurately capture the response of the evaporative fraction (EF=LE/(LE+H)) to Rn and the environmental parameters.
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.
NASA Astrophysics Data System (ADS)
Barenbrug, Theo M. A. O. M.; Peters, E. A. J. F. (Frank); Schieber, Jay D.
2002-11-01
In Brownian Dynamics simulations, the diffusive motion of the particles is simulated by adding random displacements, proportional to the square root of the chosen time step. When computing average quantities, these Brownian contributions usually average out, and the overall simulation error becomes proportional to the time step. A special situation arises if the particles undergo hard-body interactions that instantaneously change their properties, as in absorption or association processes, chemical reactions, etc. The common "naı̈ve simulation method" accounts for these interactions by checking for hard-body overlaps after every time step. Due to the simplification of the diffusive motion, a substantial part of the actual hard-body interactions is not detected by this method, resulting in an overall simulation error proportional to the square root of the time step. In this paper we take the hard-body interactions during the time step interval into account, using the relative positions of the particles at the beginning and at the end of the time step, as provided by the naı̈ve method, and the analytical solution for the diffusion of a point particle around an absorbing sphere. Öttinger used a similar approach for the one-dimensional case [Stochastic Processes in Polymeric Fluids (Springer, Berlin, 1996), p. 270]. We applied the "corrected simulation method" to the case of a simple, second-order chemical reaction. The results agree with recent theoretical predictions [K. Hyojoon and Joe S. Kook, Phys. Rev. E 61, 3426 (2000)]. The obtained simulation error is proportional to the time step, instead of its square root. The new method needs substantially less simulation time to obtain the same accuracy. Finally, we briefly discuss a straightforward way to extend the method for simulations of systems with additional (deterministic) forces.
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.
CombiROC: an interactive web tool for selecting accurate marker combinations of omics data.
Mazzara, Saveria; Rossi, Riccardo L; Grifantini, Renata; Donizetti, Simone; Abrignani, Sergio; Bombaci, Mauro
2017-03-30
Diagnostic accuracy can be improved considerably by combining multiple markers, whose performance in identifying diseased subjects is usually assessed via receiver operating characteristic (ROC) curves. The selection of multimarker signatures is a complicated process that requires integration of data signatures with sophisticated statistical methods. We developed a user-friendly tool, called CombiROC, to help researchers accurately determine optimal markers combinations from diverse omics methods. With CombiROC data from different domains, such as proteomics and transcriptomics, can be analyzed using sensitivity/specificity filters: the number of candidate marker panels rising from combinatorial analysis is easily optimized bypassing limitations imposed by the nature of different experimental approaches. Leaving to the user full control on initial selection stringency, CombiROC computes sensitivity and specificity for all markers combinations, performances of best combinations and ROC curves for automatic comparisons, all visualized in a graphic interface. CombiROC was designed without hard-coded thresholds, allowing a custom fit to each specific data: this dramatically reduces the computational burden and lowers the false negative rates given by fixed thresholds. The application was validated with published data, confirming the marker combination already originally described or even finding new ones. CombiROC is a novel tool for the scientific community freely available at http://CombiROC.eu.
CombiROC: an interactive web tool for selecting accurate marker combinations of omics data
Mazzara, Saveria; Rossi, Riccardo L.; Grifantini, Renata; Donizetti, Simone; Abrignani, Sergio; Bombaci, Mauro
2017-01-01
Diagnostic accuracy can be improved considerably by combining multiple markers, whose performance in identifying diseased subjects is usually assessed via receiver operating characteristic (ROC) curves. The selection of multimarker signatures is a complicated process that requires integration of data signatures with sophisticated statistical methods. We developed a user-friendly tool, called CombiROC, to help researchers accurately determine optimal markers combinations from diverse omics methods. With CombiROC data from different domains, such as proteomics and transcriptomics, can be analyzed using sensitivity/specificity filters: the number of candidate marker panels rising from combinatorial analysis is easily optimized bypassing limitations imposed by the nature of different experimental approaches. Leaving to the user full control on initial selection stringency, CombiROC computes sensitivity and specificity for all markers combinations, performances of best combinations and ROC curves for automatic comparisons, all visualized in a graphic interface. CombiROC was designed without hard-coded thresholds, allowing a custom fit to each specific data: this dramatically reduces the computational burden and lowers the false negative rates given by fixed thresholds. The application was validated with published data, confirming the marker combination already originally described or even finding new ones. CombiROC is a novel tool for the scientific community freely available at http://CombiROC.eu. PMID:28358118
NASA Astrophysics Data System (ADS)
Alborzpour, Jonathan P.; Tew, David P.; Habershon, Scott
2016-11-01
Solution of the time-dependent Schrödinger equation using a linear combination of basis functions, such as Gaussian wavepackets (GWPs), requires costly evaluation of integrals over the entire potential energy surface (PES) of the system. The standard approach, motivated by computational tractability for direct dynamics, is to approximate the PES with a second order Taylor expansion, for example centred at each GWP. In this article, we propose an alternative method for approximating PES matrix elements based on PES interpolation using Gaussian process regression (GPR). Our GPR scheme requires only single-point evaluations of the PES at a limited number of configurations in each time-step; the necessity of performing often-expensive evaluations of the Hessian matrix is completely avoided. In applications to 2-, 5-, and 10-dimensional benchmark models describing a tunnelling coordinate coupled non-linearly to a set of harmonic oscillators, we find that our GPR method results in PES matrix elements for which the average error is, in the best case, two orders-of-magnitude smaller and, in the worst case, directly comparable to that determined by any other Taylor expansion method, without requiring additional PES evaluations or Hessian matrices. Given the computational simplicity of GPR, as well as the opportunities for further refinement of the procedure highlighted herein, we argue that our GPR methodology should replace methods for evaluating PES matrix elements using Taylor expansions in quantum dynamics simulations.
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)
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).
Huang, Xinchuan; Schwenke, David W; Lee, Timothy J
2008-12-07
A global potential energy surface (PES) that includes short and long range terms has been determined for the NH(3) molecule. The singles and doubles coupled-cluster method that includes a perturbational estimate of connected triple excitations and the internally contracted averaged coupled-pair functional electronic structure methods have been used in conjunction with very large correlation-consistent basis sets, including diffuse functions. Extrapolation to the one-particle basis set limit was performed and core correlation and scalar relativistic contributions were included directly, while the diagonal Born-Oppenheimer correction was added. Our best purely ab initio PES, denoted "mixed," is constructed from two PESs which differ in whether the ic-ACPF higher-order correlation correction was added or not. Rovibrational transition energies computed from the mixed PES agree well with experiment and the best previous theoretical studies, but most importantly the quality does not deteriorate even up to 10 300 cm(-1) above the zero-point energy (ZPE). The mixed PES was improved further by empirical refinement using the most reliable J=0-2 rovibrational transitions in the HITRAN 2004 database. Agreement between high-resolution experiment and rovibrational transition energies computed from our refined PES for J=0-6 is excellent. Indeed, the root mean square (rms) error for 13 HITRAN 2004 bands for J=0-2 is 0.023 cm(-1) and that for each band is always
Lao, Ka Un; Schäffer, Rainer; Jansen, Georg; Herbert, John M
2015-06-09
Three new data sets for intermolecular interactions, AHB21 for anion-neutral dimers, CHB6 for cation-neutral dimers, and IL16 for ion pairs, are assembled here, with complete-basis CCSD(T) results for each. These benchmarks are then used to evaluate the accuracy of the single-exchange approximation that is used for exchange energies in symmetry-adapted perturbation theory (SAPT), and the accuracy of SAPT based on wave function and density-functional descriptions of the monomers is evaluated. High-level SAPT calculations afford poor results for these data sets, and this includes the recently proposed "gold", "silver", and "bronze standards" of SAPT, namely, SAPT2+(3)-δMP2/aug-cc-pVTZ, SAPT2+/aug-cc-pVDZ, and sSAPT0/jun-cc-pVDZ, respectively [ Parker , T. M. , et al. , J. Chem. Phys. 2014 , 140 , 094106 ]. Especially poor results are obtained for symmetric shared-proton systems of the form X(-)···H(+)···X(-), for X = F, Cl, or OH. For the anionic data set, the SAPT2+(CCD)-δMP2/aug-cc-pVTZ method exhibits the best performance, with a mean absolute error (MAE) of 0.3 kcal/mol and a maximum error of 0.7 kcal/mol. For the cationic data set, the highest-level SAPT method, SAPT2+3-δMP2/aug-cc-pVQZ, outperforms the rest of the SAPT methods, with a MAE of 0.2 kcal/mol and a maximum error of 0.4 kcal/mol. For the ion-pair data set, the SAPT2+3-δMP2/aug-cc-pVTZ performs the best among all SAPT methods with a MAE of 0.3 kcal/mol and a maximum error of 0.9 kcal/mol. Overall, SAPT2+3-δMP2/aug-cc-pVTZ affords a small and balanced MAE (<0.5 kcal/mol) for all three data sets, with an overall MAE of 0.4 kcal/mol. Despite the breakdown of perturbation theory for ionic systems at short-range, SAPT can still be saved given two corrections: a "δHF" correction, which requires a supermolecular Hartree-Fock calculation to incorporate polarization effects beyond second order, and a "δMP2" correction, which requires a supermolecular MP2 calculation to account for higher
Generation of Accurate Lateral Boundary Conditions for a Surface-Water Groundwater Interaction Model
NASA Astrophysics Data System (ADS)
Khambhammettu, P.; Tsou, M.; Panday, S. M.; Kool, J.; Wei, X.
2010-12-01
groundwater pumping / recharge in the SDM and adds the kriged residual surface as variations back to the trend. The variations could be from the scale effects of grid resolution and from the temporal averaging of stresses (pumping, recharge, etc.,). The validity of the approach is demonstrated by visual and statistical comparison of the observed and simulated heads before and after correction. For predictive simulations, an Artificial Neural Network was trained to predict heads at monitoring wells based on precipitation and pumping. These predicted head values could then be used as surrogate observations for correcting the results of the regional SDM. In summary, an appropriate approach to link a regional groundwater model to a detailed surface-water groundwater interaction model is demonstrated with an example.
NASA Astrophysics Data System (ADS)
Amador, Davi H. T.; de Oliveira, Heibbe C. B.; Sambrano, Julio R.; Gargano, Ricardo; de Macedo, Luiz Guilherme M.
2016-10-01
A prolapse-free basis set for Eka-Actinium (E121, Z = 121), numerical atomic calculations on E121, spectroscopic constants and accurate analytical form for the potential energy curve of diatomic E121F obtained at 4-component all-electron CCSD(T) level including Gaunt interaction are presented. The results show a strong and polarized bond (≈181 kcal/mol in strength) between E121 and F, the outermost frontier molecular orbitals from E121F should be fairly similar to the ones from AcF and there is no evidence of break of periodic trends. Moreover, the Gaunt interaction, although small, is expected to influence considerably the overall rovibrational spectra.
a General Transformation to Canonical Form for Potentials in Pairwise Intermolecular Interactions
NASA Astrophysics Data System (ADS)
Walton, Jay R.; Rivera-Rivera, Luis A.; Lucchese, Robert R.; Bevan, John W.
2015-06-01
A generalized formulation of explicit transformations is introduced to investigate the concept of a canonical potential in both fundamental chemical and intermolecular bonding. Different classes of representative ground electronic state pairwise interatomic interactions are referenced to a single canonical potential illustrating application of explicit transformations. Specifically, accurately determined potentials of the diatomic molecules H_2, H_2^+, HF, LiH, argon dimer, and one-dimensional dissociative coordinates in Ar-HBr, OC-HF, and OC-Cl_2 are investigated throughout their bound potentials. The advantages of the current formulation for accurately evaluating equilibrium dissociation energies and a fundamentally different unified perspective on nature of intermolecular interactions will be emphasized. In particular, this canonical approach has relevance to previous assertions that there is no very fundamental distinction between van der Waals bonding and covalent bonding or for that matter hydrogen and halogen bonds.
Zhu, Lijuan; Wang, Zhikai; Wang, Wenwen; Wang, Chunli; Hua, Shasha; Su, Zeqi; Brako, Larry; Garcia-Barrio, Minerva; Ye, Mingliang; Wei, Xuan; Zou, Hanfa; Ding, Xia; Liu, Lifang; Liu, Xing; Yao, Xuebiao
2015-01-01
Mitotic chromosome segregation is orchestrated by the dynamic interaction of spindle microtubules with the kinetochores. During chromosome alignment, kinetochore-bound microtubules undergo dynamic cycles between growth and shrinkage, leading to an oscillatory movement of chromosomes along the spindle axis. Although kinetochore protein CENP-H serves as a molecular control of kinetochore-microtubule dynamics, the mechanistic link between CENP-H and kinetochore microtubules (kMT) has remained less characterized. Here, we show that CSPP1 is a kinetochore protein essential for accurate chromosome movements in mitosis. CSPP1 binds to CENP-H in vitro and in vivo. Suppression of CSPP1 perturbs proper mitotic progression and compromises the satisfaction of spindle assembly checkpoint. In addition, chromosome oscillation is greatly attenuated in CSPP1-depleted cells, similar to what was observed in the CENP-H-depleted cells. Importantly, CSPP1 depletion enhances velocity of kinetochore movement, and overexpression of CSPP1 decreases the speed, suggesting that CSPP1 promotes kMT stability during cell division. Specific perturbation of CENP-H/CSPP1 interaction using a membrane-permeable competing peptide resulted in a transient mitotic arrest and chromosome segregation defect. Based on these findings, we propose that CSPP1 cooperates with CENP-H on kinetochores to serve as a novel regulator of kMT dynamics for accurate chromosome segregation. PMID:26378239
Zhu, Lijuan; Wang, Zhikai; Wang, Wenwen; Wang, Chunli; Hua, Shasha; Su, Zeqi; Brako, Larry; Garcia-Barrio, Minerva; Ye, Mingliang; Wei, Xuan; Zou, Hanfa; Ding, Xia; Liu, Lifang; Liu, Xing; Yao, Xuebiao
2015-11-06
Mitotic chromosome segregation is orchestrated by the dynamic interaction of spindle microtubules with the kinetochores. During chromosome alignment, kinetochore-bound microtubules undergo dynamic cycles between growth and shrinkage, leading to an oscillatory movement of chromosomes along the spindle axis. Although kinetochore protein CENP-H serves as a molecular control of kinetochore-microtubule dynamics, the mechanistic link between CENP-H and kinetochore microtubules (kMT) has remained less characterized. Here, we show that CSPP1 is a kinetochore protein essential for accurate chromosome movements in mitosis. CSPP1 binds to CENP-H in vitro and in vivo. Suppression of CSPP1 perturbs proper mitotic progression and compromises the satisfaction of spindle assembly checkpoint. In addition, chromosome oscillation is greatly attenuated in CSPP1-depleted cells, similar to what was observed in the CENP-H-depleted cells. Importantly, CSPP1 depletion enhances velocity of kinetochore movement, and overexpression of CSPP1 decreases the speed, suggesting that CSPP1 promotes kMT stability during cell division. Specific perturbation of CENP-H/CSPP1 interaction using a membrane-permeable competing peptide resulted in a transient mitotic arrest and chromosome segregation defect. Based on these findings, we propose that CSPP1 cooperates with CENP-H on kinetochores to serve as a novel regulator of kMT dynamics for accurate chromosome segregation.
An analytical fit to an accurate ab initio ( 1A 1) potential surface of H 2O
NASA Astrophysics Data System (ADS)
Redmon, Michael J.; Schatz, George C.
1981-01-01
The accurate ab initio MBPT quartic force field of Bartlett, Shavitt and Purvis has been fit to an analytical function using a method developed by Sorbie and Murrell (SM). An analysis of this surface indicates that it describes most properties of the H 2O molecule very accurately, including an exact fit to the MBPT force field, and very close to the correct energy difference between linear and equilibrium H 2O. The surface also reproduces the correct diatomic potentials in all dissociative regions, but some aspects of it in the "near asymptotic" O( 1D) + H 2 region are not quantitatively described. For example, the potential seems to be too attractive at long range for O + H 2 encounters, although it does have the correct minimum energy path geometry and correctly exhibits no barrier to O atom insertion. Comparisons of this surface with one previously developed by SM indicates generally good agreement between the two, especially after some of the SM parameters were corrected, using a numerical differentiation algorithm to evaluate them. A surface developed by Schinke and Lester (SL) is more realistic than outs in the O( 1D) + H 2 regions, but less quantitative in its description of the H 2O molecule. Overall, the present fit appears to be both realistic and quantitative for energy displacements up to 3-4; eV from H 2O equilibrium, and should therefore be useful for spectroscopic and collision dynamics studies involving H 2O.
NASA Astrophysics Data System (ADS)
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.
Hughes, Timothy J; Kandathil, Shaun M; Popelier, Paul L A
2015-02-05
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).
Yuan, Xuye; Chen, Jiajia; Lin, Yuxin; Li, Yin; Xu, Lihua; Chen, Luonan; Hua, Haiying; Shen, Bairong
2017-01-01
Leukemia is a leading cause of cancer deaths in the developed countries. Great efforts have been undertaken in search of diagnostic biomarkers of leukemia. However, leukemia is highly complex and heterogeneous, involving interaction among multiple molecular components. Individual molecules are not necessarily sensitive diagnostic indicators. Network biomarkers are considered to outperform individual molecules in disease characterization. We applied an integrative approach that identifies active network modules as putative biomarkers for leukemia diagnosis. We first reconstructed the leukemia-specific PPI network using protein-protein interactions from the Protein Interaction Network Analysis (PINA) and protein annotations from GeneGo. The network was further integrated with gene expression profiles to identify active modules with leukemia relevance. Finally, the candidate network-based biomarker was evaluated for the diagnosing performance. A network of 97 genes and 400 interactions was identified for accurate diagnosis of leukemia. Functional enrichment analysis revealed that the network biomarkers were enriched in pathways in cancer. The network biomarkers could discriminate leukemia samples from the normal controls more effectively than the known biomarkers. The network biomarkers provide a useful tool to diagnose leukemia and also aids in further understanding the molecular basis of leukemia. PMID:28243332
Potential food-drug interactions in long-term care.
Anderson, Judy K; Fox, Jodie R
2012-04-01
Medication administration at mealtimes may result in food-drug interactions. Older adults are especially at risk of food-drug interactions leading to adverse drug effects and subtherapeutic responses. Research on potential food-drug interactions is limited and dated. This study examined the frequency of potential food-drug interactions in long-term care. Forty-nine percent of drugs administered at mealtimes had potential for interaction, with cardiovascular medications given most frequently. The frequency of potential interactions makes this phenomenon critically important to review. Collaboration between nurses and pharmacists may identify optimal medication scheduling. Nurses can enhance care by identifying strategies to limit interactions through knowledge and creative, collaborative administration schedules.
Namazian, Mansoor; Coote, Michelle L
2007-08-02
Standard ab initio molecular orbital theory and density functional theory calculations have been used to calculate absolute one-electron reduction potentials of several para-quinones in acetonitrile. The high-level composite method of G3(MP2)-RAD is used for the gas-phase calculations and a continuum model of solvation, CPCM, has been employed to calculate solvation energies. To compare the theoretical reduction potentials with experiment, the reduction potentials relative to a standard calomel electrode (SCE) have also been calculated and compared to experimental values. The average error of the calculated reduction potentials using the proposed method is 0.07 V without any additional approximation. An ONIOM method in which the core is studied at G3(MP2)-RAD and the substituent effect of the rest of the molecule is studied at R(O)MP2/6-311+G(3df,2p) provides an accurate low-cost alternative to G3(MP2)-RAD for larger molecules.
Potential drug interactions with dietary and herbal supplements during hospitalization.
Levy, Ilana; Attias, Samuel; Ben-Arye, Eran; Goldstein, Lee; Schiff, Elad
2017-04-01
Dietary and herbal supplements (DHS) are widely used in the general population, including during hospitalization. Yet, their potential interactions with prescription drugs have seldom been delineated among inpatients. We aimed to evaluate potentially dangerous interactions of DHS with prescribed medications among inpatients. This was a cross-sectional prospective study involving a cohort of patients hospitalized in 12 departments of a public academic medical center (Bnai Zion Medical Center, Haifa, Israel) from 2009 to 2014. DHS users were determined via a questionnaire. The Natural Medicine database was used to search for potential DHS-drug interactions for identified DHS, and the clinical significance was evaluated using Lexi-interact online interaction analysis. Medical files were assessed for documentation of DHS use. Univariate and multivariate logistic regression analyses were used to characterize potential risk factors for DHS-drug interactions. Of 927 patients consenting to answer the questionnaire, 458 (49 %) reported DHS use. Of these, 215 (47 %) had at least one potential interaction during hospitalization (759 interactions). Of these interactions, 116 (15 %) were potentially clinically significant. Older age [OR = 1.02 (1.01-1.04), p = 0.002], males [OR = 2.11 (1.35-3.29), p = 0.001] and increased number of used DHS [OR = 4.28 (2.28-8.03), p < 0.001] or drugs [OR = 1.95 (1.17-3.26), p = 0.011] were associated with potential interactions in DHS users. Physicians documented only 16.5 % of DHS involved in these interactions in patients' medical files. In conclusion, a substantial number of inpatients use DHS with potential interactions with concomitant medications. Medical staff should be aware of this, question patients on DHS usage and check for such interactions.
NASA Astrophysics Data System (ADS)
Knight, Chris; Voth, Gregory A.
2012-05-01
The molecular simulation of condensed phase systems with electronic structure methods can be prohibitively expensive if the length and time scales necessary to observe the desired chemical phenomena are too large. One solution is to map the results of a representative electronic structure simulation onto a computationally more efficient model that reproduces the original calculation, while allowing for statistical sampling relevant to the required length and time scales. The statistical mechanical multiscale coarse-graining procedure is one methodology in which a model can be developed by integrating over the subset of fast degrees of freedom to construct a reduced representation of the original system that reproduces thermodynamic, and in some instances dynamic, properties. The coarse-graining away of electronic structure is one application of this general method, wherein the electronic degrees of freedom are integrated out and the full dimensionality of the system is mapped to that of only the nuclei. The forces on the nuclei in this reduced representation are obtained from a variational force-matching procedure applied to the Hellman-Feynman forces of the original full electron + nuclear system. This work discusses the coarse-graining procedure and its application to ab initio molecular dynamics simulations of the aqueous hydroxide ion.
NASA Astrophysics Data System (ADS)
Rostami, Samare; Ghasemi, S. Alireza; Nedaaee Oskoee, Ehsan
2016-09-01
We present an accurate and efficient algorithm to calculate the electrostatic interaction of charged point particles with partially periodic boundary conditions that are confined along the non-periodic direction by two parallel metallic plates. The method preserves the original boundary conditions, leading to an exact solution of the problem. In addition, the scaling complexity is quasilinear O ( N ln ( N ) ) , where N is the number of particles in the simulation box. Based on the superposition principle in electrostatics, the problem is split into two electrostatic problems where each can be calculated by the appropriate Poisson solver. The method is applied to NaCl ultra-thin films where its dielectric response with respect to an external bias voltage is investigated. Furthermore, the total charge induced on the metallic boundaries can be calculated to an arbitrary precision.
Li, Y Q; Zhang, P Y; Han, K L
2015-03-28
A global many-body expansion potential energy surface is reported for the electronic ground state of CH2 (+) by fitting high level ab initio energies calculated at the multireference configuration interaction level with the aug-cc-pV6Z basis set. The topographical features of the new global potential energy surface are examined in detail and found to be in good agreement with those calculated directly from the raw ab initio energies, as well as previous calculations available in the literature. In turn, in order to validate the potential energy surface, a test theoretical study of the reaction CH(+)(X(1)Σ(+))+H((2)S)→C(+)((2)P)+H2(X(1)Σg (+)) has been carried out with the method of time dependent wavepacket on the title potential energy surface. The total integral cross sections and the rate coefficients have been calculated; the results determined that the new potential energy surface can both be recommended for dynamics studies of any type and as building blocks for constructing the potential energy surfaces of larger C(+)/H containing systems.
Arcon, Juan Pablo; Defelipe, Lucas A; Modenutti, Carlos P; López, Elias D; Alvarez-Garcia, Daniel; Barril, Xavier; Turjanski, Adrián G; Martí, Marcelo A
2017-03-31
One of the most important biological processes at the molecular level is the formation of protein-ligand complexes. Therefore, determining their structure and underlying key interactions is of paramount relevance and has direct applications in drug development. Because of its low cost relative to its experimental sibling, molecular dynamics (MD) simulations in the presence of different solvent probes mimicking specific types of interactions have been increasingly used to analyze protein binding sites and reveal protein-ligand interaction hot spots. However, a systematic comparison of different probes and their real predictive power from a quantitative and thermodynamic point of view is still missing. In the present work, we have performed MD simulations of 18 different proteins in pure water as well as water mixtures of ethanol, acetamide, acetonitrile and methylammonium acetate, leading to a total of 5.4 μs simulation time. For each system, we determined the corresponding solvent sites, defined as space regions adjacent to the protein surface where the probability of finding a probe atom is higher than that in the bulk solvent. Finally, we compared the identified solvent sites with 121 different protein-ligand complexes and used them to perform molecular docking and ligand binding free energy estimates. Our results show that combining solely water and ethanol sites allows sampling over 70% of all possible protein-ligand interactions, especially those that coincide with ligand-based pharmacophoric points. Most important, we also show how the solvent sites can be used to significantly improve ligand docking in terms of both accuracy and precision, and that accurate predictions of ligand binding free energies, along with relative ranking of ligand affinity, can be performed.
Li, Y Q; Varandas, A J C
2010-09-16
An accurate single-sheeted double many-body expansion potential energy surface is reported for the title system which is suitable for dynamics and kinetics studies of the reactions of N(2D) + H2(X1Sigmag+) NH(a1Delta) + H(2S) and their isotopomeric variants. It is obtained by fitting ab initio energies calculated at the multireference configuration interaction level with the aug-cc-pVQZ basis set, after slightly correcting semiempirically the dynamical correlation using the double many-body expansion-scaled external correlation method. The function so obtained is compared in detail with a potential energy surface of the same family obtained by extrapolating the calculated raw energies to the complete basis set limit. The topographical features of the novel global potential energy surface are examined in detail and found to be in general good agreement with those calculated directly from the raw ab initio energies, as well as previous calculations available in the literature. The novel function has been built so as to become degenerate at linear geometries with the ground-state potential energy surface of A'' symmetry reported by our group, where both form a Renner-Teller pair.
Xia, Peng; Wang, Zhikai; Liu, Xing; Wu, Bing; Wang, Juncheng; Ward, Tarsha; Zhang, Liangyu; Ding, Xia; Gibbons, Gary; Shi, Yunyu; Yao, Xuebiao
2012-01-01
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.
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
Preparation of synthetic copolymers potentially capable to interact with biomacromolecules
NASA Astrophysics Data System (ADS)
Davydova, N. K.; Sinitsyna, O. V.; Zinoviev, K. E.
2012-07-01
A series of substituted amides of acrylic acid with various functional groups have been synthesized. On their basis there were obtained synthetic polymers which potentially could be employed as the probes capable of interaction with biomacromolecules. Atomic force microscopy was applied to study the interaction between DNA and the copolymers.
NASA Astrophysics Data System (ADS)
Liu, Hui; Shi, Deheng; Sun, Jinfeng; Zhu, Zunlue
2016-11-01
The potential energy curves were calculated for the 24 Λ-S states correlating with the lowest four dissociation channels of the BO+ cation. The potential energy curves were also computed for the 60 Ω states generated from the 24 Λ-S states. Calculations were made for internuclear separations from 0.08 to 1.05 nm using the CASSCF method, which was followed by the icMRCI approach with the correlation-consistent basis sets. Core-valence correlation, scalar relativistic and basis extrapolation were accounted for. Of the 24 Λ-S states, only three states (25Π, 15Σ-, and 25Σ-) were found to be repulsive; only the 15Δ state was found to be a very weakly-bound state; and the E1Π, 23Π, and 15Π states were found to be very strong bound. In addition, the B1Σ+ and 31Σ+ states have double wells by the avoided crossing between the two states. The a3Π, 13Σ-, and 23Σ- states are inverted with the spin-orbit coupling effect included. The spectroscopic parameters were determined and the vibrational properties of several Λ-S states were predicted. Comparison with available experimental data shows that the methodology employed is highly accurate for this system.
Potential drug interactions in patients given antiretroviral therapy
dos Santos, Wendel Mombaque; Secoli, Silvia Regina; Padoin, Stela Maris de Mello
2016-01-01
ABSTRACT Objective: to investigate potential drug-drug interactions (PDDI) in patients with HIV infection on antiretroviral therapy. Methods: a cross-sectional study was conducted on 161 adults with HIV infection. Clinical, socio demographic, and antiretroviral treatment data were collected. To analyze the potential drug interactions, we used the software Micromedex(r). Statistical analysis was performed by binary logistic regression, with a p-value of ≤0.05 considered statistically significant. Results: of the participants, 52.2% were exposed to potential drug-drug interactions. In total, there were 218 potential drug-drug interactions, of which 79.8% occurred between drugs used for antiretroviral therapy. There was an association between the use of five or more medications and potential drug-drug interactions (p = 0.000) and between the time period of antiretroviral therapy being over six years and potential drug-drug interactions (p < 0.00). The clinical impact was prevalent sedation and cardiotoxicity. Conclusions: the PDDI identified in this study of moderate and higher severity are events that not only affect the therapeutic response leading to toxicity in the central nervous and cardiovascular systems, but also can interfere in tests used for detection of HIV resistance to antiretroviral drugs. PMID:27878224
Meng, Qingyong; Chen, Jun; Zhang, Dong H
2016-04-21
To fast and accurately compute rate coefficients of the H/D + CH4 → H2/HD + CH3reactions, 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.
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.
NASA Astrophysics Data System (ADS)
Tan, Samuel; Barrera Acevedo, Santiago; Izgorodina, Ekaterina I.
2017-02-01
The accurate calculation of intermolecular interactions is important to our understanding of properties in large molecular systems. The high computational cost of the current "gold standard" method, coupled cluster with singles and doubles and perturbative triples (CCSD(T), limits its application to small- to medium-sized systems. Second-order Møller-Plesset perturbation (MP2) theory is a cheaper alternative for larger systems, although at the expense of its decreased accuracy, especially when treating van der Waals complexes. In this study, a new modification of the spin-component scaled MP2 method was proposed for a wide range of intermolecular complexes including two well-known datasets, S22 and S66, and a large dataset of ionic liquids consisting of 174 single ion pairs, IL174. It was found that the spin ratio, ɛΔ s=E/INT O SEIN T S S , calculated as the ratio of the opposite-spin component to the same-spin component of the interaction correlation energy fell in the range of 0.1 and 1.6, in contrast to the range of 3-4 usually observed for the ratio of absolute correlation energy, ɛs=E/OSES S , in individual molecules. Scaled coefficients were found to become negative when the spin ratio fell in close proximity to 1.0, and therefore, the studied intermolecular complexes were divided into two groups: (1) complexes with ɛΔ s< 1 and (2) complexes with ɛΔ s≥ 1 . A separate set of coefficients was obtained for both groups. Exclusion of counterpoise correction during scaling was found to produce superior results due to decreased error. Among a series of Dunning's basis sets, cc-pVTZ and cc-pVQZ were found to be the best performing ones, with a mean absolute error of 1.4 kJ mol-1 and maximum errors below 6.2 kJ mol-1. The new modification, spin-ratio scaled second-order Møller-Plesset perturbation, treats both dispersion-driven and hydrogen-bonded complexes equally well, thus validating its robustness with respect to the interaction type ranging from ionic
Dense neuron system interacting with the gravitational potential.
Thuraisingham, R A
2015-10-07
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.
Potential Drug - Drug Interactions among Medications Prescribed to Hypertensive Patients
Ganguly, Barna
2014-01-01
Context: Drug-drug interactions(DDIs) are significant but avoidable causes of iatrogenic morbidity and hospital admission. Aim: To detect potential drug-drug interactions among medications received by hypertensive patients. Materials and Methods: Patients of both sex and all adult age groups, who were attending medicine out -patient department (OPD) of a tertiary care teaching rural hospital since last six months and were being prescribed antihypertensive drug/s for essential hypertension, were selected for the study. Hypertensive patient with co-morbities diabetes mellitus, ischemic heart diseases, congestive heart failure, and chronic renal diseases were also included in the study. Potential drug drug interactions were checked with medscape drug interaction software. Results: With the help of medscape drug interaction software, 71.50% prescriptions were identified having atleast one drug-drug interaction. Total 918 DDIs were found in between 58 drug pairs. 55.23% DDIs were pharmacodynamic, 4.79% pharmacokinetic type of DDIs. 32.24% DDIs were found affecting serum potassium level. 95.42% DDIs were found significant type of DDIs. Drug drug interaction between atenolol & amlodipine was the most common DDI (136) followed by metoprolol and amlodine (88) in this study. Atenolol and amlodipine ( 25.92%) was the most common drugs to cause DDIs in our study. Conclusion: We detected a significant number of drug drug interaction in hypertensive patients. These interactions were between antihypertensive agents or between hypertensive and drug for co-morbid condition. PMID:25584241
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.
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.
Potential drug interactions with statins: Estonian register-based study
Volmer, Daisy; Hartikainen, Sirpa; Zharkovsky, Alexander
2015-01-01
In Estonia, HMG-CoA reductase inhibitors are widely used to modify lipid levels but there are no current data on additional medicines prescribed alongside the statins. The aim of this study was to identify the frequency of potential clinically relevant interactions at a national level among an outpatient population treated with statins between January and June 2008, based on the prescription database of the Estonian Health Insurance Fund. This retrospective prevalence study included 203,646 outpatients aged 50 years or older, of whom 29,367 received statin therapy. The study analysed individuals who had used at least one prescription medicine for a minimum of 7 days concomitantly with statins. Potential drug interactions were analysed using Epocrates online, Stockley’s Drug Interactions, and the drug interaction database developed in Estonia. Statins metabolised by the CYP3A4 isoenzyme were prescribed to 64% of all statin users. Medicines known to have potentially clinically significant interactions with statins were prescribed to 4.6% of patients. The drugs prescribed concomitantly most often with simvastatin were warfarin (5.7%) and amiodarone (3.9%), whereas digoxin (1.2%) and ethinylestradiol (2%) were prescribed with atorvastatin. Potential interactions were not detected in the treatment regimens of rosuvastatin, pravastatin, and fluvastatin users. PMID:28352703
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.
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.
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).
NASA Astrophysics Data System (ADS)
Ripoche, J.; Lacroix, D.; Gambacurta, D.; Ebran, J.-P.; Duguet, T.
2017-01-01
Background: Ab initio many-body methods have been developed over the past ten years to address mid-mass nuclei. In their best current level of implementation, their accuracy is of the order of a few percent error on the ground-state correlation energy. Recently implemented variants of these methods are operating a breakthrough in the description of medium-mass open-shell nuclei at a polynomial computational cost while putting state-of-the-art models of internucleon interactions to the test. Purpose: As progress in the design of internucleon interactions is made, and as questions one wishes to answer are refined in connection with increasingly available experimental data, further efforts must be made to tailor many-body methods that can reach an even higher precision for an even larger number of observable quantum states or nuclei. The objective of the present work is to contribute to such a quest by designing and testing a new many-body scheme. Methods: We formulate a truncated configuration-interaction method that consists of diagonalizing the Hamiltonian in a highly truncated subspace of the total N -body Hilbert space. The reduced Hilbert space is generated via the particle-number projected BCS state along with projected seniority-zero two- and four-quasiparticle excitations. Furthermore, the extent by which the underlying BCS state breaks U(1 ) symmetry is optimized in the presence of the projected two- and four-quasiparticle excitations. This constitutes an extension of the so-called restricted variation after projection method in use within the frame of multireference energy density functional calculations. The quality of the newly designed method is tested against exact solutions of the so-called attractive pairing Hamiltonian problem. Results: By construction, the method reproduces exact results for N =2 and N =4 . For N =(8 ,16 ,20 ) , the error in the ground-state correlation energy is less than (0.006%, 0.1%, 0.15%) across the entire range of
Herbal medication: potential for adverse interactions with analgesic drugs.
Abebe, W
2002-12-01
The use of herbal supplements in the US has increased dramatically in recent years. These products are not regulated by the Food and Drug Administration (FDA) with the same scrutiny as conventional drugs. Patients who use herbal supplements often do so in conjunction with conventional drugs. This article is a review of potential adverse interactions between some of the commonly used herbal supplements and analgesic drugs. Non-steroidal anti-inflammatory drugs (NSAIDs), particularly aspirin, have the potential to interact with herbal supplements that are known to possess antiplatelet activity (ginkgo, garlic, ginger, bilberry, dong quai, feverfew, ginseng, turmeric, meadowsweet and willow), with those containing coumarin (chamomile, motherworth, horse chestnut, fenugreek and red clover) and with tamarind, enhancing the risk of bleeding. Acetaminophen may also interact with ginkgo and possibly with at least some of the above herbs to increase the risk of bleeding. Further, the incidences of hepatotoxicity and nephrotoxicity may be augmented by acetaminophen when concomitantly used with the potentially hepatotoxic herbs Echinacea and kava, and with herbs containing salicylate (willow, meadowsweet), respectively. The concomitant use of opioid analgesics with the sedative herbal supplements, valerian, kava and chamomile, may lead to increased central nervous system (CNS) depression. The analgesic effect of opioids may also be inhibited by ginseng. It is suggested that health-care professionals should be more aware of the potential adverse interactions between herbal supplements and analgesic drugs, and take appropriate precautionary measures to avoid their possible occurrences. However, as most of the interaction information available is based on individual case reports, animal studies and in vitro data, further research is needed to confirm and assess the clinical significance of these potential interactions.
Gutten, Ondrej; Beššeová, Ivana; Rulíšek, Lubomír
2011-10-20
To address fundamental questions in bioinorganic chemistry, such as metal ion selectivity, accurate computational protocols for both the gas-phase association of metal-ligand complexes and solvation/desolvation energies of the species involved are needed. In this work, we attempt to critically evaluate the performance of the ab initio and DFT electronic structure methods available and recent solvation models in calculations of the energetics associated with metal ion complexation. On the example of five model complexes ([M(II)(CH(3)S)(H(2)O)](+), [M(II)(H(2)O)(2)(H(2)S)(NH(3))](2+), [M(II)(CH(3)S)(NH(3))(H(2)O)(CH(3)COO)], [M(II)(H(2)O)(3)(SH)(CH(3)COO)(Im)], [M(II)(H(2)S)(H(2)O)(CH(3)COO)(PhOH)(Im)](+) in typical coordination geometries) and four metal ions (Fe(2+), Cu(2+), Zn(2+), and Cd(2+); representing open- and closed-shell and the first- and second-row transition metal elements), we provide reference values for the gas-phase complexation energies, as presumably obtained using the CCSD(T)/aug-cc-pVTZ method, and compare them with cheaper methods, such as DFT and RI-MP2, that can be used for large-scale calculations. We also discuss two possible definitions of interaction energies underlying the theoretically predicted metal-ion selectivity and the effect of geometry optimization on these values. Finally, popular solvation models, such as COSMO-RS and SMD, are used to demonstrate whether quantum chemical calculations can provide the overall free enthalpy (ΔG) changes in the range of the expected experimental values for the model complexes or match the experimental stability constants in the case of three complexes for which the experimental data exist. The data presented highlight several intricacies in the theoretical predictions of the experimental stability constants: the covalent character of some metal-ligand bonds (e.g., Cu(II)-thiolate) causing larger errors in the gas-phase complexation energies, inaccuracies in the treatment of solvation of the
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.
Liang, Guiying; Liu, Xiaoting; Zhang, Xiaomei; Xu, Haifeng; Yan, Bing
2016-03-05
A high-level ab initio calculation on the ZnH(+) cation has been carried out with the multi-reference configuration interaction method plus Davison correction (MRCI+Q). The scalar relativistic effect is included by using the Douglas-Kroll-Hess (DKH) method. The calculated potential energy curves (PECs) of the 7 Λ-S states are associated with the dissociation limits of Zn(+)((2)Sg)+H((2)Sg), Zn((1)Sg)+H(+)((1)Sg), and Zn(+)((2)Pu)+H((2)Sg), respectively (The Λ-S state is labeled as (2S+1)Λ, in which Λ is the quantum number for the projection along the internuclear axis of the total electronic orbital angular momentum and S is the total electron spin). The spectroscopic constants of the bound states are determined and in good agreement with the available theoretical and experimental results. The permanent dipole moments (PDMs) of Λ-S states and the spin-orbit (SO) matrix elements between Λ-S states are also computed. The results show that the abrupt changes of the PDMs and SO matrix elements come into being for the reason of the avoided crossing between the states with the same symmetry. In addition, the non-adiabatic couplings matrix elements between Λ-S states are also evaluated. Finally, the spin-orbit couplings (SOCs) for the low-lying states are considered with Breit-Pauli operator. The SOC effect makes the 7 Λ-S states of the ZnH(+) cation split into 12 Ω states (Ω=Λ+Sz, in which Sz is projection of the total electron spin S along the internuclear Z-axis). For the (3)0(+) state, the two energy minima exhibit in the potential, which could be attributed to the formation of the new avoided crossing point. The transition dipole moments (TDMs), Franck-Condon factors, and the radiative lifetimes of the selected transitions (2)0(+)-X0(+), (3)0(+)-X0(+), (2)1-X0(+) and (3)1-X0(+) have been reported.
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.
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.
Accurate Analytic Potential Energy Function and Spectroscopic Study for G1Πg State of Dimer 7Li2
NASA Astrophysics Data System (ADS)
Shi, De-Heng; Ma, Heng; Sun, Jin-Feng; Zhu, Zun-Lue
2007-06-01
The reasonable dissociation limit for the G1Πg state of dimer 7Li2 is determined. The equilibrium internuclear distance, dissociation energy, harmonic frequency, vibrational zero energy, and adiabatic excitation energy are calculated using a symmetry-adapted-cluster configuration-interaction method in complete active space in Gaussian03 program package at such numerous basis sets as 6-311++G, 6-311++G(2df,2pd), 6-311++G(2df,p), cc-PVTZ, 6-311++G(3df,3pd), CEP-121G, 6-311++G(2df,pd), 6-311++G(d,p),6-311G(3df,3pd), D95(3df,3pd), 6-311++G(3df,2p), 6-311++G(2df), 6-311++G(df,pd) D95V++, and DGDZVP. The complete potential energy curves are obtained at these sets over a wide internuclear distance range and have least squares fitted to Murrell-Sorbie function. The conclusion shows that the basis set 6-311++G(2df,p) is a most suitable one for the G1Πg state. At this basis set, the calculated spectroscopic constants Te, De, E0, Re, ωe, ωeχe, αe, and Be are of 3.9523 eV, 0.813 06 eV, 113.56 cm-1, 0.320 15 nm, 227.96 cm-1, 1.6928 cm-1, 0.004 436 cm-1, and 0.4689 cm-1, respectively, which are in good agreement with measurements whenever available. The total 50 vibrational levels and corresponding inertial rotation constants are for the first time calculated and compared with available RKR data. And good agreement with measurements is obtained.
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.
NASA Astrophysics Data System (ADS)
Walton, Jay R.; Rivera-Rivera, Luis A.; Lucchese, Robert R.; Bevan, John W.
2015-10-01
A proof-of-concept for the accurate generation of multidimensional intermolecular interaction potentials is demonstrated. The basis for evaluating this application is the available very accurate 3-D morphed potential of Ar·HBr. Starting from the well-defined potential of the simplest molecule, the diatomic H2+, a recently developed 1-D canonical potential is used with selected 2-D polyatomic data to generate the adiabatic intermolecular interaction potential in Ar·HBr, with HBr in the vibrational ground state. This represents the first application of canonical transformations to a higher vibrationally dimensional molecular system, in this case, Ar·HBr. Results indicate intrinsic bonding characteristics inherent to both systems.
Potential social interactions are important to social attention.
Laidlaw, Kaitlin E W; Foulsham, Tom; Kuhn, Gustav; Kingstone, Alan
2011-04-05
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.
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}.
NASA Astrophysics Data System (ADS)
Bross, David H.; Parmar, Payal; Peterson, Kirk A.
2015-11-01
The first 6 ionization potentials (IPs) of the uranium atom have been calculated using multireference configuration interaction (MRCI+Q) with extrapolations to the complete basis set limit using new all-electron correlation consistent basis sets. The latter was carried out with the third-order Douglas-Kroll-Hess Hamiltonian. Correlation down through the 5s5p5d electrons has been taken into account, as well as contributions to the IPs due to the Lamb shift. Spin-orbit coupling contributions calculated at the 4-component Kramers restricted configuration interaction level, as well as the Gaunt term computed at the Dirac-Hartree-Fock level, were added to the best scalar relativistic results. The final ionization potentials are expected to be accurate to at least 5 kcal/mol (0.2 eV) and thus more reliable than the current experimental values of IP3 through IP6.
NASA Technical Reports Server (NTRS)
Desmarais, R. N.
1982-01-01
The method is capable of generating approximations of arbitrary accuracy. It is based on approximating the algebraic part of the nonelementary integrals in the kernel by exponential functions and then integrating termwise. The exponent spacing in the approximation is a geometric sequence. The coefficients and exponent multiplier of the exponential approximation are computed by least squares so the method is completely automated. Exponential approximates generated in this manner are two orders of magnitude more accurate than the exponential approximation that is currently most often used for this purpose. The method can be used to generate approximations to attain any desired trade-off between accuracy and computing cost.
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.
He-LiF surface interaction potential from fast atom diffraction
Schueller, A.; Winter, H.; Gravielle, M. S.; Miraglia, J. E.; Pruneda, J. M.
2009-12-15
Diffraction patterns produced by grazing scattering of fast atoms from insulator surfaces are used to examine the atom-surface interaction. The method is applied to He atoms colliding with a LiF(001) surface along axial crystallographic channels. The projectile-surface potential is obtained from an accurate density-functional theory calculation, which includes polarization effects and surface relaxation. For the description of the collision process we employ the surface eikonal approximation, which takes into account quantum interference between different projectile paths. The dependence of projectile spectra on the parallel and perpendicular incident energies is experimentally and theoretically analyzed, demonstrating the range of applicability of the proposed model.
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.
Dynamics of Interacting Fermions in Spin-Dependent Potentials.
Koller, Andrew P; Wall, Michael L; Mundinger, Josh; Rey, Ana Maria
2016-11-04
Recent experiments with dilute trapped Fermi gases observed that weak interactions can drastically modify spin transport dynamics and give rise to robust collective effects including global demagnetization, macroscopic spin waves, spin segregation, and spin self-rephasing. In this Letter, we develop a framework for studying the dynamics of weakly interacting fermionic gases following a spin-dependent change of the trapping potential which illuminates the interplay between spin, motion, Fermi statistics, and interactions. The key idea is the projection of the state of the system onto a set of lattice spin models defined on the single-particle mode space. Collective phenomena, including the global spreading of quantum correlations in real space, arise as a consequence of the long-ranged character of the spin model couplings. This approach achieves good agreement with prior measurements and suggests a number of directions for future experiments.
Dynamics of Interacting Fermions in Spin-Dependent Potentials
NASA Astrophysics Data System (ADS)
Koller, Andrew P.; Wall, Michael L.; Mundinger, Josh; Rey, Ana Maria
2016-11-01
Recent experiments with dilute trapped Fermi gases observed that weak interactions can drastically modify spin transport dynamics and give rise to robust collective effects including global demagnetization, macroscopic spin waves, spin segregation, and spin self-rephasing. In this Letter, we develop a framework for studying the dynamics of weakly interacting fermionic gases following a spin-dependent change of the trapping potential which illuminates the interplay between spin, motion, Fermi statistics, and interactions. The key idea is the projection of the state of the system onto a set of lattice spin models defined on the single-particle mode space. Collective phenomena, including the global spreading of quantum correlations in real space, arise as a consequence of the long-ranged character of the spin model couplings. This approach achieves good agreement with prior measurements and suggests a number of directions for future experiments.
Handley, Chris M; Hawe, Glenn I; Kell, Douglas B; Popelier, Paul L A
2009-08-14
To model liquid water correctly and to reproduce its structural, dynamic and thermodynamic properties warrants models that account accurately for electronic polarisation. We have previously demonstrated that polarisation can be represented by fluctuating multipole moments (derived by quantum chemical topology) predicted by multilayer perceptrons (MLPs) in response to the local structure of the cluster. Here we further develop this methodology of modeling polarisation enabling control of the balance between accuracy, in terms of errors in Coulomb energy and computing time. First, the predictive ability and speed of two additional machine learning methods, radial basis function neural networks (RBFNN) and Kriging, are assessed with respect to our previous MLP based polarisable water models, for water dimer, trimer, tetramer, pentamer and hexamer clusters. Compared to MLPs, we find that RBFNNs achieve a 14-26% decrease in median Coulomb energy error, with a factor 2.5-3 slowdown in speed, whilst Kriging achieves a 40-67% decrease in median energy error with a 6.5-8.5 factor slowdown in speed. Then, these compromises between accuracy and speed are improved upon through a simple multi-objective optimisation to identify Pareto-optimal combinations. Compared to the Kriging results, combinations are found that are no less accurate (at the 90th energy error percentile), yet are 58% faster for the dimer, and 26% faster for the pentamer.
Todd-Rutel, B.G.; Piekarewicz, J.
2005-09-16
An accurately calibrated relativistic parametrization is introduced to compute the ground state properties of finite nuclei, their linear response, and the structure of neutron stars. While similar in spirit to the successful NL3 parameter set, it produces an equation of state that is considerably softer--both for symmetric nuclear matter and for the symmetry energy. This softening appears to be required for an accurate description of several collective modes having different neutron-to-proton ratios. Among the predictions of this model are a symmetric nuclear-matter incompressibility of K=230 MeV and a neutron skin thickness in {sup 208}Pb of R{sub n}-R{sub p}=0.21 fm. The impact of such a softening on various neutron-star properties is also examined.
Localization of interacting Fermi gases in quasiperiodic potentials
NASA Astrophysics Data System (ADS)
Pilati, Sebastiano; Varma, Vipin Kerala
2017-01-01
We investigate the zero-temperature metal-insulator transition in a one-dimensional two-component Fermi gas in the presence of a quasiperiodic potential resulting from the superposition of two optical lattices of equal intensity but incommensurate periods. A mobility edge separating (low-energy) Anderson localized and (high-energy) extended single-particle states appears in this continuous-space model beyond a critical intensity of the quasiperiodic potential. To discern the metallic phase from the insulating phase in the interacting many-fermion system, we employ unbiased quantum Monte Carlo (QMC) simulations combined with the many-particle localization length familiar from the modern theory of the insulating state. In the noninteracting limit, the critical optical-lattice intensity for the metal-insulator transition predicted by the QMC simulations coincides with the Anderson localization transition of the single-particle eigenstates. We show that weak repulsive interactions induce a shift of this critical point towards larger intensities, meaning that repulsion favors metallic behavior. This shift appears to be linear in the interaction parameter, suggesting that even infinitesimal interactions can affect the position of the critical point.
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.
NASA Astrophysics Data System (ADS)
Gloor, Guy J.; Jackson, George; Blas, Felipe J.; del Río, Elvira Martín; de Miguel, Enrique
2004-12-01
A Helmholtz free energy density functional is developed to describe the vapor-liquid interface of associating chain molecules. The functional is based on the statistical associating fluid theory with attractive potentials of variable range (SAFT-VR) for the homogenous fluid [A. Gil-Villegas, A. Galindo, P. J. Whitehead, S. J. Mills, G. Jackson, and A. N. Burgess, J. Chem. Phys. 106, 4168 (1997)]. A standard perturbative density functional theory (DFT) is constructed by partitioning the free energy density into a reference term (which incorporates all of the short-range interactions, and is treated locally) and an attractive perturbation (which incorporates the long-range dispersion interactions). In our previous work [F. J. Blas, E. Martı´n del Rı´o, E. de Miguel, and G. Jackson, Mol. Phys. 99, 1851 (2001); G. J. Gloor, F. J. Blas, E. Martı´n del Rı´o, E. de Miguel, and G. Jackson, Fluid Phase Equil. 194, 521 (2002)] we used a mean-field version of the theory (SAFT-HS) in which the pair correlations were neglected in the attractive term. This provides only a qualitative description of the vapor-liquid interface, due to the inadequate mean-field treatment of the vapor-liquid equilibria. Two different approaches are used to include the correlations in the attractive term: in the first, the free energy of the homogeneous fluid is partitioned such that the effect of correlations are incorporated in the local reference term; in the second, a density averaged correlation function is incorporated into the perturbative term in a similar way to that proposed by Toxvaerd [S. Toxvaerd, J. Chem. Phys. 64, 2863 (1976)]. The latter is found to provide the most accurate description of the vapor-liquid surface tension on comparison with new simulation data for a square-well fluid of variable range. The SAFT-VR DFT is used to examine the effect of molecular chain length and association on the surface tension. Different association schemes (dimerization, straight and
NASA Astrophysics Data System (ADS)
Zhang, Shimin
The interaction energies between two similar plane double layers for CaCl2-type asymmetric electrolytes at positive surface potential are expanded in the power series at lower potential and smaller absolute value of integral constant as well as higher potential and larger absolute value of integral constant, respectively. When dimensionless surface potential y0 ≤ 20, the number of the series terms required to obtain the interaction energies with six significant digits are not more than eight if higher potential expressions are combined with lower potential expressions. The accurate numerical results are given and they can be used to check up the validity of approximate expressions that will be obtained. The present results are also fit for Na2SO4-type asymmetric electrolytes at negative surface potential.
LI, DAN; DING, JIAN; CHEN, ZHIXIN; CHEN, YUN; LIN, NA; CHEN, FENGLIN; WANG, XIAOZHONG
2015-01-01
The hepatitis B virus (HBV) X protein (HBx) plays an important pathogenetic role in hepatocarcinoma tumorigenesis. As HBx does not have the ability to bind to double-stranded DNA (dsDNA), protein-protein interaction is crucial for HBx functions. In a previous study, we screened a novel HBx-interacting protein, the cytochrome c oxidase subunit III (COXIII). In the present study, we aimed to accurately map the location of the binding site for the interaction of HBx with COXIII. Two fragments of HBx mutants (X1 aa1-72 and X2 aa1-117) were amplified by polymerase chain reaction (PCR) and separately inserted into the pAS2-1 plasmid. PCR and gene sequencing confirmed the correct insertion of the mutant fragments in the plasmid. The tanscription of the mutant fragments in yeast cells was demonstrated by RT-PCR and western blot analysis confirmed that they were accurately translated into fusion proteins. Hybridization on solid medium and the detection of β-galactosidase (β-gal) activity indicated that the binding site for the interaction between HBx and COXIII was located between aa72 and aa117. Specific interactions between the HBxX2 protein and COXIII were verified by co-immunoprecipitation. To the best of our knowledge, this is the first study showing to demonstrate that aa72-117 in HBx is the key region for binding with COXIII. PMID:25483779
Prevalence of the Prescription of Potentially Interacting Drugs
Tragni, Elena; Casula, Manuela; Pieri, Vasco; Favato, Giampiero; Marcobelli, Alberico; Trotta, Maria Giovanna; Catapano, Alberico Luigi
2013-01-01
The use of multiple medications is becoming more common, with a correspondingly increased risk of untoward effects and drug-related morbidity and mortality. We aimed at estimating the prevalence of prescription of relevant potentially interacting drugs and at evaluating possible predictors of potentially interacting drug exposure. We retrospectively analyzed data on prescriptions dispensed from January 2004 to August 2005 to individuals of two Italian regions with a population of almost 2.1 million individuals. We identified 27 pairs of potentially interacting drugs by examining clinical relevance, documentation, and volume of use in Italy. Subjects who received at least one prescription of both drugs were selected. Co-prescribing denotes “two prescriptions in the same day”, and concomitant medication “the prescription of two drugs with overlapping coverage”. A logistic regression analysis was conducted to examine the predictors of potential Drug-Drug Interaction (pDDIs). 957,553 subjects (45.3% of study population) were exposed to at least one of the drugs/classes of the 27 pairs. Overall, pDDIs occurred 2,465,819 times. The highest rates of concomitant prescription and of co-prescription were for ACE inhibitors+NSAIDs (6,253 and 4,621/100,000 plan participants). Considering concomitance, the male/female ratio was <1 in 17/27 pairs (from 0.31 for NSAIDs-ASA+SSRI to 0.74 for omeprazole+clopidogrel). The mean age was lowest for methotrexate pairs (+omeprazole, 59.9 years; +NSAIDs-ASA, 59.1 years) and highest for digoxin+verapamil (75.4 years). In 13/27 pairs, the mean ages were ≥70 years. On average, subjects involved in pDDIs received ≥10 drugs. The odds of exposure were more frequently higher for age ≥65 years, males, and those taking a large number of drugs. A substantial number of clinically important pDDIs were observed, particularly among warfarin users. Awareness of the most prevalent pDDIs could help practitioners in preventing concomitant use
An accurate potential energy surface for the F + H2 → HF + H reaction by the coupled-cluster method.
Chen, Jun; Sun, Zhigang; Zhang, Dong H
2015-01-14
A three dimensional potential energy surface for the F + H2 → HF + H reaction has been computed by the spin unrestricted coupled cluster method with singles, doubles, triples, and perturbative quadruples [UCCSDT(2)Q] using the augmented correlation-consistent polarised valence quadruple zeta basis set for the fluorine atom and the correlation-consistent polarised valence quadruple zeta basis set for the hydrogen atom. All the calculations are based on the restricted open-shell Hartree-Fock orbitals, together with the frozen core approximations, and the UCCSD(T)/complete basis set (CBS) correction term was included. The global potential energy surface was calculated by fitting the sampled ab initio points without any scaling factor for the correlation energy part using a neutral network function method. Extensive dynamics calculations have been carried out on the potential energy surface. The reaction rate constants, integral cross sections, product rotational states distribution, and forward and backward scattering as a function of collision energy of the F + HD → HF + D, F + HD → DF + H, and F + H2 reaction, were calculated by the time-independent quantum dynamics scattering theory using the new surface. The satisfactory agreement with the reported experimental observations previously demonstrates the accuracy of the new potential energy surface.
NASA Astrophysics Data System (ADS)
Bukowski, Robert; Szalewicz, Krzysztof; Groenenboom, Gerrit C.; van der Avoird, Ad
2008-03-01
A six-dimensional interaction potential for the water dimer has been fitted to ab initio interaction energies computed at 2510 dimer configurations. These energies were obtained by combining the supermolecular second-order energies extrapolated to the complete basis set limit from up to quadruple-zeta quality basis sets with the contribution from the coupled-cluster method including single, double, and noniterative triple excitations computed in a triple-zeta quality basis set. All basis sets were augmented by diffuse functions and supplemented by midbond functions. The energies have been fitted using an analytic form with the induction component represented by a polarizable term, making the potential directly transferable to clusters and the bulk phase. Geometries and energies of stationary points on the potential surface agree well with the results of high-level ab initio geometry optimizations.
Spatial coincidence modulates interaction between visual and somatosensory evoked potentials.
Schürmann, Martin; Kolev, Vasil; Menzel, Kristina; Yordanova, Juliana
2002-05-07
The time course of interaction between concurrently applied visual and somatosensory stimulation with respect to evoked potentials (EPs) was studied. Visual stimuli, either in the left or right hemifield, and electric stimuli to the left wrist were delivered either alone or simultaneously. Visual and somatosensory EPs were summed and compared to bimodal EPs (BiEP, response to actual combination of both modalities). Temporal coincidence of stimuli lead to sub-additive or over-additive amplitudes in BiEPs in several time windows between 75 and 275 ms. Additional effects of spatial coincidence (left wrist with left hemifield) were found between 75 and 300 ms and beyond 450 ms. These interaction effects hint at a temporo-spatial pattern of multiple brain areas participating in the process of multimodal integration.
NASA Astrophysics Data System (ADS)
Yoo, Dong Su; Ryu, Jeong Ho; Lee, Sung-Ho; Cho, Hyun; Chung, Yong-Chae
2011-06-01
The crystal structure, electronic structure, and photoluminescence properties of EuxSi6-zAlzOzN8-z (x = 0.01754, z = 0.25) green phosphor were calculated by modified version of the exchange potential proposed by Becke and Johnson [J. Chem. Phys. 124 (2006) 221101]. An interstitially doped Eu atom was found in the atomic channel parallel to the [0001] axis. The additional states originated from the hybridization of Eu 4f and Eu 5d with Si 3p and N 2p. The luminescence properties were analyzed using a quantitative calculation of the energy gap and the wavelength. The calculated emission peak wavelength of Eu from the energy gap between Eu 5d and Eu 4f was 552 nm. Conventional local or semi local density functionals always underestimate the band gap for wide gap semiconductor. In contrast, the calculated results using the semi local potential well agreed with experiment.
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.
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.
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.
Gender differences, polypharmacy, and potential pharmacological interactions in the elderly
Venturini, Carina Duarte; Engroff, Paula; Ely, Luísa Scheer; de Araújo Zago, Luísa Faria; Schroeter, Guilherme; Gomes, Irenio; De Carli, Geraldo Attilio; Morrone, Fernanda Bueno
2011-01-01
OBJECTIVE: This study aims to analyze pharmacological interactions among drugs taken by elderly patients and their age and gender differences in a population from Porto Alegre, Brazil. METHODS: We retrospectively analyzed the database provided by the Institute of Geriatric and Gerontology, Porto Alegre, Brazil. The database was composed of 438 elderly and includes information about the patients' disease, therapy regimens, utilized drugs. All drugs reported by the elderly patients were classified using the Anatomical Therapeutic and Chemical Classification System. The drug-drug interactions and their severity were assessed using the Micromedex® Healthcare Series. RESULTS: Of the 438 elderly patients in the data base, 376 (85.8%) used pharmacotherapy, 274 were female, and 90.4% of females used drugs. The average number of drugs used by each individual younger than 80 years was 3.2±2.6. Women younger than 80 years old used more drugs than men in the same age group whereas men older than 80 years increased their use of drugs in relation to other age groups. Therefore, 32.6% of men and 49.2% of women described at least one interaction, and 8.1% of men and 10.6% of women described four or more potential drug-drug interactions. Two-thirds of drug-drug interactions were moderate in both genders, and most of them involved angiotensin-converting enzyme inhibitor, non-steroidal anti-inflammatory, loop and thiazide diuretics, and β-blockers. CONCLUSION: Elderly patients should be closely monitored, based on drug class, gender, age group and nutritional status. PMID:22086515
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}.
Accurate Analytic Potential Functions for the a ^3Π_1 and X ^1Σ^+ States of {IBr}
NASA Astrophysics Data System (ADS)
Yukiya, Tokio; Nishimiya, Nobuo; Suzuki, Masao; Le Roy, Robert
2014-06-01
Spectra of IBr in various wavelength regions have been measured by a number of researchers using traditional diffraction grating and microwave methods, as well as using high-resolution laser techniques combined with a Fourier transform spectrometer. In a previous paper at this meeting, we reported a preliminary determination of analytic potential energy functions for the A ^3Π_1 and X ^1Σ^+ states of IBr from a direct-potential-fit (DPF) analysis of all of the data available at that time. That study also confirmed the presence of anomalous fluctuations in the v--dependence of the first differences of the inertial rotational constant, Δ Bv=Bv+1-Bv in the A ^3Π_1 state for vibrational levels with v'(A) in the mid 20's. However, our previous experience in a recent study of the analogous A ^3Π_1-X ^1Σ_g^+ system of Br_2 suggested that the effect of such fluctuations may be overcome if sufficient data are available. The present work therefore reports new measurements of transitions to levels in the v'(A)=23-26 region, together with a new global DPF analysis that uses ``robust" least-squares fits to average properly over the effect of such fluctuations in order to provide an optimum delineation of the underlying potential energy curve(s). L.E.Selin,Ark. Fys. 21,479(1962) E. Tiemann and Th. Moeller, Z. Naturforsch. A 30,986 (1975) E.M. Weinstock and A. Preston, J. Mol. Spectrosc. 70, 188 (1978) D.R.T. Appadoo, P.F. Bernath, and R.J. Le Roy, Can. J. Phys. 72, 1265 (1994) N. Nishimiya, T. Yukiya and M. Suzuki, J. Mol. Spectrosc. 173, 8 (1995). T. Yukiya, N. Nishimiya, and R.J. Le Roy, Paper MF12 at the 65th Ohio State University International Symposium on Molecular Spectroscopy, Columbus, Ohio, June 20-24, 2011. T. Yukiya, N. Nishimiya, Y. Samajima, K. Yamaguchi, M. Suzuki, C.D. Boone, I. Ozier and R.J. Le Roy, J. Mol. Spectrosc. 283, 32 (2013) J.K.G. Watson, J. Mol. Spectrosc. 219, 326 (2003).
Microscopic positive-energy potential based on the Gogny interaction
NASA Astrophysics Data System (ADS)
Blanchon, G.; Dupuis, M.; Arellano, H. F.; Vinh Mau, N.
2015-01-01
We present a nucleon elastic scattering calculation based on Green's function formalism in the random-phase approximation. For the first time, the finite-range Gogny effective interaction is used consistently throughout the whole calculation to account for the complex, nonlocal, and energy-dependent optical potential. Effects of intermediate single-particle resonances are included and found to play a crucial role in the account for measured reaction cross sections. Double counting of the particle-hole second-order contribution is carefully addressed. The resulting integro-differential Schrödinger equation for the scattering process is solved without localization procedures. The method is applied to neutron and proton elastic scattering from 40Ca. A successful account for differential and integral cross sections, including analyzing powers, is obtained for incident energies up to 30 MeV. Discrepancies at higher energies are related to a much-too-high volume integral of the real potential for large partial waves. This work opens the way to simultaneously assess effective interactions suitable for both nuclear structure and reactions.
Exact vibrational energies of non-rotating H 2O and D 2O using an accurate ab initio potential
NASA Astrophysics Data System (ADS)
Bowman, Joel M.; Wierzbicki, Andrzej; Zúñiga, Jose
1988-09-01
Variationally exact vibrational energies are reported for non-rotating H 2O and D 2O using the recent CCSDT-1 ab initio potential of Bartlett, Cole, Purvis, Ermler, Hsieh and Shavitt as fit to an SPF quartic force field by Ermler. Twenty vibrational states are calculated for H 2O and D 2O and compared with experimental data. The agreement with experiment is fairly good; however, when the second-order bending force constant is reduced slightly, the agreement with experiment improves significantly. For eighteen states of H 2O the largest error is 15 cm -1 and the average absolute error is 6 cm -1. For eight states of D 2O the largest error is 7 cm -1 and the average absolute error is 4 cm -1.
Murphy, Kyle R; Mann, Ian R; Rae, I Jonathan; Sibeck, David G; Watt, Clare E J
2016-08-01
Wave-particle interactions play a crucial role in energetic particle dynamics in the Earth's radiation belts. However, the relative importance of different wave modes in these dynamics is poorly understood. Typically, this is assessed during geomagnetic storms using statistically averaged empirical wave models as a function of geomagnetic activity in advanced radiation belt simulations. However, statistical averages poorly characterize extreme events such as geomagnetic storms in that storm-time ultralow frequency wave power is typically larger than that derived over a solar cycle and Kp is a poor proxy for storm-time wave power.
Mann, Ian R.; Rae, I. Jonathan; Sibeck, David G.; Watt, Clare E. J.
2016-01-01
Abstract Wave‐particle interactions play a crucial role in energetic particle dynamics in the Earth's radiation belts. However, the relative importance of different wave modes in these dynamics is poorly understood. Typically, this is assessed during geomagnetic storms using statistically averaged empirical wave models as a function of geomagnetic activity in advanced radiation belt simulations. However, statistical averages poorly characterize extreme events such as geomagnetic storms in that storm‐time ultralow frequency wave power is typically larger than that derived over a solar cycle and Kp is a poor proxy for storm‐time wave power. PMID:27867798
NASA Astrophysics Data System (ADS)
Murphy, Kyle R.; Mann, Ian R.; Rae, I. Jonathan; Sibeck, David G.; Watt, Clare E. J.
2016-08-01
Wave-particle interactions play a crucial role in energetic particle dynamics in the Earth's radiation belts. However, the relative importance of different wave modes in these dynamics is poorly understood. Typically, this is assessed during geomagnetic storms using statistically averaged empirical wave models as a function of geomagnetic activity in advanced radiation belt simulations. However, statistical averages poorly characterize extreme events such as geomagnetic storms in that storm-time ultralow frequency wave power is typically larger than that derived over a solar cycle and Kp is a poor proxy for storm-time wave power.
Tyuterev, Vladimir; Tashkun, Sergei; Rey, Michael; Kochanov, Roman; Nikitin, Andrei; Delahaye, Thibault
2013-12-19
A new spectroscopic model is developed for theoretical predictions of vibration-rotation line positions and line intensities of the methane molecule. Resonance coupling parameters of the effective polyad Hamiltionians were obtained via high-order contact transformations (CT) from ab initio potential energy surface. This allows converging vibrational and rotational levels to the accuracy of best variational calculations. Average discrepancy with centers of 100 reliably assigned experimental bands up to the triacontad range was 0.74 cm(-1) and 0.001 cm(-1) for GS rotational levels up to J = 17 in direct CT calculations without adjustable parameters. A subsequent "fine tuning" of the diagonal parameters allows achieving experimental accuracy for about 5600 Dyad and Pentad line positions, whereas all resonance coupling parameters were held fixed to ab initio values. Dipole transition moment parameters were determined from selected ab initio line strengths previously computed from a dipole moment surface by variational method. New polyad model allows generating a spectral line list for the Dyad and Pentad bands with the accuracy ~10(-3) cm(-1) for line positions combined with ab initio predictions for line intensities. The overall integrated intensity agreement with Hitran-2008 empirical database is of 4.4% for the Dyad and of 1.8% for the Pentad range.
Hyperon-Nucleon Effective Interactions Derived from Modern Mesonic Exchange Potentials.
NASA Astrophysics Data System (ADS)
Hao, Jifa
Hyperon-nucleon (YN) effective interactions are derived from the recent Jddot ulich one- and two-meson-exchange potentials. Based on a nucleon -nucleon (NN) G-matrix folded-diagram formalism, the YN effective interaction can be calculated in three steps. First we derive the model-space YN G matrix. Then the irreducible vertex function, namely the YN Q-box, is calculated from the G matrix. Finally the YN effective interaction, which is energy independent, is obtained by summing up a YN Q -box folded-diagram series to all orders. A special feature of our G-matrix calculation is an essentially exact treatment of the Pauli exclusion operator Q_{YN}. The presence of this operator has been a main source of difficulty for the YN G matrix in the past. To avoid this difficulty, previously one just adopted an approximation where the finite-hypernuclei Pauli exclusion operator is replaced by a nuclear-matter one with the nuclear-matter Fermi momentum treated as an adjustable parameter. This approximation is convenient but its accuracy is difficult to asess. Our Q_{YN} is defined in terms of shell-model hyperon and nucleon wave functions as one should, and by way of a matrix-inversion method we have been able to treat Q_{YN} exactly, except for one so-called finite-n_ {3Lambda} truncation. The accuracy of this truncation has been examined numerically, using the Jddot ulich JA and JB potentials. We have found that this truncation is quite accurate if a sufficiently large n_{3Lambda } is employed. In this way we have now obtained accurate YN G matrix, starting from modern mesonic-exchange YN potentials. Next we construct the YN Q -box for which we have considered valence-linked diagrams first- and second-order in the YN G interaction. Of particular interest is the YN core-polarization diagram, whose importance for the NN effective interactions is well known. This diagram provides the long-range interaction between valence baryons, and our calculations have indicated that this
NASA Astrophysics Data System (ADS)
Ranasinghe, Duminda S.; Margraf, Johannes T.; Jin, Yifan; Bartlett, Rodney J.
2017-01-01
Though contrary to conventional wisdom, the interpretation of all occupied Kohn-Sham eigenvalues as vertical ionization potentials is justified by several formal and numerical arguments. Similarly, the performance of density functional approximations (DFAs) for fractionally charged systems has been extensively studied as a measure of one- and many-electron self-interaction errors (MSIEs). These complementary perspectives (initially recognized in ab initio dft) are shown to lead to the unifying concept that satisfying Bartlett's IP theorem in DFA's mitigates self-interaction errors. In this contribution, we show that the IP-optimized QTP functionals (reparameterization of CAM-B3LYP where all eigenvalues are approximately equal to vertical IPs) display reduced self-interaction errors in a variety of tests including the He2+ potential curve. Conversely, the MSIE-optimized rCAM-B3LYP functional also displays accurate orbital eigenvalues. It is shown that the CAM-QTP and rCAM-B3LYP functionals show improved dissociation limits, fundamental gaps and thermochemical accuracy compared to their parent functional CAM-B3LYP.
Strongly Interacting Matter at Finite Chemical Potential: Hybrid Model Approach
NASA Astrophysics Data System (ADS)
Srivastava, P. K.; Singh, C. P.
2013-06-01
Search for a proper and realistic equation of state (EOS) for strongly interacting matter used in the study of the QCD phase diagram still appears as a challenging problem. Recently, we constructed a hybrid model description for the quark-gluon plasma (QGP) as well as hadron gas (HG) phases where we used an excluded volume model for HG and a thermodynamically consistent quasiparticle model for the QGP phase. The hybrid model suitably describes the recent lattice results of various thermodynamical as well as transport properties of the QCD matter at zero baryon chemical potential (μB). In this paper, we extend our investigations further in obtaining the properties of QCD matter at finite value of μB and compare our results with the most recent results of lattice QCD calculation.
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.
Baldassi, Carlo; Zamparo, Marco; Feinauer, Christoph; Procaccini, Andrea; Zecchina, Riccardo; Weigt, Martin; Pagnani, Andrea
2014-01-01
In the course of evolution, proteins show a remarkable conservation of their three-dimensional structure and their biological function, leading to strong evolutionary constraints on the sequence variability between homologous proteins. Our method aims at extracting such constraints from rapidly accumulating sequence data, and thereby at inferring protein structure and function from sequence information alone. Recently, global statistical inference methods (e.g. direct-coupling analysis, sparse inverse covariance estimation) have achieved a breakthrough towards this aim, and their predictions have been successfully implemented into tertiary and quaternary protein structure prediction methods. However, due to the discrete nature of the underlying variable (amino-acids), exact inference requires exponential time in the protein length, and efficient approximations are needed for practical applicability. Here we propose a very efficient multivariate Gaussian modeling approach as a variant of direct-coupling analysis: the discrete amino-acid variables are replaced by continuous Gaussian random variables. The resulting statistical inference problem is efficiently and exactly solvable. We show that the quality of inference is comparable or superior to the one achieved by mean-field approximations to inference with discrete variables, as done by direct-coupling analysis. This is true for (i) the prediction of residue-residue contacts in proteins, and (ii) the identification of protein-protein interaction partner in bacterial signal transduction. An implementation of our multivariate Gaussian approach is available at the website http://areeweb.polito.it/ricerca/cmp/code.
Spear, Jack; Fields, Lanny
2015-12-01
Interpreting and describing complex information shown in graphs are essential skills to be mastered by students in many disciplines; both are skills that are difficult to learn. Thus, interventions that produce these outcomes are of great value. Previous research showed that conditional discrimination training that established stimulus control by some elements of graphs and their printed descriptions produced some improvement in the accuracy of students' written descriptions of graphs. In the present experiment, students wrote nearly perfect descriptions of the information conveyed in interaction-based graphs after the establishment of conditional relations between graphs and their printed descriptions. This outcome was achieved with the use of special conditional discrimination training procedures that required participants to attend to many of the key elements of the graphs and the phrases in the printed descriptions that corresponded to the elements in the graphs. Thus, students learned to write full descriptions of the information represented by complex graphs by an automated training procedure that did not involve the direct training of writing.
Ciprofloxacin and Clozapine: A Potentially Fatal but Underappreciated Interaction
Proctor, George; Cummings, Michael A.; Dardashti, Laura J.; Stahl, Stephen M.
2016-01-01
Objective. Clozapine provides a 50%–60% response rate in refractory schizophrenia but has a narrow therapeutic index and is susceptible to pharmacokinetic interactions, particularly with strong inhibitors or inducers of cytochrome P450 (CYP) 1A2. Case Report. We report the case of a 28-year-old nonsmoking female with intellectual disability who was maintained for 3 years on clozapine 100 mg orally twice daily. The patient was treated for presumptive urinary tract infection with ciprofloxacin 500 mg orally twice daily and two days later collapsed and died despite resuscitation efforts. The postmortem femoral clozapine plasma level was dramatically elevated at 2900 ng/mL, and the cause of death was listed as acute clozapine toxicity. Conclusion. Given the potentially fatal pharmacokinetic interaction between clozapine and ciprofloxacin, clinicians are advised to monitor baseline clozapine levels prior to adding strong CYP450 1A2 inhibitors, reduce the clozapine dose by at least two-thirds if adding a 1A2 inhibitor such as ciprofloxacin, check subsequent steady state clozapine levels, and adjust the clozapine dose to maintain levels close to those obtained at baseline. PMID:27872784
Anticoagulant Medicine: Potential for Drug-Food Interactions
... Medications Anticoagulants and Drug-Food Interactions Anticoagulants and Drug-Food Interactions Make an Appointment Ask a Question ... care provider before making the change. Anticoagulants and Medicine There are many medicines that can interact with ...
NASA Astrophysics Data System (ADS)
Losilla, S. A.; Sundholm, D.
2012-06-01
A computational scheme to perform accurate numerical calculations of electrostatic potentials and interaction energies for molecular systems has been developed and implemented. Molecular electron and energy densities are divided into overlapping atom-centered atomic contributions and a three-dimensional molecular remainder. The steep nuclear cusps are included in the atom-centered functions making the three-dimensional remainder smooth enough to be accurately represented with a tractable amount of grid points. The one-dimensional radial functions of the atom-centered contributions as well as the three-dimensional remainder are expanded using finite element functions. The electrostatic potential is calculated by integrating the Coulomb potential for each separate density contribution, using our tensorial finite element method for the three-dimensional remainder. We also provide algorithms to compute accurate electron-electron and electron-nuclear interactions numerically using the proposed partitioning. The methods have been tested on all-electron densities of 18 reasonable large molecules containing elements up to Zn. The accuracy of the calculated Coulomb interaction energies is in the range of 10-3 to 10-6 Eh when using an equidistant grid with a step length of 0.05 a0.
Nelson, B; Liu, E; Kirby, R M; Haimes, R
2012-12-01
This paper presents the Element Visualizer (ElVis), a new, open-source scientific visualization system for use with high-order finite element solutions to PDEs in three dimensions. This system is designed to minimize visualization errors of these types of fields by querying the underlying finite element basis functions (e.g., high-order polynomials) directly, leading to pixel-exact representations of solutions and geometry. The system interacts with simulation data through runtime plugins, which only require users to implement a handful of operations fundamental to finite element solvers. The data in turn can be visualized through the use of cut surfaces, contours, isosurfaces, and volume rendering. These visualization algorithms are implemented using NVIDIA's OptiX GPU-based ray-tracing engine, which provides accelerated ray traversal of the high-order geometry, and CUDA, which allows for effective parallel evaluation of the visualization algorithms. The direct interface between ElVis and the underlying data differentiates it from existing visualization tools. Current tools assume the underlying data is composed of linear primitives; high-order data must be interpolated with linear functions as a result. In this work, examples drawn from aerodynamic simulations-high-order discontinuous Galerkin finite element solutions of aerodynamic flows in particular-will demonstrate the superiority of ElVis' pixel-exact approach when compared with traditional linear-interpolation methods. Such methods can introduce a number of inaccuracies in the resulting visualization, making it unclear if visual artifacts are genuine to the solution data or if these artifacts are the result of interpolation errors. Linear methods additionally cannot properly visualize curved geometries (elements or boundaries) which can greatly inhibit developers' debugging efforts. As we will show, pixel-exact visualization exhibits none of these issues, removing the visualization scheme as a source of
Galland, Nicolas; Kone, Soleymane; Le Questel, Jean-Yves
2012-10-01
A quantitative analysis of the interaction sites of the anti-Alzheimer drug galanthamine with molecular probes (water and benzene molecules) representative of its surroundings in the binding site of acetylcholinesterase (AChE) has been realized through pairwise potentials calculations and quantum chemistry. This strategy allows a full and accurate exploration of the galanthamine potential energy surface of interaction. Significantly different results are obtained according to the distances of approaches between the various molecular fragments and the conformation of the galanthamine N-methyl substituent. The geometry of the most relevant complexes has then been fully optimized through MPWB1K/6-31 + G(d,p) calculations, final energies being recomputed at the LMP2/aug-cc-pVTZ(-f) level of theory. Unexpectedly, galanthamine is found to interact mainly from its hydrogen-bond donor groups. Among those, CH groups in the vicinity of the ammonium group are prominent. The trends obtained provide rationales to the predilection of the equatorial orientation of the galanthamine N-methyl substituent for binding to AChE. The analysis of the interaction energies pointed out the independence between the various interaction sites and the rigid character of galanthamine. The comparison between the cluster calculations and the crystallographic observations in galanthamine-AChE co-crystals allows the validation of the theoretical methodology. In particular, the positions of several water molecules appearing as strongly conserved in galanthamine-AChE co-crystals are predicted by the calculations. Moreover, the experimental position and orientation of lateral chains of functionally important aminoacid residues are in close agreement with the ones predicted theoretically. Our study provides relevant information for a rational drug design of galanthamine based AChE inhibitors.
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.
Isolating the non-polar contributions to the intermolecular potential for water-alkane interactions.
Ballal, Deepti; Venkataraman, Pradeep; Fouad, Wael A; Cox, Kenneth R; Chapman, Walter G
2014-08-14
Intermolecular potential models for water and alkanes describe pure component properties fairly well, but fail to reproduce properties of water-alkane mixtures. Understanding interactions between water and non-polar molecules like alkanes is important not only for the hydrocarbon industry but has implications to biological processes as well. Although non-polar solutes in water have been widely studied, much less work has focused on water in non-polar solvents. In this study we calculate the solubility of water in different alkanes (methane to dodecane) at ambient conditions where the water content in alkanes is very low so that the non-polar water-alkane interactions determine solubility. Only the alkane-rich phase is simulated since the fugacity of water in the water rich phase is calculated from an accurate equation of state. Using the SPC/E model for water and TraPPE model for alkanes along with Lorentz-Berthelot mixing rules for the cross parameters produces a water solubility that is an order of magnitude lower than the experimental value. It is found that an effective water Lennard-Jones energy ε(W)/k = 220 K is required to match the experimental water solubility in TraPPE alkanes. This number is much higher than used in most simulation water models (SPC/E-ε(W)/k = 78.2 K). It is surprising that the interaction energy obtained here is also higher than the water-alkane interaction energy predicted by studies on solubility of alkanes in water. The reason for this high water-alkane interaction energy is not completely understood. Some factors that might contribute to the large interaction energy, such as polarizability of alkanes, octupole moment of methane, and clustering of water at low concentrations in alkanes, are examined. It is found that, though important, these factors do not completely explain the anomalously strong attraction between alkanes and water observed experimentally.
NASA Astrophysics Data System (ADS)
Le Roy, Robert J.; Walji, Sadru; Sentjens, Katherine
2013-06-01
Alkali hydride diatomic molecules have long been the object of spectroscopic studies. However, their small reduced mass makes them species for which the conventional semiclassical-based methods of analysis tend to have the largest errors. To date, the only quantum-mechanically accurate direct-potential-fit (DPF) analysis for one of these molecules was the one for LiH reported by Coxon and Dickinson. The present paper extends this level of analysis to NaH, and reports a DPF analysis of all available spectroscopic data for the A ^1Σ^+-X ^1Σ^+ system of NaH which yields analytic potential energy functions for these two states that account for those data (on average) to within the experimental uncertainties. W.C. Stwalley, W.T. Zemke and S.C. Yang, J. Phys. Chem. Ref. Data {20}, 153-187 (1991). J.A. Coxon and C.S. Dickinson, J. Chem. Phys. {121}, 8378 (2004).
The dispersion interaction between quantum mechanics and effective fragment potential molecules
Smith, Quentin A.; Ruedenberg, Klaus; Gordon, Mark S.; Slipchenko, Lyudmila
2012-06-26
A method for calculating the dispersion energy between molecules modeled with the general effective fragment potential (EFP2) method and those modeled using a full quantum mechanics (QM) method, e.g., Hartree-Fock (HF) or second-order perturbation theory, is presented. C6 dispersion coefficients are calculated for pairs of orbitals using dynamic polarizabilities from the EFP2 portion, and dipole integrals and orbital energies from the QM portion of the system. Dividing by the sixth power of the distance between localized molecular orbital centroids yields the first term in the commonly employed London series expansion. A C8 term is estimated from the C6 term to achieve closer agreement with symmetry adapted perturbation theory values. Two damping functions for the dispersion energy are evaluated. By using terms that are already computed during an ordinary HF or EFP2 calculation, the new method enables accurate and extremely rapid evaluation of the dispersion interaction between EFP2 and QM molecules.
Gilani, G Sarwar; Xiao, Chaowu; Lee, Nora
2008-01-01
Accurate standardized methods for the determination of amino acid in foods are required to assess the nutritional safety and compositional adequacy of sole source foods such as infant formulas and enteral nutritionals, and protein and amino acid supplements and their hydrolysates, and to assess protein claims of foods. Protein digestibility-corrected amino acid score (PDCAAS), which requires information on amino acid composition, is the official method for assessing protein claims of foods and supplements sold in the United States. PDCAAS has also been adopted internationally as the most suitable method for routine evaluation of protein quality of foods by the Food and Agriculture Organization/World Health Organization. Standardized methods for analysis of amino acids by ion-exchange chromatography have been developed. However, there is a need to develop validated methods of amino acid analysis in foods using liquid chromatographic techniques, which have replaced ion-exchange methods for quantifying amino acids in most laboratories. Bioactive peptides from animal and plant proteins have been found to potentially impact human health. A wide range of physiological effects, including blood pressure-lowering effects, cholesterol-lowering ability, antithrombotic effects, enhancement of mineral absorption, and immunomodulatory effects have been described for bioactive peptides. There is considerable commercial interest in developing functional foods containing bioactive peptides. There is also a need to develop accurate standardized methods for the characterization (amino acid sequencing) and quantification of bioactive peptides and to carry out dose-response studies in animal models and clinical trials to assess safety, potential allergenicity, potential intolerance, and efficacy of bioactive peptides. Information from these studies is needed for determining the upper safe levels of bioactive peptides and as the basis for developing potential health claims for bioactive
Antiparkinsonian potential of interaction of LEK-8829 with bromocriptine.
Zivin, M; Sprah, L; Sket, D
1998-05-22
The ergoline derivative, LEK-8829 (9,10-didehydro-N-methyl-(2-propynyl)-6-methyl-8-aminomethylerg oline), has been proposed as a potential atypical antipsychotic drug with antagonistic actions at dopamine D2 and serotonin 5-HT2 and 5-HT1A receptors (Krisch et al., 1994, 1996). LEK-8829 also induces contralateral turning in rats with 6-hydroxydopamine-induced unilateral lesion of dopamine nigrostriatal neurons. Turning is blocked by SCH-23390 (R(+)-chloro-8-hydroxy-3-methyl-1-phenyl-2,3,4,5-tetrahydro-1H-3-benzaze pine), a dopamine D1 receptor antagonist. It has been suggested that LEK-8829 could have beneficial effects in parkinsonian patients suffering from psychotic episodes induced as a side-effect of antiparkinsonian treatment with dopamine D2 receptor agonists. Therefore, we now investigated the interaction of LEK-8829 with the dopamine D2 receptor agonist bromocriptine (2-bromo-alpha-ergokryptine) in 6-hydroxydopamine-lesioned rats. Treatment with either LEK-8829 (3 mg kg(-1)) or bromocriptine (3 mg kg(-1)) induced a vigorous contralateral turning response. The cumulated number of turns induced by the treatment with both drugs combined was not significantly different from the cumulated number of turns induced by single-drug treatment. The pretreatment with SCH-23390 (1 mg kg(-1)) did not have a significant effect on the bromocriptine-induced turning but significantly decreased the turning observed after the combined LEK-8829/bromocriptine treatment. We conclude that in the 6-hydroxydopamine model, the turning behaviour mediated by the LEK-8829/bromocriptine combination may be the result of opposing activity of both drugs at dopamine D2 receptors with concomitant stimulation of dopamine D1 receptors by LEK-8829. Therefore, LEK-8829 may have a potential for the therapy of parkinsonism complicated by dopamine D2 receptor agonist drug-induced psychosis.
Probiotics: Interaction with gut microbiome and antiobesity potential.
Arora, Tulika; Singh, Satvinder; Sharma, Raj Kumar
2013-04-01
Obesity is a metabolic disorder afflicting people globally. There has been a pivotal advancement in the understanding of the intestinal microbiota composition and its implication in extraintestinal (metabolic) diseases. Therefore, any agent modulating gut microbiota may produce an influential effect in preventing the pathogenesis of disease. Probiotics are live microbes that, when administered in adequate amounts, have been shown to confer health benefits to the host. Over the years, probiotics have been a part of the human diet in the form of different fermented foods consumed around the world. Their influence on different physiologic functions in the host is increasingly being documented. The antiobesity potential of probiotics is also gaining wide attention because of increasing evidence of the role of gut microbiota in energy homeostasis and fat accumulation. Probiotics have also been shown to interact with the resident bacterial members already present in the gut by altering their properties, which may also affect the metabolic pathways involved in the regulation of fat metabolism. The underlying pathways governing the antiobesity effects of probiotics remain unclear. However, it is hoped that the evidence presented and discussed in this review will encourage and thus drive more extensive research in this field.
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.
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.
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
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}.
NASA Astrophysics Data System (ADS)
Sahni, Viraht; Qian, Zhixin
2007-03-01
In previous work, it has been shown that for spherically symmetric or sphericalized systems, the asymptotic near nucleus structure of the electron-interaction potential is vee(r) = vee(0) + βr + γr^2. In this paper we prove via time-independent Quantal Density Functional Theory[1](Q-DFT): (i) correlations due to the Pauli exclusion principle and Coulomb repulsion do not contribute to the linear structure;(ii) these Pauli and Coulomb correlations contribute quadratically; (iii) the linear structure is solely due to Correlation-Kinetic effects, the coefficient β being determined analytically. By application of adiabatic coupling constant perturbation theory via QDFT we further prove: (iv) the Kohn-Sham (KS-DFT) `exchange' potential vx(r) approaches the nucleus linearly, this structure being due solely to lowest- order Correlation-Kinetic effects: (v) the KS-DFT `correlation' potential vc(r) also approaches the nucleus linearly, being solely due to higher-order Correlation-Kinetic contributions. The above conclusions are equally valid for system of arbitrary symmetry, provided spherical averages of the properties are employed. 1 Quantal Density Functional Theory, V. Sahni (Springer-Verlag 2004)
Cybulski, H; Krems, R V; Sadeghpour, H R; Dalgarno, A; Kłos, J; Groenenboom, G C; van der Avoird, A; Zgid, D; Chałasiński, G
2005-03-01
A detailed analysis of the He-NH((3)Sigma(-)) van der Waals complex is presented. We discuss ab initio calculations of the potential energy surface and fitting procedures with relevance to cold collisions, and we present accurate calculations of bound energy levels of the triatomic complex as well as collisional properties of NH molecules in a buffer gas of (3)He. The influence of the external magnetic field used to trap the NH molecules and the effect of the atom-molecule interaction potential on the collisionally induced Zeeman relaxation are explored. It is shown that minute variations of the interaction potential due to different fitting procedures may alter the Zeeman relaxation rate at ultralow temperatures by as much as 50%.
Bulut, Niyazi; Kłos, Jacek; Alexander, Millard H
2012-03-14
We present converged exact quantum wave packet calculations of reaction probabilities, integral cross sections, and thermal rate coefficients for the title reaction. Calculations have been carried out on the ground 1(2)A' global adiabatic potential energy surface of Deskevich et al. [J. Chem. Phys. 124, 224303 (2006)]. Converged wave packet reaction probabilities at selected values of the total angular momentum up to a partial wave of J = 140 with the HCl reagent initially selected in the v = 0, j = 0-16 rovibrational states have been obtained for the collision energy range from threshold up to 0.8 eV. The present calculations confirm an important enhancement of reactivity with rotational excitation of the HCl molecule. First, accurate integral cross sections and rate constants have been calculated and compared with the available experimental data.
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.
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.
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.
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.
NASA Astrophysics Data System (ADS)
Calvo, F.; Falvo, Cyril; Parneix, Pascal
2013-01-01
An explicit polarizable potential for the naphthalene-argon complex has been derived assuming only atomic contributions, aiming at large scale simulations of naphthalene under argon environment. The potential was parametrized from dedicated quantum chemical calculations at the CCSD(T) level, and satisfactorily reproduces available structural and energetic properties. Combining this potential with a tight-binding model for naphthalene, collisional energy transfer is studied by means of dedicated molecular dynamics simulations, nuclear quantum effects being accounted for in the path-integral framework. Except at low target temperature, nuclear quantum effects do not alter the average energies transferred by the collision or the collision duration. However, the distribution of energy transferred is much broader in the quantum case due to the significant zero-point energy and the higher density of states. Using an ab initio potential for the Ar-Ar interaction, the IR absorption spectrum of naphthalene solvated by argon clusters or an entire Ar matrix is computed via classical and centroid molecular dynamics. The classical spectra exhibit variations with growing argon environment that are absent from quantum spectra. This is interpreted by the greater fluxional character experienced by the argon atoms due to vibrational delocalization.
NASA Astrophysics Data System (ADS)
Holka, Filip; Szalay, Péter G.; Fremont, Julien; Rey, Michael; Peterson, Kirk A.; Tyuterev, Vladimir G.
2011-03-01
High level ab initio potential energy functions have been constructed for LiH in order to predict vibrational levels up to dissociation. After careful tests of the parameters of the calculation, the final adiabatic potential energy function has been composed from: (a) an ab initio nonrelativistic potential obtained at the multireference configuration interaction with singles and doubles level including a size-extensivity correction and quintuple-sextuple ζ extrapolations of the basis, (b) a mass-velocity-Darwin relativistic correction, and (c) a diagonal Born-Oppenheimer (BO) correction. Finally, nonadiabatic effects have also been considered by including a nonadiabatic correction to the kinetic energy operator of the nuclei. This correction is calculated from nonadiabatic matrix elements between the ground and excited electronic states. The calculated vibrational levels have been compared with those obtained from the experimental data [J. A. Coxon and C. S. Dickinson, J. Chem. Phys. 134, 9378 (2004)]. It was found that the calculated BO potential results in vibrational levels which have root mean square (rms) deviations of about 6-7 cm-1 for LiH and ˜3 cm-1 for LiD. With all the above mentioned corrections accounted for, the rms deviation falls down to ˜1 cm-1. These results represent a drastic improvement over previous theoretical predictions of vibrational levels for all isotopologues of LiH.
Holka, Filip; Szalay, Péter G; Fremont, Julien; Rey, Michael; Peterson, Kirk A; Tyuterev, Vladimir G
2011-03-07
High level ab initio potential energy functions have been constructed for LiH in order to predict vibrational levels up to dissociation. After careful tests of the parameters of the calculation, the final adiabatic potential energy function has been composed from: (a) an ab initio nonrelativistic potential obtained at the multireference configuration interaction with singles and doubles level including a size-extensivity correction and quintuple-sextuple ζ extrapolations of the basis, (b) a mass-velocity-Darwin relativistic correction, and (c) a diagonal Born-Oppenheimer (BO) correction. Finally, nonadiabatic effects have also been considered by including a nonadiabatic correction to the kinetic energy operator of the nuclei. This correction is calculated from nonadiabatic matrix elements between the ground and excited electronic states. The calculated vibrational levels have been compared with those obtained from the experimental data [J. A. Coxon and C. S. Dickinson, J. Chem. Phys. 134, 9378 (2004)]. It was found that the calculated BO potential results in vibrational levels which have root mean square (rms) deviations of about 6-7 cm(-1) for LiH and ∼3 cm(-1) for LiD. With all the above mentioned corrections accounted for, the rms deviation falls down to ∼1 cm(-1). These results represent a drastic improvement over previous theoretical predictions of vibrational levels for all isotopologues of LiH.
Calvo, F; Falvo, Cyril; Parneix, Pascal
2013-01-21
An explicit polarizable potential for the naphthalene-argon complex has been derived assuming only atomic contributions, aiming at large scale simulations of naphthalene under argon environment. The potential was parametrized from dedicated quantum chemical calculations at the CCSD(T) level, and satisfactorily reproduces available structural and energetic properties. Combining this potential with a tight-binding model for naphthalene, collisional energy transfer is studied by means of dedicated molecular dynamics simulations, nuclear quantum effects being accounted for in the path-integral framework. Except at low target temperature, nuclear quantum effects do not alter the average energies transferred by the collision or the collision duration. However, the distribution of energy transferred is much broader in the quantum case due to the significant zero-point energy and the higher density of states. Using an ab initio potential for the Ar-Ar interaction, the IR absorption spectrum of naphthalene solvated by argon clusters or an entire Ar matrix is computed via classical and centroid molecular dynamics. The classical spectra exhibit variations with growing argon environment that are absent from quantum spectra. This is interpreted by the greater fluxional character experienced by the argon atoms due to vibrational delocalization.
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
Czakó, Gábor
2013-04-07
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
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...
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.
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.
NASA Astrophysics Data System (ADS)
Huang, Xinchuan; Schwenke, David W.; Lee, Timothy J.
2014-03-01
A purely ab initio potential energy surface (PES) was refined with selected 32S16O2 HITRAN data. Compared to HITRAN, the root-mean-squares error (σRMS) 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 34S16O2 band origins, higher energy 32S16O2 band origins and missing 32S16O2 IR bands have been verified by most recent experiments and available HITRAN data. We conclude that the Ames-1 PES is able to predict 32/34S16O2 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 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.
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.
NASA Astrophysics Data System (ADS)
Hu, Hao; Lu, Zhenyu; Parks, Jerry M.; Burger, Steven K.; Yang, Weitao
2008-01-01
To accurately determine the reaction path and its energetics for enzymatic and solution-phase reactions, we present a sequential sampling and optimization approach that greatly enhances the efficiency of the ab initio quantum mechanics/molecular mechanics minimum free-energy path (QM/MM-MFEP) method. In the QM/MM-MFEP method, the thermodynamics of a complex reaction system is described by the potential of mean force (PMF) surface of the quantum mechanical (QM) subsystem with a small number of degrees of freedom, somewhat like describing a reaction process in the gas phase. The main computational cost of the QM/MM-MFEP method comes from the statistical sampling of conformations of the molecular mechanical (MM) subsystem required for the calculation of the QM PMF and its gradient. In our new sequential sampling and optimization approach, we aim to reduce the amount of MM sampling while still retaining the accuracy of the results by first carrying out MM phase-space sampling and then optimizing the QM subsystem in the fixed-size ensemble of MM conformations. The resulting QM optimized structures are then used to obtain more accurate sampling of the MM subsystem. This process of sequential MM sampling and QM optimization is iterated until convergence. The use of a fixed-size, finite MM conformational ensemble enables the precise evaluation of the QM potential of mean force and its gradient within the ensemble, thus circumventing the challenges associated with statistical averaging and significantly speeding up the convergence of the optimization process. To further improve the accuracy of the QM/MM-MFEP method, the reaction path potential method developed by Lu and Yang [Z. Lu and W. Yang, J. Chem. Phys. 121, 89 (2004)] is employed to describe the QM/MM electrostatic interactions in an approximate yet accurate way with a computational cost that is comparable to classical MM simulations. The new method was successfully applied to two example reaction processes, the
Hu Hao; Lu Zhenyu; Parks, Jerry M.; Burger, Steven K.; Yang Weitao
2008-01-21
To accurately determine the reaction path and its energetics for enzymatic and solution-phase reactions, we present a sequential sampling and optimization approach that greatly enhances the efficiency of the ab initio quantum mechanics/molecular mechanics minimum free-energy path (QM/MM-MFEP) method. In the QM/MM-MFEP method, the thermodynamics of a complex reaction system is described by the potential of mean force (PMF) surface of the quantum mechanical (QM) subsystem with a small number of degrees of freedom, somewhat like describing a reaction process in the gas phase. The main computational cost of the QM/MM-MFEP method comes from the statistical sampling of conformations of the molecular mechanical (MM) subsystem required for the calculation of the QM PMF and its gradient. In our new sequential sampling and optimization approach, we aim to reduce the amount of MM sampling while still retaining the accuracy of the results by first carrying out MM phase-space sampling and then optimizing the QM subsystem in the fixed-size ensemble of MM conformations. The resulting QM optimized structures are then used to obtain more accurate sampling of the MM subsystem. This process of sequential MM sampling and QM optimization is iterated until convergence. The use of a fixed-size, finite MM conformational ensemble enables the precise evaluation of the QM potential of mean force and its gradient within the ensemble, thus circumventing the challenges associated with statistical averaging and significantly speeding up the convergence of the optimization process. To further improve the accuracy of the QM/MM-MFEP method, the reaction path potential method developed by Lu and Yang [Z. Lu and W. Yang, J. Chem. Phys. 121, 89 (2004)] is employed to describe the QM/MM electrostatic interactions in an approximate yet accurate way with a computational cost that is comparable to classical MM simulations. The new method was successfully applied to two example reaction processes, the
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.
Bell, T G; Smith, W L; Oxender, W D
1986-01-01
Prostaglandins are vasoactive agents which have potent and varied effects depending on the species, conditions and organs tested. The clinician wishing to gain a significant overview of the field from current research literature has a demanding task for himself. A review of biologic interactions is exactly what is needed in a consideration of possible clinical applications of prostaglandins. Thus, it is necessary first to recount the last five years' advances in prostaglandin research. Only then will the listing and discussion of some diseases soon to benefit from the application of research be meaningful.
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.
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.
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 D7 is obtained by perturbation methods. Collision-induced absorption spectra are computed quantum mechanically and compared with existing measurements.
Maraviroc: in vitro assessment of drug–drug interaction potential
Hyland, Ruth; Dickins, Maurice; Collins, Claire; Jones, Hannah; Jones, Barry
2008-01-01
AIMS To characterize the cytochrome P450 enzyme(s) responsible for the N-dealkylation of maraviroc in vitro, and predict the extent of clinical drug–drug interactions (DDIs). METHODS Human liver and recombinant CYP microsomes were used to identify the CYP enzyme responsible for maraviroc N-dealkylation. Studies comprised enzyme kinetics and evaluation of the effects of specific CYP inhibitors. In vitro data were then used as inputs for simulation of DDIs with ketoconazole, ritonavir, saquinavir and atazanvir, using the Simcyp™ population-based absorption, distribution, metabolism and elimination (ADME) simulator. Study designs for simulations mirrored those actually used in the clinic. RESULTS Maraviroc was metabolized to its N-dealkylated product via a single CYP enzyme characterized by a Km of 21 µM and Vmax of 0.45 pmol pmol−1 min−1 in human liver microsomes and was inhibited by ketoconazole (CYP3A4 inhibitor). In a panel of recombinant CYP enzymes, CYP3A4 was identified as the major CYP responsible for maraviroc metabolism. Using recombinant CYP3A4, N-dealkylation was characterized by a Km of 13 µM and a Vmax of 3 pmol pmol−1 CYP min−1. Simulations therefore focused on the effect of CYP3A4 inhibitors on maraviroc pharmacokinetics. The simulated median AUC ratios were in good agreement with observed clinical changes (within twofold in all cases), although, in general, there was a trend for overprediction in the magnitude of the DDI. CONCLUSION Maraviroc is a substrate for CYP3A4, and exposure will therefore be modulated by CYP3A4 inhibitors. Simcyp™ has successfully simulated the extent of clinical interactions with CYP3A4 inhibitors, further validating this software as a good predictor of CYP-based DDIs. WHAT IS ALREADY KNOWN ABOUT THE SUBJECTMaraviroc is known to undergo oxidative metabolism in vivo and is a substrate for cytochrome P450 (CYP).Simcyp™ has recently become more widely used for the prediction of CYP-mediated drug
Nikitin, A V; Rey, M; Rodina, A; Krishna, B M; Tyuterev, Vl G
2016-11-17
Nine-dimensional potential energy surface (PES) and dipole moment surface (DMS) of the germane molecule are constructed using extended ab initio CCSD(T) calculations at 19 882 points. PES analytical representation is determined as an expansion in nonlinear symmetry adapted products of orthogonal and internal coordinates involving 340 parameters up to eighth order. Minor empirical refinement of the equilibrium geometry and of four quadratic parameters of the PES computed at the CCSD(T)/aug-cc-pVQZ-DK level of the theory yielded the accuracy below 1 cm(-1) for all experimentally known vibrational band centers of five stable isotopologues of (70)GeH4, (72)GeH4, (73)GeH4, (74)GeH4, and (76)GeH4 up to 8300 cm(-1). The optimized equilibrium bond re = 1.517 594 Å is very close to best ab initio values. Rotational energies up to J = 15 are calculated using potential expansion in normal coordinate tensors with maximum errors of 0.004 and 0.0006 cm(-1) for (74)GeH4 and (76)GeH4. The DMS analytical representation is determined through an expansion in symmetry-adapted products of internal nonlinear coordinates involving 967 parameters up to the sixth order. Vibration-rotation line intensities of five stable germane isotopologues were calculated from purely ab initio DMS using nuclear motion variational calculations with a full account of the tetrahedral symmetry of the molecules. For the first time a good overall agreement of main absorption features with experimental rotationally resolved Pacific Northwest National Laboratory spectra was achieved in the entire range of 700-5300 cm(-1). It was found that very accurate description of state-dependent isotopic shifts is mandatory to correctly describe complex patterns of observed spectra at natural isotopic abundance resulting from the superposition of five stable isotopologues. The data obtained in this work will be made available through the TheoReTS information system.
Korth, Martin; Thiel, Walter
2011-09-13
Semiempirical quantum mechanical (SQM) methods offer a fast approximate treatment of the electronic structure and the properties of large molecules. Careful benchmarks are required to establish their accuracy. Here, we report a validation of standard SQM methods using a subset of the comprehensive GMTKN24 database for general main group thermochemistry, kinetics, and noncovalent interactions, which has recently been introduced to evaluate density functional theory (DFT) methods ( J. Chem. Theory Comput. 2010 , 6 , 107 ). For all SQM methods considered presently, parameters are available for the elements H, C, N, and O, and consequently, we have extracted from the GMTKN24 database all species containing only these four elements (excluding multireference cases). The resulting GMTKN24-hcno database has 370 entries (derived from 593 energies) compared with 715 entries (derived from 1033 energies) in the original GMTKN24 database. The current benchmark covers established standard SQM methods (AM1, PM6), more recent approaches with orthogonalization corrections (OM1, OM2, OM3), and the self-consistent-charge density functional tight binding method (SCC-DFTB). The results are compared against each other and against DFT results using standard functionals. We find that the OMx methods outperform AM1, PM6, and SCC-DFTB by a significant margin, with a substantial gain in accuracy especially for OM2 and OM3. These latter methods are quite accurate even in comparison with DFT, with an overall mean absolute deviation of 6.6 kcal/mol for PBE and 7.9 kcal/mol for OM3. The OMx methods are also remarkably robust with regard to the unusual bonding situations encountered in the "mindless" MB08-165 test set, for which all other SQM methods fail badly.
Quasielastic nucleon transfer and the heavy-ion interaction potential
NASA Astrophysics Data System (ADS)
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.
1986-02-01
Quasielastic nucleon-transfer cross sections have been mea- sured at energies ~=35% above the Coulomb barrier for 58,64Ni + 112,116,120,124Sn. 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.
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
2013-04-05
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).
Pharmacological potential of biogenic amine–polyamine interactions beyond neurotransmission
Sánchez-Jiménez, F; Ruiz-Pérez, M V; Urdiales, J L; Medina, M A
2013-01-01
Histamine, serotonin and dopamine are biogenic amines involved in intercellular communication with multiple effects on human pathophysiology. They are products of two highly homologous enzymes, histidine decarboxylase and l-aromatic amino acid decarboxylase, and transmit their signals through different receptors and signal transduction mechanisms. Polyamines derived from ornithine (putrescine, spermidine and spermine) are mainly involved in intracellular effects related to cell proliferation and death mechanisms. This review summarizes structural and functional evidence for interactions between components of all these amine metabolic and signalling networks (decarboxylases, transporters, oxidases, receptors etc.) at cellular and tissue levels, distinct from nervous and neuroendocrine systems, where the crosstalk among these amine-related components can also have important pathophysiological consequences. The discussion highlights aspects that could help to predict and discuss the effects of intervention strategies. Linked Articles This article is part of a themed issue on Histamine Pharmacology Update. To view the other articles in this issue visit http://dx.doi.org/10.1111/bph.2013.170.issue-1 PMID:23347064
Paracetamol and simvastatin: a potential interaction resulting in hepatotoxicity.
Gumbrevičius, Gintautas; Sveikata, Audrius; Sveikatienė, Renata; Stankevičius, Edgaras
2012-01-01
The safety profile of paracetamol and simvastatin is sufficiently well known, although no interactions between these two medicinal products have been described in the scientific literature so far. A 66-year-old female patient who experienced myocardial infarction and underwent coronary artery bypass grafting 9 years ago was taking simvastatin at a daily dose of 10 mg. Liver enzyme tests were carried out regularly, and their results were always normal. Later on, the patient took 6 tablets of fixed combination medicinal product Gripex(TM) (paracetamol, pseudoephedrine, and dextromethorphan) per day due to a fever. The daily dose of paracetamol taken by the patient totaled 1.95 g. The patient developed severe jaundice, nausea, vomiting; blood bilirubin levels increased more than 3 times; alanine transaminase, more than 10 times; and asparagine transaminase, more than 5 times. Paracetamol is metabolized by CYP enzymes (CYP2E1, 1A2, 2A6, 3A4) to a reactive metabolite, N-acetyl-p-benzoquinone-imine (NAPQI). Under conditions of excessive NAPQI formation or reduction in glutathione stores by approximately 70%, NAPQI covalently binds to the cysteinyl sulfhydryl groups of cellular proteins, forming NAPQI-protein adducts. Simvastatin is a substrate of CYP3A4 enzyme. Clinical and pharmacological data, available in the published literature, allow the assumption that simvastatin may induce CYP3A4 and result in increased hepatoxicity of paracetamol.
Severe potential drug-drug interactions in older adults with dementia and associated factors
Bogetti-Salazar, Michele; González-González, Cesar; Juárez-Cedillo, Teresa; Sánchez-García, Sergio; Rosas-Carrasco, Oscar
2016-01-01
OBJECTIVE: To identify the main severe potential drug-drug interactions in older adults with dementia and to examine the factors associated with these interactions. METHOD: This was a cross-sectional study. The enrolled patients were selected from six geriatrics clinics of tertiary care hospitals across Mexico City. The patients had received a clinical diagnosis of dementia based on the current standards and were further divided into the following two groups: those with severe drug-drug interactions (contraindicated/severe) (n=64) and those with non-severe drug-drug interactions (moderate/minor/absent) (n=117). Additional socio-demographic, clinical and caregiver data were included. Potential drug-drug interactions were identified using Micromedex Drug Reax 2.0® database. RESULTS: A total of 181 patients were enrolled, including 57 men (31.5%) and 124 women (68.5%) with a mean age of 80.11±8.28 years. One hundred and seven (59.1%) patients in our population had potential drug-drug interactions, of which 64 (59.81%) were severe/contraindicated. The main severe potential drug-drug interactions were caused by the combinations citalopram/anti-platelet (11.6%), clopidogrel/omeprazole (6.1%), and clopidogrel/aspirin (5.5%). Depression, the use of a higher number of medications, dementia severity and caregiver burden were the most significant factors associated with severe potential drug-drug interactions. CONCLUSIONS: Older people with dementia experience many severe potential drug-drug interactions. Anti-depressants, antiplatelets, anti-psychotics and omeprazole were the drugs most commonly involved in these interactions. Despite their frequent use, anti-dementia drugs were not involved in severe potential drug-drug interactions. The number and type of medications taken, dementia severity and depression in patients in addition to caregiver burden should be considered to avoid possible drug interactions in this population. PMID:26872079
Orchid–pollinator interactions and potential vulnerability to biological invasion
Chupp, Adam D.; Battaglia, Loretta L.; Schauber, Eric M.; Sipes, Sedonia D.
2015-01-01
an indirect threat to plant–pollinator interactions. PMID:26286221
Orchid-pollinator interactions and potential vulnerability to biological invasion.
Chupp, Adam D; Battaglia, Loretta L; Schauber, Eric M; Sipes, Sedonia D
2015-08-17
an indirect threat to plant-pollinator interactions.
On the theory of interaction potentials in ionic crystals
NASA Astrophysics Data System (ADS)
Acevedo, Roberto; Soto-Bubert, Andrés
2008-11-01
The aim of this research work is to report a more comprehensive and detailed study of both, the intermolecular and intramolecular potencial functions with reference to the various families of the elpasolite type crystals. The cohesive energy has been thought as a sum of three terms; the long range (Coulombic), the Born and the van der Waals contributions to the total energy. The Born-Mayer-Buckingham potential1 has been employed in all of these current studies and a number of convergence tests are analyzed from a formal viewpoint. Our work has been focused to the following systems: Cs2NaLnF6, Cs2NaLnCl6, Cs2NaLnBr6, Rb2NaLnF6 and Cs2KLnF6 in the Fm3m space group. A substantial amount of theoretical models have been analyzed and several computing simulations have been undertaken to estimate the reticular energies and the corresponding heat of formation for these crystals. To achieve this goal, a Born-Haber thermodynamic cycle has been introduced in our model. It is shown that the calculated energy values are reasonable and follow the expected trend along the lanthanide series in the periodic chart. We also discuss the advantages and disadvantages of the current and proposed generalized model. The most likely sources for improvement are discussed in detail. New convergence tests as well as some master equations have been introduced to study the various diagonal contributions to the total energy.
Homayoon, Zahra
2014-09-28
A new, full (nine)-dimensional potential energy surface and dipole moment surface to describe the NO{sup +}(H{sub 2}O) cluster is reported. The PES is based on fitting of roughly 32 000 CCSD(T)-F12/aug-cc-pVTZ electronic energies. The surface is a linear least-squares fit using a permutationally invariant basis with Morse-type variables. The PES is used in a Diffusion Monte Carlo study of the zero-point energy and wavefunction of the NO{sup +}(H{sub 2}O) and NO{sup +}(D{sub 2}O) complexes. Using the calculated ZPE the dissociation energies of the clusters are reported. Vibrational configuration interaction calculations of NO{sup +}(H{sub 2}O) and NO{sup +}(D{sub 2}O) using the MULTIMODE program are performed. The fundamental, a number of overtone, and combination states of the clusters are reported. The IR spectrum of the NO{sup +}(H{sub 2}O) cluster is calculated using 4, 5, 7, and 8 modes VSCF/CI calculations. The anharmonic, coupled vibrational calculations, and IR spectrum show very good agreement with experiment. Mode coupling of the water “antisymmetric” stretching mode with the low-frequency intermolecular modes results in intensity borrowing.
Szabó, István; Telekes, Hajnalka; Czakó, Gábor
2015-06-28
We develop a full-dimensional global analytical potential energy surface (PES) for the F(-) + CH3F reaction by fitting about 50 000 energy points obtained by an explicitly correlated composite method based on the second-order Møller-Plesset perturbation-F12 and coupled-cluster singles, doubles, and perturbative triples-F12a methods and the cc-pVnZ-F12 [n = D, T] basis sets. The PES accurately describes the (a) back-side attack Walden inversion mechanism involving the pre- and post-reaction (b) ion-dipole and (c) hydrogen-bonded complexes, the configuration-retaining (d) front-side attack and (e) double-inversion substitution pathways, as well as (f) the proton-abstraction channel. The benchmark quality relative energies of all the important stationary points are computed using the focal-point analysis (FPA) approach considering electron correlation up to coupled-cluster singles, doubles, triples, and perturbative quadruples method, extrapolation to the complete basis set limit, core-valence correlation, and scalar relativistic effects. The FPA classical(adiabatic) barrier heights of (a), (d), and (e) are -0.45(-0.61), 46.07(45.16), and 29.18(26.07) kcal mol(-1), respectively, the dissociation energies of (b) and (c) are 13.81(13.56) and 13.73(13.52) kcal mol(-1), respectively, and the endothermicity of (f) is 42.54(38.11) kcal mol(-1). Quasiclassical trajectory computations of cross sections, scattering (θ) and initial attack (α) angle distributions, as well as translational and internal energy distributions are performed for the F(-) + CH3F(v = 0) reaction using the new PES. Apart from low collision energies (Ecoll), the SN2 excitation function is nearly constant, the abstraction cross sections rapidly increase with Ecoll from a threshold of ∼40 kcal mol(-1), and retention trajectories via double inversion are found above Ecoll = ∼ 30 kcal mol(-1), and at Ecoll = ∼ 50 kcal mol(-1), the front-side attack cross sections start to increase very rapidly. At
NASA Astrophysics Data System (ADS)
Szabó, István; Telekes, Hajnalka; Czakó, Gábor
2015-06-01
We develop a full-dimensional global analytical potential energy surface (PES) for the F- + CH3F reaction by fitting about 50 000 energy points obtained by an explicitly correlated composite method based on the second-order Møller-Plesset perturbation-F12 and coupled-cluster singles, doubles, and perturbative triples-F12a methods and the cc-pVnZ-F12 [n = D, T] basis sets. The PES accurately describes the (a) back-side attack Walden inversion mechanism involving the pre- and post-reaction (b) ion-dipole and (c) hydrogen-bonded complexes, the configuration-retaining (d) front-side attack and (e) double-inversion substitution pathways, as well as (f) the proton-abstraction channel. The benchmark quality relative energies of all the important stationary points are computed using the focal-point analysis (FPA) approach considering electron correlation up to coupled-cluster singles, doubles, triples, and perturbative quadruples method, extrapolation to the complete basis set limit, core-valence correlation, and scalar relativistic effects. The FPA classical(adiabatic) barrier heights of (a), (d), and (e) are -0.45(-0.61), 46.07(45.16), and 29.18(26.07) kcal mol-1, respectively, the dissociation energies of (b) and (c) are 13.81(13.56) and 13.73(13.52) kcal mol-1, respectively, and the endothermicity of (f) is 42.54(38.11) kcal mol-1. Quasiclassical trajectory computations of cross sections, scattering (θ) and initial attack (α) angle distributions, as well as translational and internal energy distributions are performed for the F- + CH3F(v = 0) reaction using the new PES. Apart from low collision energies (Ecoll), the SN2 excitation function is nearly constant, the abstraction cross sections rapidly increase with Ecoll from a threshold of ˜40 kcal mol-1, and retention trajectories via double inversion are found above Ecoll = ˜ 30 kcal mol-1, and at Ecoll = ˜ 50 kcal mol-1, the front-side attack cross sections start to increase very rapidly. At low Ecoll, the
NASA Astrophysics Data System (ADS)
Shi, Deheng; Li, Peiling; Sun, Jinfeng; Zhu, Zunlue
2014-01-01
The potential energy curves (PECs) of 28 Ω states generated from 9 Λ-S states (X2Π, 14Π, 16Π, 12Σ+, 14Σ+, 16Σ+, 14Σ-, 24Π and 14Δ) are studied for the first time using an ab initio quantum chemical method. All the 9 Λ-S states correlate to the first two dissociation limits, N(4Su) + Se(3Pg) and N(4Su) + Se(3Dg), of NSe radical. Of these Λ-S states, the 16Σ+, 14Σ+, 16Π, 24Π and 14Δ are found to be rather weakly bound states. The 12Σ+ is found to be unstable and has double wells. And the 16Σ+, 14Σ+, 14Π and 16Π are found to be the inverted ones with the SO coupling included. The PEC calculations are made by the complete active space self-consistent field method, which is followed by the internally contracted multireference configuration interaction approach with the Davidson modification. The spin-orbit coupling is accounted for by the state interaction approach with the Breit-Pauli Hamiltonian. The convergence of the present calculations is discussed with respect to the basis set and the level of theory. Core-valence correlation corrections are included with a cc-pCVTZ basis set. Scalar relativistic corrections are calculated by the third-order Douglas-Kroll Hamiltonian approximation at the level of a cc-pV5Z basis set. All the PECs are extrapolated to the complete basis set limit. The variation with internuclear separation of spin-orbit coupling constants is discussed in brief for some Λ-S states with one shallow well on each PEC. The spectroscopic parameters of 9 Λ-S and 28 Ω states are determined by fitting the first ten vibrational levels whenever available, which are calculated by solving the rovibrational Schrödinger equation with Numerov's method. The splitting energy in the X2Π Λ-S state is determined to be about 864.92 cm-1, which agrees favorably with the measurements of 891.80 cm-1. Moreover, other spectroscopic parameters of Λ-S and Ω states involved here are also in fair agreement with available measurements. It
NASA Technical Reports Server (NTRS)
Partridge, Harry; Stallcop, James R.; Levin, Eugene; Arnold, Jim (Technical Monitor)
2001-01-01
The interactions of a He atom with a heavier atom are examined for 26 different elements, which are consecutive members selected from three rows (Li - Ne, Na - Ar, and K,Ca, Ga - Kr) and column 12 (Zn,Cd) of the periodic table. Interaction energies are determined wing high-quality ab initio calculations for the states of the molecule that would be formed from each pair of atoms in their ground states. Potential energies are tabulated for a broad range of Interatomic separation distances. The results show, for example, that the energy of an alkali interaction at small separations is nearly the same as that of a rare-gas interaction with the same electron configuration for the dosed shells. Furthermore, the repulsive-range parameter for this region is very short compared to its length for the repulsion dominated by the alkali-valence electron at large separations (beyond about 3-4 a(sub 0)). The potential energies in the region of the van der Waals minimum agree well with the most accurate results available. The ab initio energies are applied to calculate scattering cross sections and obtain the collision integrals that are needed to determine transport properties to second order. The theoretical values of Li-He total scattering cross sections and the rare-gas atom-He transport properties agree well (to within about 1%) with the corresponding measured data. Effective potential energies are constructed from the ab initio energies; the results have been shown to reproduce known transport data and can be readily applied to predict unknown transport properties for like-atom interactions.
Potential of Drug Interactions among Hospitalized Cancer Patients in a Developing Country
Tavakoli-Ardakani, Maria; Kazemian, Kaveh; Salamzadeh, Jamshid; Mehdizadeh, Mahshid
2013-01-01
Cancer patients are more susceptible to adverse drug-drug interactions (DDIs) due to receiving multiple medications especially chemotherapy medications, hormonal agents and supportive care drugs. The aim of this study is to describe the prevalence of potential DDIs and to identify risk factors for these potential interactions in hospitalized cancer patients in a developing country. A cross-sectional study conducted by reviewing charts of 224 consecutive in hospitalized patients in hematology-oncology ward of a teaching hospital in Tehran, during a 12 month period from July 2009 to July 2010. “Drug Interaction Facts 2008, 2009: The Authority on Drug Interactions” was used for screening the potential drug-drug interactions. Potential interactions were classified by levels of severity and documentation. The median age of patients was 50 years, the length of hospital stay for patient was 5 days and the number of drugs per patient was 8 drugs. Two hundred and twenty-eight potential interactions were detected. Nearly 14% of the interactions were major and 60% were moderate. Approximately 9% and 10% potential interactions were graded as established and probable. In multivariate analysis, being older than 61 years old, suffering from hematologic cancer, source of cancer in different specific organs (esophagus, testis and cervices more than other sources), and number of ordered drugs for patients were independent predictors of having at least one potential DDI in hospital order. Suffering from hematologic cancer, source of cancer in different organs, length of hospital stay and number of ordered drugs for patients were independent predictors for number of interactions per patients. Having a DDI seems to be more likely to occur in patients older than 61 years old. Hematologic cancers, having more medications in physician’s order, longer length of hospital stay, esophageal cancer, testicular cancer and cervical cancer have related to having a DDI and also having more
Janke, Svenja M.; Auerbach, Daniel J.; Kandratsenka, Alexander; Wodtke, Alec M.
2015-09-28
We have constructed a potential energy surface (PES) for H-atoms interacting with fcc Au(111) based on fitting the analytic form of the energy from Effective Medium Theory (EMT) to ab initio energy values calculated with density functional theory. The fit used input from configurations of the H–Au system with Au atoms at their lattice positions as well as configurations with the Au atoms displaced from their lattice positions. It reproduces the energy, in full dimension, not only for the configurations used as input but also for a large number of additional configurations derived from ab initio molecular dynamics (AIMD) trajectories at finite temperature. Adiabatic molecular dynamics simulations on this PES reproduce the energy loss behavior of AIMD. EMT also provides expressions for the embedding electron density, which enabled us to develop a self-consistent approach to simulate nonadiabatic electron-hole pair excitation and their effect on the motion of the incident H-atoms. For H atoms with an energy of 2.7 eV colliding with Au, electron-hole pair excitation is by far the most important energy loss pathway, giving an average energy loss ≈3 times that of the adiabatic case. This increased energy loss enhances the probability of the H-atom remaining on or in the Au slab by a factor of 2. The most likely outcome for H-atoms that are not scattered also depends prodigiously on the energy transfer mechanism; for the nonadiabatic case, more than 50% of the H-atoms which do not scatter are adsorbed on the surface, while for the adiabatic case more than 50% pass entirely through the 4 layer simulation slab.
Janke, Svenja M; Auerbach, Daniel J; Wodtke, Alec M; Kandratsenka, Alexander
2015-09-28
We have constructed a potential energy surface (PES) for H-atoms interacting with fcc Au(111) based on fitting the analytic form of the energy from Effective Medium Theory (EMT) to ab initio energy values calculated with density functional theory. The fit used input from configurations of the H-Au system with Au atoms at their lattice positions as well as configurations with the Au atoms displaced from their lattice positions. It reproduces the energy, in full dimension, not only for the configurations used as input but also for a large number of additional configurations derived from ab initio molecular dynamics (AIMD) trajectories at finite temperature. Adiabatic molecular dynamics simulations on this PES reproduce the energy loss behavior of AIMD. EMT also provides expressions for the embedding electron density, which enabled us to develop a self-consistent approach to simulate nonadiabatic electron-hole pair excitation and their effect on the motion of the incident H-atoms. For H atoms with an energy of 2.7 eV colliding with Au, electron-hole pair excitation is by far the most important energy loss pathway, giving an average energy loss ≈3 times that of the adiabatic case. This increased energy loss enhances the probability of the H-atom remaining on or in the Au slab by a factor of 2. The most likely outcome for H-atoms that are not scattered also depends prodigiously on the energy transfer mechanism; for the nonadiabatic case, more than 50% of the H-atoms which do not scatter are adsorbed on the surface, while for the adiabatic case more than 50% pass entirely through the 4 layer simulation slab.
ERIC Educational Resources Information Center
Huffman, Celia A.
2012-01-01
This study looked at the potential relationship that may exist between students' intelligence strengths, in particular their spatial and kinesthetic strengths, and their combined cognitive and metacognitive levels of interaction with a CD-ROM storybook. The multiple intelligence strengths of a sample of students, measured via the MIDAS/My…
Theoretical study of HCN-water interaction: five dimensional potential energy surfaces.
Sánchez, Ernesto Quintas; Dubernet, Marie-Lise
2017-03-01
A new five-dimensional potential energy surface is calculated at the coupled-cluster CCSD(T) level of theory for the HCN-water system, treating both monomers as rigid rotors. The associated methodology, which combines extensive ab initio calculations of moderate accuracy (CCSD(T)/AVDZ) and a fitting procedure involving a much lower angular coverage with more accurate ab initio calculations (CCSD(T)/CBS), is described in detail. This methodology provides a time-saving approach to compute quantitatively accurate potential energy surfaces with reasonable computational effort. Our potential reproduces the main features reported in the literature, and will allow us to perform the first quantum and semi-classical simulations of the collisional dynamic on this system.
Potential of the neutron lloyd's mirror interferometer for the search for new interactions
Pokotilovski, Yu. N.
2013-04-15
We discuss the potential of the neutron Lloyd's mirror interferometer in a search for new interactions at small scales. We consider three hypothetical interactions that may be tested using the interferometer. The chameleon scalar field proposed to solve the enigma of accelerating expansion of the Universe produces interaction between particles and matter. The axion-like spin-dependent coupling between a neutron and nuclei or/and electrons may result in a P- and T-noninvariant interaction with matter. Hypothetical non-Newtonian gravitational interactions mediates an additional short-range potential between neutrons and bulk matter. These interactions between the neutron and the mirror of a Lloyd-type neutron interferometer cause a phase shift of neutron waves. We estimate the sensitivity and systematic effects of possible experiments.
Ab initio Potential-Energy Surfaces and Electron-Spin-Exchange Cross Sections for H-O2 Interactions
NASA Technical Reports Server (NTRS)
Stallcop, James R.; Partridge, Harry; Levin, Eugene
1996-01-01
Accurate quartet- and doublet-state potential-energy surfaces for the interaction of a hydrogen atom and an oxygen molecule in their ground states have been determined from an ab initio calculation using large-basis sets and the internally contracted multireference configuration interaction method. These potential surfaces have been used to calculate the H-O2 electron-spin-exchange cross section; the square root of the cross section (in a(sub 0)), not taking into account inelastic effects, can be obtained approximately from the expressions 2.390E(sup -1/6) and 5.266-0.708 log10(E) at low and high collision energies E (in E(sub h)), respectively. These functional forms, as well as the oscillatory structure of the cross section found at high energies, are expected from the nature of the interaction energy. The mean cross section (the cross section averaged over a Maxwellian velocity distribution) agrees reasonably well with the results of measurements.
One of the challenges facing toxicology and risk assessment is that numerous host and environmental factors may modulate vulnerability and risk. An area of increasing interest is the potential for chemicals to interact with background aging and disease processes, an interaction...
Double Folding Potential of Different Interaction Models for 16O + 12C Elastic Scattering
NASA Astrophysics Data System (ADS)
Hamada, Sh.; Bondok, I.; Abdelmoatmed, M.
2016-12-01
The elastic scattering angular distributions for 16O + 12C nuclear system have been analyzed using double folding potential of different interaction models: CDM3Y1, CDM3Y6, DDM3Y1 and BDM3Y1. We have extracted the renormalization factor N r for the different concerned interaction models. Potential created by BDM3Y1 model of interaction has the shallowest depth which reflects the necessity to use higher renormalization factor. The experimental angular distributions for 16O + 12C nuclear system in the energy range 115.9-230 MeV exhibited unmistakable refractive features and rainbow phenomenon.
NASA Astrophysics Data System (ADS)
Cotner, Eric
2016-09-01
Scalar particles are a common prediction of many beyond the Standard Model theories. If they are light and cold enough, there is a possibility they may form Bose-Einstein condensates, which will then become gravitationally bound. These boson stars are solitonic solutions to the Einstein-Klein-Gordon equations but may be approximated in the nonrelativistic regime with a coupled Schrödinger-Poisson system. General properties of single soliton states are derived, including the possibility of quartic self-interactions. Binary collisions between two solitons are then studied, and the effects of different mass ratios, relative phases, self-couplings, and separation distances are characterized, leading to an easy conceptual understanding of how these parameters affect the collision outcome in terms of conservation of energy. Applications to dark matter are discussed.
Wong, Yong Foo; Chin, Sung-Tong; Perlmutter, Patrick; Marriott, Philip J
2015-03-27
To explore the possible obligate interactions between the phytopathogenic fungus and Aquilaria malaccensis which result in generation of a complex array of secondary metabolites, we describe a comprehensive two-dimensional gas chromatography (GC × GC) method, coupled to accurate mass time-of-flight mass spectrometry (TOFMS) for the untargeted and comprehensive metabolic profiling of essential oils from naturally infected A. malaccensis trees. A polar/non-polar column configuration was employed, offering an improved separation pattern of components when compared to other column sets. Four different grades of the oils displayed quite different metabolic patterns, suggesting the evolution of a signalling relationship between the host tree (emergence of various phytoalexins) and fungi (activation of biotransformation). In total, ca. 550 peaks/metabolites were detected, of which tentative identification of 155 of these compounds was reported, representing between 20.1% and 53.0% of the total ion count. These are distributed over the chemical families of monoterpenic and sesquiterpenic hydrocarbons, oxygenated monoterpenes and sesquiterpenes (comprised of ketone, aldehyde, oxide, alcohol, lactone, keto-alcohol and diol), norterpenoids, diterpenoids, short chain glycols, carboxylic acids and others. The large number of metabolites detected, combined with the ease with which they are located in the 2D separation space, emphasises the importance of a comprehensive analytical approach for the phytochemical analysis of plant metabolomes. Furthermore, the potential of this methodology in grading agarwood oils by comparing the obtained metabolic profiles (pattern recognition for unique metabolite chemical families) is discussed. The phytocomplexity of the agarwood oils signified the production of a multitude of plant-fungus mediated secondary metabolites as chemical signals for natural ecological communication. To the best of our knowledge, this is the most complete
NASA Astrophysics Data System (ADS)
Ebrahimian, N.; Safiee, Z.
2017-03-01
We consider a polarized Fermi mixture (with normal-superfluid phase separation), subjected to artificial vector potential. We concentrate on the BCS regime with various interaction strengths and numerically obtain the polarisability of the system. We obtain the functional dependence of the polarisability of the system on frequency and the relevant physical parameters, namely the interaction strength, the mass ratio, the average and imbalance chemical potentials. Also, we find the special frequency (ωs), for which the rate of the response of system to the potential is changed and the cut-off frequency (ωcutoff), for which the response starts to become infinity. We investigate the behavior of the curves of polarisability versus proper physical parameters for ω <ωs and ωs < ω <ωcutoff at a nonzero temperature and interpret the existence of special and cut-off frequencies via the propagator concept (of particles or holes). Also, we offer the explanation of the minimum energy required for the occurrence of the pair-breaking process and the existence of the cut-off frequency, which is different with respect to the conventional superfluid Fermi gas, and is related to the relevant physical parameters. Finally, the system's response can be controlled by relevant physical parameters, such as interaction strength.
Ramakrishnan, Gayatri; Srinivasan, Narayanaswamy; Padmapriya, Ponnan; Natarajan, Vasant
2015-01-01
Plasmodium falciparum, a causative agent of malaria, is a well-characterized obligate intracellular parasite known for its ability to remodel host cells, particularly erythrocytes, to successfully persist in the host environment. However, the current levels of understanding from the laboratory experiments on the host–parasite interactions and the strategies pursued by the parasite to remodel host erythrocytes are modest. Several computational means developed in the recent past to predict host–parasite/pathogen interactions have generated testable hypotheses on feasible protein–protein interactions. We demonstrate the utility of protein structure-based protocol in the recognition of potential interacting proteins across P. falciparum and host erythrocytes. In concert with the information on the expression and subcellular localization of host and parasite proteins, we have identified 208 biologically feasible interactions potentially brought about by 59 P. falciparum and 30 host erythrocyte proteins. For selected cases, we have evaluated the physicochemical viability of the predicted interactions in terms of surface complementarity, electrostatic complementarity, and interaction energies at protein interface regions. Such careful inspection of molecular and mechanistic details generates high confidence on the predicted host–parasite protein–protein interactions. The predicted host–parasite interactions generate many experimentally testable hypotheses that can contribute to the understanding of possible mechanisms undertaken by the parasite in host erythrocyte remodeling. Thus, the key protein players recognized in P. falciparum can be explored for their usefulness as targets for chemotherapeutic intervention. PMID:26740742
NASA Astrophysics Data System (ADS)
Ghoshal, Arijit; Ho, Yew Kam
2017-04-01
We have investigated the resonances in the {{{e}}}+-{{He}}{(}3{{{S}}}{{e}}) system interacting with screened potentials by using the stabilization method. Two types of screened potential have been considered: static screened Coulomb potential and exponential cosine-screened Coulomb potential. A model potential has been used to describe the interaction between the outer electron and the {{{He}}}+ ionic core. We have found two resonances below the {{Ps}}(n=2)-{{{He}}}+ threshold. For the unscreened case, our results are in nice agreement with some of the most accurate results available in the literature.
Cannon, John G. D.; Sherman, Rachel M.; Wang, Victoria M. Y.; Newman, Grace A.
2015-01-01
The role of amino acid-RNA nucleobase interactions in the evolution of RNA translation and protein-mRNA autoregulation remains an open area of research. We describe the inference of pairwise amino acid-RNA nucleobase interaction preferences using structural data from known RNA-protein complexes. We observed significant matching between an amino acid’s nucleobase affinity and corresponding codon content in both the standard genetic code and mitochondrial variants. Furthermore, we showed that knowledge of nucleobase preferences allows statistically significant prediction of protein primary sequence from mRNA using purely physiochemical information. Interestingly, ribosomal primary sequences were more accurately predicted than non-ribosomal sequences, suggesting a potential role for direct amino acid-nucleobase interactions in the genesis of amino acid-based ribosomal components. Finally, we observed matching between amino acid-nucleobase affinities and corresponding mRNA sequences in 35 evolutionarily diverse proteomes. We believe these results have important implications for the study of the evolutionary origins of the genetic code and protein-mRNA cross-regulation. PMID:26656258
NASA Astrophysics Data System (ADS)
Kedziera, Dariusz; Mentel, Łukasz; Żuchowski, Piotr S.; Knoop, Steven
2015-06-01
We have obtained accurate ab initio +4Σ quartet potentials for the diatomic metastable triplet helium+alkali-metal (Li, Na, K, Rb) systems, using all-electron restricted open-shell coupled cluster singles and doubles with noniterative triples corrections CCSD(T) calculations and accurate calculations of the long-range C6 coefficients. These potentials provide accurate ab initio quartet scattering lengths, which for these many-electron systems is possible, because of the small reduced masses and shallow potentials that result in a small amount of bound states. Our results are relevant for ultracold metastable triplet helium+alkali-metal mixture experiments.
NASA Astrophysics Data System (ADS)
Rybynok, V. O.; Kyriacou, P. A.
2007-10-01
Diabetes is one of the biggest health challenges of the 21st century. The obesity epidemic, sedentary lifestyles and an ageing population mean prevalence of the condition is currently doubling every generation. Diabetes is associated with serious chronic ill health, disability and premature mortality. Long-term complications including heart disease, stroke, blindness, kidney disease and amputations, make the greatest contribution to the costs of diabetes care. Many of these long-term effects could be avoided with earlier, more effective monitoring and treatment. Currently, blood glucose can only be monitored through the use of invasive techniques. To date there is no widely accepted and readily available non-invasive monitoring technique to measure blood glucose despite the many attempts. This paper challenges one of the most difficult non-invasive monitoring techniques, that of blood glucose, and proposes a new novel approach that will enable the accurate, and calibration free estimation of glucose concentration in blood. This approach is based on spectroscopic techniques and a new adaptive modelling scheme. The theoretical implementation and the effectiveness of the adaptive modelling scheme for this application has been described and a detailed mathematical evaluation has been employed to prove that such a scheme has the capability of extracting accurately the concentration of glucose from a complex biological media.
Mardirossian, Narbe; Head-Gordon, Martin
2016-09-13
The 14 Minnesota density functionals published between the years 2005 and early 2016 are benchmarked on a comprehensive database of 4986 data points (84 data sets) involving molecules composed of main-group elements. The database includes noncovalent interactions, isomerization energies, thermochemistry, and barrier heights, as well as equilibrium bond lengths and equilibrium binding energies of noncovalent dimers. Additionally, the sensitivity of the Minnesota density functionals to the choice of basis set and integration grid is explored for both noncovalent interactions and thermochemistry. Overall, the main strength of the hybrid Minnesota density functionals is that the best ones provide very good performance for thermochemistry (e.g., M06-2X), barrier heights (e.g., M08-HX, M08-SO, MN15), and systems heavily characterized by self-interaction error (e.g., M06-2X, M08-HX, M08-SO, MN15), while the main weakness is that none of them are state-of-the-art for the full spectrum of noncovalent interactions and isomerization energies (although M06-2X is recommended from the 10 hybrid Minnesota functionals). Similarly, the main strength of the local Minnesota density functionals is that the best ones provide very good performance for thermochemistry (e.g., MN15-L), barrier heights (e.g., MN12-L), and systems heavily characterized by self-interaction error (e.g., MN12-L and MN15-L), while the main weakness is that none of them are state-of-the-art for the full spectrum of noncovalent interactions and isomerization energies (although M06-L is clearly the best from the four local Minnesota functionals). As an overall guide, M06-2X and MN15 are perhaps the most broadly useful hybrid Minnesota functionals, while M06-L and MN15-L are perhaps the most broadly useful local Minnesota functionals, although each has different strengths and weaknesses.
Zhao, Yan; Truhlar, Donald G.
2008-03-20
The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Graphene sheets are the building blocks of carbon nanotubes and a variety of functionalized nanomaterials. Methods to be used for computer-aided design of such materials or for the study of aromatic-aromatic interactions in biopolymers and other soft materials should be validated for smaller systems where reliable estimates of interaction energies are available. In this work, we first validated the M06-2X functional against the S22 database of noncovalent interaction energies of biological importance. We then applied the M06-2X functional to study aromatic-aromatic interactions in coronene dimers. We located six stationary points on the potential energy surface of coronene dimer, we calculated the potential energy curves for the sandwich, T-shaped, and parallel-displaced configurations of this prototype of aromatic-aromatic interactions, and we found that a parallel displaced configuration is the global minimum. The potential curves for the coronene dimers will aid the development of new force fields and potential energy functions that are computationally efficient and capable of modeling large graphene or aromatic clusters.
NASA Astrophysics Data System (ADS)
da Silva, João Bosco P.; Hallwass, Fernando; da Silva, Aluizio G.; Moreira, Diogo Rodrigo; Ramos, Mozart N.; Espíndola, José Wanderlan P.; de Oliveira, Ana Daura T.; Brondani, Dalci José; Leite, Ana Cristina L.; Merz, Kenneth M.
2015-08-01
DFT calculations were used to access information about structure, energy and electronic properties of series of phenyl- and phenoxymethyl-(thio)semicarbazone derivatives with demonstrated activity against the larvae of Aedes aegypti in stage L4. The way as the thiosemicarbazone derivatives can interact with solvents like DMSO and water were analyzed from the comparison between calculated and experimental 1H NMR chemical shifts. The evidences of thiosemicarbazone derivatives making H-bond interaction to solvent have provide us insights on how they can interact with a potential A. aegypti's biological target, the Sterol Carrier Protein-2.
Nonlinear pressure dependence of the interaction potential of dense protein solutions.
Schroer, Martin A; Markgraf, Jonas; Wieland, D C Florian; Sahle, Christoph J; Möller, Johannes; Paulus, Michael; Tolan, Metin; Winter, Roland
2011-04-29
The influence of pressure on the structure and protein-protein interaction potential of dense protein solutions was studied and analyzed using small-angle x-ray scattering in combination with a liquid state theoretical approach. The structural as well as the interaction parameters of dense lysozyme solutions are affected by pressure in a nonlinear way. The structural properties of water lead to a modification of the protein-protein interactions below 4 kbar, which might have significant consequences for the stability of proteins in extreme natural environments.
An improved He-CO interaction potential from a multiproperty analysis
NASA Astrophysics Data System (ADS)
Gianturco, F. A.; Sanna, N.; Serna-Molinera, S.
Following previous tests of the existing potential energy surface (PES) for the He-CO gaseous mixture (F. A. Gianturco, N. Sanna and S. Serna, 1993, J. Chem. Phys., 98, 3833) that used quantum and classical calculations of several non-equilibrium properties, the present work modifies specific parts of that interaction in order to improve agreement with experimental diffusion and viscosity coefficients while leaving unaltered the existing good accord with molecular beam data. It is finally shown that the modified PES thus obtained agrees very well with existing experimental data and provides the best available description of the interaction potential for the title system.
NASA Technical Reports Server (NTRS)
Stallcop, James R.; Partridge, Harry; Levin, Eugene; Langhoff, Stephen R. (Technical Monitor)
1995-01-01
Collision integrals are fundamental quantities required to determine the transport properties of the environment surrounding aerospace vehicles in the upper atmosphere. These collision integrals can be determined as a function of temperature from the potential energy curves describing the atomic and molecular collisions. Ab initio calculations provide a practical method of computing the required interaction potentials. In this work we will discuss recent advances in scattering calculations with an emphasis on the accuracy that is obtainable. Results for interactions of the atoms and ionized atoms of nitrogen and oxygen will be reviewed and their application to the determination of transport properties, such as diffusion and viscosity coefficients, will be examined.
Cosmological model with fermion and tachyon fields interacting via Yukawa-type potential
NASA Astrophysics Data System (ADS)
Ribas, Marlos O.; Devecchi, Fernando P.; Kremer, Gilberto M.
2016-02-01
A model for the universe with tachyonic and fermionic fields interacting through a Yukawa-type potential is investigated. It is shown that the tachyonic field answers for the initial accelerated regime and for the subsequent decelerated regime so that it behaves as an inflaton at early times and as a matter field at intermediate times, while the fermionic field has the role of a dark energy constituent, since it leads to an accelerated regime at later times. The interaction between the fields via a Yukawa-type potential controls the duration of the decelerated era, since a stronger coupling makes a shorter decelerated period.
Chen, Jun; Sun, Zhigang E-mail: zhangdh@dicp.ac.cn; Zhang, Dong H. E-mail: zhangdh@dicp.ac.cn
2015-01-14
A three dimensional potential energy surface for the F + H{sub 2} → HF + H reaction has been computed by the spin unrestricted coupled cluster method with singles, doubles, triples, and perturbative quadruples [UCCSDT(2){sub Q}] using the augmented correlation-consistent polarised valence quadruple zeta basis set for the fluorine atom and the correlation-consistent polarised valence quadruple zeta basis set for the hydrogen atom. All the calculations are based on the restricted open-shell Hartree-Fock orbitals, together with the frozen core approximations, and the UCCSD(T)/complete basis set (CBS) correction term was included. The global potential energy surface was calculated by fitting the sampled ab initio points without any scaling factor for the correlation energy part using a neutral network function method. Extensive dynamics calculations have been carried out on the potential energy surface. The reaction rate constants, integral cross sections, product rotational states distribution, and forward and backward scattering as a function of collision energy of the F + HD → HF + D, F + HD → DF + H, and F + H{sub 2} reaction, were calculated by the time-independent quantum dynamics scattering theory using the new surface. The satisfactory agreement with the reported experimental observations previously demonstrates the accuracy of the new potential energy surface.
Zhang, Chi; Liu, Song; Zhou, Yaoqi
2006-04-01
Molecular networks in cells are organized into functional modules, where genes in the same module interact densely with each other and participate in the same biological process. Thus, identification of modules from molecular networks is an important step toward a better understanding of how cells function through the molecular networks. Here, we propose a simple, automatic method, called MC(2), to identify functional modules by enumerating and merging cliques in the protein-interaction data from large-scale experiments. Application of MC(2) to the S. cerevisiae protein-interaction data produces 84 modules, whose sizes range from 4 to 69 genes. The majority of the discovered modules are significantly enriched with a highly specific process term (at least 4 levels below root) and a specific cellular component in Gene Ontology (GO) tree. The average fraction of genes with the most enriched GO term for all modules is 82% for specific biological processes and 78% for specific cellular components. In addition, the predicted modules are enriched with coexpressed proteins. These modules are found to be useful for annotating unknown genes and uncovering novel functions of known genes. MC(2) is efficient, and takes only about 5 min to identify modules from the current yeast gene interaction network with a typical PC (Intel Xeon 2.5 GHz CPU and 512 MB memory). The CPU time of MC(2) is affordable (12 h) even when the number of interactions is increased by a factor of 10. MC(2) and its results are publicly available on http://theory.med.buffalo.edu/MC2.
Baranowska-Łączkowska, Angelika; Fernández, Berta
2014-01-30
In order to obtain efficient basis sets for the evaluation of van der Waals complex intermolecular potentials, we carry out systematic basis set studies. For this, interaction energies at representative geometries on the potential energy surfaces are evaluated using the CCSD(T) correlation method and large polarized LPol-n and augmented polarization-consistent aug-pc-2 basis sets extended with different sets of midbond functions. On the basis of the root mean square errors calculated with respect to the values for the most accurate potentials available, basis sets are selected for fitting the corresponding interaction energies and getting analytical potentials. In this work, we study the Ne-N2 van der Waals complex and after the above procedure, the aug-pc-2-3321 and the LPol-ds-33221 basis set results are fitted. The obtained potentials are characterized by T-shaped global minima at distances between the Ne atom and the N2 center of mass of 3.39 Å, with interaction energies of -49.36 cm(-1) for the aug-pc-2-3321 surface and -50.28 cm(-1) for the LPol-ds-33221 surface. Both sets of results are in excellent agreement with the reference surface. To check the potentials further microwave transition frequencies are calculated that agree well with the experimental and the aV5Z-33221 values. The success of this study suggests that it is feasible to carry out similar accurate calculations of interaction energies and ro-vibrational spectra at reduced cost for larger complexes than has been possible hitherto.
de Oliveira-Filho, Antonio G S; Ornellas, Fernando R; Bowman, Joel M
2014-12-26
We report reaction cross sections, energy disposal, and rate constants for the OH + HBr → Br + H2O and OH + DBr → Br + HDO reactions from quasiclassical trajectory calculations using an ab initio potential energy surface [ de Oliveira-Filho , A. G. S. ; Ornellas , F. R. ; Bowman , J. M. J. Phys. Chem. Lett. 2014 , 5 , 706 - 712 ]. Comparison with available experiments are made and generally show good agreement.
NASA Astrophysics Data System (ADS)
Sarkar, Vaskar; Dutta, Aloke K.
2006-11-01
A novel approach of defining the threshold voltage for long channel MOSFETs has been presented in this paper, where it has been proposed that it corresponds to the gate-to-source voltage for which the drift and diffusion components of the total drain current become equal to each other. In order to avoid the greater computation time associated with the numerical solution of these two components, an analytical expression of the surface potential, corresponding to the threshold condition, is given here, which has the same functional form as the one proposed by Tsividis. The fuzzy parameter n, appearing in this expression of the surface potential, is expressed as a function of the substrate doping density ( NA) and the oxide thickness ( tox). The threshold voltage values, obtained analytically from the relation between the surface potential at the threshold condition and the closed-form technology-mapped expression of the fuzzy parameter n, show an excellent match with those obtained from SILVACO simulations for a wide range of NA and tox, with the maximum error being only about 4%. The comparison of the percent error values of the threshold voltage obtained from this proposed model with those obtained from the other two recently proposed methods, all with respect to SILVACO simulation results, further verifies the validity of our completely analytical, mathematically simple, and straight-forward approach, proposed in this work here.
Tsai, Hsin-Hui; Lin, Hsiang-Wen; Lu, Ying-Hung; Chen, Yi-Ling; Mahady, Gail B.
2013-01-01
Background The risks attributed to drug-herb interactions, even when known, are often ignored or underestimated, especially for those involving anti-clotting drugs and Chinese medicines. The aim of this study was to structurally search and evaluate the existing evidence-based data associated with potential drug interactions between anticoagulant/antiplatelet drugs and Chinese herbal medicines (CHMs) and evaluate the documented mechanisms, consequences, and/or severity of interactions. Methodology and Findings Information related to anticoagulant/antiplatelet drug-CHM interactions was retrieved from eight interaction-based textbooks, four web resources and available primary biomedical literature. The primary literature searches were conducted in English and/or Chinese from January 2000 through December 2011 using the secondary databases (e.g., PubMed, Airiti Library, China Journal full-text database). The search terms included the corresponding medical subject headings and key words. Herbs or natural products not used as a single entity CHM or in Chinese Medicinal Prescriptions were excluded from further review. The corresponding mechanisms and severity ratings of interactions were retrieved using MicroMedex®, Lexicomp® and Natural Medicines Comprehensive Database®. Finally, we found 90 single entity CHMs contributed to 306 documented drug-CHM interactions. A total of 194 (63.4%) interactions were verified for its evidence describing possible mechanisms and severity. Of them, 155 interactions (79.9%) were attributable to pharmacodynamic interactions, and almost all were rated as moderate to severe interactions. The major consequences of these interactions were increased bleeding risks due to the additive anticoagulant or antiplatelet effects of the CHMs, specifically danshen, dong quai, ginger, ginkgo, licorice, and turmeric. Conclusions/Significance Conventional anticoagulants and antiplatelet drugs were documented to have harmful interactions with some commonly
Khan, Shagufta H; Ahmad, Faizan; Ahmad, Nihal; Flynn, Daniel C; Kumar, Raj
2011-06-01
A vast network of genes is inter-linked through protein-protein interactions and is critical component of almost every biological process under physiological conditions. Any disruption of the biologically essential network leads to pathological conditions resulting into related diseases. Therefore, proper understanding of biological functions warrants a comprehensive knowledge of protein-protein interactions and the molecular mechanisms that govern such processes. The importance of protein-protein interaction process is highlighted by the fact that a number of powerful techniques/methods have been developed to understand how such interactions take place under various physiological and pathological conditions. Many of the key protein-protein interactions are known to participate in disease-associated signaling pathways, and represent novel targets for therapeutic intervention. Thus, controlling protein-protein interactions offers a rich dividend for the discovery of new drug targets. Availability of various tools to study and the knowledge of human genome have put us in a unique position to understand highly complex biological network, and the mechanisms involved therein. In this review article, we have summarized protein-protein interaction networks, techniques/methods of their binding/kinetic parameters, and the role of these interactions in the development of potential tools for drug designing.
Potential P-glycoprotein pharmacokinetic interaction of telaprevir with morphine or methadone.
Fudin, Jeffrey; Fontenelle, Dania Vanesta; Fudin, Hannah Rebecca; Carlyn, Cynthia; Hinden, Debra Ann; Ashley, Christopher C
2013-08-01
Telaprevir (TVR) effects on P-glycloprotein and cytochrome P450 (CYP) may significantly elevate serum levels of morphine and methadone. Recent literature points to major interactions when combining TVR with warfarin or rifampin. Opioid interactions are especially dangerous in hepatitis C patients, as coinfection with human immunodeficiency virus (HIV) and hepatitis C virus (HCV) occurs in 50-90% of HIV-infected drug users that are prescribed opioids for chronic pain and/or methadone for maintenance. TVR has been shown to significantly inhibit the active transport enzyme pGP and may therefore increase intestinal morphine absorption. TVR also inhibits hepatic CYP3A4 that are responsible for metabolizing methadone. Patients requiring opioid analgesics must be carefully monitored because of potential for elevated opioid levels and overdose risk. Current recommendations minimize potential drug interactions between telaprevir and opioids, especially methadone, based on a single 7-day trial. We outline the various pharmacokinetic mechanisms involved when combining TVR with methadone or morphine and recommend that current data are not sufficiently robust to minimize the potentially significant interaction with opioids, especially methadone. Clinicians must be mindful of these understated interactions, know that the opioid dose may need to be significantly increased or reduced, and use caution during upward titration of opioids affected by these enzyme systems.
Wang, Yimin; Bowman, Joel M; Kamarchik, Eugene
2016-03-21
We report full-dimensional, ab initio-based potentials and dipole moment surfaces for NaCl, NaF, Na(+)H2O, F(-)H2O, and Cl(-)H2O. The NaCl and NaF potentials are diabatic ones that dissociate to ions. These are obtained using spline fits to CCSD(T)/aug-cc-pV5Z energies. In addition, non-linear least square fits using the Born-Mayer-Huggins potential are presented, providing accurate parameters based strictly on the current ab initio energies. The long-range behavior of the NaCl and NaF potentials is shown to go, as expected, accurately to the point-charge Coulomb interaction. The three ion-H2O potentials are permutationally invariant fits to roughly 20,000 coupled cluster CCSD(T) energies (awCVTZ basis for Na(+) and aVTZ basis for Cl(-) and F(-)), over a large range of distances and H2O intramolecular configurations. These potentials are switched accurately in the long range to the analytical ion-dipole interactions, to improve computational efficiency. Dipole moment surfaces are fits to MP2 data; for the ion-ion cases, these are well described in the intermediate- and long-range by the simple point-charge expression. The performance of these new fits is examined by direct comparison to additional ab initio energies and dipole moments along various cuts. Equilibrium structures, harmonic frequencies, and electronic dissociation energies are also reported and compared to direct ab initio results. These indicate the high fidelity of the new PESs.
Hua -Gen Yu; Han, Huixian; Guo, Hua
2016-03-29
Vibrational energy levels of the ammonium cation (NH4+) and its deuterated isotopomers are calculated using a numerically exact kinetic energy operator on a recently developed nine-dimensional permutation invariant semiglobal potential energy surface fitted to a large number of high-level ab initio points. Like CH4, the vibrational levels of NH4+ and ND4+ exhibit a polyad structure, characterized by a collective quantum number P = 2(v1 + v3) + v2 + v4. As a result, the low-lying vibrational levels of all isotopomers are assigned and the agreement with available experimental data is better than 1 cm–1.
Folch, Benjamin; Rooman, Marianne; Dehouck, Yves
2008-01-01
The temperature dependence of the interactions that stabilize protein structures is a long-standing issue, the elucidation of which would enable the prediction and the rational modification of the thermostability of a target protein. It is tackled here by deriving distance-dependent amino acid pair potentials from four datasets of proteins with increasing melting temperatures (Tm). The temperature dependence of the interactions is determined from the differences in the shape of the potentials derived from the four datasets. Note that, here, we use an unusual dataset definition, which is based on the Tm values, rather than on the living temperature of the host organisms. Our results show that the stabilizing weight of hydrophobic interactions (between Ile, Leu, and Val) remains constant as the temperature increases, compared to the other interactions. In contrast, the two minima of the Arg--Glu and Arg--Asp salt bridge potentials show a significant Tm dependence. These two minima correspond to two geometries: the fork--fork geometry, where the side chains point toward each other, and the fork--stick geometry, which involves the N(epsilon) side chain atom of Arg. These two types of salt bridges were determined to be significantly more stabilizing at high temperature. Moreover, a preference for more-compact salt bridges is noticeable in heat-resistant proteins, especially for the fork--fork geometry. The Tm-dependent potentials that have been defined here should be useful for predicting thermal stability changes upon mutation.
Potential Energy Curves and Associated Line Shape of Alkali-Metal and Noble-Gas Interactions
2014-10-20
xii I. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.1 Motivation...150 xii POTENTIAL ENERGY CURVES AND ASSOCIATED LINE SHAPE OF ALKALI-METAL AND NOBLE-GAS INTERACTIONS I. Introduction 1.1 Motivation...starting point for all modern developments of a quantum picture of pressure broadening, and show how this theory reduces to the classical theory under
ERIC Educational Resources Information Center
Filicková, Marta; Ropovik, Ivan; Bobaková, Monika; Kovalcíková, Iveta
2015-01-01
The main aim of the study was to explore the relationship between fluid intelligence (gf), attentional control (AC), and learning potential (LP), and to investigate the interaction effect between gf and AC on LP. The sample comprised 210 children attending the fourth grade of a standard elementary school. It was hypothesized that the extent of the…
Munier-Jolain, Nathalie; Salon, Christophe
2003-11-01
The composition of the translocates reaching the seeds of pea plants having various nitrogen (N) nutrition regimes was investigated under field situations. Sucrose flow in the phloem sap increased with the node number, but was not significantly different between N nutrition levels. Because N deficiency reduced the number of flowering nodes and the number of seeds per pod, the sucrose flow bleeding from cut peduncles was divided by the number of seeds to give the amount of assimilates available per seed. The sucrose concentration in phloem sap supplied to seeds at the upper nodes was higher than that at the lower nodes. The flow of sucrose delivered to the seeds during the cell division period was correlated with seed growth potential. Seeds from the more N-stressed plants had both the highest seed growth rate and received a higher sucrose flux per seed during the cell division period. As seed growth rate is highly correlated with the number of cotyledonary cells produced during the cell division period, sucrose flow in phloem sap is proposed to be an important determinant of mitotic activity in seed embryos. The carbon (C)/N ratio of the flow of translocates towards seeds was higher under conditions of N-deficiency than with optimal N nutrition, indicating that N flux towards seeds, in itself, is not the main determinant of seed growth potential.
de Oliveira-Filho, Antonio G S; Ornellas, Fernando R; Peterson, Kirk A
2012-05-07
In this work, we report the construction of potential energy surfaces for the (3)A('') and (3)A(') states of the system O((3)P) + HBr. These surfaces are based on extensive ab initio calculations employing the MRCI+Q/CBS+SO level of theory. The complete basis set energies were estimated from extrapolation of MRCI+Q/aug-cc-VnZ(-PP) (n = Q, 5) results and corrections due to spin-orbit effects obtained at the CASSCF/aug-cc-pVTZ(-PP) level of theory. These energies, calculated over a region of the configuration space relevant to the study of the reaction O((3)P) + HBr → OH + Br, were used to generate functions based on the many-body expansion. The three-body potentials were interpolated using the reproducing kernel Hilbert space method. The resulting surface for the (3)A('') electronic state contains van der Waals minima on the entrance and exit channels and a transition state 6.55 kcal/mol higher than the reactants. This barrier height was then scaled to reproduce the value of 5.01 kcal/mol, which was estimated from coupled cluster benchmark calculations performed to include high-order and core-valence correlation, as well as scalar relativistic effects. The (3)A(') surface was also scaled, based on the fact that in the collinear saddle point geometry these two electronic states are degenerate. The vibrationally adiabatic barrier heights are 3.44 kcal/mol for the (3)A('') and 4.16 kcal/mol for the (3)A(') state.
Simulation-Based Fitting of Protein-Protein Interaction Potentials to SAXS Experiments
Kim, Seung Joong; Dumont, Charles; Gruebele, Martin
2008-07-08
We present a new method for computing interaction potentials of solvated proteins directly from small-angle x-ray scattering data. An ensemble of proteins is modeled by Monte Carlo or molecular dynamics simulation. The global x-ray scattering of the whole model ensemble is then computed at each snapshot of the simulation, and averaged to obtain the x-ray scattering intensity. Finally, the interaction potential parameters are adjusted by an optimization algorithm, and the procedure is iterated until the best agreement between simulation and experiment is obtained. This new approach obviates the need for approximations that must be made in simplified analytical models. We apply the method to lambda repressor fragment 6-85 and fyn-SH3. With the increased availability of fast computer clusters, Monte Carlo and molecular dynamics analysis using residue-level or even atomistic potentials may soon become feasible.
A model of a nonlinear DNA-protein interaction system with Killingbeck potential and its stability
NASA Astrophysics Data System (ADS)
Syahroni, E.; Suparmi, A.; Cari, C.; Fuad, A.
2016-11-01
In this paper, we presented a model of a nonlinear DNA-protein interaction system. The interaction system consisted of a molecule of protein bound with a single chain of DNA. The interaction between DNA chain, especially adenine and thymine, and DNA-protein bound to glutamine and adenine. The forms of these bonds are adapted from the hydrogen bonds. The Killingbeack potential were used to describe both of the interactions. We proposed the Hamiltonian equation to describe the general model of interaction. The interaction model is satisfied when a protein molecule triggers pulses on a DNA chain. An initial shift in position of protein xm should trigger the shift in position of DNA ym , or alter the state. However, an initial shift in DNA, yn , should not alter the state of a rest protein (i.e. xm = 0), otherwise, the protein would not steadily bind. We also investigated the stability of the model from the DNA-protein interaction with Lyapunov function. The stability of system can be determined when we obtained the equilibrium point.
Le, Hung M; Dinh, Thach S; Le, Hieu V
2011-10-13
The singlet-triplet transformation and molecular dissociation of ozone (O(3)) gas is investigated by performing quasi-classical molecular dynamics (MD) simulations on an ab initio potential energy surface (PES) with visible and near-infrared excitations. MP4(SDQ) level of theory with the 6-311g(2d,2p) basis set is executed for three different electronic spin states (singlet, triplet, and quintet). In order to simplify the potential energy function, an approximation is adopted by ignoring the spin-orbit coupling and allowing the molecule to switch favorably and instantaneously to the spin state that is more energetically stable (lowest in energy among the three spin states). This assumption has previously been utilized to study the SiO(2) system as reported by Agrawal et al. (J. Chem. Phys. 2006, 124 (13), 134306). The use of such assumption in this study probably makes the upper limits of computed rate coefficients the true rate coefficients. The global PES for ozone is constructed by fitting 5906 ab initio data points using a 60-neuron two-layer feed-forward neural network. The mean-absolute error and root-mean-squared error of this fit are 0.0446 eV (1.03 kcal/mol) and 0.0756 eV (1.74 kcal/mol), respectively, which reveal very good fitting accuracy. The parameter coefficients of the global PES are reported in this paper. In order to identify the spin state with high confidence, we propose the use of a pattern-recognition neural network, which is trained to predict the spin state of a given configuration (with a prediction accuracy being 95.6% on a set of testing data points). To enhance the prediction effectiveness, a buffer series of five points are validated to confirm the spin state during the MD process to gain better confidence. Quasi-classical MD simulations from 1.2 to 2.4 eV of total internal energy (including zero-point energy) result in rate coefficients of singlet-triplet transformation in the range of 0.027 ps(-1) to 1.21 ps(-1). Also, we find very
Kinetic and interaction components of the exact time-dependent correlation potential
Luo, Kai; Fuks, Johanna I.; Sandoval, Ernesto D.; Maitra, Neepa T.; Elliott, Peter
2014-05-14
The exact exchange-correlation (xc) potential of time-dependent density functional theory has been shown to have striking features. For example, step and peak features are generically found when the system is far from its ground-state, and these depend nonlocally on the density in space and time. We analyze the xc potential by decomposing it into kinetic and interaction components and comparing each with their exact-adiabatic counterparts, for a range of dynamical situations in model one-dimensional two-electron systems. We find that often, but not always, the kinetic contribution is largely responsible for these features that are missed by the adiabatic approximation. The adiabatic approximation often makes a smaller error for the interaction component, which we write in two parts, one being the Coulomb potential due to the time-dependent xc hole. Non-adiabatic features of the kinetic component were also larger than those of the interaction component in cases that we studied when there is negligible step structure. In ground-state situations, step and peak structures arise in cases of static correlation, when more than one determinant is essential to describe the interacting state. We investigate the time-dependent natural orbital occupation numbers and find the corresponding relation between these and the dynamical step is more complex than for the ground-state case.
Galvão, B R L; Varandas, A J C
2009-12-31
A new global potential energy surface is reported for the (4)A'' ground electronic state of the N(3) system from double many-body expansion theory and an extensive set of accurate ab initio energies extrapolated to the complete basis set limit. It shows three equivalent metastable potential wells for C(2v) geometries that are separated from the three N((4)S) + N(2) asymptotes by energy barriers as predicted from previous ab initio work. The potential well and barrier height now predicted lie 42.9 and 45.9 kcal mol(-1) above the atom-diatom dissociation limit, respectively, being about 1 kcal mol(-1) lower than previous theoretical estimates. The ab initio calculations here reported predict also a (4)B(1)/(4)A(2) conical intersection and reveal a new minimum with D(3h) symmetry that lies 147 kcal mol(-1) above the atom-diatom asymptote. All major topographical features of the potential energy surface are accurately described by the DMBE function, including the weakly bound van der Waals minima at large atom-diatom separations.
NASA Astrophysics Data System (ADS)
Song, W.; Rossky, P. J.; Maroncelli, M.
2003-11-01
We have tested the ability of the OPLS-AA models (optimized potentials for liquid simulations) of alkanes and perfluoroalkanes recently developed by Jorgensen and co-workers to represent the unusual mixing behavior of alkane+perfluoroalkane systems. We find that these all-atom Lennard-Jones (6-12)+Coulomb representations, together with the usual Lorentz-Berthelot combining rules, fail to reproduce the weaker-than-anticipated interactions between these two classes of molecules. Systematic disagreements with experiment are found in the case of second pressure virial coefficients, gas solubilities, and liquid-liquid mixing properties. These discrepancies are not specific to the choice of OPLS-AA potentials, but are rather linked to the failure of the geometric mean combining rule for relating unlike atom interactions. In all cases examined, a reduction in the strength of cross H+F interactions by ˜25% relative to the geometric mean is required in order to achieve reasonable agreement with experiment. Several less commonly used combining rules were also examined. Although some of these rules are able to provide a reasonable description of the interactions among perfluoroalkane and alkane species, they fail to provide a consistent treatment when atoms other than C, H, and F are considered, as is necessary for modeling the interaction of the former molecules with rare-gas atoms.
Reader, Arran T; Holmes, Nicholas P
2016-01-01
Social interaction is an essential part of the human experience, and much work has been done to study it. However, several common approaches to examining social interactions in psychological research may inadvertently either unnaturally constrain the observed behaviour by causing it to deviate from naturalistic performance, or introduce unwanted sources of variance. In particular, these sources are the differences between naturalistic and experimental behaviour that occur from changes in visual fidelity (quality of the observed stimuli), gaze (whether it is controlled for in the stimuli), and social potential (potential for the stimuli to provide actual interaction). We expand on these possible sources of extraneous variance and why they may be important. We review the ways in which experimenters have developed novel designs to remove these sources of extraneous variance. New experimental designs using a 'two-person' approach are argued to be one of the most effective ways to develop more ecologically valid measures of social interaction, and we suggest that future work on social interaction should use these designs wherever possible.
Doyon, William M; Thomas, Alyse M; Ostroumov, Alexey; Dong, Yu; Dani, John A
2013-10-15
Epidemiological studies consistently find correlations between nicotine and alcohol use, yet the neural mechanisms underlying their interaction remain largely unknown. Nicotine and alcohol (i.e., ethanol) share many common molecular and cellular targets that provide potential substrates for nicotine-alcohol interactions. These targets for interaction often converge upon the mesocorticolimbic dopamine system, where the link to drug self-administration and reinforcement is well documented. Both nicotine and alcohol activate the mesocorticolimbic dopamine system, producing downstream dopamine signals that promote the drug reinforcement process. While nicotine primarily acts via nicotinic acetylcholine receptors, alcohol acts upon a wider range of receptors and molecular substrates. The complex pharmacological profile of these two drugs generates overlapping responses that ultimately intersect within the mesocorticolimbic dopamine system to promote drug use. Here we will examine overlapping targets between nicotine and alcohol and provide evidence for their interaction. Based on the existing literature, we will also propose some potential targets that have yet to be directly tested. Mechanistic studies that examine nicotine-alcohol interactions would ultimately improve our understanding of the factors that contribute to the associations between nicotine and alcohol use.
NASA Astrophysics Data System (ADS)
Famulari, Antonino; Specchio, Roberto; Sironi, Maurizio; Raimondi, Mario
1998-02-01
Recently, a controversy has come to light in literature regarding the structure of water in nonambient conditions. Disagreement is evident between the site-site pair correlation functions of water derived from neutron diffraction and those obtained by computer simulations which employ effective pairwise potentials to express the intermolecular interactions. In this paper the SCFMI method (self-consistent field for molecular interaction) followed by nonorthogonal CI (configuration interaction) calculations was used to determine a new water-water interaction potential, which is BSSE (basis set superposition error) free in an a priori fashion. Extensive calculations were performed on water dimer and trimer and a new parametrization of a NCC-like (Niesar-Corongiu-Clementi) potential was accomplished. This was employed in the molecular-dynamics simulation of water. The effect of temperature and density variations was examined. Acceptable agreement between site-site correlation functions derived from neutron diffraction data and from computer simulation was reached. In particular, a weakening of the hydrogen bonded structure was observed on approaching the critical point, which reproduces the experimental behavior. The simulations were performed using the MOTECC (modern techniques in computational chemistry) suite of programs. The present results show the importance of BSSE-free nonorthogonal orbitals in an accurate description of the intermolecular potential of water.
Boschen, Jeffery S.; Theis, Daniel; Ruedenberg, Klaus; Windus, Theresa L.
2013-12-07
The diatomic carbon molecule has a complex electronic structure with a large number of low-lying electronic excited states. In this work, the potential energy curves (PECs) of the four lowest lying singlet states (X-1 Sigma(+)(g), A(1)Pi(u), B-1 Delta(g), and B'(1)Sigma(+)(g)) were obtained by high-level ab initio calculations. Valence electron correlation was accounted for by the correlation energy extrapolation by intrinsic scaling (CEEIS) method. Additional corrections to the PECs included core-valence correlation and relativistic effects. Spin-orbit corrections were found to be insignificant. The impact of using dynamically weighted reference wave functions in conjunction with CEEIS was examined and found to give indistinguishable results from the even weighted method. The PECs showed multiple curve crossings due to the B-1 Delta(g) state as well as an avoided crossing between the two (1)Sigma(+)(g) states. Vibrational energy levels were computed for each of the four electronic states, as well as rotational constants and spectroscopic parameters. Comparison between the theoretical and experimental results showed excellent agreement overall. Equilibrium bond distances are reproduced to within 0.05 %. The dissociation energies of the states agree with experiment to within similar to 0.5 kcal/mol, achieving "chemical accuracy." Vibrational energy levels show average deviations of similar to 20 cm(-1) or less. The B-1 Delta(g) state shows the best agreement with a mean absolute deviation of 2.41 cm(-1). Calculated rotational constants exhibit very good agreement with experiment, as do the spectroscopic constants.
Association of COMT and COMT-DRD2 interaction with creative potential
Zhang, Shun; Zhang, Muzi; Zhang, Jinghuan
2014-01-01
Several lines of evidence suggest that genes involved in dopamine (DA) transmission may contribute to creativity. Among these genes, the catechol-O-methyltransferase gene (COMT) and the dopamine D2 receptor gene (DRD2) are the most promising candidates. Our previous study has revealed evidence for the involvement of DRD2 in creative potential. The present study extended our previous study by systematically exploring the association of COMT with creative potential as well as the interaction between COMT and DRD2. Twelve single nucleotide polymorphisms (SNPs) covering COMT were genotyped in 543 healthy Chinese college students whose creative potentials were assessed by divergent thinking tests. Single SNP analysis showed that rs174697 was nominally associated with verbal originality, two SNPs (rs737865 and rs5993883) were nominally associated with figural fluency, and two SNPs (rs737865 and rs4680) were nominally associated with figural originality. Haplotype analysis showed that, the TCT and CCT haplotype (rs737865-rs174675-rs5993882) were nominally associated with figural originality, and the TATGCAG and CGCGGGA haplotype (rs4646312-rs6269-rs4633-rs6267-rs4818-rs4680-rs769224) were nominally associated with figural originality and verbal flexibility, respectively. However, none of these nominal findings survived correction for multiple testing. Gene–gene interaction analysis identified one significant four-way interaction of rs174675 (COMT), rs174697 (COMT), rs1076560 (DRD2), and rs4436578 (DRD2) on verbal fluency, one significant four-way interaction of rs174675 (COMT), rs4818 (COMT), rs1076560 (DRD2), and rs4648317 (DRD2) on verbal flexibility, and one significant three-way interaction of rs5993883 (COMT), rs4648319 (DRD2), and rs4648317 (DRD2) on figural flexibility. In conclusion, the present study provides nominal evidence for the involvement of COMT in creative potential and suggests that DA related genes may act in coordination to contribute to creativity
Cencek, Wojciech; Przybytek, Michał; Komasa, Jacek; Mehl, James B; Jeziorski, Bogumił; Szalewicz, Krzysztof
2012-06-14
The adiabatic, relativistic, and quantum electrodynamics (QED) contributions to the pair potential of helium were computed, fitted separately, and applied, together with the nonrelativistic Born-Oppenheimer (BO) potential, in calculations of thermophysical properties of helium and of the properties of the helium dimer. An analysis of the convergence patterns of the calculations with increasing basis set sizes allowed us to estimate the uncertainties of the total interaction energy to be below 50 ppm for interatomic separations R smaller than 4 bohrs and for the distance R = 5.6 bohrs. For other separations, the relative uncertainties are up to an order of magnitude larger (and obviously still larger near R = 4.8 bohrs where the potential crosses zero) and are dominated by the uncertainties of the nonrelativistic BO component. These estimates also include the contributions from the neglected relativistic and QED terms proportional to the fourth and higher powers of the fine-structure constant α. To obtain such high accuracy, it was necessary to employ explicitly correlated Gaussian expansions containing up to 2400 terms for smaller R (all R in the case of a QED component) and optimized orbital bases up to the cardinal number X = 7 for larger R. Near-exact asymptotic constants were used to describe the large-R behavior of all components. The fitted potential, exhibiting the minimum of -10.996 ± 0.004 K at R = 5.608 0 ± 0.000 1 bohr, was used to determine properties of the very weakly bound (4)He(2) dimer and thermophysical properties of gaseous helium. It is shown that the Casimir-Polder retardation effect, increasing the dimer size by about 2 Å relative to the nonrelativistic BO value, is almost completely accounted for by the inclusion of the Breit-interaction and the Araki-Sucher contributions to the potential, of the order α(2) and α(3), respectively. The remaining retardation effect, of the order of α(4) and higher, is practically negligible for the bound
Andrade, Chittaranjan
2014-04-01
In vitro and in vivo laboratory data show that pomegranate juice consistently inhibits intestinal CYP2C9 and CYP3A4 enzymes. Pomegranate juice may therefore increase the bioavailability of drugs that are metabolized by these enzymes. However, studies in humans find that pomegranate juice does not increase exposure to either CYP2C9 or CYP3A4 substrates. These contradictory findings suggest that potential drug interactions identified in the laboratory may not necessarily translate into clinically significant drug interactions in humans, and hence that laboratory data are insufficient grounds upon which clinical decisions may be based.
Delocalization of Weakly Interacting Bosons in a 1D Quasiperiodic Potential
NASA Astrophysics Data System (ADS)
Michal, V. P.; Altshuler, B. L.; Shlyapnikov, G. V.
2014-07-01
We consider weakly interacting bosons in a 1D quasiperiodic potential (Aubry-Azbel-Harper model) in the regime where all single-particle states are localized. We show that the interparticle interaction may lead to the many-body delocalization and we obtain the finite-temperature phase diagram. Counterintuitively, in a wide range of parameters the delocalization requires stronger coupling as the temperature increases. This means that the system of bosons can undergo a transition from a fluid to insulator (glass) state under heating.
Yigit, Cemil; Dzubiella, Joachim; Heyda, Jan
2015-08-14
We introduce a set of charged patchy particle models (CPPMs) in order to systematically study the influence of electrostatic charge patchiness and multipolarity on macromolecular interactions by means of implicit-solvent, explicit-ion Langevin dynamics simulations employing the Gromacs software. We consider well-defined zero-, one-, and two-patched spherical globules each of the same net charge and (nanometer) size which are composed of discrete atoms. The studied mono- and multipole moments of the CPPMs are comparable to those of globular proteins with similar size. We first characterize ion distributions and electrostatic potentials around a single CPPM. Although angle-resolved radial distribution functions reveal the expected local accumulation and depletion of counter- and co-ions around the patches, respectively, the orientation-averaged electrostatic potential shows only a small variation among the various CPPMs due to space charge cancellations. Furthermore, we study the orientation-averaged potential of mean force (PMF), the number of accumulated ions on the patches, as well as the CPPM orientations along the center-to-center distance of a pair of CPPMs. We compare the PMFs to the classical Derjaguin-Verwey-Landau-Overbeek theory and previously introduced orientation-averaged Debye-Hückel pair potentials including dipolar interactions. Our simulations confirm the adequacy of the theories in their respective regimes of validity, while low salt concentrations and large multipolar interactions remain a challenge for tractable theoretical descriptions.
Concomitant therapy in people with epilepsy: potential drug-drug interactions and patient awareness.
Eyal, Sara; Rasaby, Sivan; Ekstein, Dana
2014-02-01
People with epilepsy (PWE) may use prescription and over-the-counter (OTC) drugs for the treatment of concomitant diseases. Combinations of these drugs, as well as dietary supplements, with antiepileptic drugs (AEDs) may lead to reduced control of seizures and of coexisting medical conditions and increased risk of adverse drug reactions (ADRs). The aims of this study were to obtain comprehensive lists of medications, dietary supplements, botanicals, and specific food components used by adult PWE and to evaluate the potential for interactions involving AEDs and patients' awareness of such potential interactions. We conducted a prospective, questionnaire-based study of PWE attending the Hadassah-Hebrew University Epilepsy Clinic over a period of 7months. The questionnaire interview included the listing of medications, medicinal herbs, dietary supplements, and specific food components consumed and the knowledge of potential drug-drug interactions (DDIs), and it was conducted by a pharmacist. Drug-drug interactions were analyzed via the Micromedex online database. Out of 179 patients who attended the clinic over the study period, we interviewed 73 PWE, of which 71 were included in our final analysis. The mean number of AEDs consumed per subject was 1.7 (SD: 0.8, range: 1-4). Forty (56%) subjects were also treated with other prescription and/or OTC medications, and thirty-four (48%) took dietary supplements. Drug families most prone to DDIs involving AEDs included antipsychotic agents, selective serotonin reuptake inhibitors, and statins. Two-thirds of study participants (67%) knew that DDIs may lead to ADRs, but only half (56%) were aware of the potential for reduced seizure control. Only 44% always reported treatment with AEDs to medical professionals. This study provides for the first time a comprehensive picture of prescription and OTC drugs and food supplements used by PWE. Despite a considerable potential for DDIs involving AEDs, patient awareness is limited
Hb lepore/β0-thalassaemia with α+-thalassaemia interactions, a potential diagnostic pitfall.
Alauddin, Hafiza; Mohamad Nasir, Suziana; Ahadon, Madzlifah; Raja Sabudin, Raja Zahratul Azma; Ithnin, Azlin; Hussin, Noor Hamidah; Alias, Hamidah; Loh, C-Khai; Abdul Latiff, Zarina; Abdul Murad, Nor Azian; Othman, Ainoon
2015-12-01
Haemoglobin (Hb) Lepore is a variant Hb consisting of two α-globin and two δβ-globin chains. In a heterozygote, it is associated with clinical findings of thalassaemia minor, but interactions with other haemoglobinopathies can lead to various clinical phenotypes and pose diagnostic challenges. We reported a pair of siblings from a Malay family, who presented with pallor and hepatosplenomegaly at the ages of 21 months and 14 months old. The red cell indices and peripheral blood smears of both patients showed features of thalassaemia intermedia. Other laboratory investigations of the patients showed conflicting results. However, laboratory investigation results of the parents had led to a presumptive diagnosis of compound heterozygote Hb Lepore/β-thalassaemia and co-inheritance α+-thalassaemia (-α3.7). Hb Lepore has rarely been detected in Southeast Asian countries, particularly in Malaysia. These two cases highlight the importance of family studies for accurate diagnosis, hence appropriate clinical management and genetic counseling.
NASA Astrophysics Data System (ADS)
Carelli, Fabio; Gianturco, Francesco Antonio
2016-06-01
The interaction of low-energy scattering electrons/positrons with molecular targets characterized by a "supercritical" permanent dipole moment (≳2.0 D) presents special physical characteristics that affect their spatial distributions, around the nuclear network of the molecular partners, both above and below the energy thresholds. Such special states are described as either dipole scattering states (DSS) above thresholds or as dipole bound states (DBS) below thresholds. The details of their respective behaviour will be presented and discussed in this work in the case of the purinic DNA bases of adenine and guanine. The behavior of the additional electron, in particular, will be discussed in detail by providing new computational results that will be related to the findings from recent experiments on the same DNA bases, confirming the transient electron's behaviour surmised by them. This work is affectionately dedicated to Michael Allan on the occasion of his official retirement. We wish to this dear friend and outstanding scientist many years to come in the happy pursuit of his many scientific interests.Contribution to the Topical Issue "Advances in Positron and Electron Scattering", edited by Paulo Limao-Vieira, Gustavo Garcia, E. Krishnakumar, James Sullivan, Hajime Tanuma and Zoran Petrovic.
Gibbs, Gerald V.; Cox, David; Crawford, T Daniel; Rosso, Kevin M.; Ross, Nancy; Downs, R. T.
2006-02-28
A classification of the HF bonded interactions comprising a large number of molecules has been proposed by Espinosa et al. [J. Chem. Phys. 117, 5529 (2002)] based on the ratio |V(rc)|/G(rc) where |V(rc)| is the magnitude of the local potential energy density and G(rc) is the local kinetic density evaluated at the bond critical points, rc. A calculation of the ratio for the MO bonded interactions comprising a relatively large number of molecules and earth materials, together with the constraints imposed by the values of Ñ2ρ(rc) and the local electronic energy density H(rc) = G(rc) + V(rc) in the HF study, yielded the same classification for the oxides as found for the fluorides. This is true despite the different trends of the bond critical point and local energy properties with the bond length displayed by the HF and MO bonded interactions. LiO, NaO and MgO bonded interactions classify as closed shell ionic bonds, BeO, AlO, SiO, BO and PO bonded interactions classify as bonds of intermediate character and NO bonded interactions classify as shared covalent bonds. CO and SO bonded interactions classify as both intermediate and covalent bonded interactions. The CO triple bonded interaction classifies as a bond of intermediate character and the CO single bonded interaction classifies as a covalent bond whereas their H(rc) value indicates that they are both covalent bonds. The |V(rc)|/G(rc) ratios for the BeO, AlO and SiO bonded interactions indicate that they have a substantial component of ionic character despite their classification as bonds of intermediate character. The trend between |V(rc)|/G(rc) and the character of the bonded interaction is consistent with trends expected from electronegativity considerations. The connection between the net charges and the experimental SiO bond length evaluated for the Si and O atoms comprising two orthosilicates are examined in terms of the |V(rc)|/G(rc) values.
Scalar-fluid interacting dark energy: Cosmological dynamics beyond the exponential potential
NASA Astrophysics Data System (ADS)
Dutta, Jibitesh; Khyllep, Wompherdeiki; Tamanini, Nicola
2017-01-01
We extend the dynamical systems analysis of scalar-fluid interacting dark energy models performed in C. G. Boehmer et al., Phys. Rev. D 91, 123002 (2015), 10.1103/PhysRevD.91.123002 by considering scalar field potentials beyond the exponential type. The properties and stability of critical points are examined using a combination of linear analysis, computational methods and advanced mathematical techniques, such as center manifold theory. We show that the interesting results obtained with an exponential potential can generally be recovered also for more complicated scalar field potentials. In particular, employing power law and hyperbolic potentials as examples, we find late time accelerated attractors, transitions from dark matter to dark energy domination with specific distinguishing features, and accelerated scaling solutions capable of solving the cosmic coincidence problem.
NASA Astrophysics Data System (ADS)
Meyer, Sam; Everaers, Ralf
2015-02-01
The histone-DNA interaction in the nucleosome is a fundamental mechanism of genomic compaction and regulation, which remains largely unknown despite increasing structural knowledge of the complex. In this paper, we propose a framework for the extraction of a nanoscale histone-DNA force-field from a collection of high-resolution structures, which may be adapted to a larger class of protein-DNA complexes. We applied the procedure to a large crystallographic database extended by snapshots from molecular dynamics simulations. The comparison of the structural models first shows that, at histone-DNA contact sites, the DNA base-pairs are shifted outwards locally, consistent with locally repulsive forces exerted by the histones. The second step shows that the various force profiles of the structures under analysis derive locally from a unique, sequence-independent, quadratic repulsive force-field, while the sequence preferences are entirely due to internal DNA mechanics. We have thus obtained the first knowledge-derived nanoscale interaction potential for histone-DNA in the nucleosome. The conformations obtained by relaxation of nucleosomal DNA with high-affinity sequences in this potential accurately reproduce the experimental values of binding preferences. Finally we address the more generic binding mechanisms relevant to the 80% genomic sequences incorporated in nucleosomes, by computing the conformation of nucleosomal DNA with sequence-averaged properties. This conformation differs from those found in crystals, and the analysis suggests that repulsive histone forces are related to local stretch tension in nucleosomal DNA, mostly between adjacent contact points. This tension could play a role in the stability of the complex.
Sumpter, Bobby G; Sherrill, David; Sinnokrot, Mutasem O; Marshall, Michael S.; Hohenstein, Edward G.; Walker, Ross; Gould, Ian R
2009-01-01
Several popular force fields, namely, CHARMM, AMBER, OPLS-AA, and MM3, have been tested for their ability to reproduce highly accurate quantum mechani- cal potential energy curves for noncovalent interactions in the benzene dimer, the benzene-CH4 complex, and the benzene-H2S complex. All of the force fields are semi-quantitatively correct, but none of them is consistently reliable quantitatively. Re-optimization of Lennard-Jones parameters and symmetry-adapted perturbation theory analysis for the benzene dimer suggests that better agreement cannot be expected unless more flexible functional forms (particularly for the electrostatic contributions)are employed for the empirical force fields.
Potential costs of heterospecific sexual interactions in golden orbweb spiders (Nephila spp.).
Quiñones-Lebrón, Shakira G; Kralj-Fišer, Simona; Gregorič, Matjaž; Lokovšek, Tjaša; Čandek, Klemen; Haddad, Charles R; Kuntner, Matjaž
2016-11-15
Though not uncommon in other animals, heterospecific mating is rarely reported in arachnids. We investigated sexual interactions among four closely related and syntopical African golden orbweb spiders, Nephila inaurata, N. fenestrata, N. komaci, and N. senegalensis. In two South African localities, female webs were often inhabited by heterospecific males that sometimes outnumbered conspecifics. Species association of males with females was random in nature. In subsequent laboratory choice experiments, N. inaurata males chose heterospecific females in 30% of trials. We also observed natural mating interactions between N. inaurata males and N. komaci females, and between N. komaci males and N. inaurata females in laboratory experiments. While heterospecific mating in the laboratory never produced offspring, conspecific mating did. We discuss potential ecological and evolutionary consequences of heterospecific mating interactions in Nephila that may be particularly costly to the rarer species.
Potential costs of heterospecific sexual interactions in golden orbweb spiders (Nephila spp.)
Quiñones-Lebrón, Shakira G.; Kralj-Fišer, Simona; Gregorič, Matjaž; Lokovšek, Tjaša; Čandek, Klemen; Haddad, Charles R.; Kuntner, Matjaž
2016-01-01
Though not uncommon in other animals, heterospecific mating is rarely reported in arachnids. We investigated sexual interactions among four closely related and syntopical African golden orbweb spiders, Nephila inaurata, N. fenestrata, N. komaci, and N. senegalensis. In two South African localities, female webs were often inhabited by heterospecific males that sometimes outnumbered conspecifics. Species association of males with females was random in nature. In subsequent laboratory choice experiments, N. inaurata males chose heterospecific females in 30% of trials. We also observed natural mating interactions between N. inaurata males and N. komaci females, and between N. komaci males and N. inaurata females in laboratory experiments. While heterospecific mating in the laboratory never produced offspring, conspecific mating did. We discuss potential ecological and evolutionary consequences of heterospecific mating interactions in Nephila that may be particularly costly to the rarer species. PMID:27845369
Interaction potential of microparticles in a plasma: role of collisions with plasma particles.
Khrapak, S A; Ivlev, A V; Morfill, G
2001-10-01
The interaction potential of two charged microparticles in a plasma is studied. Violation of the plasma equilibrium around the dust particles due to plasma-particle inelastic collisions results in three effects: long-range (non-Yukawa) electrostatic repulsion, attraction due to ion shadowing, and attraction or repulsion due to neutral shadowing (depending on the sign of the temperature difference between the particle surface and neutral gas). An analytical expression for the total potential is obtained and compared with previous theoretical results. The relative contribution of these effects is studied in two limiting cases-an isotropic bulk plasma and the plasma sheath region. The results obtained are compared with existing experimental results on pair particle interaction. The possibility of the so-called dust molecule formation is discussed.
Liu, Zhiquan; Cui, Fuyi; Ma, Hua; Fan, Zhenqiang; Zhao, Zhiwei; Hou, Zhenling; Liu, Dongmei; Jia, Xuebin
2013-08-01
The potential water quality problems caused by the interaction between nitrobezene (NB) and Microcystis aeruginosa was investigated by studying the growth inhibition, the haloacetic acids formation potential (HAAFP) and the secretion of microcystin-LR (MC-LR). The results showed that NB can inhibit the growth of M. aeruginosa, and the value of EC50 increased with the increase of initial algal density. Although NB can hardly react with chlorine to form HAAs, the presence of NB can enhance the HAAFP productivity. The secretion of the intracellular MC-LR is constant under the steady experimental conditions. However, the presence of NB can reduce the MC-LR productivity of M. aeruginosa. Overall, the increased disinfection risk caused by the interaction has more important effect on the safety of drinking water quality than the benefit of the decreased MC-LR productivity, and should be serious considered when the water contained NB and M. aeruginosa is used as drinking water source.
Life history determines genetic structure and evolutionary potential of host–parasite interactions
Barrett, Luke G.; Thrall, Peter H.; Burdon, Jeremy J.; Linde, Celeste C.
2009-01-01
Measures of population genetic structure and diversity of disease-causing organisms are commonly used to draw inferences regarding their evolutionary history and potential to generate new variation in traits that determine interactions with their hosts. Parasite species exhibit a range of population structures and life-history strategies, including different transmission modes, life-cycle complexity, off-host survival mechanisms and dispersal ability. These are important determinants of the frequency and predictability of interactions with host species. Yet the complex causal relationships between spatial structure, life history and the evolutionary dynamics of parasite populations are not well understood. We demonstrate that a clear picture of the evolutionary potential of parasitic organisms and their demographic and evolutionary histories can only come from understanding the role of life history and spatial structure in influencing population dynamics and epidemiological patterns. PMID:18947899
Castro-Smirnov, Fidel Antonio; Piétrement, Olivier; Aranda, Pilar; Bertrand, Jean-Rémi; Ayache, Jeanne; Le Cam, Eric; Ruiz-Hitzky, Eduardo; Lopez, Bernard S
2016-11-03
Nanofibers of sepiolite, a natural silicate belonging to the clay minerals family, might constitute a potential promising nanocarrier for the non-viral transfer of bio-molecules. We show here that sepiolite nanofibers efficiently bind different types of DNA molecules through electrostatic interactions, hydrogen bonding, cation bridges, and van der Waals forces. Moreover, Fourier-transform infrared spectroscopy identified the external silanol groups as the main sites of interaction with the DNA. Furthermore, as a proof of concept, we show that sepiolite is able to stably transfer plasmid DNA into mammalian cells and that the efficiency can be optimized. Indeed, sonication of sepiolite 100-fold stimulated DNA transfection efficiency. These results open the way to the use of sepiolite-based biohybrids as a novel class of nanoplatform for gene transfer with potential clinical applications.
NASA Astrophysics Data System (ADS)
Castro-Smirnov, Fidel Antonio; Piétrement, Olivier; Aranda, Pilar; Bertrand, Jean-Rémi; Ayache, Jeanne; Le Cam, Eric; Ruiz-Hitzky, Eduardo; Lopez, Bernard S.
2016-11-01
Nanofibers of sepiolite, a natural silicate belonging to the clay minerals family, might constitute a potential promising nanocarrier for the non-viral transfer of bio-molecules. We show here that sepiolite nanofibers efficiently bind different types of DNA molecules through electrostatic interactions, hydrogen bonding, cation bridges, and van der Waals forces. Moreover, Fourier-transform infrared spectroscopy identified the external silanol groups as the main sites of interaction with the DNA. Furthermore, as a proof of concept, we show that sepiolite is able to stably transfer plasmid DNA into mammalian cells and that the efficiency can be optimized. Indeed, sonication of sepiolite 100-fold stimulated DNA transfection efficiency. These results open the way to the use of sepiolite-based biohybrids as a novel class of nanoplatform for gene transfer with potential clinical applications.
Castro-Smirnov, Fidel Antonio; Piétrement, Olivier; Aranda, Pilar; Bertrand, Jean-Rémi; Ayache, Jeanne; Le Cam, Eric; Ruiz-Hitzky, Eduardo; Lopez, Bernard S.
2016-01-01
Nanofibers of sepiolite, a natural silicate belonging to the clay minerals family, might constitute a potential promising nanocarrier for the non-viral transfer of bio-molecules. We show here that sepiolite nanofibers efficiently bind different types of DNA molecules through electrostatic interactions, hydrogen bonding, cation bridges, and van der Waals forces. Moreover, Fourier-transform infrared spectroscopy identified the external silanol groups as the main sites of interaction with the DNA. Furthermore, as a proof of concept, we show that sepiolite is able to stably transfer plasmid DNA into mammalian cells and that the efficiency can be optimized. Indeed, sonication of sepiolite 100-fold stimulated DNA transfection efficiency. These results open the way to the use of sepiolite-based biohybrids as a novel class of nanoplatform for gene transfer with potential clinical applications. PMID:27808269
Thiel, M. van; Ree, F.H.; Haselman, L.C.
1995-03-01
Statistical mechanical chemical equilibrium calculations of the properties of high-pressure high-temperature reactive C,H,N,O mixtures are made to derive an accurate self-consistent set of inter-molecular potentials for the product molecules. Previous theoretical efforts to predict such properties relied in part on Corresponding States theory and shock wave data of argon. More recent high-pressure Hugoniot measurements on a number of elements and molecules allow more accurate determination of the potentials of these materials, and explicit inclusion of additional dissociation products. The present discussion briefly reviews the previous analysis and the method used to produce a self-consistent set of potentials from shock data on N{sub 2}, O{sub 2}, H{sub 2}, NO, an N{sub 2} + O{sub 2} mixture, carbon, CO{sub 2}, and CO, as well as some simple explosive product mixtures from detonation of hexanitrobenzene, PETN, and a mixture of hydrazine nitrate, hydrazine and water. The results are tested using the data from an HMX explosive formulations. The effect of the non-equilibrium nature of carbon clusters is estimated using data for TNT as a standard to determine a nonequilibrium equation of state for carbon. The resulting parameter set is used in a survey of 27 explosives. For the subset that contains no fluorine or two-phase carbon effects the rms deviation from experimental detonation velocity is 1.2%.
Specific anion effects on the pressure dependence of the protein-protein interaction potential.
Möller, Johannes; Grobelny, Sebastian; Schulze, Julian; Steffen, Andre; Bieder, Steffen; Paulus, Michael; Tolan, Metin; Winter, Roland
2014-04-28
We present a study on ion specific effects on the intermolecular interaction potential V(r) of dense protein solutions under high hydrostatic pressure conditions. Small-angle X-ray scattering in combination with a liquid-state theoretical approach was used to determine the effect of structure breaking/making salt anions (Cl(-), SO4(2-), PO4(3-)) on the intermolecular interaction of lysozyme molecules. It was found that besides the Debye-Hückel charge screening effect, reducing the repulsiveness of the interaction potential V(r) at low salt concentrations, a specific ion effect is observed at high salt concentrations for the multivalent kosmotropic anions, which modulates also the pressure dependence of the protein-protein interaction potential. Whereas sulfate and phosphate strongly influence the pressure dependence of V(r), chloride anions do not. The strong structure-making effect of the multivalent anions, dominating for the triply charged PO4(3-), renders the solution structure less bulk-water-like at high salt concentrations, which leads to an altered behavior of the pressure dependence of V(r). Hence, the particular structural properties of the salt solutions are able to influence the spatial organization and the intermolecular interactions of the proteins, in particular upon compression. These results are of interest for exploring the combined effects of ionic strength, temperature and pressure on the phase behavior of protein solutions, but may also be of relevance for understanding pressure effects on the hydration behavior of biological matter under extreme environmental conditions.
Herbal medicines in Brazil: pharmacokinetic profile and potential herb-drug interactions.
Mazzari, Andre L D A; Prieto, Jose M
2014-01-01
A plethora of active compounds found in herbal medicines can serve as substrate for enzymes involved in the metabolism of xenobiotics. When a medicinal plant is co-administered with a conventional drug and little or no information is known about the pharmacokinetics of the plant metabolites, there is an increased risk of potential herb-drug interactions. Moreover, genetic polymorphisms in a population may act to predispose individuals to adverse reactions. The use of herbal medicines is rapidly increasing in many countries, particularly Brazil where the vast biodiversity is a potential source of new and more affordable treatments for numerous conditions. Accordingly, the Brazilian Unified Public Health System (SUS) produced a list of 71 plant species of interest, which could be made available to the population in the near future. Physicians at SUS prescribe a number of essential drugs and should herbal medicines be added to this system the chance of herb-drug interactions further increases. A review of the effects of these medicinal plants on Phase 1 and Phase 2 metabolic mechanisms and the transporter P-glycoprotein was conducted. The results have shown that approximately half of these medicinal plants lack any pharmacokinetic data. Moreover, most of the studies carried out are in vitro. Only a few reports on herb-drug interactions with essential drugs prescribed by SUS were found, suggesting that very little attention is being given to the safety of herbal medicines. Here we have taken this information to discuss the potential interactions between herbal medicines and essential drugs prescribed to Brazilian patients whilst taking into account the most common polymorphisms present in the Brazilian population. A number of theoretical interactions are pinpointed but more pharmacokinetic studies and pharmacovigilance data are needed to ascertain their clinical significance.
Potential drug–drug interactions in Alzheimer patients with behavioral symptoms
Pasqualetti, Giuseppe; Tognini, Sara; Calsolaro, Valeria; Polini, Antonio; Monzani, Fabio
2015-01-01
The use of multi drug regimens among the elderly population has increased tremendously over the last decade although the benefits of medications are always accompanied by potential harm, even when prescribed at recommended doses. The elderly populations are particularly at an increased risk of adverse drug reactions considering comorbidity, poly-therapy, physiological changes affecting the pharmacokinetics and pharmacodynamics of many drugs and, in some cases, poor compliance due to cognitive impairment and/or depression. In this setting, drug–drug interaction may represent a serious and even life-threatening clinical condition. Moreover, the inability to distinguish drug-induced symptoms from a definitive medical diagnosis often results in addition of yet another drug to treat the symptoms, which in turn increases drug–drug interactions. Cognitive enhancers, including acetylcholinesterase inhibitors and memantine, are the most widely prescribed agents for Alzheimer’s disease (AD) patients. Behavioral and psychological symptoms of dementia, including psychotic symptoms and behavioral disorders, represent noncognitive disturbances frequently observed in AD patients. Antipsychotic drugs are at high risk of adverse events, even at modest doses, and may interfere with the progression of cognitive impairment and interact with several drugs including anti-arrhythmics and acetylcholinesterase inhibitors. Other medications often used in AD patients are represented by anxiolytic, like benzodiazepine, or antidepressant agents. These agents also might interfere with other concomitant drugs through both pharmacokinetic and pharmacodynamic mechanisms. In this review we focus on the most frequent drug–drug interactions, potentially harmful, in AD patients with behavioral symptoms considering both physiological and pathological changes in AD patients, and potential pharmacodynamic/pharmacokinetic drug interaction mechanisms. PMID:26392756
Herbal medicines in Brazil: pharmacokinetic profile and potential herb-drug interactions
Mazzari, Andre L. D. A.; Prieto, Jose M.
2014-01-01
A plethora of active compounds found in herbal medicines can serve as substrate for enzymes involved in the metabolism of xenobiotics. When a medicinal plant is co-administered with a conventional drug and little or no information is known about the pharmacokinetics of the plant metabolites, there is an increased risk of potential herb-drug interactions. Moreover, genetic polymorphisms in a population may act to predispose individuals to adverse reactions. The use of herbal medicines is rapidly increasing in many countries, particularly Brazil where the vast biodiversity is a potential source of new and more affordable treatments for numerous conditions. Accordingly, the Brazilian Unified Public Health System (SUS) produced a list of 71 plant species of interest, which could be made available to the population in the near future. Physicians at SUS prescribe a number of essential drugs and should herbal medicines be added to this system the chance of herb-drug interactions further increases. A review of the effects of these medicinal plants on Phase 1 and Phase 2 metabolic mechanisms and the transporter P-glycoprotein was conducted. The results have shown that approximately half of these medicinal plants lack any pharmacokinetic data. Moreover, most of the studies carried out are in vitro. Only a few reports on herb-drug interactions with essential drugs prescribed by SUS were found, suggesting that very little attention is being given to the safety of herbal medicines. Here we have taken this information to discuss the potential interactions between herbal medicines and essential drugs prescribed to Brazilian patients whilst taking into account the most common polymorphisms present in the Brazilian population. A number of theoretical interactions are pinpointed but more pharmacokinetic studies and pharmacovigilance data are needed to ascertain their clinical significance. PMID:25071580
Effect of taurine and potential interactions with caffeine on cardiovascular function.
Schaffer, Stephen W; Shimada, Kayoko; Jong, Chian Ju; Ito, Takashi; Azuma, Junichi; Takahashi, Kyoko
2014-05-01
The major impetus behind the rise in energy drink popularity among adults is their ability to heighten mental alertness, improve physical performance and supply energy. However, accompanying the exponential growth in energy drink usage have been recent case reports and analyses from the National Poison Data System, raising questions regarding the safety of energy drinks. Most of the safety concerns have centered on the effect of energy drinks on cardiovascular and central nervous system function. Although the effects of caffeine excess have been widely studied, little information is available on potential interactions between the other active ingredients of energy drinks and caffeine. One of the active ingredients often mentioned as a candidate for interactions with caffeine is the beta-amino acid, taurine. Although taurine is considered a conditionally essential nutrient for humans and is thought to play a key role in several human diseases, clinical studies evaluating the effects of taurine are limited. However, based on this review regarding possible interactions between caffeine and taurine, we conclude that taurine should neutralize several untoward effects of caffeine excess. In agreement with this conclusion, the European Union's Scientific Committee on Food published a report in March 2003 summarizing its investigation into potential interactions of the ingredients in energy drinks. At the cardiovascular level, they concluded that "if there are any interactions between caffeine and taurine, taurine might reduce the cardiovascular effects of caffeine." Although these interactions remain to be further examined in humans, the physiological functions of taurine appear to be inconsistent with the adverse cardiovascular symptoms associated with excessive consumption of caffeine-taurine containing beverages.
Low potential for interactions between melagatran/ximelagatran and other drugs, food, or alcohol.
Wolzt, Michael; Sarich, Troy S; Eriksson, Ulf G
2005-08-01
Vitamin K antagonists including warfarin are associated with numerous interactions with other drugs and foods. In clinical practice, this complicates the task of maintaining plasma levels of warfarin within a narrow therapeutic window and so maximizing protection against thromboembolic events while minimizing the risk of complications, particularly bleeding. In contrast, ximelagatran has a low potential for pharmacokinetic drug:drug and food interactions. There is no significant metabolism of melagatran, and the main route of elimination of melagatran is renal excretion that appears to occur via glomerular filtration. Most importantly, cytochrome P450 isoenzymes that mediate many drug:drug interactions are not involved in the biotransformation of ximelagatran to melagatran. No significant pharmacokinetic interactions have been observed when oral ximelagatran is administered with a range of agents, including diclofenac, diazepam, nifedipine, digoxin, atorvastatin, or amiodarone. The low potential for drug:drug interactions with ximelagatran is also supported by an analysis of the pharmacokinetic data from clinical studies in patients with atrial fibrillation receiving long-term treatment with oral ximelagatran. Increases of mean melagatran area under the curve and maximum plasma concentration ( Cmax) of up to approximately 80% have been observed when ximelagatran is co-administered with the macrolide antibiotics erythromycin or azithromycin, and the mechanism for this interaction is currently under investigation. The bioavailability of melagatran is not altered by co-administration with food or alcohol. The melagatran-induced prolongation of activated partial thromboplastin time (APTT), an ex vivo coagulation time assay used as a measure of thrombin inhibition, is not altered by other drugs [including digoxin, atorvastatin, acetylsalicylic acid (ASA), and amiodarone], food, or alcohol. The effect of melagatran on capillary bleeding time, which is prolonged as a
Multi-time Schrödinger equations cannot contain interaction potentials
Petrat, Sören; Tumulka, Roderich
2014-03-15
Multi-time wave functions are wave functions that have a time variable for every particle, such as ϕ(t{sub 1},x{sub 1},...,t{sub N},x{sub N}). They arise as a relativistic analog of the wave functions of quantum mechanics but can be applied also in quantum field theory. The evolution of a wave function with N time variables is governed by N Schrödinger equations, one for each time variable. These Schrödinger equations can be inconsistent with each other, i.e., they can fail to possess a joint solution for every initial condition; in fact, the N Hamiltonians need to satisfy a certain commutator condition in order to be consistent. While this condition is automatically satisfied for non-interacting particles, it is a challenge to set up consistent multi-time equations with interaction. We prove for a wide class of multi-time Schrödinger equations that the presence of interaction potentials (given by multiplication operators) leads to inconsistency. We conclude that interaction has to be implemented instead by creation and annihilation of particles, which, in fact, can be done consistently [S. Petrat and R. Tumulka, “Multi-time wave functions for quantum field theory,” Ann. Physics (to be published)]. We also prove the following result: When a cut-off length δ > 0 is introduced (in the sense that the multi-time wave function is defined only on a certain set of spacelike configurations, thereby breaking Lorentz invariance), then the multi-time Schrödinger equations with interaction potentials of range δ are consistent; however, in the desired limit δ → 0 of removing the cut-off, the resulting multi-time equations are interaction-free, which supports the conclusion expressed in the title.
Intermolecular interactions in the crystal structures of potential HIV-1 integrase inhibitors.
Majerz-Maniecka, Katarzyna; Musiol, Robert; Nitek, Wojciech; Oleksyn, Barbara J; Mouscadet, Jean-Francois; Le Bret, Marc; Polanski, Jaroslaw
2006-02-15
2-[(2,5-dichloro-4-nitro-phenylamino)-methoxy-methyl]-8-hydroxy-quinoline 1 and 2-methyl-quinoline-5,8-dione-5-oxime 2 were obtained as potential HIV-1 integrase inhibitors and analyzed by X-ray crystallography. Semiempirical theoretical calculations of energy preferred conformations were also carried out. The crystal structures of both compounds are stabilized via hydrogen bonds and pi-pi stacking interactions. The planarity of compound 1 is caused by intramolecular hydrogen bonds.
Self-consistent calculations of rare-gas-transition-metal interaction potentials
NASA Astrophysics Data System (ADS)
Drakova, D.; Doyen, G.; v. Trentini, F.
1985-11-01
A model Hamiltonian is used to calculate potential-energy surfaces for He and Ne on the (110) faces of Ni, Cu, Pd, and Ag. The calculations are nonperturbative, self-consistent, and contain no parameters which are fittable with respect to the gas-solid interaction. Static image-force effects are included. The theory represents the first quantum-mechanical approach to rare-gas-transition-metal potentials which includes the interaction of the rare-gas orbitals with the d electrons in a consistent way. Corrugation is found to be approximately proportional to the d-electron charge density. The sp band is represented by a Sommerfeld model with hybridization gap, which does not contribute to the corrugation. Part of the potential arises through the hybridization of the rare-gas orbitals with the unoccupied metal states. This interference energy is roughly a factor of 2 larger for neon than for helium, leading to larger corrugations of the neon potentials as compared with the helium potentials. This is in agreement with recent experiments, but in contrast to earlier theoretical predictions. The theoretically calculated corrugations and well depths compare reasonably to the experimental data where available. The computed values of corrugation for He increase in the order Ni, Cu, Ag, and Pd. This agrees with experiments where soft potentials have been fitted to the scattering data, although the predicted He/Ni(110) corrugation is overly large by more than a factor of 2. With increasing energy, the He corrugation increases slightly in the calculations. The dependence is nearly constant for Ni and strongest for Pd. For Ne/Ni(110) and Ne/Pd(110) corrugation decreases with energy. Image-force effects are found to be important for the corrugation and softness of the neon potentials.
2012-01-01
Background Leptospirosis is considered a re-emerging infectious disease caused by pathogenic spirochaetes of the genus Leptospira. Pathogenic leptospires have the ability to survive and disseminate to multiple organs after penetrating the host. Leptospires were shown to express surface proteins that interact with the extracellular matrix (ECM) and to plasminogen (PLG). This study examined the interaction of two putative leptospiral proteins with laminin, collagen Type I, collagen Type IV, cellular fibronectin, plasma fibronectin, PLG, factor H and C4bp. Results We show that two leptospiral proteins encoded by LIC11834 and LIC12253 genes interact with laminin in a dose - dependent and saturable mode, with dissociation equilibrium constants (KD) of 367.5 and 415.4 nM, respectively. These proteins were named Lsa33 and Lsa25 (Leptospiral surface adhesin) for LIC11834 and LIC12253, respectively. Metaperiodate - treated laminin reduced Lsa25 - laminin interaction, suggesting that sugar moieties of this ligand participate in this interaction. The Lsa33 is also PLG - binding receptor, with a KD of 23.53 nM, capable of generating plasmin in the presence of an activator. Although in a weak manner, both proteins interact with C4bp, a regulator of complement classical route. In silico analysis together with proteinase K and immunoflorescence data suggest that these proteins might be surface exposed. Moreover, the recombinant proteins partially inhibited leptospiral adherence to immobilized laminin and PLG. Conclusions We believe that these multifunctional proteins have the potential to participate in the interaction of leptospires to hosts by mediating adhesion and by helping the bacteria to escape the immune system and to overcome tissue barriers. To our knowledge, Lsa33 is the first leptospiral protein described to date with the capability of binding laminin, PLG and C4bp in vitro. PMID:22463075
Christensen, Anders S. E-mail: cui@chem.wisc.edu; Cui, Qiang E-mail: cui@chem.wisc.edu; Elstner, Marcus
2015-08-28
Semi-empirical quantum mechanical methods traditionally expand the electron density in a minimal, valence-only electron basis set. The minimal-basis approximation causes molecular polarization to be underestimated, and hence intermolecular interaction energies are also underestimated, especially for intermolecular interactions involving charged species. In this work, the third-order self-consistent charge density functional tight-binding method (DFTB3) is augmented with an auxiliary response density using the chemical-potential equalization (CPE) method and an empirical dispersion correction (D3). The parameters in the CPE and D3 models are fitted to high-level CCSD(T) reference interaction energies for a broad range of chemical species, as well as dipole moments calculated at the DFT level; the impact of including polarizabilities of molecules in the parameterization is also considered. Parameters for the elements H, C, N, O, and S are presented. The Root Mean Square Deviation (RMSD) interaction energy is improved from 6.07 kcal/mol to 1.49 kcal/mol for interactions with one charged species, whereas the RMSD is improved from 5.60 kcal/mol to 1.73 for a set of 9 salt bridges, compared to uncorrected DFTB3. For large water clusters and complexes that are dominated by dispersion interactions, the already satisfactory performance of the DFTB3-D3 model is retained; polarizabilities of neutral molecules are also notably improved. Overall, the CPE extension of DFTB3-D3 provides a more balanced description of different types of non-covalent interactions than Neglect of Diatomic Differential Overlap type of semi-empirical methods (e.g., PM6-D3H4) and PBE-D3 with modest basis sets.
Lewis, J M; Stott, K E; Monnery, D; Seden, K; Beeching, N J; Chaponda, M; Khoo, S; Beadsworth, M B J
2016-02-01
Drug-drug interactions between antiretroviral therapy and other drugs are well described. Gastric acid-reducing agents are one such class. However, few data exist regarding the frequency of and indications for prescription, nor risk assessment in the setting of an HIV cohort receiving antiretroviral therapy. To assess prevalence of prescription of gastric acid-reducing agents and drug-drug interaction within a UK HIV cohort, we reviewed patient records for the whole cohort, assessing demographic data, frequency and reason for prescription of gastric acid-reducing therapy. Furthermore, we noted potential drug-drug interaction and whether risk had been documented and mitigated. Of 701 patients on antiretroviral therapy, 67 (9.6%) were prescribed gastric acid-reducing therapy. Of these, the majority (59/67 [88.1%]) were prescribed proton pump inhibitors. We identified four potential drug-drug interactions, which were appropriately managed by temporally separating the administration of gastric acid-reducing agent and antiretroviral therapy, and all four of these patients remained virally suppressed. Gastric acid-reducing therapy, in particular proton pump inhibitor therapy, appears common in patients prescribed antiretroviral therapy. Whilst there remains a paucity of published data, our findings are comparable to those in other European cohorts. Pharmacovigilance of drug-drug interactions in HIV-positive patients is vital. Education of patients and staff, and accurate data-gathering tools, will enhance patient safety.
Potential for interaction of kava and St. John's wort with drugs.
Singh, Yadhu N
2005-08-22
The present interest and widespread use of herbal remedies has created the possibility of interaction between them and pharmaceutical drugs if they are used simultaneously. Before the recent reports of apparent hepatotoxicity associated with its use, kava (Piper methysticum Forst. F.), was one of the top 10 selling herbal remedies in Europe and North America. This adverse effect was not previously encountered with the traditional beverage which was prepared as a water infusion in contrast to the commercial products which are extracted with organic solvents. Kavalactones, the active principles in kava, are potent inhibitors of several of the CYP 450 enzymes, suggesting a high potential for causing pharmacokinetic interactions with drugs and other herbs which are metabolized by the same CYP 450 enzymes. Furthermore, some kavalactones have been shown to possess pharmacological effects, such as blockade of GABA receptors and sodium and calcium ion channels, which may lead to pharmacodynamic interactions with other substances which possess similar pharmacological proprieties. St. John's wort (Hypericum perforatum L.), used extensively for the treatment of mild to moderate clinical depression, has long been considered safer than the conventional pharmaceutical agents. However, its ability, through its active constituents hypericin, pseudohypericin and hyperforin, to induce intestinal P-glycoprotein/MRD1 and both intestinal and hepatic CYP3A4 enzyme, could markedly reduce the distribution and disposition of their co-substrates. In addition, St. John's wort is a potent uptake inhibitor of the neurotransmitters serotonin, norepinephrine and dopamine all of which have a role in mood control. Consequently, the very real potential for a pharmacodynamic interaction between the herb and pharmaceutical drugs which share this mechanism of action and, like St. John's wort, are used for mood elevation. However, presently there is very little evidence to substantiate actual
Semi-Empirical Effective Interactions for Inelastic Scattering Derived from the Reid Potential
NASA Astrophysics Data System (ADS)
Fiase, J. O.; Sharma, L. K.; Winkoun, D. P.; Hosaka, A.
2001-09-01
An effective local interaction suitable for inelastic scattering is constructed from the Reid soft - core potential. We proceed in two stages: We first calculated a set of relative two - body matrix elements in a variational approach using the Reid soft-core potential folded with two-body correlation functions. In the second stage we constructed a potential for inelastic scattering by fitting the matrix elements to a sum of Yukawa central, tensor and spin-orbit terms to the set of relative two - body matrix elements obtained in the first stage by a least squares fitting procedure. The ranges of the new potential were selected to ensure the OPEP tails in the relevant channels as well as the short - range part of the interaction. It is found that the results of our variational techniques are very similar to the G - matrix calculations of Bertsch and co - workers in the singlet - even, triplet - even, tensor - even and spin-orbit odd channels thus putting our calculations of two - body matrix elements of nuclear forces in these channels on a sound footing. However, there exist major differences in the singlet - odd, triplet - odd, tensor - odd and spin - orbit even channels which casts some doubt on our understanding of nuclear forces in these channels.
NASA Astrophysics Data System (ADS)
Ahlrichs, R.; Brode, S.; Buck, U.; Dekieviet, M.; Lauenstein, Ch.; Rudolph, A.; Schmidt, B.
1990-12-01
Optimized geometries and binding energies are calculated for ethene (ethylene) dimers, trimers, and tetramers based on a pairwise additive dimer potential. From these results intermolecular frequencies and relative abundancies (catchment areas) of the different isomers are obtained and compared with the results of accurate measurements of the photodissociation upon absorption of one photon of a CO2 laser in the region of the v 7 monomer absorption band at 949 cm-1. The clusters are size selected in a scattering experiment and show for a cluster size from n=2 to n=6 a frequency maximum shifted by 3 cm-1 to the blue compared with the monomer. The result is explained by the predominance of chains and chain-like structures of the clusters in the photodissociation process. The chains consist of cross-like dimer sub-units.
Meng, Qingyong Chen, Jun Zhang, Dong H.
2015-09-14
The ring polymer molecular dynamics (RPMD) calculations are performed to calculate rate constants for the title reaction on the recently constructed potential energy surface based on permutation invariant polynomial (PIP) neural-network (NN) fitting [J. Li et al., J. Chem. Phys. 142, 204302 (2015)]. By inspecting convergence, 16 beads are used in computing free-energy barriers at 300 K ≤ T ≤ 1000 K, while different numbers of beads are used for transmission coefficients. The present RPMD rates are in excellent agreement with quantum rates computed on the same potential energy surface, as well as with the experimental measurements, demonstrating further that the RPMD is capable of producing accurate rates for polyatomic chemical reactions even at rather low temperatures.
Lin, Shi Ying; Sun, Zhigang; Guo, Hua; Zhang, Dong Hui; Honvault, Pascal; Xie, Daiqian; Lee, Soo-Y
2008-01-31
We present accurate quantum calculations of the integral cross section and rate constant for the H + O2 --> OH + O combustion reaction on a recently developed ab initio potential energy surface using parallelized time-dependent and Chebyshev wavepacket methods. Partial wave contributions up to J = 70 were computed with full Coriolis coupling, which enabled us to obtain the initial state-specified integral cross sections up to 2.0 eV of the collision energy and thermal rate constants up to 3000 K. The integral cross sections show a large reaction threshold due to the quantum endothermicity of the reaction, and they monotonically increase with the collision energy. As a result, the temperature dependence of the rate constant is of the Arrhenius type. In addition, it was found that reactivity is enhanced by reactant vibrational excitation. The calculated thermal rate constant shows a significant improvement over that obtained on the DMBE IV potential, but it still underestimates the experimental consensus.
Bonneté, F; Vivarès, D
2002-10-01
It has been shown for several years that the second virial coefficient, A(2), can be helpfully used to describe the thermodynamic behavior of biological macromolecules in solution prior to crystallization. The coefficient, which reflects either repulsive or attractive interactions between particles, can allow a rapid determination of crystallization conditions. Different biological systems, from 14 kDa to 4600 kDa, were studied by small angle X-ray scattering. With large macromolecules, the A(2) values were found at the low end of the crystallization slot described by George & Wilson [(1994) Acta Cryst. D50, 361-365]. This led us to investigate the physical meaning of the second virial coefficient and to propose the use of the dimensionless second virial coefficient independent of the molecular weight and the size of the particle, which only takes into account the interaction potential between macromolecules, to predict successful crystallization conditions for large macromolecules. With this normalized coefficient (a(2)), the effect of salt on small proteins becomes equivalent to the effect of PEG on large macromolecules in terms of interaction potentials.
Subsystem-DFT potential-energy curves for weakly interacting systems.
Schlüns, Danny; Klahr, Kevin; Mück-Lichtenfeld, Christian; Visscher, Lucas; Neugebauer, Johannes
2015-06-14
Kohn-Sham density-functional theory (DFT) within the local-density approximation (LDA) or the generalized-gradient approximation (GGA) is known to fail for the correct description of London dispersion interactions. Often, not even bound potential-energy surfaces are obtained for van der Waals complexes, unless special correction schemes are employed. In contrast to that, there has been some evidence for the fact that subsystem-based density functional theory produces interaction energies for weakly bound systems which are superior to Kohn-Sham DFT results without dispersion corrections. This is usually attributed to an error cancellation between the approximate exchange-correlation and non-additive kinetic-energy functionals employed in subsystem DFT. Here, we investigate the accuracy of subsystem DFT for weakly interacting systems in detail, paying special attention to the shape of the potential-energy surfaces (PESs). Our test sets include the extensive S22x5 and S66x8 data sets. Our results indicate that subsystem DFT PESs strongly vary depending on the functional. LDA results are usually quite good, but behave differently from their KS counterparts. GGA results from the popular Perdew-Wang (PW91) set of functionals produce PESs that are often, but not in general overbinding. Results from Becke-Perdew (BP86) GGAs, by contrast, show the typical problems known from the corresponding KS results. We provide some preliminary results for empirical corrections for both PW91 and BP86 in subsystem DFT.
Murtaza, Ghulam; Khan, Muhammad Yasir Ghani; Azhar, Saira; Khan, Shujaat Ali; Khan, Tahir M
2016-03-01
Drug-drug interactions (DDIs) may result in the alteration of therapeutic response. Sometimes they may increase the untoward effects of many drugs. Hospitalized cardiac patients need more attention regarding drug-drug interactions due to complexity of their disease and therapeutic regimen. This research was performed to find out types, prevalence and association between various predictors of potential drug-drug interactions (pDDIs) in the Department of Cardiology and to report common interactions. This study was performed in the hospitalized cardiac patients at Ayub Teaching Hospital, Abbottabad, Pakistan. Patient charts of 2342 patients were assessed for pDDIs using Micromedex® Drug Information. Logistic regression was applied to find predictors of pDDIs. The main outcome measure in the study was the association of the potential drug-drug interactions with various factors such as age, gender, polypharmacy, and hospital stay of the patients. We identified 53 interacting-combinations that were present in total 5109 pDDIs with median number of 02 pDDIs per patient. Overall, 91.6% patients had at least one pDDI; 86.3% were having at least one major pDDI, and 84.5% patients had at least one moderate pDDI. Among 5109 identified pDDIs, most were of moderate (55%) or major severity (45%); established (24.2%), theoretical (18.8%) or probable (57%) type of scientific evidence. Top 10 common pDDIs included 3 major and 7 moderate interactions. Results obtained by multivariate logistic regression revealed a significant association of the occurrence of pDDIs in patient with age of 60 years or more (p < 0.001), hospital stay of 7 days or longer (p < 0.001) and taking 7 or more drugs (p < 0.001). We found a high prevalence for pDDIs in the Department of Cardiology, most of which were of moderate severity. Older patients, patients with longer hospital stay and with elevated number of prescribed drugs were at higher risk of pDDIs.
Clarke, Michael T; Soto, Gloria; Nelson, Keith
2017-03-01
For children with typical development, language is learned through everyday discursive interaction. Adults mediate child participation in such interactions through the deployment of a range of co-constructive strategies, including repeating, questioning, prompting, expanding, and reformulating the child's utterances. Adult reformulations of child utterances, also known as recasts, have also been shown to relate to the acquisition of linguistic structures in children with language and learning disabilities and children and adults learning a foreign language. In this paper we discuss the theoretical basis and empirical evidence for the use of different types of recasts as a major language learning catalyst, and what may account for their facilitative effects. We consider the occurrence of different types of recasts in AAC-mediated interactions and their potential for language facilitation, within the typical operational and linguistic constraints of such interactions. We also consider the benefit of explicit and corrective forms of recasts for language facilitation in conversations with children who rely on AAC. We conclude by outlining future research directions.
Entangling spin-spin interactions of ions in individually controlled potential wells
NASA Astrophysics Data System (ADS)
Wilson, Andrew; Colombe, Yves; Brown, Kenton; Knill, Emanuel; Leibfried, Dietrich; Wineland, David
2014-03-01
Physical systems that cannot be modeled with classical computers appear in many different branches of science, including condensed-matter physics, statistical mechanics, high-energy physics, atomic physics and quantum chemistry. Despite impressive progress on the control and manipulation of various quantum systems, implementation of scalable devices for quantum simulation remains a formidable challenge. As one approach to scalability in simulation, here we demonstrate an elementary building-block of a configurable quantum simulator based on atomic ions. Two ions are trapped in separate potential wells that can individually be tailored to emulate a number of different spin-spin couplings mediated by the ions' Coulomb interaction together with classical laser and microwave fields. We demonstrate deterministic tuning of this interaction by independent control of the local wells and emulate a particular spin-spin interaction to entangle the internal states of the two ions with 0.81(2) fidelity. Extension of the building-block demonstrated here to a 2D-network, which ion-trap micro-fabrication processes enable, may provide a new quantum simulator architecture with broad flexibility in designing and scaling the arrangement of ions and their mutual interactions. This research was funded by the Office of the Director of National Intelligence (ODNI), Intelligence Advanced Research Projects Activity (IARPA), ONR, and the NIST Quantum Information Program.
Assessment of Potential Herb-Drug Interactions among Nigerian Adults with Type-2 Diabetes
Ezuruike, Udoamaka; Prieto, Jose M.
2016-01-01
It is becoming increasingly evident that patients with diabetes do not rely only on prescription drugs for their disease management. The use of herbal medicines is one of the self-management practices adopted by these patients, often without the knowledge of their healthcare practitioners. This study assessed the potential for pharmacokinetic herb-drug interactions (HDIs) amongst Nigerian adult diabetic patients. This was done through a literature analysis of the pharmacokinetic profile of their herbal medicines and prescription drugs, based on information obtained from 112 patients with type-2 diabetes attending two secondary health care facilities in Nigeria. Fifty percent of the informants used herbal medicines alongside their prescription drugs. Worryingly, 60% of the patients taking herbal medicines did not know their identity, thus increasing the risk of unidentified HDIs. By comparing the pharmacokinetic profile of eight identified herbs taken by the patients for the management of diabetes against those of the prescription drugs, several scenarios of potential HDIs were identified and their clinical relevance is discussed. The lack of clinical predictors points toward cultural factors as the influence for herb use, making it more difficult to identify these patients and in turn monitor potential HDIs. In identifying these possible interactions, we have highlighted the need for healthcare professionals to promote a proactive monitoring of patients' use of herbal medicines. PMID:27559312
Antinucleon-nucleus interaction near threshold from the Paris N bar N potential
NASA Astrophysics Data System (ADS)
Friedman, E.; Gal, A.; Loiseau, B.; Wycech, S.
2015-11-01
A general algorithm for handling the energy dependence of hadron-nucleon amplitudes in the nuclear medium, consistently with their density dependence, has been recently applied to antikaons, eta mesons and pions interacting with nuclei. Here we apply this approach to antiprotons below threshold, analyzing experimental results for antiprotonic atoms across the periodic table. It is also applied to antiproton and antineutron interactions with nuclei up to 400 MeV/c, comparing with elastic scattering and annihilation cross sections. The underlying p bar N scattering amplitudes are derived from the Paris N bar N potential, including in-medium modifications. Emphasis is placed on the role of the P-wave amplitudes with respect to the repulsive S-wave amplitudes.
Experimental modelling of lightning interaction phenomena with a free potential conducting objects
NASA Technical Reports Server (NTRS)
Chernov, E. N.; Lupeiko, A. V.; Petrov, N. I.
1991-01-01
Laboratory experiments were conducted to investigate the physical processes of the development of air discharge and its interaction with free potential conducting objects. The space-time development of lightning in gaps was recorded by a motion picture camera and an optoelectronic transducer. The electric field at different points in the gap was measured using a Pockels device both in the leader stage and in the stage of the return stroke. Experimental results of the streamer zone length measurements in the gaps with lengths up to 65 meters are presented. The physical processes occurring during the interaction of positive and negative long sparks with isolated objects were investigated. The striking probability of isolated conducting spheres with different diameters and the dependence of the strike on the location of the gap are investigated.
Research on the potential use of interactive materials on astronomy education
NASA Astrophysics Data System (ADS)
Voelzke, Marcos Rincon; Macedo, Josue
2016-07-01
This study presents results of a survey conducted at the Federal Institution of Education, Science and Technology in the North of Minas Gerais (IFNMG), and aimed to investigate the potentialities of the use of interactive materials in the teaching of astronomy. An advanced training course with involved learning activities about basic concepts of astronomy was offered to thirty-two Licenciate students in Physics, Mathematics and Biological Sciences, using the mixed methodology, combined with the three pedagogical moments. Among other aspects, the viability of the use of resources was noticed, involving digital technologies and interactive materials on teaching of astronomy, which may contribute to the broadening of methodological options for future teachers and meet their training needs.
Thrush, Simon F; Hewitt, Judi E; Parkes, Samantha; Lohrer, Andrew M; Pilditch, Conrad; Woodin, Sarah A; Wethey, David S; Chiantore, Mariachiara; Asnaghi, Valentina; De Juan, Silvia; Kraan, Casper; Rodil, Ivan; Savage, Candida; Van Colen, Carl
2014-06-01
Thresholds profoundly affect our understanding and management of ecosystem dynamics, but we have yet to develop practical techniques to assess the risk that thresholds will be crossed. Combining ecological knowledge of critical system interdependencies with a large-scale experiment, we tested for breaks in the ecosystem interaction network to identify threshold potential in real-world ecosystem dynamics. Our experiment with the bivalves Macomona liliana and Austrovenus stutchburyi on marine sandflats in New Zealand demonstrated that reductions in incident sunlight changed the interaction network between sediment biogeochemical fluxes, productivity, and macrofauna. By demonstrating loss of positive feedbacks and changes in the architecture of the network, we provide mechanistic evidence that stressors lead to break points in dynamics, which theory predicts predispose a system to a critical transition.
Mechanisms of radiation interaction with DNA: Potential implications for radiation protection
Sinclair, W.K.; Fry, R.J.M.
1987-01-01
An overview of presentations and discussions which took place at the US Department of Energy/Commission of European Communities (DOE/CEC) workshop on ''Mechanisms of Radiation Interaction with DNA: Potential Implications for Radiation Protection,'' held at San Diego, California, January 21-22, 1987, is provided. The Department has traditionally supported fundamental research on interactions of ionizing radiation with different biological systems and at all levels of biological organization. The aim of this workshop was to review the base of knowledge in the area of mechanisms of radiation action at the DNA level, and to explore ways in which this information can be applied to the development of scientifically sound concepts and procedures for use in the field of radiation protection.
Solid phase stability of a double-minimum interaction potential system
Suematsu, Ayumi; Yoshimori, Akira Saiki, Masafumi; Matsui, Jun; Odagaki, Takashi
2014-06-28
We study phase stability of a system with double-minimum interaction potential in a wide range of parameters by a thermodynamic perturbation theory. The present double-minimum potential is the Lennard-Jones-Gauss potential, which has a Gaussian pocket as well as a standard Lennard-Jones minimum. As a function of the depth and position of the Gaussian pocket in the potential, we determine the coexistence pressure of crystals (fcc and bcc). We show that the fcc crystallizes even at zero pressure when the position of the Gaussian pocket is coincident with the first or third nearest neighbor site of the fcc crystal. The bcc crystal is more stable than the fcc crystal when the position of the Gaussian pocket is coincident with the second nearest neighbor sites of the bcc crystal. The stable crystal structure is determined by the position of the Gaussian pocket. These results show that we can control the stability of the solid phase by tuning the potential function.
Solid phase stability of a double-minimum interaction potential system
NASA Astrophysics Data System (ADS)
Suematsu, Ayumi; Yoshimori, Akira; Saiki, Masafumi; Matsui, Jun; Odagaki, Takashi
2014-06-01
We study phase stability of a system with double-minimum interaction potential in a wide range of parameters by a thermodynamic perturbation theory. The present double-minimum potential is the Lennard-Jones-Gauss potential, which has a Gaussian pocket as well as a standard Lennard-Jones minimum. As a function of the depth and position of the Gaussian pocket in the potential, we determine the coexistence pressure of crystals (fcc and bcc). We show that the fcc crystallizes even at zero pressure when the position of the Gaussian pocket is coincident with the first or third nearest neighbor site of the fcc crystal. The bcc crystal is more stable than the fcc crystal when the position of the Gaussian pocket is coincident with the second nearest neighbor sites of the bcc crystal. The stable crystal structure is determined by the position of the Gaussian pocket. These results show that we can control the stability of the solid phase by tuning the potential function.
The (H2)2 potential surface and the interaction between hydrogen molecules at low temperatures
NASA Astrophysics Data System (ADS)
Burton, Peter G.; Senff, Ulrich E.
1982-06-01
The (H2)2 rigid rotor interaction potential has been calculated for the intermolecular distance range R = 3.0-11.0 a.u. for six relative orientations to estimate both the isotropic and anisotropic components of the full intermolecular potential. A partially optimized basis set limited in size to 78 independent Gaussian functions was used throughout the energy calculations, which required only very small corrections for basis set unsaturation effects. Correlation effects were computed both at the variational (single and) double excitation PNOCI level and using the CEPA2-PNO approximation to estimate higher order excitation effects. While the latter rigid-rotor surface may overestimate the strength of the H2-H2 interaction in the vicinity of the well by a few wave numbers in the rigid-rotor PNOCI surface from the present study, which we regard as an upper bound to the true rigid-rotor surface, is also slightly deeper than almost all previous theoretical and empirical ''fit'' potentials in the well region. Since low energy scattering experiments lack sensitivity to the precise well depth because of the long de Broglie wavelengths appropriate to scattering at energies comparable with the well depth, the significance of the current disagreement on the well depth between the rigid-rotor level of the theory (which puts it at least 27.5 cm-1) and experiment is uncertain. However, coupled with the present uncertainty stemming from the CI formalism of ˜±3 cm-1, is a further uncertainty due to the expected increase in intramolecular zero-point energies due to hindered H2 vibration within the dimer. A zero-point increase within each H2 at Re of 0.1% would effectively raise the rigid-rotor potentials by some 4 cm-1, bringing the well depth into line with experimental estimates. In the low energy part of the repulsive wall of the potential (where the relative importance of these small effects diminishes), which has been probed rather sensitively by recent rotationally
Host-Microbiome Interaction and Cancer: Potential Application in Precision Medicine.
Contreras, Alejandra V; Cocom-Chan, Benjamin; Hernandez-Montes, Georgina; Portillo-Bobadilla, Tobias; Resendis-Antonio, Osbaldo
2016-01-01
It has been experimentally shown that host-microbial interaction plays a major role in shaping the wellness or disease of the human body. Microorganisms coexisting in human tissues provide a variety of benefits that contribute to proper functional activity in the host through the modulation of fundamental processes such as signal transduction, immunity and metabolism. The unbalance of this microbial profile, or dysbiosis, has been correlated with the genesis and evolution of complex diseases such as cancer. Although this latter disease has been thoroughly studied using different high-throughput (HT) technologies, its heterogeneous nature makes its understanding and proper treatment in patients a remaining challenge in clinical settings. Notably, given the outstanding role of host-microbiome interactions, the ecological interactions with microorganisms have become a new significant aspect in the systems that can contribute to the diagnosis and potential treatment of solid cancers. As a part of expanding precision medicine in the area of cancer research, efforts aimed at effective treatments for various kinds of cancer based on the knowledge of genetics, biology of the disease and host-microbiome interactions might improve the prediction of disease risk and implement potential microbiota-directed therapeutics. In this review, we present the state of the art of sequencing and metabolome technologies, computational methods and schemes in systems biology that have addressed recent breakthroughs of uncovering relationships or associations between microorganisms and cancer. Together, microbiome studies extend the horizon of new personalized treatments against cancer from the perspective of precision medicine through a synergistic strategy integrating clinical knowledge, HT data, bioinformatics, and systems biology.
Host-Microbiome Interaction and Cancer: Potential Application in Precision Medicine
Contreras, Alejandra V.; Cocom-Chan, Benjamin; Hernandez-Montes, Georgina; Portillo-Bobadilla, Tobias; Resendis-Antonio, Osbaldo
2016-01-01
It has been experimentally shown that host-microbial interaction plays a major role in shaping the wellness or disease of the human body. Microorganisms coexisting in human tissues provide a variety of benefits that contribute to proper functional activity in the host through the modulation of fundamental processes such as signal transduction, immunity and metabolism. The unbalance of this microbial profile, or dysbiosis, has been correlated with the genesis and evolution of complex diseases such as cancer. Although this latter disease has been thoroughly studied using different high-throughput (HT) technologies, its heterogeneous nature makes its understanding and proper treatment in patients a remaining challenge in clinical settings. Notably, given the outstanding role of host-microbiome interactions, the ecological interactions with microorganisms have become a new significant aspect in the systems that can contribute to the diagnosis and potential treatment of solid cancers. As a part of expanding precision medicine in the area of cancer research, efforts aimed at effective treatments for various kinds of cancer based on the knowledge of genetics, biology of the disease and host-microbiome interactions might improve the prediction of disease risk and implement potential microbiota-directed therapeutics. In this review, we present the state of the art of sequencing and metabolome technologies, computational methods and schemes in systems biology that have addressed recent breakthroughs of uncovering relationships or associations between microorganisms and cancer. Together, microbiome studies extend the horizon of new personalized treatments against cancer from the perspective of precision medicine through a synergistic strategy integrating clinical knowledge, HT data, bioinformatics, and systems biology. PMID:28018236
Das, T.K.; Chakrabarti, B.
2004-12-01
We study a system of A identical interacting bosons trapped by an external field by solving ab initio the many-body Schroedinger equation. A complete solution by using, for example, the traditional hyperspherical harmonics (HH) basis develops serious practical problems due to the large degeneracy of HH basis. Symmetrization of the wave function, calculation of the matrix elements, etc., become an immensely formidable task as A increases. Instead of the HH basis, here we use a new basis, called 'potential harmonics' (PH) basis, which is a subset of HH basis. We assume that the contribution to the orbital and grand orbital [in 3(A-1)-dimensional space of the reduced motion] quantum numbers comes only from the interacting pair. This implies inclusion of two-body correlations only and disregard of all higher-body correlations. Such an assumption is ideally suited for the Bose-Einstein condensate (BEC), which is required, for experimental realization of BEC, to be extremely dilute. Hence three and higher-body collisions are almost totally absent. Unlike the (3A-4) hyperspherical variables in HH basis, the PH basis involves only three active variables, corresponding to three quantum numbers--the orbital l, azimuthal m, and the grand orbital 2K+l quantum numbers for any arbitrary A. It drastically reduces the number of coupled equations and calculation of the potential matrix becomes tremendously simplified, as it involves integrals over only three variables for any A. One can easily incorporate realistic atom-atom interactions in a straightforward manner. We study the ground and excited state properties of the condensate for both attractive and repulsive interactions for various particle number. The ground state properties are compared with those calculated from the Gross-Pitaevskii equation. We notice that our many-body results converge towards the mean field results as the particle number increases.
Overlapping Regions in HIV-1 Genome Act as Potential Sites for Host–Virus Interaction
Saha, Deeya; Podder, Soumita; Ghosh, Tapash C.
2016-01-01
More than a decade, overlapping genes in RNA viruses became a subject of research which has explored various effect of gene overlapping on the evolution and function of viral genomes like genome size compaction. Additionally, overlapping regions (OVRs) are also reported to encode elevated degree of protein intrinsic disorder (PID) in unspliced RNA viruses. With the aim to explore the roles of OVRs in HIV-1 pathogenesis, we have carried out an in-depth analysis on the association of gene overlapping with PID in 35 HIV1- M subtypes. Our study reveals an over representation of PID in OVR of HIV-1 genomes. These disordered residues endure several vital, structural features like short linear motifs (SLiMs) and protein phosphorylation (PP) sites which are previously shown to be involved in massive host–virus interaction. Moreover, SLiMs in OVRs are noticed to be more functionally potential as compared to that of non-overlapping region. Although, density of experimentally verified SLiMs, resided in 9 HIV-1 genes, involved in host–virus interaction do not show any bias toward clustering into OVR, tat and rev two important proteins mediates host–pathogen interaction by their experimentally verified SLiMs, which are mostly localized in OVR. Finally, our analysis suggests that the acquisition of SLiMs in OVR is mutually exclusive of the occurrence of disordered residues, while the enrichment of PPs in OVR is solely dependent on PID and not on overlapping coding frames. Thus, OVRs of HIV-1 genomes could be demarcated as potential molecular recognition sites during host–virus interaction. PMID:27867372
Nagata, Takeshi; Fedorov, Dmitri G; Sawada, Toshihiko; Kitaura, Kazuo
2012-09-13
Based on the proposed new expression of the polarization energy for the fragment molecular orbital (FMO) method interfaced with effective fragment potentials (EFPs), we develop an analysis of the solute(FMO)-solvent(EFP) interactions by defining individual fragment contributions for both solute and solvent. The obtained components are compared to all-electron calculations where water is treated as FMO fragments in the pair interaction energy decomposition analysis. The new energy expression is shown to be accurate, and the developed energy analysis is applied to the solvated griffithsin-carbohydrate complex. The details of the ligand recognition are revealed in the context with their interplay with the solvent effects. Tyr residue fragments are shown to reduce the desolvation penalty for Asp, which strongly binds the ligand.
In vitro and in vivo Evaluation of CYP1A Interaction Potential of Terminalia Arjuna Bark
Varghese, Alice; Pandita, Nancy; Gaud, R. S.
2014-01-01
Terminalia arjuna Wight and Arn. (Combretaceae) is a tree having an extensive medicinal potential in cardiovascular disorders. Triterpenoids are mainly responsible for cardiovascular properties. Aqueous, hydroalcoholic and alcoholic extract of T. arjuna, arjunic acid and arjungenin were examined for their potential to inhibit CYP1A enzyme in rat and human liver microsomes. IC50 values of aqueous, hydroalcoholic and alcoholic extract of T. arjuna was found to be 11.4, 28.9 and 44.6 μg/ml in rat liver microsomes while 30.0, 29.7 and 39.0 μg/ml in human liver microsomes, respectively for CYP1A. However IC50 values of arjunic acid and arjungenin for both rat liver microsomes and human liver microsomes were found to be >50 μM. Arjunic acid and arjungenin did not show inhibition of CYP1A enzyme up to concentrations of 50 μM. These in vitro data indicate that Terminalia arjuna extracts contain constituents that can potently inhibit the activity of CYP1A, which could in turn lead to undesirable pharmacokinetic drug–herb interactions in vivo. Based on the in vitro data, interaction potential of the aqueous extract of Terminalia arjuna orally in rats was investigated. A probe substrate, phenacetin, was used to index the activity of CYP1A. In vivo pharmacokinetic study of coadministration of aqueous extract of Terminalia arjuna and phenacetin, revealed that the aqueous extract did not lead to any significant change in the pharmacokinetic parameters of phenacetin as compared with control group. Though there was no in vivo–in vitro correlation, drug interactions could arise with drugs having a narrow therapeutic range and extensively cleared by CYP1A enzyme, which could lead to undesirable side effects. PMID:24843187
Mason, Tom H E; Stephens, Philip A; Apollonio, Marco; Willis, Stephen G
2014-12-01
The altitudinal shifts of many montane populations are lagging behind climate change. Understanding habitual, daily behavioural rhythms, and their climatic and environmental influences, could shed light on the constraints on long-term upslope range-shifts. In addition, behavioural rhythms can be affected by interspecific interactions, which can ameliorate or exacerbate climate-driven effects on ecology. Here, we investigate the relative influences of ambient temperature and an interaction with domestic sheep (Ovis aries) on the altitude use and activity budgets of a mountain ungulate, the Alpine chamois (Rupicapra rupicapra). Chamois moved upslope when it was hotter but this effect was modest compared to that of the presence of sheep, to which they reacted by moving 89-103 m upslope, into an entirely novel altitudinal range. Across the European Alps, a range-shift of this magnitude corresponds to a 46% decrease in the availability of suitable foraging habitat. This highlights the importance of understanding how factors such as competition and disturbance shape a given species' realised niche when predicting potential future responses to change. Furthermore, it exposes the potential for manipulations of species interactions to ameliorate the impacts of climate change, in this case by the careful management of livestock. Such manipulations could be particularly appropriate for species where competition or disturbance already strongly restricts their available niche. Our results also reveal the potential role of behavioural flexibility in responses to climate change. Chamois reduced their activity when it was warmer, which could explain their modest altitudinal migrations. Considering this behavioural flexibility, our model predicts a small 15-30 m upslope shift by 2100 in response to climate change, less than 4% of the altitudinal shift that would be predicted using a traditional species distribution model-type approach (SDM), which assumes that species' behaviour
Potential Role of Elicitins in the Interaction between Phytophthora Species and Tobacco
Kamoun, Sophien; Young, Mary; Förster, Helga; Coffey, Michael D.; Tyler, Brett M.
1994-01-01
The potential role of extracellular elicitor proteins (elicitins) from Phytophthora species as avirulence factors in the interaction between Phytophthora and tobacco was examined. A survey of 85 Phytophthora isolates representing 14 species indicated that production of elicitin is almost ubiquitous except for isolates of Phytophthora parasitica from tobacco. The production of elicitins by isolates of P. parasitica correlated without exception with low or no virulence on tobacco. Genetic analysis was conducted by using a cross between two isolates of P. parasitica, segregating for production of elicitin and virulence on tobacco. Virulence assays of the progeny on tobacco confirmed the correlation between production of elicitin and low virulence. Images PMID:16349258
Minimizing the injury potential of deploying airbag interactions with car occupants.
Mertz, Harold J; Prasad, Priya; Dalmotas, Dainius
2013-11-01
Minimizing the injury potential of the interactions between deploying airbags and car occupants is the major issue with the design of airbag systems. This concern was identified in 1964 by Carl Clark when he presented the results of human volunteer and dummy testing of the "Airstop" system that was being developed for aircraft. The following is a chronological summary of the actions taken by the car manufacturers, airbag suppliers, SAE and ISO task groups, research institutes and universities, and consumer and government groups to address this issue.
Evaluation of Potential Drug-Drug Interactions with Antidepressants in Two Tertiary Care Hospitals
Rafi, Muhammad Salman; Naqvi, Syed Baqir Shyum; Khan, Muhammad Umair; Fayyaz, Muhammad; Ashraf, Nida; Khan, Maqsood Ahmed; Ahmad, Akram
2015-01-01
Background Limited resources of healthcare system and high use of antidepressants have raised some serious concerns regarding proper surveillance system of prescribed medicines. Not much literature is available from Pakistan regarding the potential drug-drug interactions (pDDIs) associated with antidepressants. Objective The objective of this study was to assess the frequency of pDDIs associated with antidepressants, their severity, significance and their association with patient characteristics. Materials and Methods A prospective, observational study was conducted in two major hospitals of Karachi for the period of three months. Patient profiles, medication charts, and physician notes were thoroughly reviewed to gather all the relevant information. Inclusion and exclusion criteria were set prior to data collection. The collected data was then analysed using Micromedex Drug-REAX System. Descriptive and binomial logistic regression analysis was used to express results. Results Of 245 prescriptions reviewed, 141 prescriptions had at least one pDDI (57.5%). A total of 181 pDDIs were identified in prescription containing antidepressant. The ratio of pDDI per prescriptions was 0.78. 42.5% interactions were moderate in severity, 30% of interactions were rapid in onset, and 43% were considered as significant interactions. Polypharmacy (OR=3.41, p< 0.001) and presence of chronic problems (OR=2.14, p=0.002) were significantly associated with the occurrence of pDDIs. Citalopram and diclofenac (11.6%) was commonly prescribed interacting pair in this study. Conclusion The findings of this study recorded high frequency of antidepressants associated pDDIs. Our results confirm the significant association of polypharmacy with the occurrence of pDDIs with antidepressants. Future studies are warranted to establish these results by including hospitals in different parts of the country. PMID:26393139
Gufford, Brandon T; Chen, Gang; Vergara, Ana G; Lazarus, Philip; Oberlies, Nicholas H; Paine, Mary F
2015-09-01
Women at high risk of developing breast cancer are prescribed selective estrogen response modulators, including raloxifene, as chemoprevention. Patients often seek complementary and alternative treatment modalities, including herbal products, to supplement prescribed medications. Milk thistle preparations, including silibinin and silymarin, are top-selling herbal products that may be consumed by women taking raloxifene, which undergoes extensive first-pass glucuronidation in the intestine. Key constituents in milk thistle, flavonolignans, were previously shown to be potent inhibitors of intestinal UDP-glucuronosyl transferases (UGTs), with IC50s ≤ 10 μM. Taken together, milk thistle preparations may perpetrate unwanted interactions with raloxifene. The objective of this work was to evaluate the inhibitory effects of individual milk thistle constituents on the intestinal glucuronidation of raloxifene using human intestinal microsomes and human embryonic kidney cell lysates overexpressing UGT1A1, UGT1A8, and UGT1A10, isoforms highly expressed in the intestine that are critical to raloxifene clearance. The flavonolignans silybin A and silybin B were potent inhibitors of both raloxifene 4'- and 6-glucuronidation in all enzyme systems. The Kis (human intestinal microsomes, 27-66 µM; UGT1A1, 3.2-8.3 µM; UGT1A8, 19-73 µM; and UGT1A10, 65-120 µM) encompassed reported intestinal tissue concentrations (20-310 µM), prompting prediction of clinical interaction risk using a mechanistic static model. Silibinin and silymarin were predicted to increase raloxifene systemic exposure by 4- to 5-fold, indicating high interaction risk that merits further evaluation. This systematic investigation of the potential interaction between a widely used herbal product and chemopreventive agent underscores the importance of understanding natural product-drug interactions in the context of cancer prevention.
NASA Astrophysics Data System (ADS)
Campos, L. Q. Costa; Apolinario, S. W. S.
2015-01-01
We implement Brownian dynamics to investigate the static properties of colloidal particles confined anisotropically and interacting via a potential which can be tailored in a repulsive-attractive-respulsive fashion as the interparticle distance increases. A diverse number of structural phases are self-assembled, which were classified according to two aspects, that is, their macroscopic and microscopic patterns. Concerning the microscopic phases we found the quasicrystalline, triangular, square, and mixed orderings, where this latter is a combination of square and triangular cells in a 3 ×2 proportion, i.e., the so-called (33,42) Archimedian lattice. On the macroscopic level the system could self-organize in a compact or perforated single cluster surrounded or not by fringes. All the structural phases are summarized in detailed phases diagrams, which clearly show that the different phases are extended as the confinement potential becomes more anisotropic.
Interacting particles in a periodically moving potential: traveling wave and transport.
Chatterjee, Rakesh; Chatterjee, Sakuntala; Pradhan, Punyabrata; Manna, S S
2014-02-01
We study a system of interacting particles in a periodically moving external potential, within the simplest possible description of paradigmatic symmetric exclusion process on a ring. The model describes diffusion of hardcore particles where the diffusion dynamics is locally modified at a uniformly moving defect site, mimicking the effect of the periodically moving external potential. The model, though simple, exhibits remarkably rich features in particle transport, such as polarity reversal and double peaks in particle current upon variation of defect velocity and particle density. By tuning these variables, the most efficient transport can be achieved in either direction along the ring. These features can be understood in terms of a traveling density wave propagating in the system. Our results could be experimentally tested, e.g., in a system of colloidal particles driven by a moving optical tweezer.
Boulanger, Mathieu; Giraudet, Guillaume; Faubert, Jocelyn
2017-01-01
Humans routinely scan their environment for useful information using saccadic eye movements and/or coordinated movements of the eyes and other body segments such the head and the torso. Most previous eye movement studies were conducted with seated subject and showed that single saccades and sequences of saccades (e.g. double-step saccades) made to briefly flashed stimuli were equally accurate and precise. As one can easily appreciate, most gaze shifts performed daily by a given person are not produced from a seated position, but rather from a standing position either as subjects perform an action from an upright stance or as they walk from one place to another. In the experiments presented here, we developed a new dual-task paradigm in order to study the interaction between the gaze control system and the postural system. Healthy adults (n = 12) were required to both maintain balance and produce accurate single-step and double-step eye saccades from a standing position. Visually-induced changes in head sway were evoked using wide-field background stimuli that either moved in the mediolateral direction or in the anteroposterior direction. We found that, as in the seated condition, single- and double-step saccades were very precise and accurate when made from a standing position, but that a tighter control of head sway was necessary in the more complex double-step saccades condition for equivalent results to be obtained. Our perturbation results support the "common goal" hypothesis that state that if necessary, as was the case during the more complex oculomotor task, context-dependent modulations of the postural system can be triggered to reduced instability and therefore support the accomplishment of a suprapostural goal.
Giraudet, Guillaume; Faubert, Jocelyn
2017-01-01
Humans routinely scan their environment for useful information using saccadic eye movements and/or coordinated movements of the eyes and other body segments such the head and the torso. Most previous eye movement studies were conducted with seated subject and showed that single saccades and sequences of saccades (e.g. double-step saccades) made to briefly flashed stimuli were equally accurate and precise. As one can easily appreciate, most gaze shifts performed daily by a given person are not produced from a seated position, but rather from a standing position either as subjects perform an action from an upright stance or as they walk from one place to another. In the experiments presented here, we developed a new dual-task paradigm in order to study the interaction between the gaze control system and the postural system. Healthy adults (n = 12) were required to both maintain balance and produce accurate single-step and double-step eye saccades from a standing position. Visually-induced changes in head sway were evoked using wide-field background stimuli that either moved in the mediolateral direction or in the anteroposterior direction. We found that, as in the seated condition, single- and double-step saccades were very precise and accurate when made from a standing position, but that a tighter control of head sway was necessary in the more complex double-step saccades condition for equivalent results to be obtained. Our perturbation results support the “common goal” hypothesis that state that if necessary, as was the case during the more complex oculomotor task, context-dependent modulations of the postural system can be triggered to reduced instability and therefore support the accomplishment of a suprapostural goal. PMID:28296958
Potential disturbance interactions with a single IGV in an F109 turbofan engine
NASA Astrophysics Data System (ADS)
Kirk, Joel F.
A common cause of aircraft engine failure is the high cycle fatigue of engine blades and stators. One of the primary causes of these failures is due to blade row interactions, which cause an aerodynamic excitation to be resonant with a mechanical natural frequency. Traditionally, the primary source of such aerodynamic excitations has been practically limited to viscous wakes from upstream components. However, more advanced designs require that blade rows be very highly loaded and closely spaced. This results in aerodynamic excitation from potential fields of down stream engine components, in addition to the known wake excitations. An experimental investigation of the potential field from the fan of a Honeywell F109 turbofan engine has been completed. The investigation included velocity measurements upstream of the fan, addition of an airfoil shaped probe upstream of the fan on which surface pressure measurements were acquired, and measurement of the velocity in the interaction region between the probe and the fan. This investigation sought to characterize the response on the upstream probe due to the fan potential field and the interaction between a viscous wake and the potential field; as such, all test conditions were for subsonic fan speeds. The results from the collected data show that fan-induced potential disturbances propagate upstream at acoustic velocities, to produce vane surface-pressure amplitudes as high as 40 percent Joel F. Kirk of the inlet, mean total pressure. Further, these fan-induced pressure amplitudes display large variations between the two vane surfaces. An argument is made that the structure of the pressure response is consistent with the presence of two distinct sources of unsteady forcing disturbances. The disturbances on the incoming-rotation-facing surface of the IGV propagated upstream at a different speed than those on the outgoing-rotation-facing surface, indicating that one originated from a rotating source and the other from a
Kravchenko, Julia; Corsini, Emanuela; Williams, Marc A; Decker, William; Manjili, Masoud H; Otsuki, Takemi; Singh, Neetu; Al-Mulla, Faha; Al-Temaimi, Rabeah; Amedei, Amedeo; Colacci, Anna Maria; Vaccari, Monica; Mondello, Chiara; Scovassi, A Ivana; Raju, Jayadev; Hamid, Roslida A; Memeo, Lorenzo; Forte, Stefano; Roy, Rabindra; Woodrick, Jordan; Salem, Hosni K; Ryan, Elizabeth P; Brown, Dustin G; Bisson, William H; Lowe, Leroy; Lyerly, H Kim
2015-06-01
An increasing number of studies suggest an important role of host immunity as a barrier to tumor formation and progression. Complex mechanisms and multiple pathways are involved in evading innate and adaptive immune responses, with a broad spectrum of chemicals displaying the potential to adversely influence immunosurveillance. The evaluation of the cumulative effects of low-dose exposures from the occupational and natural environment, especially if multiple chemicals target the same gene(s) or pathway(s), is a challenge. We reviewed common environmental chemicals and discussed their potential effects on immunosurveillance. Our overarching objective was to review related signaling pathways influencing immune surveillance such as the pathways involving PI3K/Akt, chemokines, TGF-β, FAK, IGF-1, HIF-1α, IL-6, IL-1α, CTLA-4 and PD-1/PDL-1 could individually or collectively impact immunosurveillance. A number of chemicals that are common in the anthropogenic environment such as fungicides (maneb, fluoxastrobin and pyroclostrobin), herbicides (atrazine), insecticides (pyridaben and azamethiphos), the components of personal care products (triclosan and bisphenol A) and diethylhexylphthalate with pathways critical to tumor immunosurveillance. At this time, these chemicals are not recognized as human carcinogens; however, it is known that they these chemicalscan simultaneously persist in the environment and appear to have some potential interfere with the host immune response, therefore potentially contributing to promotion interacting with of immune evasion mechanisms, and promoting subsequent tumor growth and progression.
Kravchenko, Julia; Corsini, Emanuela; Williams, Marc A.; Decker, William; Manjili, Masoud H.; Otsuki, Takemi; Singh, Neetu; Al-Mulla, Faha; Al-Temaimi, Rabeah; Amedei, Amedeo; Colacci, Anna Maria; Vaccari, Monica; Mondello, Chiara; Scovassi, A. Ivana; Raju, Jayadev; Hamid, Roslida A.; Memeo, Lorenzo; Forte, Stefano; Roy, Rabindra; Woodrick, Jordan; Salem, Hosni K.; Ryan, Elizabeth P.; Brown, Dustin G.; Lowe, Leroy; Lyerly, H.Kim
2015-01-01
An increasing number of studies suggest an important role of host immunity as a barrier to tumor formation and progression. Complex mechanisms and multiple pathways are involved in evading innate and adaptive immune responses, with a broad spectrum of chemicals displaying the potential to adversely influence immunosurveillance. The evaluation of the cumulative effects of low-dose exposures from the occupational and natural environment, especially if multiple chemicals target the same gene(s) or pathway(s), is a challenge. We reviewed common environmental chemicals and discussed their potential effects on immunosurveillance. Our overarching objective was to review related signaling pathways influencing immune surveillance such as the pathways involving PI3K/Akt, chemokines, TGF-β, FAK, IGF-1, HIF-1α, IL-6, IL-1α, CTLA-4 and PD-1/PDL-1 could individually or collectively impact immunosurveillance. A number of chemicals that are common in the anthropogenic environment such as fungicides (maneb, fluoxastrobin and pyroclostrobin), herbicides (atrazine), insecticides (pyridaben and azamethiphos), the components of personal care products (triclosan and bisphenol A) and diethylhexylphthalate with pathways critical to tumor immunosurveillance. At this time, these chemicals are not recognized as human carcinogens; however, it is known that they these chemicalscan simultaneously persist in the environment and appear to have some potential interfere with the host immune response, therefore potentially contributing to promotion interacting with of immune evasion mechanisms, and promoting subsequent tumor growth and progression. PMID:26002081
NASA Astrophysics Data System (ADS)
Zarghami, Ahad; Looije, Niels; Van den Akker, Harry
2015-08-01
The pseudopotential lattice Boltzmann model (PP-LBM) is a very popular model for simulating multiphase systems. In this model, phase separation occurs via a short-range attraction between different phases when the interaction potential term is properly chosen. Therefore, the potential term is expected to play a significant role in the model and to affect the accuracy and the stability of the computations. The original PP-LBM suffers from some drawbacks such as being capable of dealing with low density ratios only, thermodynamic inconsistency, and spurious velocities. In this paper, we aim to analyze the PP-LBM with the view to simulate single-component (non-)isothermal multiphase systems at large density ratios and in spite of the presence of spurious velocities. For this purpose, the performance of two popular potential terms and of various implementation schemes for these potential terms is examined. Furthermore, the effects of different parameters (i.e., equation of state, viscosity, etc.) on the simulations are evaluated, and, finally, recommendations for a proper simulation of (non-)isothermal multiphase systems are presented.
Huang, Zhenxing; Huang, Ming; Mi, Chenyu; Wang, Tao; Chen, Dong; Teng, Yue
2016-01-01
2-mercaptothiazoline (2-MT) is widely used in many industrial fields, but its residue is potentially harmful to the environment. In this study, to evaluate the biological toxicity of 2-MT at protein level, the interaction between 2-MT and the pivotal antioxidant enzyme—catalase (CAT) was investigated using multiple spectroscopic techniques and molecular modeling. The results indicated that the CAT fluorescence quenching caused by 2-MT should be dominated by a static quenching mechanism through formation of a 2-MT/CAT complex. Furthermore, the identifications of the binding constant, binding forces, and the number of binding sites demonstrated that 2-MT could spontaneously interact with CAT at one binding site mainly via Van der Waals’ forces and hydrogen bonding. Based on the molecular docking simulation and conformation dynamic characterization, it was found that 2-MT could bind into the junctional region of CAT subdomains and that the binding site was close to enzyme active sites, which induced secondary structural and micro-environmental changes in CAT. The experiments on 2-MT toxicity verified that 2-MT significantly inhibited CAT activity via its molecular interaction, where 2-MT concentration and exposure time both affected the inhibitory action. Therefore, the present investigation provides useful information for understanding the toxicological mechanism of 2-MT at the molecular level. PMID:27537873
NASA Astrophysics Data System (ADS)
Li, Xiao; Farber, Steven
2016-10-01
The social interaction potential (SIP) metric measures urban structural constraints on social interaction opportunities of a metropolitan region based on the time geographic concept of joint accessibility. Previous implementations of the metric used an interaction surface based on census tracts and the locations of their centroids. This has been shown to be a shortcoming, as the metric strongly depends on the scale of the zoning system in the region, making it difficult to compare the SIP metric between metropolitan regions. This research explores the role of spatial representation in the SIP metric and identifies a suitable grid-based representation that allows for comparison between regions while retaining cost-effectiveness with respect to computational burden. We also report on findings from an extensive sensitivity analysis investigating the SIP metric's input parameters such as a travel flow congestion factor and the length of the allowable time budget for social activities. The results provide new insights on the role of the modifiable areal unit problem in the computation of time geographic measures of accessibility.
Hidden Sources of Grapefruit in Beverages: Potential Interactions with Immunosuppressant Medications
Auten, Ashley A.; Beauchamp, Lauren N.; Joshua Taylor
2013-01-01
Purpose: The interaction between grapefruit-containing beverages and immunosuppressants is not well defined in the literature. This study was conducted to investigate possible sources of grapefruit juice or grapefruit extract in common US-manufactured beverages. The goal was to identify those products that might serve as hidden sources of dietary grapefruit intake, increasing a transplant patient’s risk for drug interactions. Methods: A careful review of the ingredients of the 3 largest US beverage manufacturer’s product lines was conducted through manufacturer correspondence, product labeling examination, and online nutrition database research. Focus was placed on citrus-flavored soft drinks, teas, and juice products and their impact on a patient’s immunosuppressant regimens. Results: Twenty-three beverages were identified that contained grapefruit. Five did not contain the word “grapefruit” in the product name. In addition to the confirmed grapefruit-containing products, 17 products were identified as possibly containing grapefruit juice or grapefruit extract. Conclusion: A greater emphasis should be placed upon properly educating patients regarding hidden sources of grapefruit in popular US beverages and the potential for food-drug interactions. PMID:24421511
Parojcić, Jelena; Corrigan, Owen I
2008-06-01
Ibuprofen is a widely used NSAID which is often co-administered with antacids because of its gastro-irritant effects. Literature data suggest that antacid interactions may increase or decrease the drug's absorption rate and onset of action and that the interaction may be formulation specific. In the present study, literature data on ibuprofen absorption were evaluated in order to gain insight into the nature of the in vivo effect. Solubility determinations in reactive media containing magnesium or aluminium and dissolution studies in the presence of antacid suspension were performed in an attempt to simulate in vitro the effects observed in vivo. The results obtained indicate that magnesium hydroxide enhances ibuprofen solubility, dissolution and bioavailability, while aluminium hydroxide has a retarding effect. Solubility studies indicated formation of a soluble solid ibuprofen phase in the presence of Mg2+, in contrast, an insoluble ibuprofen salt was formed with Al3+. The introduction of magnesium based antacid suspension into the dissolution media resulted in a formulation specific increase in drug dissolution rate with the most pronounced effect observed for the slowest release tablet formulation. The results obtained indicate the potential for in vitro studies to predict physicochemical interactions that are likely to influence drug absorption rate in vivo.
Organic cation transporter-mediated drug-drug interaction potential between berberine and metformin.
Kwon, Mihwa; Choi, Young A; Choi, Min-Koo; Song, Im-Sook
2015-01-01
Berberine, the main active component of the herbal medicine Rhizoma Coptidis, has been reported to have hypoglycemic and insulin-sensitizing effects and, therefore, could be combined with metformin therapy. Thus, we assessed the potential drug-drug interactions between berberine and metformin. We investigated the in vitro inhibitory potency of berberine on metformin uptake in HEK293 cells overexpressing organic cation transporter (OCT) 1 and 2. To investigate whether this inhibitory effect of berberine on OCT1 and OCT2 could change the pharmacokinetics of metformin in vivo, we measured the effect of berberine co-administration on the pharmacokinetics of metformin at a single intravenous dose of 2 mg/kg metformin and 10 mg/kg berberine. In HEK293 cells, berberine inhibited OCT1- and OCT2-mediated metformin uptake in a concentration dependent manner and IC50 values for OCT1 and OCT2 were 7.28 and 11.3 μM, respectively. Co-administration of berberine increased the initial plasma concentration and AUC of metformin and decreased systemic clearance and volume of distribution of metformin in rats, suggesting that berberine inhibited disposition of metformin, which is governed by OCT1 and OCT2. Berberine inhibited the transport activity of OCT1 and OCT2 and showed significant potential drug-drug interactions with metformin in in vivo rats.
A heuristic model for potential geomorphic influences on trophic interactions in streams
NASA Astrophysics Data System (ADS)
Doyle, Martin W.
2006-07-01
Whereas certain linkages between stream channel morphology and stream ecology are fairly well-understood, how geomorphology influences trophic interactions remains largely unknown. As a first step, a simple, heuristic model is developed that couples reach-scale geomorphic morphology with trophic dynamics between vegetation, detritus, herbivores, and predators. Predation is assumed to increase with depth beyond a threshold depth, and herbivory is assumed to decrease with velocity beyond a threshold velocity. Results show that the modeled food chain is sensitive to channel geometry, particularly around the threshold conditions for predators and herbivores. Importantly, geomorphic influences are not isolated to a particular trophic level, but rather are transferred through the food chain via top-down and bottom-up effects. The modeled system is particularly sensitive to changes in the end-members of the food chain: vegetation and predators. Results illustrate that geomorphic disturbances, known to affect a single trophic level (e.g., fish), likely impact multiple trophic levels in the stream ecosystem via trophic interactions. Such impacts at the multiple trophic level are poorly understood. While limited by the lack of empirical long-term data for testing and calibration, this simple model provides a structure for generating hypotheses, collecting targeted data, and assessing the potential impacts of stream disturbance or restoration on entire stream ecosystems. Further, the model illustrates the potential for future coupled stream models to explore spatial and temporal linkages.
NASA Astrophysics Data System (ADS)
Karthick, T.; Balachandran, V.; Perumal, S.
2015-04-01
Thiophene derivatives have been focused in the past decades due to their remarkable biological and pharmacological activities. In connection with that the conformational stability, spectroscopic characterization, molecular (inter- and intra-) interactions, and molecular docking studies on thiophene-2-carboxylicacid have been performed in this work by experimental FT-IR and theoretical quantum chemical computations. Experimentally recorded FT-IR spectrum in the region 4000-400 cm-1 has been compared with the scaled theoretical spectrum and the spectral peaks have been assigned on the basis of potential energy distribution results obtained from MOLVIB program package. The conformational stability of monomer and dimer conformers has been examined. The presence of inter- and intramolecular interactions in the monomer and dimer conformers have been explained by natural bond orbital analysis. The UV-Vis spectra of the sample in different solvents have been simulated and solvent effects were predicted by polarisable continuum model with TD-DFT/B3LYP/6-31+G(d,p) method. To test the biological activity of the sample, molecular docking (ligand-protein) simulations have been performed using SWISSDOCK web server. The full fitness (FF) score and binding affinity values revealed that thiophene-2-carboxylicacid can act as potential inhibitor against inflammation.
Pressure Effects on the Intermolecular Interaction Potential of Condensed Protein Solutions.
Winter, Roland
2015-01-01
Knowledge of the intermolecular interaction potential of proteins as a function of their solution conditions is essential for understanding protein aggregation, crystallization, and the phase behavior of proteins in general. Here, we report on a combined small-angle X-ray scattering and liquid-state theoretical approach to study dense lysozyme solutions as a function of temperature and pressure, but also in the presence of salts and osmolytes of different nature. We show that the pressure-dependent interaction potential of lysozyme changes in a nonlinear fashion over a wide range of temperatures, salt and protein concentrations, indicating that changes of the bulk water structure mediate the pressure dependence of the intermolecular forces. We present also results on the effect of high hydrostatic pressure on the phase behavior of dense lysozyme solutions in the liquid-liquid phase-coexistence region. As also shown in this study, the application of pressure can be used to fine-tune the second virial coefficient of protein solutions, which can be used to control nucleation rates and hence protein crystallization, or to prevent protein aggregation. Moreover, these results are also important for understanding the hydration behavior of biological matter under extreme environmental conditions, and the high stability of dense protein solutions (as they occur intracellularly) in organisms thriving under hydrostatic pressure conditions such as in the deep sea, where pressures up to the 100 MPa-level are reached.
NASA Astrophysics Data System (ADS)
Baba, Toshitaka; Allgeyer, Sebastien; Hossen, Jakir; Cummins, Phil R.; Tsushima, Hiroaki; Imai, Kentaro; Yamashita, Kei; Kato, Toshihiro
2017-03-01
In this study, we considered the accurate calculation of far-field tsunami waveforms by using the shallow water equations and accounting for the effects of Boussinesq dispersion, seawater density stratification, elastic loading, and gravitational potential change in a finite difference scheme. By comparing numerical simulations that included and excluded each of these effects with the observed waveforms of the 2011 Tohoku tsunami, we found that all of these effects are significant and resolvable in the far field by the current generation of deep ocean-bottom pressure gauges. Our calculations using previously published, high-resolution models of the 2011 Tohoku tsunami source exhibited excellent agreement with the observed waveforms to a degree that has previously been possible only with near-field or regional observations. We suggest that the ability to model far-field tsunamis with high accuracy has important implications for tsunami source and hazard studies.
The Potential for Signal Integration and Processing in Interacting Map Kinase Cascades
Schwacke, John H.; Voit, Eberhard O.
2009-01-01
The cellular response to environmental stimuli requires biochemical information processing through which sensory inputs and cellular status are integrated and translated into appropriate responses by way of interacting networks of enzymes. One such network, the Mitogen Activated Protein (MAP) kinase cascade is a highly conserved signal transduction module that propagates signals from cell surface receptors to various cytosolic and nuclear targets by way of a phosphorylation cascade. We have investigated the potential for signal processing within a network of interacting feed-forward kinase cascades typified by the MAP kinase cascade. A genetic algorithm was used to search for sets of kinetic parameters demonstrating representative key input-output patterns of interest. We discuss two of the networks identified in our study, one implementing the exclusive-or function (XOR) and another implementing what we refer to as an in-band detector (IBD) or two-sided threshold. These examples confirm the potential for logic and amplitude-dependent signal processing in interacting MAP kinase cascades demonstrating limited cross-talk. Specifically, the XOR function allows the network to respond to either one, but not both signals simultaneously, while the IBD permits the network to respond exclusively to signals within a given range of strength, and to suppress signals below as well as above this range. The solution to the XOR problem is interesting in that it requires only two interacting pathways, crosstalk at only one layer, and no feedback or explicit inhibition. These types of responses are not only biologically relevant but constitute signal processing modules that can be combined to create other logical functions and that, in contrast to amplification, cannot be achieved with a single cascade or with two non-interacting cascades. Our computational results revealed surprising similarities between experimental data describing the JNK/MKK4/MKK7 pathway and the solution for
Li, Y. Q.; Ma, F. C.; Sun, M. T.
2013-10-21
A full three-dimensional global potential energy surface is reported first time for the title system, which is important for the photodissociation processes. It is obtained using double many-body expansion theory and an extensive set of accurate ab initio energies extrapolated to the complete basis set limit. Such a work can be recommended for dynamics studies of the N({sup 2}D) + H{sub 2} reaction, a reliable theoretical treatment of the photodissociation dynamics and as building blocks for constructing the double many-body expansion potential energy surface of larger nitrogen/hydrogen containing systems. In turn, a preliminary theoretical study of the reaction N({sup 2}D)+H{sub 2}(X{sup 1}Σ{sub g}{sup +})(ν=0,j=0)→NH(a{sup 1}Δ)+H({sup 2}S) has been carried out with the method of quasi-classical trajectory on the new potential energy surface. Integral cross sections and thermal rate constants have been calculated, providing perhaps the most reliable estimate of the integral cross sections and the rate constants known thus far for such a reaction.
Pan, Weiran; Li, Gang; Yang, Xiaoxiao; Miao, Jinming
2015-04-01
This study aims to explore the potential mechanism of glioma through bioinformatic approaches. The gene expression profile (GSE4290) of glioma tumor and non-tumor samples was downloaded from Gene Expression Omnibus database. A total of 180 samples were available, including 23 non-tumor and 157 tumor samples. Then the raw data were preprocessed using robust multiarray analysis, and 8,890 differentially expressed genes (DEGs) were identified by using t-test (false discovery rate < 0.0005). Furthermore, 16 known glioma related genes were abstracted from Genetic Association Database. After mapping 8,890 DEGs and 16 known glioma related genes to Human Protein Reference Database, a glioma associated protein-protein interaction network (GAPN) was constructed. In addition, 51 sub-networks in GAPN were screened out through Molecular Complex Detection (score ≥ 1), and sub-network 1 was found to have the closest interaction (score = 3). What' more, for the top 10 sub-networks, Gene Ontology (GO) enrichment analysis (p value < 0.05) was performed, and DEGs involved in sub-network 1 and 2, such as BRMS1L and CCNA1, were predicted to regulate cell growth, cell cycle, and DNA replication via interacting with known glioma related genes. Finally, the overlaps of DEGs and human essential, housekeeping, tissue-specific genes were calculated (p value = 1.0, 1.0, and 0.00014, respectively) and visualized by Venn Diagram package in R. About 61% of human tissue-specific genes were DEGs as well. This research shed new light on the pathogenesis of glioma based on DEGs and GAPN, and our findings might provide potential targets for clinical glioma treatment.
Spin-orbit configuration interaction calculation of the potential energy curves of iodine oxide
Roszak, S.; Krauss, M.; Alekseyev, A.B.; Liebermann, H.P.; Buenker, R.J.
2000-04-06
An ab initio configuration interaction (CI) study including spin-orbit coupling is carried out for the ground and excited states of the IO radical by employing relativistic effective core potentials. The computed spectroscopic constants are in good agreement with available experimental data, with some tendency to underestimate the strength of bonding. The first excited state, a{sup 4}{Sigma}{sup {minus}}, which has not yet been observed experimentally, is predicted to be bound by 30.1 kJ/mol and to have a significantly larger equilibrium distance than the ground state. It is split by spin-orbit interaction into 1/2 and 3/2 components, with the 1/2 component being the lower one with a calculated spin-orbit splitting of 210 cm{sup {minus}1}. The most interesting state in the low-energy IO spectrum, A{sub 1}{sup 2}{Pi}{sub 3/2}, is shown to be predissociated due to interaction with a number of repulsive electronic states. Predissociation of the A{sup 1}, {nu}{prime} = 0, 1 vibrational levels is attributed to a fairly weak spin-orbit coupling with the {sup 2}{Delta}{sub 3/2} state, while rotationally dependent predissociation of the {nu}{prime} = 2 level is explained by the coupling with the 1/2(III) state having mainly {sup 2}{Sigma}{sup {minus}} character. Strong predissociation of the {nu}{prime} {ge} 4 levels is attributed to interaction with the higher-lying {Omega} = 3/2 states, with predominantly {sup 4}{Sigma}{sup +} and {sup 4}{Delta} origin.
Murdoch, D L; Thomson, G D; Thompson, G G; Murray, G D; Brodie, M J; McInnes, G T
1991-01-01
1. Potential pharmacodynamic and pharmacokinetic interactions between verapamil and propranolol were evaluated in two double-blind, randomised, balanced, crossover studies employing the same six healthy males. 2. The first study examined the effect of repeated propranolol administration on the pharmacodynamics and pharmacokinetics of verapamil after single oral and intravenous doses. The second explored the pharmacodynamics and pharmacokinetics of verapamil and propranolol alone and in combination after single and repeated oral doses. 3. The magnitude of the prolongation of PR interval induced by oral and intravenous verapamil was not affected by pre-treatment with propranolol. When verapamil and propranolol were co-administered as single doses, effects on PR interval were additive but, following repeated doses, a trend towards greater than additive prolongation was seen. The arithmetic sum of the effects of the two drugs was 23% (95% C.I. 8-38%) but the measured increase after the combination was 40% (95% C.I. 26-54%). 4. The extent of reduction in heart rate and blood pressure at rest and after exercise following repeated doses of propranolol was not influenced by single oral or intravenous doses of verapamil. The heart rate and blood pressure responses to single and repeated oral doses of verapamil and propranolol in combination were significantly greater than those after either drug alone and approximated to the arithmetic sum of the individual responses. 5. Although repeated administration of propranolol reduced hepatic blood flow as assessed by indocyanine green clearance, there was no evidence of an interaction between the drugs at this level. 6. The pharmacokinetics of verapamil and norverapamil were not significantly affected by prior propranolol. After single doses of verapamil and propranolol in combination, the maximum plasma concentration of propranolol was increased and the oral clearance of verapamil reduced. No pharmacokinetic interaction was
Monte Carlo simulations of fluids whose particles interact with a logarithmic potential.
Heyes, D M; Rickayzen, G; Powles, J G
2008-04-07
Monte Carlo simulations of a model fluid in which the particles interact via a continuous potential that has a logarithmic divergence at a pair separation of sigma, which we introduced in J. G. Powles et al., Proc. R. Soc. London, Ser. A 455, 3725 (1999), have been carried out. The potential has the form, phi(r)= -epsilon ln(fr), where epsilon sets the energy scale and fr=1-(sigma/r)m. The value of m chosen was 12 but the qualitative trends depend only weakly on the value of m, providing it is greater than 3. The potential is entirely repulsive and has a logarithmic divergence as approximately -ln(r/sigma-1) in the r-->sigma limit. Predictions of the previous paper that the internal energy can be computed at all temperatures using the standard statistical mechanics formula for continuous potentials are verified here. The pressure can be calculated using the usual virial expression for continuous potentials, although there are practical limitations in resolving the increasingly important contribution from the r-->sigma limit at reduced temperatures greater than approximately 5. The mean square force F2 and infinite frequency shear Ginfinity and bulk Kinfinity moduli are only finite for T*=kBT/epsilon<1. The logarithmic fluid's physical properties become increasingly more like that of the hard sphere fluid with increasing temperature, showing a sharp transition in the behavior of the mean square force and infinite frequency elastic constants at T*=1. The logarithmic fluid is shown to exhibit a solid-fluid phase transition.
Monte Carlo simulations of fluids whose particles interact with a logarithmic potential
NASA Astrophysics Data System (ADS)
Heyes, D. M.; Rickayzen, G.; Powles, J. G.
2008-04-01
Monte Carlo simulations of a model fluid in which the particles interact via a continuous potential that has a logarithmic divergence at a pair separation of σ, which we introduced in J. G. Powles et al., Proc. R. Soc. London, Ser. A 455, 3725 (1999), have been carried out. The potential has the form, ϕ(r )=-ɛln(f(r)), where ɛ sets the energy scale and f(r )=1-(σ/r)m. The value of m chosen was 12 but the qualitative trends depend only weakly on the value of m, providing it is greater than 3. The potential is entirely repulsive and has a logarithmic divergence as ˜-ln(r/σ-1) in the r →σ limit. Predictions of the previous paper that the internal energy can be computed at all temperatures using the standard statistical mechanics formula for continuous potentials are verified here. The pressure can be calculated using the usual virial expression for continuous potentials, although there are practical limitations in resolving the increasingly important contribution from the r →σ limit at reduced temperatures greater than ˜5. The mean square force ⟨F2⟩ and infinite frequency shear G∞ and bulk K∞ moduli are only finite for T*=kBT/ɛ<1. The logarithmic fluid's physical properties become increasingly more like that of the hard sphere fluid with increasing temperature, showing a sharp transition in the behavior of the mean square force and infinite frequency elastic constants at T*=1. The logarithmic fluid is shown to exhibit a solid-fluid phase transition.
Moss, Andrew
2013-12-01
Angiopoietin-1 and -2 are endogenous ligands for the vascular endothelial receptor tyrosine kinase Tie2. Signalling by angiopoietin-1 promotes vascular endothelial cell survival and the sprouting and reorganisation of blood vessels, as well as inhibiting activation of the vascular endothelial barrier to reduce leakage and leucocyte migration into tissues. Angiopoietin-2 generally has an opposing action, and is released naturally at times of vascular growth and inflammation. There is a significant body of emerging evidence that promoting the actions of angiopoietin-1 through Tie2 is of benefit in pathologies of vascular activation, such as sepsis, stroke, diabetic retinopathy and asthma. Similarly, methods to inhibit the actions of angiopoietin-2 are emerging and have been demonstrated to be of preclinical and clinical benefit in reducing tumour angiogenesis. Here the author reviews the evidence for potential benefits of modulation of the interaction of angiopoietins with Tie2, and the potential applications. Additionally, methods for delivery of the complex protein angiopoietin-1 are discussed, as well as potentially deleterious consequences of administering angiopoietin-1.
Kiyatkin, Eugene A; Ren, Suelynn; Wakabayashi, Ken T; Baumann, Michael H; Shaham, Yavin
2016-01-01
MDMA-induced hyperthermia is highly variable, unpredictable, and greatly potentiated by the social and environmental conditions of recreational drug use. Current strategies to treat pathological MDMA-induced hyperthermia in humans are palliative and marginally effective, and there are no specific pharmacological treatments to counteract this potentially life-threatening condition. Here, we tested the efficacy of mixed adrenoceptor blockers carvedilol and labetalol, and the atypical antipsychotic clozapine, in reversing MDMA-induced brain and body hyperthermia. We injected rats with a moderate non-toxic dose of MDMA (9 mg/kg) during social interaction, and we administered potential treatment drugs after the development of robust hyperthermia (>2.5 °C), thus mimicking the clinical situation of acute MDMA intoxication. Brain temperature was our primary focus, but we also simultaneously recorded temperatures from the deep temporal muscle and skin, allowing us to determine the basic physiological mechanisms of the treatment drug action. Carvedilol was modestly effective in attenuating MDMA-induced hyperthermia by moderately inhibiting skin vasoconstriction, and labetalol was ineffective. In contrast, clozapine induced a marked and immediate reversal of MDMA-induced hyperthermia via inhibition of brain metabolic activation and blockade of skin vasoconstriction. Our findings suggest that clozapine, and related centrally acting drugs, might be highly effective for reversing MDMA-induced brain and body hyperthermia in emergency clinical situations, with possible life-saving results.
Kiyatkin, Eugene A; Ren, Suelynn; Wakabayashi, Ken T; Baumann, Michael H; Shaham, Yavin
2016-01-01
MDMA-induced hyperthermia is highly variable, unpredictable, and greatly potentiated by the social and environmental conditions of recreational drug use. Current strategies to treat pathological MDMA-induced hyperthermia in humans are palliative and marginally effective, and there are no specific pharmacological treatments to counteract this potentially life-threatening condition. Here, we tested the efficacy of mixed adrenoceptor blockers carvedilol and labetalol, and the atypical antipsychotic clozapine, in reversing MDMA-induced brain and body hyperthermia. We injected rats with a moderate non-toxic dose of MDMA (9 mg/kg) during social interaction, and we administered potential treatment drugs after the development of robust hyperthermia (>2.5 °C), thus mimicking the clinical situation of acute MDMA intoxication. Brain temperature was our primary focus, but we also simultaneously recorded temperatures from the deep temporal muscle and skin, allowing us to determine the basic physiological mechanisms of the treatment drug action. Carvedilol was modestly effective in attenuating MDMA-induced hyperthermia by moderately inhibiting skin vasoconstriction, and labetalol was ineffective. In contrast, clozapine induced a marked and immediate reversal of MDMA-induced hyperthermia via inhibition of brain metabolic activation and blockade of skin vasoconstriction. Our findings suggest that clozapine, and related centrally acting drugs, might be highly effective for reversing MDMA-induced brain and body hyperthermia in emergency clinical situations, with possible life-saving results. PMID:26105141
Accurate Finite Difference Algorithms
NASA Technical Reports Server (NTRS)
Goodrich, John W.
1996-01-01
Two families of finite difference algorithms for computational aeroacoustics are presented and compared. All of the algorithms are single step explicit methods, they have the same order of accuracy in both space and time, with examples up to eleventh order, and they have multidimensional extensions. One of the algorithm families has spectral like high resolution. Propagation with high order and high resolution algorithms can produce accurate results after O(10(exp 6)) periods of propagation with eight grid points per wavelength.
Accurate monotone cubic interpolation
NASA Technical Reports Server (NTRS)
Huynh, Hung T.
1991-01-01
Monotone piecewise cubic interpolants are simple and effective. They are generally third-order accurate, except near strict local extrema where accuracy degenerates to second-order due to the monotonicity constraint. Algorithms for piecewise cubic interpolants, which preserve monotonicity as well as uniform third and fourth-order accuracy are presented. The gain of accuracy is obtained by relaxing the monotonicity constraint in a geometric framework in which the median function plays a crucial role.
NASA Astrophysics Data System (ADS)
Zhalnina, K.; Cho, H. J.; Hao, Z.; Mansoori, N.; Karaoz, U.; Jenkins, S.; White, R. A., III; Lipton, M. S.; Deng, K.; Zhou, J.; Pett-Ridge, J.; Northen, T.; Firestone, M. K.; Brodie, E.
2015-12-01
In the rhizosphere, metabolic processes of plants and microorganisms are closely coupled, and together with soil minerals, their interactions regulate the turnover of soil organic C (SOC). Plants provide readily assimilable metabolites for microorganisms through exudation, and it has been hypothesized that increasing concentrations of exudate C may either stimulate or suppress rates of SOC mineralization (rhizosphere priming). Both positive and negative rhizosphere priming has been widely observed, however the underlying mechanisms remain poorly understood. To begin to identify the molecular mechanisms underlying rhizosphere priming, we isolated a broad range of soil bacteria from a Mediterranean grassland dominated by annual grass. Thirty-nine heterotrophic bacteria were selected for genome sequencing and both rRNA gene analysis and metagenome coverage suggest that these isolates represent naturally abundant strain variants. We analyzed their genomes for potential metabolic traits related to life in the rhizosphere and the decomposition of polymeric SOC. While the two dominant groups, Alphaproteobacteria and Actinobacteria, were enriched in polymer degrading enzymes, Alphaproteobacterial isolates contained greater gene copies of transporters related to amino acid, organic acid and auxin uptake or export, suggesting an enhanced metabolic potential for life in the root zone. To verify this metabolic potential, we determined the enzymatic activities of these isolates and revealed preferences of strains to degrade certain polymers (xylan, cellulose or lignin). Fourier Transform Infrared spectroscopy is being used to determine which polymeric components of plant roots are targeted by specific strains and how exudates may impact their degradation. To verify the potential of isolates to assimilate root exudates and export key metabolites we are using LC-MS/MS based exometabolomic profiling. The traits hypothesized and verified here (transporters, enzymes, exudate uptake
Potential of mean force for human lysozyme camelid vhh hl6 antibody interaction studies
NASA Astrophysics Data System (ADS)
Wang, Yeng-Tseng; Liao, Jun-Min; Chen, Cheng-Lung; Su, Zhi-Yuan; Chen, Chang-Hung; Hu, Jeu-Jiun
2008-04-01
Calculating antigen-antibody interaction energies is crucial for understanding antigen-antibody associations in immunology. To shed further light into this equation, we study a separation of human lysozyme-camelid vhh hl6 antibody (cAb-HuL6) complex. The c-terminal end-to-end stretching of the lysozyme-antibody complex structures have been studied using potential of mean force (PMF) calculations based on molecular dynamics (MD) and explicit water model. For the lysozyme-antibody complex, there are six important intermediates in the c-terminal extensions process. Inclusion of our simulations may help to understand the binding mechanics of lysozyme-cAb-HuL6 antibody complex.
Teng, Yue; Zou, Luyi; Huang, Ming; Zong, Wansong
2014-12-01
2-Mercaptobenzimidazole (MBI) is widely utilized as a corrosion inhibitor, copper-plating brightener and rubber accelerator. The residue of MBI in the environment possesses a potential risk to human health. In this work, the toxic interaction of MBI with the important antioxidant enzyme catalase (CAT) was investigated using spectroscopic and molecular docking methods under physiological conditions. MBI can spontaneously bind with CAT with one binding site through hydrogen bonds and van der Waals forces to form MBI-CAT complex. The molecular docking study revealed that MBI bound into the CAT interface of chains B and C, which led to some conformational and microenvironmental changes of CAT and further resulted in the inhibition of CAT activity. This present study provides direct evidence at a molecular level to show that exposure to MBI could induce changes in the structure and function of the enzyme CAT.
Helical configurations of elastic rods in the presence of a long-range interaction potential
NASA Astrophysics Data System (ADS)
De Lillo, S.; Lupo, G.; Sommacal, M.
2010-02-01
Recently, the integrability of the stationary Kirchhoff equations describing an elastic rod folded in the shape of a circular helix was proven. In this paper we explicitly work out the solutions to the stationary Kirchhoff equations in the presence of a long-range potential which describes the average constant force due to a Morse-type interaction acting among the points of the rod. The average constant force results to be parallel to the normal vector to the central line of the folded rod; this condition remarkably permits to preserve the integrability (indeed the solvability) of the corresponding Kirchhoff equations if the elastic rod features constant or periodic stiffnesses and vanishing intrinsic twist. Furthermore, we discuss the elastic energy density with respect to the radius and pitch of the helix, showing the existence of stationary points, namely stable and unstable configurations, for plausible choices of the featured parameters corresponding to a real bio-polymer.
The solar wind interaction with Mars as seen by the Viking retarding potential analyzers
NASA Astrophysics Data System (ADS)
Cragin, B. L.; Hanson, W. B.; Sanatani, S.
1982-06-01
Both energy spectra and continuous monitoring periods of the total flux above 15 eV are available, from Viking retarding potential analyzer measurements of electron fluxes not exceeding 75 eV out to 16,000 km above the Mars surface. Although the mean electron current at energies above 15 eV increases monotonically by almost two orders of magnitude from 9000 to 700 km in Viking 1 data, no clear signature of the bow shock is seen. Total current wave power shows a peak near 1700 km altitude. It is suggested that there may be a highly turbulent shock structure masking a clear signature of the bow shock in the time-averaged data, and it is concluded that the interaction model consistent with the bow shock at 1700 km, together with ionosphere measurements, indicates a permanent magnetic field able to stand off the solar wind during the Viking 1 entry.
Olive, Michael Foster
2014-01-01
Throughout the 20th century a body of literature concerning the long lasting effects of early environment was produced. Adverse experiences in early life, or early life stress (ELS), is associated with a higher risk for developing various psychiatric illnesses. The mechanisms driving the complex interplay between ELS and adult phenotype has baffled many investigators for decades. Over the last decade, the new field of neuroepigenetics has emerged as one possible mechanism by which ELS can have far reaching effects on adult phenotype, behavior, and risk for psychiatric illness. Here we review two commonly investigated epigenetic mechanisms, histone modifications and DNA methylation, and the emerging field of neuroepigenetics as they relate to ELS. We discuss the current animal literature demonstrating ELS induced epigenetic modulation of gene expression that results in altered adult phenotypes. We also briefly discuss other areas in which neuroepigenetics has emerged as a potential mechanism underlying environmental and genetic interactions. PMID:25003947
Baskerville, Tracey A; Douglas, Alison J
2010-06-01
Dopamine is an important neuromodulator that exerts widespread effects on the central nervous system (CNS) function. Disruption in dopaminergic neurotransmission can have profound effects on mood and behavior and as such is known to be implicated in various neuropsychiatric behavioral disorders including autism and depression. The subsequent effects on other neurocircuitries due to dysregulated dopamine function have yet to be fully explored. Due to the marked social deficits observed in psychiatric patients, the neuropeptide, oxytocin is emerging as one particular neural substrate that may be influenced by the altered dopamine levels subserving neuropathologic-related behavioral diseases. Oxytocin has a substantial role in social attachment, affiliation and sexual behavior. More recently, it has emerged that disturbances in peripheral and central oxytocin levels have been detected in some patients with dopamine-dependent disorders. Thus, oxytocin is proposed to be a key neural substrate that interacts with central dopamine systems. In addition to psychosocial improvement, oxytocin has recently been implicated in mediating mesolimbic dopamine pathways during drug addiction and withdrawal. This bi-directional role of dopamine has also been implicated during some components of sexual behavior. This review will discuss evidence for the existence dopamine/oxytocin positive interaction in social behavioral paradigms and associated disorders such as sexual dysfunction, autism, addiction, anorexia/bulimia, and depression. Preliminary findings suggest that whilst further rigorous testing has to be conducted to establish a dopamine/oxytocin link in human disorders, animal models seem to indicate the existence of broad and integrated brain circuits where dopamine and oxytocin interactions at least in part mediate socio-affiliative behaviors. A profound disruption to these pathways is likely to underpin associated behavioral disorders. Central oxytocin pathways may serve as a
The emotion potential of simple sentences: additive or interactive effects of nouns and adjectives?
Lüdtke, Jana; Jacobs, Arthur M.
2015-01-01
The vast majority of studies on affective processes in reading focus on single words. The most robust finding is a processing advantage for positively valenced words, which has been replicated in the rare studies investigating effects of affective features of words during sentence or story comprehension. Here we were interested in how the different valences of words in a sentence influence its processing and supralexical affective evaluation. Using a sentence verification task we investigated how comprehension of simple declarative sentences containing a noun and an adjective depends on the valences of both words. The results are in line with the assumed general processing advantage for positive words. We also observed a clear interaction effect, as can be expected from the affective priming literature: sentences with emotionally congruent words (e.g., The grandpa is clever) were verified faster than sentences containing emotionally incongruent words (e.g., The grandpa is lonely). The priming effect was most prominent for sentences with positive words suggesting that both, early processing as well as later meaning integration and situation model construction, is modulated by affective processing. In a second rating task we investigated how the emotion potential of supralexical units depends on word valence. The simplest hypothesis predicts that the supralexical affective structure is a linear combination of the valences of the nouns and adjectives (Bestgen, 1994). Overall, our results do not support this: The observed clear interaction effect on ratings indicate that especially negative adjectives dominated supralexical evaluation, i.e., a sort of negativity bias in sentence evaluation. Future models of sentence processing thus should take interactive affective effects into account. PMID:26321975
Theile, Dirk; Hohmann, Nicolas; Kiemel, Dominik; Gattuso, Giuseppe; Barreca, Davide; Mikus, Gerd; Haefeli, Walter Emil; Schwenger, Vedat; Weiss, Johanna
2017-01-15
Adverse drug interactions due to grapefruit juice are well known prompting warnings even in drug labels. Similar issues have not been reported for clementines and available data is scarce, despite of genetic descent. We observed substantially increased tacrolimus trough concentrations in a renal transplant patient consuming high clementine amounts and, thus, scrutinised the effects of clementine juice on drug metabolism and drug transporters in vitro and compared it to the effects of mandarin and grapefruit juice. All citrus juices profoundly induced several drug transporters and drug metabolising enzymes, whereas the effects of grapefruit juice were most pronounced (e.g. 156-fold and 34-fold induction of cytochrome P450 (CYP) 3A4 mRNA by grapefruit juice and clementine juice, respectively). However, the juices also inhibited e.g. CYP3A4, raising the question which effect prevails in vivo. Using an enzymatic activity assay, we demonstrated that at least in vitro CYP3A4 inhibition prevails for both grapefruit and clementine juice, whereas for CYP1A2 induction appears to predominate. Thus, inhibition of CYP3A4 is presumably the underlying reason for the observed increase in the concentrations of the CYP3A4 substrate tacrolimus in the patient. Taken together, our data indicate that clementine juice as well as grapefruit juice and to a lesser extent also mandarin juice can induce several important drug metabolising enzymes and drug transporters, but also inhibit some of these proteins. Our data indicate that clementine juice similar to grapefruit juice bears the potential for profound interactions with drugs potentially leading to adverse drug effects e.g. through over-exposure to CYP3A4 substrates.
Final Report - Assessment of Potential Phosphate Ion-Cementitious Materials Interactions
Naus, Dan J; Mattus, Catherine H; Dole, Leslie Robert
2007-06-01
The objectives of this limited study were to: (1) review the potential for degradation of cementitious materials due to exposure to high concentrations of phosphate ions; (2) provide an improved understanding of any significant factors that may lead to a requirement to establish exposure limits for concrete structures exposed to soils or ground waters containing high levels of phosphate ions; (3) recommend, as appropriate, whether a limitation on phosphate ion concentration in soils or ground water is required to avoid degradation of concrete structures; and (4) provide a "primer" on factors that can affect the durability of concrete materials and structures in nuclear power plants. An assessment of the potential effects of phosphate ions on cementitious materials was made through a review of the literature, contacts with concrete research personnel, and conduct of a "bench-scale" laboratory investigation. Results of these activities indicate that: no harmful interactions occur between phosphates and cementitious materials unless phosphates are present in the form of phosphoric acid; phosphates have been incorporated into concrete as set retarders, and phosphate cements have been used for infrastructure repair; no standards or guidelines exist pertaining to applications of reinforced concrete structures in high-phosphate environments; interactions of phosphate ions and cementitious materials has not been a concern of the research community; and laboratory results indicate similar performance of specimens cured in phosphate solutions and those cured in a calcium hydroxide solution after exposure periods of up to eighteen months. Relative to the "primer," a separate NUREG report has been prepared that provides a review of pertinent factors that can affect the durability of nuclear power plant reinforced concrete structures.
Chow, Cheryl-Emiliane T.; Winget, Danielle M.; White, Richard A.; Hallam, Steven J.; Suttle, Curtis A.
2015-01-01
Viral diversity and virus-host interactions in oxygen-starved regions of the ocean, also known as oxygen minimum zones (OMZs), remain relatively unexplored. Microbial community metabolism in OMZs alters nutrient and energy flow through marine food webs, resulting in biological nitrogen loss and greenhouse gas production. Thus, viruses infecting OMZ microbes have the potential to modulate community metabolism with resulting feedback on ecosystem function. Here, we describe viral communities inhabiting oxic surface (10 m) and oxygen-starved basin (200 m) waters of Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island, British Columbia using viral metagenomics and complete viral fosmid sequencing on samples collected between April 2007 and April 2010. Of 6459 open reading frames (ORFs) predicted across all 34 viral fosmids, 77.6% (n = 5010) had no homology to reference viral genomes. These fosmids recruited a higher proportion of viral metagenomic sequences from Saanich Inlet than from nearby northeastern subarctic Pacific Ocean (Line P) waters, indicating differences in the viral communities between coastal and open ocean locations. While functional annotations of fosmid ORFs were limited, recruitment to NCBI's non-redundant “nr” database and publicly available single-cell genomes identified putative viruses infecting marine thaumarchaeal and SUP05 proteobacteria to provide potential host linkages with relevance to coupled biogeochemical cycling processes in OMZ waters. Taken together, these results highlight the power of coupled analyses of multiple sequence data types, such as viral metagenomic and fosmid sequence data with prokaryotic single cell genomes, to chart viral diversity, elucidate genomic and ecological contexts for previously unclassifiable viral sequences, and identify novel host interactions in natural and engineered ecosystems. PMID:25914678
Therapeutic potential of mitotic interaction between the nucleoporin Tpr and aurora kinase A.
Kobayashi, Akiko; Hashizume, Chieko; Dowaki, Takayuki; Wong, Richard W
2015-01-01
Spindle poles are defined by centrosomes; therefore, an abnormal number or defective structural organization of centrosomes can lead to loss of spindle bipolarity and genetic integrity. Previously, we showed that Tpr (translocated promoter region), a component of the nuclear pore complex (NPC), interacts with Mad1 and dynein to promote proper chromosome segregation during mitosis. Tpr also associates with p53 to induce autophagy. Here, we report that Tpr depletion induces mitotic catastrophe and enhances the rate of tetraploidy and polyploidy. Mechanistically, Tpr interacts, via its central domain, with Aurora A but not Aurora B kinase. In Tpr-depleted cells, the expression levels, centrosomal localization and phosphorylation of Aurora A were all reduced. Surprisingly, an Aurora A inhibitor, Alisertib (MLN8237), also disrupted centrosomal localization of Tpr and induced mitotic catastrophe and cell death in a time- and dose-dependent manner. Strikingly, over-expression of Aurora A disrupted Tpr centrosomal localization only in cells with supernumerary centrosomes but not in bipolar cells. Our results highlight the mutual regulation between Tpr and Aurora A and further confirm the importance of nucleoporin function in spindle pole organization, bipolar spindle assembly, and mitosis; functions that are beyond the conventional nucleocytoplasmic transport and NPC structural roles of nucleoporins. Furthermore, the central coiled-coil domain of Tpr binds to and sequesters extra Aurora A to safeguard bipolarity. This Tpr domain merits further investigation for its ability to inhibit Aurora kinase and as a potential therapeutic agent in cancer treatment.
Ruedl, G; Ploner, P; Linortner, I; Schranz, A; Fink, C; Patterson, C; Nachbauer, W; Burtscher, M
2011-08-01
The aim of this study was to investigate the interaction of potential intrinsic and extrinsic risk factors in ACL injured recreational female skiers. 93 female recreational skiers who had suffered a non-contact ACL injury and 93 age-matched controls completed a self-reported questionnaire relating to intrinsic risk factors (menstrual history, BMI, previous knee injuries, self reported weekly sports participation) and extrinsic risk factors (type of ski used, time of last binding adjustment, snow condition, weather and slope difficulty). A logistic regression model revealed the following independent ACL injury risk factors for female recreational skiers: icy snow conditions (odds ratio, 24.33; 95% confidence interval, 6.8-86.5, P<0.001), skiing during snowfall (odds ratio, 16.63; 95% confidence interval, 1.8-152.1, P=0.013), use of traditional skis (odds ratio, 10.49; 95% confidence interval, 2.0-54.5, P=0.005), and preovulatory phase of menstrual cycle (odds ratio, 2.59; 95% confidence interval, 1.2-5.5, P=0.013). In conclusion, ACL injuries in female recreational skiers are the result of a complex interaction of intrinsic and extrinsic risk factors.
Potential P-glycoprotein-mediated drug-drug interactions of antimalarial agents in Caco-2 cells.
Oga, Enoche F; Sekine, Shuichi; Shitara, Yoshihisa; Horie, Toshiharu
2012-07-01
Antimalarials are widely used in African and Southeast Asian countries, where they are combined with other drugs for the treatment of concurrent ailments. The potential for P-glycoprotein (P-gp)-mediated drug-drug interactions (DDIs) between antimalarials and P-gp substrates was examined using a Caco-2 cell-based model. Selected antimalarials were initially screened for their interaction with P-gp based on the inhibition of rhodamine-123 (Rho-123) transport in Caco-2 cells. Verapamil (100 μM) and quinidine (1 μM) were used as positive inhibition controls. Lumefantrine, amodiaquin, and artesunate all showed blockade of Rho-123 transport. Subsequently, the inhibitory effect of these antimalarials on the bi-directional passage of digoxin (DIG) was examined. All of the drugs decreased basal-to-apical (B-A) P-gp-mediated DIG transport at concentrations of 100 μM and 1 mM. These concentrations may reflect therapeutic doses for amodiaquin and artesunate. Therefore, clinically relevant DDIs may occur between certain antimalarials and P-gp substrates in general.
NASA Astrophysics Data System (ADS)
Yin, Chih-Chien; Li, Arvin Huang-Te; Chao, Sheng D.
2013-11-01
We have calculated the intermolecular interaction energies of the chloroform dimer in 12 orientations using the second-order Møller-Plesset perturbation theory. Single point energies of important geometries were calibrated by the coupled cluster with single and double and perturbative triple excitation method. Dunning's correlation consistent basis sets up to aug-cc-pVQZ have been employed in extrapolating the interaction energies to the complete basis set limit values. With the ab initio potential data we constructed a 5-site force field model for molecular dynamics simulations. We compared the simulation results with recent experiments and obtained quantitative agreements for the detailed atomwise radial distribution functions. Our results were also consistent with previous results using empirical force fields with polarization effects. Moreover, the calculated diffusion coefficients reproduced the experimental data over a wide range of thermodynamic conditions. To the best of our knowledge, this is the first ab initio force field which is capable of competing with existing empirical force fields for liquid chloroform.
NASA Astrophysics Data System (ADS)
Orphan, V. J.; Skennerton, C.; Chadwick, G.; Haroon, F.; Tyson, G. W.; Leu, A.; Hatzenpichler, R.; Woyke, T.; Malmstrom, R.; Yu, H.; Scheller, S.
2015-12-01
Cooperative metabolic interactions between multiple groups of methanotrophic 'ANME' archaea and sulfate-reducing bacteria represent the primary sink for methane within continental margin sediments. These syntrophic associations are frequently observed as structured multi-celled consortia in methane seeps, often comprising a substantial proportion of the microbial biomass within near seafloor seep sediments. Since their discovery nearly 15 years ago, a number of distinct ANME groups and multiple sulfate-reducing bacterial partners have been described from seep environments worldwide. Attempts to reconstruct the genomes of some ANME organisms have been reported, however the ecological physiology and metabolic interactions of distinct ANME lineages and their bacterial partners remains poorly understood. Here, we used a fluorescence azide-alkyne click chemistry technique known as BONCAT combined with FAC sorting to examine patterns in microbial membership and the genomes of single, metabolically active ANME-bacterial consortia recovered from methane seep sediments. This targeted consortia-level sequencing approach revealed significant diversity in the ANME-bacterial associations in situ as well as insights into the potential syntrophic mechanisms underpinning these enigmatic methane-fueled partnerships.
Arora, Pooja; Slipchenko, Lyudmila V; Webb, Simon P; DeFusco, Albert; Gordon, Mark S
2010-07-01
The simplest variational method for treating electronic excited states, configuration interaction with single excitations (CIS), has been interfaced with the effective fragment potential (EFP) method to provide an effective and computationally efficient approach for studying the qualitative effects of solvents on the electronic spectra of molecules. Three different approaches for interfacing a non-self-consistent field (SCF) excited-state quantum mechanics (QM) method and the EFP method are discussed. The most sophisticated and complex approach (termed fully self consistent) calculates the excited-state electron density with fully self-consistent accounting for the polarization (induction) energy of effective fragments. The simplest approach (method 1) includes a strategy that indirectly adds the EFP perturbation to the CIS wave function and energy via modified Hartree-Fock molecular orbitals, so that there is no direct EFP interaction with the excited-state density. An intermediate approach (method 2) accomplishes the latter in a noniterative perturbative manner. Theoretical descriptions of the three approaches are presented, and test results of solvent-induced shifts using methods 1 and 2 are compared with fully ab initio values. These comparisons illustrate that, at least for the test cases examined here, modification of the ground-state Hartree-Fock orbitals is the largest and most important factor in the calculated solvent-induced shifts. Method 1 is then employed to study the aqueous solvation of coumarin 151 and compared with experimental measurements.
Inhibition of human liver aldehyde oxidase: implications for potential drug-drug interactions.
Barr, John T; Jones, Jeffrey P
2011-12-01
During the course of our research efforts to understand the kinetics of human aldehyde oxidase as a xenobiotic-clearing enzyme, we investigated the effect of eight different inhibitors on the oxidation of the probe substrate phthalazine. Saturation kinetic parameters for phthalazine oxidation in human liver cytosol were found to be the following: K(m) = 8.0 ± 0.4 μM and V(max) = 4.3 ± 0.1 nmol · min(-1) · mg protein(-1). Inhibitory potency of the inhibitors tested ranged from 0.1 to 5 μM. Of the eight different inhibitor compounds tested, seven were observed to inhibit through a mixed mode and one through a strictly competitive mode. A ratio of the K(ii) and K(is) values was used to assess the relative competitiveness of each inhibitor. For the mixed inhibitors, the mode of inhibition varied from mostly uncompetitive to predominantly competitive (K(ii)/K(is) values ranging from 0.1 to 15). The implications for potential drug-drug interactions and inhibition mechanism are discussed. We found two inhibitors, clozapine and chlorpromazine, that have a moderate predicted risk of drug-drug interactions based on the K(i) value relative to the inhibitor concentration in human plasma, having a calculated [I]/K(i) value of 0.4 and 0.8, respectively.
Ziajahromi, Shima; Neale, Peta A; Leusch, Frederic D L
2016-11-01
Wastewater treatment plant (WWTP) effluent has been identified as a potential source of microplastics in the aquatic environment. Microplastics have recently been detected in wastewater effluent in Western Europe, Russia and the USA. As there are only a handful of studies on microplastics in wastewater, it is difficult to accurately determine the contribution of wastewater effluent as a source of microplastics. However, even the small amounts of microplastics detected in wastewater effluent may be a remarkable source given the large volumes of wastewater treatment effluent discharged to the aquatic environment annually. Further, there is strong evidence that microplastics can interact with wastewater-associated contaminants, which has the potential to transport chemicals to aquatic organisms after exposure to contaminated microplastics. In this review we apply lessons learned from the literature on microplastics in the aquatic environment and knowledge on current wastewater treatment technologies, with the aim of identifying the research gaps in terms of (i) the fate of microplastics in WWTPs, (ii) the potential interaction of wastewater-based microplastics with trace organic contaminants and metals, and (iii) the risk for aquatic organisms.
Proskurnin, Mikhail A; Zhidkova, Tatyana V; Volkov, Dmitry S; Sarimollaoglu, Mustafa; Galanzha, Ekaterina I; Mock, Donald; Nedosekin, Dmitry A; Zharov, Vladimir P
2011-10-01
Recently, photoacoustic (PA) flow cytometry (PAFC) has been developed for in vivo detection of circulating tumor cells and bacteria targeted by nanoparticles. Here, we propose multispectral PAFC with multiple dyes having distinctive absorption spectra as multicolor PA contrast agents. As a first step of our proof-of-concept, we characterized high-speed PAFC capability to monitor the clearance of three dyes (Indocyanine Green [ICG], Methylene Blue [MB], and Trypan Blue [TB]) in an animal model in vivo and in real time. We observed strong dynamic PA signal fluctuations, which can be associated with interactions of dyes with circulating blood cells and plasma proteins. PAFC demonstrated enumeration of circulating red and white blood cells labeled with ICG and MB, respectively, and detection of rare dead cells uptaking TB directly in bloodstream. The possibility for accurate measurements of various dye concentrations including Crystal Violet and Brilliant Green were verified in vitro using complementary to PAFC photothermal (PT) technique and spectrophotometry under batch and flow conditions. We further analyze the potential of integrated PAFC/PT spectroscopy with multiple dyes for rapid and accurate measurements of circulating blood volume without a priori information on hemoglobin content, which is impossible with existing optical techniques. This is important in many medical conditions including surgery and trauma with extensive blood loss, rapid fluid administration, and transfusion of red blood cells. The potential for developing a robust clinical PAFC prototype that is safe for human, and its applications for studying the liver function are further highlighted.
Information flow in interaction networks II: channels, path lengths, and potentials.
Stojmirović, Aleksandar; Yu, Yi-Kuo
2012-04-01
In our previous publication, a framework for information flow in interaction networks based on random walks with damping was formulated with two fundamental modes: emitting and absorbing. While many other network analysis methods based on random walks or equivalent notions have been developed before and after our earlier work, one can show that they can all be mapped to one of the two modes. In addition to these two fundamental modes, a major strength of our earlier formalism was its accommodation of context-specific directed information flow that yielded plausible and meaningful biological interpretation of protein functions and pathways. However, the directed flow from origins to destinations was induced via a potential function that was heuristic. Here, with a theoretically sound approach called the channel mode, we extend our earlier work for directed information flow. This is achieved by constructing a potential function facilitating a purely probabilistic interpretation of the channel mode. For each network node, the channel mode combines the solutions of emitting and absorbing modes in the same context, producing what we call a channel tensor. The entries of the channel tensor at each node can be interpreted as the amount of flow passing through that node from an origin to a destination. Similarly to our earlier model, the channel mode encompasses damping as a free parameter that controls the locality of information flow. Through examples involving the yeast pheromone response pathway, we illustrate the versatility and stability of our new framework.
Huthmacher, Carola; Gille, Christoph; Holzhütter, Hermann-Georg
2008-06-07
Protein-protein interactions are operative at almost every level of cell structure and function as, for example, formation of sub-cellular organelles, packaging of chromatin, muscle contraction, signal transduction, and regulation of gene expression. Public databases of reported protein-protein interactions comprise hundreds of thousands interactions, and this number is steadily growing. Elucidating the implications of protein-protein interactions for the regulation of the underlying cellular or extra-cellular reaction network remains a great challenge for computational biochemistry. In this work, we have undertaken a systematic and comprehensive computational analysis of reported enzyme-enzyme interactions in the metabolic networks of the model organisms Escherichia coli and Saccharomyces cerevisiae. We grouped all enzyme pairs according to the topological distance that the catalyzed reactions have in the metabolic network and performed a statistical analysis of reported enzyme-enzyme interactions within these groups. We found a higher frequency of reported enzyme-enzyme interactions within the group of enzymes catalyzing reactions that are adjacent in the network, i.e. sharing at least one metabolite. As some of these interacting enzymes have already been implicated in metabolic channeling our analysis may provide a useful screening for candidates of this phenomenon. To check for a possible regulatory role of interactions between enzymes catalyzing non-neighboring reactions, we determined potentially regulatory enzymes using connectivity in the network and absolute change of Gibbs free energy. Indeed a higher portion of reported interactions pertain to such potentially regulatory enzymes.
Dham, Ashok K; McBane, George C; McCourt, Frederick R W; Meath, William J
2010-01-14
results that agree similarly well for all but one of the properties considered. When the present comparisons are combined with the ability to give accurate spectroscopic transition frequencies for the Ne-CO van der Waals complex, only the XC potential energy surfaces give results that agree well with all extant experimental data for the Ne-CO interaction.
Raffeiner, Philipp; Röck, Ruth; Schraffl, Andrea; Hartl, Markus; Hart, Jonathan R; Janda, Kim D; Vogt, Peter K; Stefan, Eduard; Bister, Klaus
2014-10-15
The oncogenic bHLH-LZ transcription factor Myc forms binary complexes with its binding partner Max. These and other bHLH-LZ-based protein-protein interactions (PPI) in the Myc-Max network are essential for the physiological and oncogenic activities of Myc. We have generated a genetically determined and highly specific protein-fragment complementation assay based on Renilla luciferase to analyze the dynamic interplay of bHLH-LZ transcription factors Myc, Max, and Mxd1 in vivo. We also applied this PPI reporter to quantify alterations of nuclear Myc-Max complexes in response to mutational events, competitive binding by the transcriptional repressor Mxd1, or perturbations by small-molecule Myc inhibitors, including recently identified potent PPI inhibitors from a Kröhnke pyridine library. We show that the specificity of Myc-Max PPI reduction by the pyridine inhibitors directly correlates with their efficient and highly specific potential to interfere with the proliferation of human and avian tumor cells displaying deregulated Myc expression. In a direct comparison with known Myc inhibitors using human and avian cell systems, the pyridine compounds reveal a unique inhibitory potential even at sub-micromolar concentrations combined with remarkable specificity for the inhibition of Myc-driven tumor cell proliferation. Furthermore, we show in direct comparisons using defined avian cell systems that different Max PPI profiles for the variant members of the Myc protein family (c-Myc, v-Myc, N-Myc, L-Myc) correlate with their diverse oncogenic potential and their variable sensitivity to the novel pyridine inhibitors.
Interaction potential of Trigonella foenum graceum through cytochrome P450 mediated inhibition
Ahmmed, Sk Milan; Mukherjee, Pulok K.; Bahadur, Shiv; Kar, Amit; Mukherjee, Kakali; Karmakar, Sanmoy; Bandyopadhyay, Arun
2015-01-01
Objective: The seeds of Trigonella foenum-graecum (TFG) (family: Leguminosae) are widely consumed both as a spice in food and Traditional Medicine in India. The present study was undertaken to evaluate the inhibitory effect of standardized extract of TFG and its major constituent trigonelline (TG) on rat liver microsome (RLM) and cytochrome P450 (CYP450) drug metabolizing isozymes (CYP3A4 and CYP2D6), which may indicate the possibility of a probable unwanted interaction. Materials and Methods: Reverse phase-high performance liquid chromatography method was developed to standardize the hydroalcoholic seed extract with standard TG. The inhibitory potential of the extract and TG was evaluated on RLM and CYP isozymes using CYP450-carbon monoxide (CYP450-CO) complex assay and fluorescence assay, respectively. Results: The content of TG in TFG was found to be 3.38% (w/w). The CYP-CO complex assay showed 23.32% inhibition on RLM. Fluorescence study revealed that the extract and the biomarker had some inhibition on CYP450 isozymes e.g. CYP3A4 and CYP2D6 (IC50 values of the extract: 102.65 ± 2.63–142.23 ± 2.61 µg/ml and TG: 168.73 ± 4.03–180.90 ± 2.49 µg/ml) which was very less compared to positive controls ketoconazole and quinidine. Inhibition potential of TFG was little higher than TG but very less compared to positive controls. Conclusions: From the present study, we may conclude that the TFG or TG has very less potential to inhibit the CYP isozymes (CYP3A4, CYP2D6), so administration of this plant extract or its biomarker TG may be safe. PMID:26600643
The Interaction of Fatigue and Potentiation Following an Acute Bout of Unilateral Squats
Andrews, Samantha K.; Horodyski, Jesse M.; MacLeod, Daniel A.; Whitten, Joseph; Behm, David G.
2016-01-01
A prior conditioning resistance exercise can augment subsequent performance of the affected muscles due to the effects of post-activation potentiation (PAP). The non-local muscle fatigue literature has illustrated the global neural effects of unilateral fatigue. However, no studies have examined the possibility of acute non-local performance enhancements. The objective of the study was to provide a conditioning stimulus in an attempt to potentiate the subsequent jump performance of the affected limb and determine if there were performance changes in the contralateral limb. Using a randomized allocation, 14 subjects (6 females, 8 males) completed three conditions on separate days: 1) unilateral, dominant leg, Bulgarian split squat protocol with testing of the exercised leg, 2) unilateral, dominant leg, Bulgarian split squat protocol with testing of the contralateral, non-exercised leg and 3) control session with testing of the non-dominant leg. Pre- and post-testing consisted of countermovement (CMJ) and drop jumps (DJ). The exercised leg exhibited CMJ height increases of 3.5% (p = 0.008; d = 0.28), 4.0% (p = 0.011; d = 0.33) and 3.2% (p = 0.013; d = 0.26) at 1, 5, and 10 min post-intervention respectively. The contralateral CMJ height had 2.0% (p = 0.034; d = 0.18), 1.2% (p = 0.2; d = 0.12), and 2.1% (p = 0.05; d = 0.17) deficits at 1, 5, and 10 min post-intervention respectively. Similar relative results were found for CMJ power. There were no significant interactions for DJ measures or control CMJ measures. The findings suggest that PAP effects were likely predominant for the exercised leg whereas the conditioning exercise provided trivial magnitude although statistically significant neural impairments for the contralateral limb. Key points Post-activation potentiation of unilateral CMJ height was achieved following 5 sequential squats at 50% 1RM, 2 squats at 70% 1RM, 1 squat at 90% 1RM with 3 min rest periods. The conditioning exercises did not elicit
Hermann, Andreas; Krawczyk, Robert P.; Lein, Matthias; Schwerdtfeger, Peter; Hamilton, I. P.; Stewart, James J. P.
2007-07-15
The many-body expansion of the interaction potential between atoms and molecules is analyzed in detail for different types of interactions involving up to seven atoms. Elementary clusters of Ar, Na, Si, and, in particular, Au are studied, using first-principles wave-function- and density-functional-based methods to obtain the individual n-body contributions to the interaction energies. With increasing atom number the many-body expansion converges rapidly only for long-range weak interactions. Large oscillatory behavior is observed for other types of interactions. This is consistent with the fact that Au clusters up to a certain size prefer planar structures over the more compact three-dimensional Lennard-Jones-type structures. Several Au model potentials and semiempirical PM6 theory are investigated for their ability to reproduce the quantum results. We further investigate small water clusters as prototypes of hydrogen-bonded systems. Here, the many-body expansion converges rapidly, reflecting the localized nature of the hydrogen bond and justifying the use of two-body potentials to describe water-water interactions. The question of whether electron correlation contributions can be successfully modeled by a many-body interaction potential is also addressed.
NASA Technical Reports Server (NTRS)
Jones, Henry E.
1997-01-01
A study of the full-potential modeling of a blade-vortex interaction was made. A primary goal of this study was to investigate the effectiveness of the various methods of modeling the vortex. The model problem restricts the interaction to that of an infinite wing with an infinite line vortex moving parallel to its leading edge. This problem provides a convenient testing ground for the various methods of modeling the vortex while retaining the essential physics of the full three-dimensional interaction. A full-potential algorithm specifically tailored to solve the blade-vortex interaction (BVI) was developed to solve this problem. The basic algorithm was modified to include the effect of a vortex passing near the airfoil. Four different methods of modeling the vortex were used: (1) the angle-of-attack method, (2) the lifting-surface method, (3) the branch-cut method, and (4) the split-potential method. A side-by-side comparison of the four models was conducted. These comparisons included comparing generated velocity fields, a subcritical interaction, and a critical interaction. The subcritical and critical interactions are compared with experimentally generated results. The split-potential model was used to make a survey of some of the more critical parameters which affect the BVI.
Kennedy-Dixon, Tracia-Gay; Gossell-Williams, Maxine; Hall, Jannel; Anglin-Brown, Blossom
2015-01-01
Objective: To identify major potential drug-drug interactions (DDIs) on prescriptions filled at the University Health Centre Pharmacy, Mona Campus, Jamaica. Methods: This investigation utilised a cross-sectional analysis on all prescriptions with more than one drug that were filled at the Health Centre Pharmacy between November 2012 and February 2013. Potential DDIs were identified using the online Drug Interactions Checker database of Drugs.com. Results: During the period of the study, a total of 2814 prescriptions were analysed for potential DDIs. The prevalence of potential DDIs found during the study period was 49.82%. Major potential DDIs accounted for 4.7 % of the total number of interactions detected, while moderate potential DDIs and minor potential DDIs were 80.8 % and 14.5 % respectively. The three most frequently occurring major potential DDIs were amlodipine and simvastatin (n=46), amiloride and losartan (n=27) and amiloride and lisinopril (n=16). Conclusion: This study has highlighted the need for educational initiatives to ensure that physicians and pharmacists collaborate in an effort to minimise the risks to the patients. These interactions are avoidable for the most part, as the use of online tools can facilitate the selection of therapeutic alternatives or guide decisions for closer patient monitoring and thus reduce the risks of adverse events. PMID:26759615
Chen, Qian; Cho, Hoduk; Manthiram, Karthish; ...
2015-03-23
We demonstrate a generalizable strategy to use the relative trajectories of pairs and groups of nanocrystals, and potentially other nanoscale objects, moving in solution which can now be obtained by in situ liquid phase transmission electron microscopy (TEM) to determine the interaction potentials between nanocrystals. Such nanoscale interactions are crucial for collective behaviors and applications of synthetic nanocrystals and natural biomolecules, but have been very challenging to measure in situ at nanometer or sub-nanometer resolution. Here we use liquid phase TEM to extract the mathematical form of interaction potential between nanocrystals from their sampled trajectories. We show the power ofmore » this approach to reveal unanticipated features of nanocrystal–nanocrystal interactions by examining the anisotropic interaction potential between charged rod-shaped Au nanocrystals (Au nanorods); these Au nanorods assemble, in a tip-to-tip fashion in the liquid phase, in contrast to the well-known side-by-side arrangements commonly observed for drying-mediated assembly. These observations can be explained by a long-range and highly anisotropic electrostatic repulsion that leads to the tip-selective attachment. As a result, Au nanorods stay unassembled at a lower ionic strength, as the electrostatic repulsion is even longer-ranged. Our study not only provides a mechanistic understanding of the process by which metallic nanocrystals assemble but also demonstrates a method that can potentially quantify and elucidate a broad range of nanoscale interactions relevant to nanotechnology and biophysics.« less
2015-01-01
We demonstrate a generalizable strategy to use the relative trajectories of pairs and groups of nanocrystals, and potentially other nanoscale objects, moving in solution which can now be obtained by in situ liquid phase transmission electron microscopy (TEM) to determine the interaction potentials between nanocrystals. Such nanoscale interactions are crucial for collective behaviors and applications of synthetic nanocrystals and natural biomolecules, but have been very challenging to measure in situ at nanometer or sub-nanometer resolution. Here we use liquid phase TEM to extract the mathematical form of interaction potential between nanocrystals from their sampled trajectories. We show the power of this approach to reveal unanticipated features of nanocrystal–nanocrystal interactions by examining the anisotropic interaction potential between charged rod-shaped Au nanocrystals (Au nanorods); these Au nanorods assemble, in a tip-to-tip fashion in the liquid phase, in contrast to the well-known side-by-side arrangements commonly observed for drying-mediated assembly. These observations can be explained by a long-range and highly anisotropic electrostatic repulsion that leads to the tip-selective attachment. As a result, Au nanorods stay unassembled at a lower ionic strength, as the electrostatic repulsion is even longer-ranged. Our study not only provides a mechanistic understanding of the process by which metallic nanocrystals assemble but also demonstrates a method that can potentially quantify and elucidate a broad range of nanoscale interactions relevant to nanotechnology and biophysics. PMID:27162944
Accurate methods for large molecular systems.
Gordon, Mark S; Mullin, Jonathan M; Pruitt, Spencer R; Roskop, Luke B; Slipchenko, Lyudmila V; Boatz, Jerry A
2009-07-23
Three exciting new methods that address the accurate prediction of processes and properties of large molecular systems are discussed. The systematic fragmentation method (SFM) and the fragment molecular orbital (FMO) method both decompose a large molecular system (e.g., protein, liquid, zeolite) into small subunits (fragments) in very different ways that are designed to both retain the high accuracy of the chosen quantum mechanical level of theory while greatly reducing the demands on computational time and resources. Each of these methods is inherently scalable and is therefore eminently capable of taking advantage of massively parallel computer hardware while retaining the accuracy of the corresponding electronic structure method from which it is derived. The effective fragment potential (EFP) method is a sophisticated approach for the prediction of nonbonded and intermolecular interactions. Therefore, the EFP method provides a way to further reduce the computational effort while retaining accuracy by treating the far-field interactions in place of the full electronic structure method. The performance of the methods is demonstrated using applications to several systems, including benzene dimer, small organic species, pieces of the alpha helix, water, and ionic liquids.
Radiom, Milad Ducker, William; Robbins, Brian; Paul, Mark
2015-02-15
The hydrodynamic interaction of two closely spaced micron-scale spheres undergoing Brownian motion was measured as a function of their separation. Each sphere was attached to the distal end of a different atomic force microscopy cantilever, placing each sphere in a stiff one-dimensional potential (0.08 Nm{sup −1}) with a high frequency of thermal oscillations (resonance at 4 kHz). As a result, the sphere’s inertial and restoring forces were significant when compared to the force due to viscous drag. We explored interparticle gap regions where there was overlap between the two Stokes layers surrounding each sphere. Our experimental measurements are the first of their kind in this parameter regime. The high frequency of oscillation of the spheres means that an analysis of the fluid dynamics would include the effects of fluid inertia, as described by the unsteady Stokes equation. However, we find that, for interparticle separations less than twice the thickness of the wake of the unsteady viscous boundary layer (the Stokes layer), the hydrodynamic interaction between the Brownian particles is well-approximated by analytical expressions that neglect the inertia of the fluid. This is because elevated frictional forces at narrow gaps dominate fluid inertial effects. The significance is that interparticle collisions and concentrated suspensions at this condition can be modeled without the need to incorporate fluid inertia. We suggest a way to predict when fluid inertial effects can be ignored by including the gap-width dependence into the frequency number. We also show that low frequency number analysis can be used to determine the microrheology of mixtures at interfaces.
2016-01-01
Background Botulinum neurotoxins are produced by Clostridium botulinum bacteria. There are eight serologically distinct botulinum neurotoxin isoforms (serotypes A–H). Currently, botulinum neurotoxin serotype A (BoNT⁄A) is commonly used for the treatment of many disorders, such as hyperactive musculoskeletal disorders, dystonia, and pain. However, the effectiveness of BoNT⁄A for pain alleviation and the mechanisms that mediate the analgesic effects of BoNT⁄A remain unclear. To define the antinociceptive mechanisms by which BoNT/A functions, the interactions between BoNT⁄A and the transient receptor potential vanilloid subfamily 1 (TRPV1) were investigated using immunofluorescence, co-immunoprecipitation, and western blot analysis in primary mouse embryonic dorsal root ganglion neuronal cultures. Results 1) Three-week-old cultured dorsal root ganglion neurons highly expressed transient TRPV1, synaptic vesicle 2A (SV2A) and synaptosomal-associated protein 25 (SNAP-25). SV2A and SNAP-25 are the binding receptor and target protein, respectively, of BoNT⁄A. 2) TRPV1 colocalized with both BoNT⁄A and cleaved SNAP-25 when BoNT⁄A was added to dorsal root ganglia neuronal cultures. 3) After 24 hours of BoNT⁄A treatment (1 nmol⁄l), both TRPV1 and BoNT⁄A positive bands were detected in western blots of immunoprecipitated pellets. 4) Blocking TRPV1 with a specific antibody decreased the cleavage of SNAP-25 by BoNT⁄A. Conclusion BoNT/A interacts with TRPV1 both structurally and functionally in cultured mouse embryonic dorsal root ganglion neurons. These results suggest that an alternative mechanism is used by BoNT⁄A to mediate pain relief. PMID:26745805
Organo-mineral interactions mask the true sorption potential of biochars in soils.
Singh, Neera; Kookana, Rai S
2009-03-01
The sorption of carbaryl (1-naphthyl methyl carbamate) and ethion [O,O,O',O'-tetraethyl S,S'-methylene bis(phosphorodithioate)] was studied in whole soils as well as after treatment of soil with 2% hydrofluoric acid (HF) to remove paramagnetic materials and to oxidize most forms of labile carbon by photo-oxidation with high energy (UV) on < 53 microm fractions. The sorption coefficient (K(d)) values for carbaryl and ethion in soils did not follow the order of their organic carbon (OC) content, and specially their char content However, the K(oc) values in < 53 microm fractions after hydrofluoric acid/photo-oxidation with high energy (hydrofluoric acid/ultraviolet; HF/UV) treatment were found to be much higher than those in bulk untreated soils. The effect of organic matter chemistry was determined by correlating K(oc) values of contaminants in bulk soils or 53 microm fractions against sample aromaticity. A poor correlation of K(oc) in bulk soil and aromatic C values of both carbaryl and ethion was observed. However, the correlation between the K(oc) and the aromatic fraction of C after the HF/UV treatment improved significantly, reflecting the contribution of char fraction of carbon in soils towards sorption of pesticides. The increase in sorption after HF/UV treatment suggested that the sorption potential of biochars, which are expected to contribute significantly to contaminant sorption due to their high surface area, can remain masked by the organo-mineral interactions of char in whole soils. This has implications for the modification of surfaces of the freshly applied biochars in soils due to organo-mineral interactions.
Interspecies interactions and potential Influenza A virus risk in small swine farms in Peru
2012-01-01
Background The recent avian influenza epidemic in Asia and the H1N1 pandemic demonstrated that influenza A viruses pose a threat to global public health. The animal origins of the viruses confirmed the potential for interspecies transmission. Swine are hypothesized to be prime "mixing vessels" due to the dual receptivity of their trachea to human and avian strains. Additionally, avian and human influenza viruses have previously been isolated in swine. Therefore, understanding interspecies contact on smallholder swine farms and its potential role in the transmission of pathogens such as influenza virus is very important. Methods This qualitative study aimed to determine swine-associated interspecies contacts in two coastal areas of Peru. Direct observations were conducted at both small-scale confined and low-investment swine farms (n = 36) and in open areas where swine freely range during the day (n = 4). Interviews were also conducted with key stakeholders in swine farming. Results In both locations, the intermingling of swine and domestic birds was common. An unexpected contact with avian species was that swine were fed poultry mortality in 6/20 of the farms in Chancay. Human-swine contacts were common, with a higher frequency on the confined farms. Mixed farming of swine with chickens or ducks was observed in 36% of all farms. Human-avian interactions were less frequent overall. Use of adequate biosecurity and hygiene practices by farmers was suboptimal at both locations. Conclusions Close human-animal interaction, frequent interspecies contacts and suboptimal biosecurity and hygiene practices pose significant risks of interspecies influenza virus transmission. Farmers in small-scale swine production systems constitute a high-risk population and need to be recognized as key in preventing interspecies pathogen transfer. A two-pronged prevention approach, which offers educational activities for swine farmers about sound hygiene and biosecurity practices and
NASA Astrophysics Data System (ADS)
Ebrahimi, Davoud; Whittle, Andrew J.; Pellenq, Roland J.-M.
2014-04-01
Face-to-face and edge-to-edge free energy interactions of Wyoming Na-montmorillonite platelets were studied by calculating potential of mean force along their center to center reaction coordinate using explicit solvent (i.e., water) molecular dynamics and free energy perturbation methods. Using a series of configurations, the Gay-Berne potential was parametrized and used to examine the meso-scale aggregation and properties of platelets that are initially random oriented under isothermal-isobaric conditions. Aggregates of clay were defined by geometrical analysis of face-to-face proximity of platelets with size distribution described by a log-normal function. The isotropy of the microstructure was assessed by computing a scalar order parameter. The number of platelets per aggregate and anisotropy of the microstructure both increases with platelet plan area. The system becomes more ordered and aggregate size increases with increasing pressure until maximum ordered state at confining pressure of 50 atm. Further increase of pressure slides platelets relative to each other leading to smaller aggregate size. The results show aggregate size of (3-8) platelets for sodium-smectite in agreement with experiments (3-10). The geometrical arrangement of aggregates affects mechanical properties of the system. The elastic properties of the meso-scale aggregate assembly are reported and compared with nanoindentation experiments. It is found that the elastic properties at this scale are close to the cubic systems. The elastic stiffness and anisotropy of the assembly increases with the size of the platelets and the level of external pressure.
Alvim, Mariana Macedo; da Silva, Lidiane Ayres; Leite, Isabel Cristina Gonçalves; Silvério, Marcelo Silva
2015-01-01
Objective To evaluate the incidence of potential drug-drug interactions in an intensive care unit of a hospital, focusing on antimicrobial drugs. Methods This cross-sectional study analyzed electronic prescriptions of patients admitted to the intensive care unit of a teaching hospital between January 1 and March 31, 2014 and assessed potential drug-drug interactions associated with antimicrobial drugs. Antimicrobial drug consumption levels were expressed in daily doses per 100 patient-days. The search and classification of the interactions were based on the Micromedex® system. Results The daily prescriptions of 82 patients were analyzed, totaling 656 prescriptions. Antimicrobial drugs represented 25% of all prescription drugs, with meropenem, vancomycin and ceftriaxone being the most prescribed medications. According to the approach of daily dose per 100 patient-days, the most commonly used antimicrobial drugs were cefepime, meropenem, sulfamethoxazole + trimethoprim and ciprofloxacin. The mean number of interactions per patient was 2.6. Among the interactions, 51% were classified as contraindicated or significantly severe. Highly significant interactions (clinical value 1 and 2) were observed with a prevalence of 98%. Conclusion The current study demonstrated that antimicrobial drugs are frequently prescribed in intensive care units and present a very high number of potential drug-drug interactions, with most of them being considered highly significant. PMID:26761473
Zhang, Xiao-Fei; Du, Zhi-Jing; Tan, Ren-Bing; Dong, Rui-Fang; Chang, Hong; Zhang, Shou-Gang
2014-07-15
We consider a pair of coupled nonlinear Schrödinger equations modeling a rotating two-component Bose–Einstein condensate with tunable interactions and harmonic potential, with emphasis on the structure of vortex states by varying the strength of inter-component interaction, rotational frequency, and the aspect ratio of the harmonic potential. Our results show that the inter-component interaction greatly enhances the effect of rotation. For the case of isotropic harmonic potential and small inter-component interaction, the initial vortex structure remains unchanged. As the ratio of inter- to intra-component interactions increases, each component undergoes a transition from a vortex lattice (vortex line) in an isotropic (anisotropic) harmonic potential to an alternatively arranged stripe pattern, and eventually to the interwoven “serpentine” vortex sheets. Moreover, in the case of anisotropic harmonic potential the system can develop to a rotating droplet structure. -- Highlights: •Different vortex structures are obtained within the full parameter space. •Effects of system parameters on the ground state structure are discussed. •Phase transition between different vortex structures is also examined. •Present one possible way to obtain the rotating droplet structure. •Provide many possibilities to manipulate vortex in two-component BEC.
MOLECULAR INTERACTION POTENTIALS FOR THE DEVELOPMENT OF STRUCTURE-ACTIVITY RELATIONSHIPS
Abstract
One reasonable approach to the analysis of the relationships between molecular structure and toxic activity is through the investigation of the forces and intermolecular interactions responsible for chemical toxicity. The interaction between the xenobiotic and the bio...
Interactions of aspirin and other potential etiologic factors in an animal model of Reye syndrome.
Deshmukh, D R; Maassab, H F; Mason, M
1982-12-01
Recent studies of Reye syndrome (RS) patients have suggested aspirin treatment as a possible factor in the etiology of this often fatal childhood disorder. the relationship of aspirin treatment to other factors that have been strongly implicated (influenza, ammonia toxicity) cannot be examined directly in patients because aspirin treatment is usually initiated by family members in the prodromal period before RS is diagnosed. In this report we describe the use of an animal model for RS in examining the interactions of these several potential etiological factors. Hyperammonemia and coma were produced in young male ferrets by a brief feeding of an arginine-deficient diet. The effects of influenza infection or aspirin treatment (or both) of control and hyperammonemic ferrets on their serum levels of ammonia, glutamic-oxaloacetic transaminase (GOT;L-aspartate:2-oxoglutarate aminotransferase, EC 2.6.1.1), ornithine carbamoyltransferase (OCT; carbamoylphosphate:L-ornithine carbamoyltransferase, EC 2.1.3.3), bilirubin, and salicylate were studied. Liver levels of lipids, proteins, and several urea-cycle enzymes were also determined in the comatose ferrets and compared with those of untreated controls and of controls treated with influenza or aspirin, or both. Synergism of these three factors (hyperammonemia, influenza infection, and aspirin treatment) in causing RS-like alterations in these parameters was observed.
Formalizing the potential of stereoscopic 3D user experience in interactive entertainment
NASA Astrophysics Data System (ADS)
Schild, Jonas; Masuch, Maic
2015-03-01
The use of stereoscopic 3D vision affects how interactive entertainment has to be developed as well as how it is experienced by the audience. The large amount of possibly impacting factors and variety as well as a certain subtlety of measured effects on user experience make it difficult to grasp the overall potential of using S3D vision. In a comprehensive approach, we (a) present a development framework which summarizes possible variables in display technology, content creation and human factors, and (b) list a scheme of S3D user experience effects concerning initial fascination, emotions, performance, and behavior as well as negative feelings of discomfort and complexity. As a major contribution we propose a qualitative formalization which derives dependencies between development factors and user effects. The argumentation is based on several previously published user studies. We further show how to apply this formula to identify possible opportunities and threats in content creation as well as how to pursue future steps for a possible quantification.
Siewit, Christina L; Gengler, Bridget; Vegas, Esera; Puckett, Rachel; Louie, Maggie C
2010-05-01
Cadmium is an environmental contaminant that enters the body through diet or cigarette smoke. It affects multiple cellular processes, including cell proliferation, differentiation, and apoptosis. Recently, cadmium has been shown to function as an endocrine disruptor, to stimulate estrogen receptor alpha (ERalpha) activity and promote uterine and mammary gland growth in mice. Although cadmium exposure has been associated with the development of breast cancer, the mechanism of action of cadmium remains unclear. To address this deficit, we examined the effects of cadmium treatment on breast cancer cells. We found that ERalpha is required for both cadmium-induced cell growth and modulation of gene expression. We also determined that ERalpha translocates to the nucleus in response to cadmium exposure. Additionally, we provide evidence that cadmium potentiates the interaction between ERalpha and c-Jun and enhances recruitment of this transcription factor complex to the proximal promoters of cyclin D1 and c-myc, thus increasing their expression. This study provides a mechanistic link between cadmium exposure and ERalpha and demonstrates that cadmium plays an important role in the promotion of breast cancer.
The two-body interaction potential in the STF tensor formalism: an application to binary asteroids
NASA Astrophysics Data System (ADS)
Compère, A.; Lemaître, A.
2014-08-01
The symmetric trace free (STF) tensor formalism, developed by Hartmann et al. (Celest Mech Dyn Astron 60:139-159. doi: 10.1007/BF00693097, 1994), is a nice tool, not much used in Celestial Mechanics. It is fully equivalent to the usual spherical harmonics but permits more elegant and compact formulations. The coupling between the gravitational fields of extended bodies with this formalism has been used in Mathis and Le Poncin-Lafitte (Astron Astrophys 497:889-910. doi: 10.1051/0004-6361/20079054, 2009) for binary stars or planetary systems, but not yet applied to binary asteroids. However, binary asteroids are common in the Solar System and usually their study requires a full two rigid body approach. The formulation of the two-body interaction potential in the STF formalism in the full two rigid body problem is detailed and completed in this article. An application to the binary asteroid (66391) 1999 KW4 is presented with a comparison of our results with other results of the literature for validation.
Buenker, Robert J; Liebermann, Heinz-Peter
2009-09-21
Ab initio multireference single- and double-excitation configuration interaction calculations have been carried out to compute the potential curves and annihilation rates (ARs) of positronic molecular complexes of a series of alkali monoxides. The dissociation limit for the lowest states of these systems consists of the positive alkali ion ground state (M(+)) and the OPs (e(+)O(-)) complex formed by attaching the positron to O(-), even though the ground state of the corresponding neutral molecule always correlates with uncharged fragments (M+O). The positron affinity of the neutral oxide (2)Pi state is greater than that of (2)Sigma(+) in each case, so that the e(+)MO ground state always has (3,1)Pi symmetry, despite the fact that both KO and RbO have (2)Sigma(+) ground states. The bonding in the positronic systems is highly ionic at all internuclear distances and this causes their ARs to decrease gradually as the positive alkali ion approaches the OPs fragment.
Mechanisms of radiation interaction with DNA: Potential implications for radiation protection
Not Available
1988-01-01
The Office of Health and Environmental Research (OHER) of the US Department of Energy conducts a broad multidisciplinary research program which includes basic biophysics, biophysical chemistry, molecular and cellular biology as well as experimental animal studies and opportunistic human studies. This research is directed at understanding how low levels of radiation of various qualities produce the spectrum of biological effects that are seen for such exposures. This workshop was entitled ''Mechanisms of Radiation Interaction with DNA: Potential Implications for Radiation Protection.'' It ws jointly sponsored by the Department of Energy and the Commission of European Communities. The aim of the workshop was to review the base of knowledge in the area of mechanisms of radiation action at the DNA level, and to explore ways in which this information can be applied to the development of scientifically sound concepts and procedures for use in the field of radiation protection. The overview of research provided by this multidisciplinary group will be helpful to the Office in program planning. This report includes a summary of the presentations, extended abstracts, the meeting agenda, research recommendations, and a list of participants. Individual papers are processed separately for the data base.
Piculell, Bridget J; Hoeksema, Jason D; Thompson, John N
2008-01-01
Background Geographic selection mosaics, in which species exert different evolutionary impacts on each other in different environments, may drive diversification in coevolving species. We studied the potential for geographic selection mosaics in plant-mycorrhizal interactions by testing whether the interaction between bishop pine (Pinus muricata D. Don) and one of its common ectomycorrhizal fungi (Rhizopogon occidentalis Zeller and Dodge) varies in outcome, when different combinations of plant and fungal genotypes are tested under a range of different abiotic and biotic conditions. Results We used a 2 × 2 × 2 × 2 factorial experiment to test the main and interactive effects of plant lineage (two maternal seed families), fungal lineage (two spore collections), soil type (lab mix or field soil), and non-mycorrhizal microbes (with or without) on the performance of plants and fungi. Ecological outcomes, as assessed by plant and fungal performance, varied widely across experimental environments, including interactions between plant or fungal lineages and soil environmental factors. Conclusion These results show the potential for selection mosaics in plant-mycorrhizal interactions, and indicate that these interactions are likely to coevolve in different ways in different environments, even when initially the genotypes of the interacting species are the same across all environments. Hence, selection mosaics may be equally as effective as genetic differences among populations in driving divergent coevolution among populations of interacting species. PMID:18507825
ERIC Educational Resources Information Center
Zirpoli, Thomas J.; Bell, Richard Q.
1987-01-01
Perceived unresponsiveness may be more critical to parent-child interaction than a severe disability itself. Controlling adult behaviors may reflect high levels of caregiver motivation and extinction burst effects. Reductions in the amount of caregiver-child interactions may be the outcome of previously unrewarded interaction attempts and…
BIOACCESSIBILITY TESTS ACCURATELY ESTIMATE ...
Hazards of soil-borne Pb to wild birds may be more accurately quantified if the bioavailability of that Pb is known. To better understand the bioavailability of Pb to birds, we measured blood Pb concentrations in Japanese quail (Coturnix japonica) fed diets containing Pb-contaminated soils. Relative bioavailabilities were expressed by comparison with blood Pb concentrations in quail fed a Pb acetate reference diet. Diets containing soil from five Pb-contaminated Superfund sites had relative bioavailabilities from 33%-63%, with a mean of about 50%. Treatment of two of the soils with P significantly reduced the bioavailability of Pb. The bioaccessibility of the Pb in the test soils was then measured in six in vitro tests and regressed on bioavailability. They were: the “Relative Bioavailability Leaching Procedure” (RBALP) at pH 1.5, the same test conducted at pH 2.5, the “Ohio State University In vitro Gastrointestinal” method (OSU IVG), the “Urban Soil Bioaccessible Lead Test”, the modified “Physiologically Based Extraction Test” and the “Waterfowl Physiologically Based Extraction Test.” All regressions had positive slopes. Based on criteria of slope and coefficient of determination, the RBALP pH 2.5 and OSU IVG tests performed very well. Speciation by X-ray absorption spectroscopy demonstrated that, on average, most of the Pb in the sampled soils was sorbed to minerals (30%), bound to organic matter 24%, or present as Pb sulfate 18%. Ad
Chang, Bong Ho; Bae, Young Chan
2003-01-01
We investigate lysozyme-lysozyme and lysozyme-salt interactions in electrolyte solutions using a molecular-thermodynamic model. An equation of state based on the statistical mechanical perturbation theory is applied to describe the interactions. The perturbation term includes a new square-well potential of mean force, which implies the information about the lysozyme surface and salt type. The attractive energy of the potential of mean force is correlated with experimental cloud-point temperatures of lysozyme in various solution conditions. The same attractive energy is used to predict osmotic pressure of a given system with no additional parameters. The new potential shows a satisfactory improvement in understanding the interactions between lysozymes in aqueous salt solutions.
Ab initio potential energy surfaces describing the interaction of CH(X2Π) with H2
NASA Astrophysics Data System (ADS)
Dagdigian, Paul J.
2016-09-01
We have determined four-dimensional ab initio quasi-diabatic potential energy surfaces describing the interaction of CH(X2Π) with H2, under the assumption of fixed CH and H2 internuclear separations. These calculations employed the multi-reference configuration interaction method [MRCISD+Q(Davidson)]. The computed points were fit to an analytical form suitable for time-independent quantum scattering calculations of rotationally inelastic cross sections and rate constants.
NASA Astrophysics Data System (ADS)
Ikot, Akpan N.; Maghsoodi, Elham; Hassanabadi, Hassan; Obu, Joseph A.
2014-05-01
In this paper, we obtain the approximate analytical bound-state solutions of the Dirac particle with the generalized Yukawa potential within the framework of spin and pseudospin symmetries for the arbitrary к state with a generalized tensor interaction. The generalized parametric Nikiforov-Uvarov method is used to obtain the energy eigenvalues and the corresponding wave functions in closed form. We also report some numerical results and present figures to show the effect of the tensor interaction.
Correia, Rion Brattig; Li, Lang; Rocha, Luis M
2016-01-01
Much recent research aims to identify evidence for Drug-Drug Interactions (DDI) and Adverse Drug reactions (ADR) from the biomedical scientific literature. In addition to this "Bibliome", the universe of social media provides a very promising source of large-scale data that can help identify DDI and ADR in ways that have not been hitherto possible. Given the large number of users, analysis of social media data may be useful to identify under-reported, population-level pathology associated with DDI, thus further contributing to improvements in population health. Moreover, tapping into this data allows us to infer drug interactions with natural products-including cannabis-which constitute an array of DDI very poorly explored by biomedical research thus far. Our goal is to determine the potential of Instagram for public health monitoring and surveillance for DDI, ADR, and behavioral pathology at large. Most social media analysis focuses on Twitter and Facebook, but Instagram is an increasingly important platform, especially among teens, with unrestricted access of public posts, high availability of posts with geolocation coordinates, and images to supplement textual analysis. Using drug, symptom, and natural product dictionaries for identification of the various types of DDI and ADR evidence, we have collected close to 7000 user timelines spanning from October 2010 to June 2015.We report on 1) the development of a monitoring tool to easily observe user-level timelines associated with drug and symptom terms of interest, and 2) population-level behavior via the analysis of co-occurrence networks computed from user timelines at three different scales: monthly, weekly, and daily occurrences. Analysis of these networks further reveals 3) drug and symptom direct and indirect associations with greater support in user timelines, as well as 4) clusters of symptoms and drugs revealed by the collective behavior of the observed population. This demonstrates that Instagram
CORREIA, RION BRATTIG; LI, LANG; ROCHA, LUIS M.
2015-01-01
Much recent research aims to identify evidence for Drug-Drug Interactions (DDI) and Adverse Drug reactions (ADR) from the biomedical scientific literature. In addition to this “Bibliome”, the universe of social media provides a very promising source of large-scale data that can help identify DDI and ADR in ways that have not been hitherto possible. Given the large number of users, analysis of social media data may be useful to identify under-reported, population-level pathology associated with DDI, thus further contributing to improvements in population health. Moreover, tapping into this data allows us to infer drug interactions with natural products—including cannabis—which constitute an array of DDI very poorly explored by biomedical research thus far. Our goal is to determine the potential of Instagram for public health monitoring and surveillance for DDI, ADR, and behavioral pathology at large. Most social media analysis focuses on Twitter and Facebook, but Instagram is an increasingly important platform, especially among teens, with unrestricted access of public posts, high availability of posts with geolocation coordinates, and images to supplement textual analysis. Using drug, symptom, and natural product dictionaries for identification of the various types of DDI and ADR evidence, we have collected close to 7000 user timelines spanning from October 2010 to June 2015. We report on 1) the development of a monitoring tool to easily observe user-level timelines associated with drug and symptom terms of interest, and 2) population-level behavior via the analysis of co-occurrence networks computed from user timelines at three different scales: monthly, weekly, and daily occurrences. Analysis of these networks further reveals 3) drug and symptom direct and indirect associations with greater support in user timelines, as well as 4) clusters of symptoms and drugs revealed by the collective behavior of the observed population. This demonstrates that
Huang, Xinchuan E-mail: Timothy.J.Lee@nasa.gov; Schwenke, David W.; Lee, Timothy J. E-mail: Timothy.J.Lee@nasa.gov
2014-03-21
A purely ab initio potential energy surface (PES) was refined with selected {sup 32}S{sup 16}O{sub 2} HITRAN data. Compared to HITRAN, the root-mean-squares error (σ{sub RMS}) for all J = 0–80 rovibrational energy levels computed on the refined PES (denoted Ames-1) is 0.013 cm{sup −1}. Combined with a CCSD(T)/aug-cc-pV(Q+d)Z dipole moment surface (DMS), an infrared (IR) line list (denoted Ames-296K) has been computed at 296 K and covers up to 8000 cm{sup −1}. Compared to the HITRAN and CDMS databases, the intensity agreement for most vibrational bands is better than 85%–90%. Our predictions for {sup 34}S{sup 16}O{sub 2} band origins, higher energy {sup 32}S{sup 16}O{sub 2} band origins and missing {sup 32}S{sup 16}O{sub 2} IR bands have been verified by most recent experiments and available HITRAN data. We conclude that the Ames-1 PES is able to predict {sup 32/34}S{sup 16}O{sub 2} band origins below 5500 cm{sup −1} with 0.01–0.03 cm{sup −1} uncertainties, and the Ames-296K line list provides continuous, reliable and accurate IR simulations. The K{sub a}-dependence of both line position and line intensity errors is discussed. The line list will greatly facilitate SO{sub 2} IR spectral experimental analysis, as well as elimination of SO{sub 2} lines in high-resolution astronomical observations.
Martins, Madlles Q.; Fortunato, Ana S.; Rodrigues, Weverton P.; Partelli, Fábio L.; Campostrini, Eliemar; Lidon, Fernando C.; DaMatta, Fábio M.; Ramalho, José C.; Ribeiro-Barros, Ana I.
2017-01-01
World coffee production has faced increasing challenges associated with ongoing climatic changes. Several studies, which have been almost exclusively based on temperature increase, have predicted extensive reductions (higher than half by 2,050) of actual coffee cropped areas. However, recent studies showed that elevated [CO2] can strongly mitigate the negative impacts of heat stress at the physiological and biochemical levels in coffee leaves. In addition, it has also been shown that coffee genotypes can successfully cope with temperatures above what has been traditionally accepted. Altogether, this information suggests that the real impact of climate changes on coffee growth and production could be significantly lower than previously estimated. Gene expression studies are an important tool to unravel crop acclimation ability, demanding the use of adequate reference genes. We have examined the transcript stability of 10 candidate reference genes to normalize RT-qPCR expression studies using a set of 24 cDNAs from leaves of three coffee genotypes (CL153, Icatu, and IPR108), grown under 380 or 700 μL CO2 L−1, and submitted to increasing temperatures from 25/20°C (day/night) to 42/34°C. Samples were analyzed according to genotype, [CO2], temperature, multiple stress interaction ([CO2], temperature) and total stress interaction (genotype, [CO2], and temperature). The transcript stability of each gene was assessed through a multiple analytical approach combining the Coeficient of Variation method and three algorithms (geNorm, BestKeeper, NormFinder). The transcript stability varied according to the type of stress for most genes, but the consensus ranking obtained with RefFinder, classified MDH as the gene with the highest mRNA stability to a global use, followed by ACT and S15, whereas α-TUB and CYCL showed the least stable mRNA contents. Using the coffee expression profiles of the gene encoding the large-subunit of ribulose-1,5-bisphosphate carboxylase
Xantheas, Sotiris S; Werhahn, Jasper C
2014-08-14
Based on the formulation of the analytical expression of the potential V(r) describing intermolecular interactions in terms of the dimensionless variables r* = r/r(m) and ɛ* = V/ɛ, where r(m) is the separation at the minimum and ɛ the well depth, we propose more generalized scalable forms for the commonly used Mie, Lennard-Jones, Morse, and Buckingham exponential-6 potential energy functions. These new generalized forms have an additional parameter from the original forms and revert to the original ones for some choice of that parameter. In this respect, the original forms of those potentials can be considered as special cases of the more general forms that are introduced. We also propose a scalable, non-revertible to the original one, 4-parameter extended Morse potential.
NASA Astrophysics Data System (ADS)
Mousavi, Mohsen; Shojaei, Mohammad Reza
2016-11-01
The relativistic Dirac equation under spin and pseudo-spin symmetries is investigated for Manning—Rosen plus quasi-Hellman potentials with tensor interaction. For the first time we consider the Hulthen plus Yukawa for tensor interaction. The Formula method is used to obtain the energy eigen-values and wave functions. We also discuss about the energy eigen-values and the Dirac spinors for the Manning—Rosen plus quasi-Hellman potentials for the spin and pseudo-spin symmetry with Formula method. To show the accuracy of the present model, some numerical results are shown in both pseudo-spin and spin symmetry limits.
Accurate spectral color measurements
NASA Astrophysics Data System (ADS)
Hiltunen, Jouni; Jaeaeskelaeinen, Timo; Parkkinen, Jussi P. S.
1999-08-01
Surface color measurement is of importance in a very wide range of industrial applications including paint, paper, printing, photography, textiles, plastics and so on. For a demanding color measurements spectral approach is often needed. One can measure a color spectrum with a spectrophotometer using calibrated standard samples as a reference. Because it is impossible to define absolute color values of a sample, we always work with approximations. The human eye can perceive color difference as small as 0.5 CIELAB units and thus distinguish millions of colors. This 0.5 unit difference should be a goal for the precise color measurements. This limit is not a problem if we only want to measure the color difference of two samples, but if we want to know in a same time exact color coordinate values accuracy problems arise. The values of two instruments can be astonishingly different. The accuracy of the instrument used in color measurement may depend on various errors such as photometric non-linearity, wavelength error, integrating sphere dark level error, integrating sphere error in both specular included and specular excluded modes. Thus the correction formulas should be used to get more accurate results. Another question is how many channels i.e. wavelengths we are using to measure a spectrum. It is obvious that the sampling interval should be short to get more precise results. Furthermore, the result we get is always compromise of measuring time, conditions and cost. Sometimes we have to use portable syste or the shape and the size of samples makes it impossible to use sensitive equipment. In this study a small set of calibrated color tiles measured with the Perkin Elmer Lamda 18 and the Minolta CM-2002 spectrophotometers are compared. In the paper we explain the typical error sources of spectral color measurements, and show which are the accuracy demands a good colorimeter should have.
Fellows, R.J.; Harvey, S.D.; Cataldo, D.A.; Mitchell, W.
1995-12-31
Munitions materiel such as trinitrotoluene (TNT) and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and their combustion/decomposition products can accumulate/cycle in terrestrial environs. High soil organic matter and fertility have been previously shown to negatively correlate with both TNT or RDX uptake in plants such as grass, wheat, and bean. The present study was therefore conducted using low fertility soil to assess uptake and distribution patterns of C-radiolabelled TNT and RDX (15 and 30 {micro}g/g) within corn (Zea mays), spinach (Spinacea oleraceae), carrot (Daucus carota), and alfalfa (Medicago sativa) grown to maturity in growth chambers. Uptake by the plants at maturity (90- to 120-days) ranged from 1.8 to 2.7% of total amended {sup 14}C-TNT for carrots and corn respectively and 17 to 33% of total amended {sup 14}C-RDX for corn and carrots respectively. Distribution patterns of total radiolabel indicate that the TNT-derived label was primarily retained within the roots (60 to 85%) while the RDX-derived label was distributed to the shoots (85 to 97%). Less than 0.01 {micro}g/g dry wt. TNT was found in all analyzed shoot tissues with > 90% of the TNT-derived radiolabel in the form of polar metabolites. Concentrations of RDX in shoot tissues of corn exceeded 180 {micro}g/g dry wt. Alfalfa grown in unfertilized, fertilized (NO{sub 3}), or unfertilized-inoculated (Rhizobia) soil exhibited a 70 to 100% increase in dry wt. after 45 days in the TNT-amended (15 {micro}g/g) fertilized and unfertilized-inoculated plants versus the controls. A potential TNT/nitrogen interaction will be discussed.
Potential interaction between zinc ions and a cyclodextrin-based diclofenac formulation.
Hamdan, Imad I; El-Sabawi, Dina; Abdel Jalil, Mariam
2016-01-01
Complexes of diclofenac sodium (DF-Na) with hydroxypropyl betacyclodextrin (HPβCD) were prepared by co-evaporation in a 1:1 ratio and characterized in light of previously reported data. Phase solubility diagrams were obtained for DF-Na with HPβCD in the presence and absence of zinc ions. Dissolution profiles were obtained for DF-Na and its HPβCD complex at acidic (pH 1.2) as well as in phosphate buffer (pH 6.8), in the presence and absence of zinc. HPβCD, as expected, was shown to improve the dissolution of DF-Na in acidic medium but not in phosphate buffer (pH 6.8). The presence of zinc ions decreased the in vitro dissolution of DF-HPβCD complex in acidic medium (pH 1.2) but not in phosphate buffer (pH 6.8). It was confirmed that the precipitate that was formed by zinc ions in the presence of HPβCD and DF-Na contained no cyclodextrin and most likely it was a mixture of the complexes: DF2-Zn and DF-Zn with some molecules of water. In vivo experiments on rats have shown that HPβCD has no statistically significant effect on absorption or bioavailability of DF-Na in spite of the observed improvement of its in vitro dissolution by HPβCD. Moreover, zinc ions were shown to decrease the absorption rate of DF-Na in rats model but did neither significantly alter the absorption nor bioavailability of DF-HPβCD complex. The zinc induced precipitates of DF were shown to have significantly different crystalline properties when HPβCD was present. Therefore, the pharmaceutical details of a DF-Na preparation should be considered when designing the formulation and predicting possible interaction between DF-Na (or other potential NSAIDs) and zinc metal.
Potential interaction between zinc ions and a cyclodextrin-based diclofenac formulation.
Hamdan, Imad I; El-Sabawi, Dina; Abdel Jalil, Mariam
2016-03-01
Complexes of diclofenac sodium (DF-Na) with hydroxypropyl betacyclodextrin (HPβCD) were prepared by co-evaporation in a 1:1 ratio and characterized in light of previously reported data. Phase solubility diagrams were obtained for DF-Na with HPβCD in the presence and absence of zinc ions. Dissolution profiles were obtained for DF-Na and its HPβCD complex at acidic (pH 1.2) as well as in phosphate buffer (pH 6.8), in the presence and absence of zinc. HPβCD, as expected, was shown to improve the dissolution of DF-Na in acidic medium but not in phosphate buffer (pH 6.8). The presence of zinc ions decreased the in vitro dissolution of DF-HPβCD complex in acidic medium (pH 1.2) but not in phosphate buffer (pH 6.8). It was confirmed that the precipitate that was formed by zinc ions in the presence of HPβCD and DF-Na contained no cyclodextrin and most likely it was a mixture of the complexes: DF2-Zn and DF-Zn with some molecules of water. In vivo experiments on rats have shown that HPβCD has no statistically significant effect on absorption or bioavailability of DF-Na in spite of the observed improvement of its in vitro dissolution by HPβCD. Moreover, zinc ions were shown to decrease the absorption rate of DF-Na in rats model but did neither significantly alter the absorption nor bioavailability of DF-HPβCD complex. The zinc induced precipitates of DF were shown to have significantly different crystalline properties when HPβCD was present. Therefore, the pharmaceutical details of a DF-Na preparation should be considered when designing the formulation and predicting possible interaction between DF-Na (or other potential NSAIDs) and zinc metal.
Chang, Andres; Hackett, Brent A; Winter, Christine C; Buchholz, Ursula J; Dutch, Rebecca Ellis
2012-09-01
The recently identified human metapneumovirus (HMPV) is a worldwide respiratory virus affecting all age groups and causing pneumonia and bronchiolitis in severe cases. Despite its clinical significance, no specific antiviral agents have been approved for treatment of HMPV infection. Unlike the case for most paramyxoviruses, the fusion proteins (F) of a number of strains, including the clinical isolate CAN97-83, can be triggered by low pH. We recently reported that residue H435 in the HRB linker domain acts as a pH sensor for HMPV CAN97-83 F, likely through electrostatic repulsion forces between a protonated H435 and its surrounding basic residues, K295, R396, and K438, at low pH. Through site-directed mutagenesis, we demonstrated that a positive charge at position 435 is required but not sufficient for F-mediated membrane fusion. Arginine or lysine substitution at position 435 resulted in a hyperfusogenic F protein, while replacement with aspartate or glutamate abolished fusion activity. Studies with recombinant viruses carrying mutations in this region confirmed its importance. Furthermore, a second region within the F(2) domain identified as being rich in charged residues was found to modulate fusion activity of HMPV F. Loss of charge at residues E51, D54, and E56 altered local folding and overall stability of the F protein, with dramatic consequences for fusion activity. As a whole, these studies implicate charged residues and potential electrostatic interactions in function, pH sensing, and overall stability of HMPV F.
Zhang, Nan; Liu, Yong; Jeong, Hyunyoung
2015-01-01
Tyrosine kinase inhibitors (TKIs) are anticancer drugs that may be co-administered with other drugs. The aims of this study are to investigate the inhibitory effects of TKIs on UDP-glucuronosyltransferase (UGT) activities, and to quantitatively evaluate their potential to cause drug-drug interactions (DDIs). Inhibition kinetic profiles of a panel of UGT enzymes (UGT1A1, 1A3, 1A4, 1A6, 1A7, 1A8, 1A9, 1A10, 2B4, 2B7, 2B15, and 2B17) by four TKIs (axitinib, imatinib, lapatinib and vandetanib) were characterized by using hepatic microsomes and recombinant proteins. Lapatinib exhibited potent competitive inhibition against UGT1A1 activity with a Ki of 0.5 μM. Imatinib was found to exhibit broad inhibition on several UGTs, particularly potent competitive inhibition against UGT2B17 with a Ki of 0.4 μM. The TKIs also exerted intermediate inhibition against several UGTs (i.e., UGT1A7 by lapatinib; UGT1A1 by imatinib; UGT1A4, 1A7 and 1A9 by axitinib; and UGT1A9 by vandetanib). Results from modeling for the quantitative prediction of DDI risk indicated that the coadministration of lapatinib or imatinib at clinical doses could result in a significant increase in AUC of drugs primarily cleared by UGT1A1 or 2B17. Lapatinib and imatinib may cause clinically significant DDIs when co-administered UGT1A1 or 2B17 substrates. PMID:26642944
Bouyoucos, Ian; Bushnell, Peter; Brill, Richard
2014-02-01
Atlantic sturgeon (Acipenser oxyrhynchus) populations have been declared either endangered or threatened under the U.S. Endangered Species Act. Effective measures to repel sturgeon from fishing gear would be beneficial to both fish and fishers because they could reduce both fishery-associated mortality and the need for seasonal and area closures of specific fisheries. Some chondrostean fishes (e.g., sturgeons and paddlefishes) can detect weak electric field gradients (possibly as low as 5 Μv/cm) due to arrays of electroreceptors (ampullae of Lorenzini) on their snout and gill covers. Weak electric fields, such as those produced by electropositive metals (typically mixtures of the lanthanide elements), could therefore potentially be used as a deterrent. To test this idea, we recorded the behavioral responses of juvenile Atlantic sturgeon (31-43 cm fork length) to electropositive metal (primarily a mixture of the lanthanide elements neodymium and praseodymium) both in the presence and absence of food stimuli. Trials were conducted in an approximately 2.5 m diameter × 0.3 m deep tank, and fish behaviors were recorded with an overhead digital video camera. Video records were subsequently digitized (x, y coordinate system), the distance between the fish and the electropositive metal calculated, and data summarized by compiling frequency distributions with 5-cm bins. Juvenile sturgeon showed clear avoidance of electropositive metal but only when food was present. On the basis of our results, we conclude that the electropositive metals, or other sources of weak electric fields, may eventually be used to reduce the interactions of Atlantic sturgeon with fishing gear, but further investigation is needed.
Woelke, Anna Lena; von Eichborn, Joachim; Murgueitio, Manuela S; Worth, Catherine L; Castiglione, Filippo; Preissner, Robert
2011-01-01
Peptide vaccination in cancer therapy is a promising alternative to conventional methods. However, the parameters for this personalized treatment are difficult to access experimentally. In this respect, in silico models can help to narrow down the parameter space or to explain certain phenomena at a systems level. Herein, we develop two empirical interaction potentials specific to B-cell and T-cell receptor complexes and validate their applicability in comparison to a more general potential. The interaction potentials are applied to the model VaccImm which simulates the immune response against solid tumors under peptide vaccination therapy. This multi-agent system is derived from another immune system simulator (C-ImmSim) and now includes a module that enables the amino acid sequence of immune receptors and their ligands to be taken into account. The multi-agent approach is combined with approved methods for prediction of major histocompatibility complex (MHC)-binding peptides and the newly developed interaction potentials. In the analysis, we critically assess the impact of the different modules on the simulation with VaccImm and how they influence each other. In addition, we explore the reasons for failures in inducing an immune response by examining the activation states of the immune cell populations in detail.In summary, the present work introduces immune-specific interaction potentials and their application to the agent-based model VaccImm which simulates peptide vaccination in cancer therapy.
Woelke, Anna Lena; von Eichborn, Joachim; Murgueitio, Manuela S.; Worth, Catherine L.; Castiglione, Filippo; Preissner, Robert
2011-01-01
Peptide vaccination in cancer therapy is a promising alternative to conventional methods. However, the parameters for this personalized treatment are difficult to access experimentally. In this respect, in silico models can help to narrow down the parameter space or to explain certain phenomena at a systems level. Herein, we develop two empirical interaction potentials specific to B-cell and T-cell receptor complexes and validate their applicability in comparison to a more general potential. The interaction potentials are applied to the model VaccImm which simulates the immune response against solid tumors under peptide vaccination therapy. This multi-agent system is derived from another immune system simulator (C-ImmSim) and now includes a module that enables the amino acid sequence of immune receptors and their ligands to be taken into account. The multi-agent approach is combined with approved methods for prediction of major histocompatibility complex (MHC)-binding peptides and the newly developed interaction potentials. In the analysis, we critically assess the impact of the different modules on the simulation with VaccImm and how they influence each other. In addition, we explore the reasons for failures in inducing an immune response by examining the activation states of the immune cell populations in detail. In summary, the present work introduces immune-specific interaction potentials and their application to the agent-based model VaccImm which simulates peptide vaccination in cancer therapy. PMID:21858048
Leão, Danyllo Fábio Lessa; de Moura, Cristiano Soares; de Medeiros, Danielle Souto
2014-01-01
Drug interactions are risk factors for the occurrence of adverse drug reactions. The risk for drug interactions includes factors related to prescription that are intrinsic to the patient. This study sought to evaluate the potential drug interactions in primary care prescriptions in Vitória da Conquista in the state of Bahia to fill the knowledge gap on this topic in Brazil. Information about several variables derived from the primary health care prescriptions was collected and drug interactions were evaluated based on information from Medscape and Micromedex(R) databases. Polypharmacy frequency and its association with the occurrence of drug interactions were also evaluated. Results revealed a 48,9% frequency of drug interactions, 74,9% of moderate or greater severity, 8,6% of prescriptions in polypharmacy that in the chi-square test showed a positive association with the occurrence of drug interactions (p < 0,001). Prescriptions from primary care in Vitória da Conquista in the state of Bahia showed a high frequency of drug interactions, however it is necessary to analyze other risk factors for their occurrence at this level of health care.
NASA Astrophysics Data System (ADS)
Pattabhiraman, Harini; Dijkstra, Marjolein
2017-03-01
A two-dimensional dodecagonal quasicrystal was previously reported by Dotera et al (2014 Nature 506 208) in a system of particles interacting with a hard core of diameter σ and a repulsive square shoulder of diameter δ =1.40σ . In the current work, we examine the formation of this quasicrystal using bond orientational order parameters, correlation functions and tiling distributions. We find that this dodecagonal quasicrystal forms from a fluid phase. We further study the effect of the width of the repulsive shoulder by simulating the system over a range of values of δ. For the range of densities and temperatures considered, we observe the formation of the dodecagonal quasicrystal between δ =1.30σ and 1.44σ . We also study the effect of shape of the interaction potential by simulating the system using three other interaction potentials with two length scales, namely hard-core plus a linear ramp, modified exponential, or Buckingham (exp-6) potential. We observe the presence of the quasicrystal in all three systems. However, depending on the shape of the potential, the formation of the quasicrystal takes place at lower temperatures (or higher interaction strengths). Using free-energy calculations, we demonstrate that the quasicrystal is thermodynamically stable in the square-shoulder and linear-ramp system.
ERIC Educational Resources Information Center
Wang, Yan; Zhang, Ming; Moon, Changjong; Hu, Qubai; Wang, Baiping; Martin, George; Sun, Zhongsheng; Wang, Hongbing
2009-01-01
FE65 is expressed predominantly in the brain and interacts with the C-terminal domain of [beta]-amyloid precursor protein (APP). We examined hippocampus-dependent memory and in vivo long-term potentiation (LTP) at the CA1 synapses with isoform-specific FE65 knockout (p97FE65[superscript -/-]) mice. When examined using the Morris water maze,…
Pattabhiraman, Harini; Dijkstra, Marjolein
2017-03-08
A two-dimensional dodecagonal quasicrystal was previously reported by Dotera et al (2014 Nature 506 208) in a system of particles interacting with a hard core of diameter σ and a repulsive square shoulder of diameter [Formula: see text]. In the current work, we examine the formation of this quasicrystal using bond orientational order parameters, correlation functions and tiling distributions. We find that this dodecagonal quasicrystal forms from a fluid phase. We further study the effect of the width of the repulsive shoulder by simulating the system over a range of values of δ. For the range of densities and temperatures considered, we observe the formation of the dodecagonal quasicrystal between [Formula: see text] and [Formula: see text]. We also study the effect of shape of the interaction potential by simulating the system using three other interaction potentials with two length scales, namely hard-core plus a linear ramp, modified exponential, or Buckingham (exp-6) potential. We observe the presence of the quasicrystal in all three systems. However, depending on the shape of the potential, the formation of the quasicrystal takes place at lower temperatures (or higher interaction strengths). Using free-energy calculations, we demonstrate that the quasicrystal is thermodynamically stable in the square-shoulder and linear-ramp system.
Thompson, Aidan P; Plimpton, Steven J; Mattson, William
2009-10-21
Three distinct forms are derived for the force virial contribution to the pressure and stress tensor of a collection of atoms interactin