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Sample records for molecular potential energy

  1. Potential energy hypersurface and molecular flexibility

    NASA Astrophysics Data System (ADS)

    Koča, Jaroslav

    1993-02-01

    The molecular flexibility phenomenon is discussed from the conformational potential energy(hyper) surface (PES) point of view. Flexibility is considered as a product of three terms: thermodynamic, kinetic and geometrical. Several expressions characterizing absolute and relative molecular flexibility are introduced, depending on a subspace studied of the entire conformational space, energy level E of PES as well as absolute temperature. Results obtained by programs DAISY, CICADA and PANIC in conjunction with molecular mechanics program MMX for flexibility analysis of isopentane, 2,2-dimethylpentane and isohexane molecules are introduced.

  2. Calculation of molecular free energies in classical potentials

    NASA Astrophysics Data System (ADS)

    Farhi, Asaf; Singh, Bipin

    2016-02-01

    Free energies of molecules can be calculated by quantum chemistry computations or by normal mode classical calculations. However, the first can be computationally impractical for large molecules and the second is based on the assumption of harmonic dynamics. We present a novel, accurate and complete calculation of molecular free energies in standard classical potentials. In this method we transform the molecule by relaxing potential terms which depend on the coordinates of a group of atoms in that molecule and calculate the free energy difference associated with the transformation. Then, since the transformed molecule can be treated as non-interacting systems, the free energy associated with these atoms is analytically or numerically calculated. This two-step calculation can be applied to calculate free energies of molecules or free energy difference between (possibly large) molecules in a general environment. We demonstrate the method in free energy calculations for methanethiol and butane molecules in vacuum and solvent. We suggest the potential application of free energy calculation of chemical reactions in classical molecular simulations.

  3. Generalized Potential Energy Finite Elements for Modeling Molecular Nanostructures.

    PubMed

    Chatzieleftheriou, Stavros; Adendorff, Matthew R; Lagaros, Nikos D

    2016-10-24

    The potential energy of molecules and nanostructures is commonly calculated in the molecular mechanics formalism by superimposing bonded and nonbonded atomic energy terms, i.e. bonds between two atoms, bond angles involving three atoms, dihedral angles involving four atoms, nonbonded terms expressing the Coulomb and Lennard-Jones interactions, etc. In this work a new, generalized numerical simulation is presented for studying the mechanical behavior of three-dimensional nanostructures at the atomic scale. The energy gradient and Hessian matrix of such assemblies are usually computed numerically; a potential energy finite element model is proposed herein where these two components are expressed analytically. In particular, generalized finite elements are developed that express the interactions among atoms in a manner equivalent to that invoked in simulations performed based on the molecular dynamics method. Thus, the global tangent stiffness matrix for any nanostructure is formed as an assembly of the generalized finite elements and is directly equivalent to the Hessian matrix of the potential energy. The advantages of the proposed model are identified in terms of both accuracy and computational efficiency. In the case of popular force fields (e.g., CHARMM), the computation of the Hessian matrix by implementing the proposed method is of the same order as that of the gradient. This analysis can be used to minimize the potential energy of molecular systems under nodal loads in order to derive constitutive laws for molecular systems where the entropy and solvent effects are neglected and can be approximated as solids, such as double stranded DNA nanostructures. In this context, the sequence dependent stretch modulus for some typical base pairs step is calculated.

  4. Forces on nuclei moving on autoionizing molecular potential energy surfaces.

    PubMed

    Moiseyev, Nimrod

    2017-01-14

    Autoionization of molecular systems occurs in diatomic molecules and in small biochemical systems. Quantum chemistry packages enable calculation of complex potential energy surfaces (CPESs). The imaginary part of the CPES is associated with the autoionization decay rate, which is a function of the molecular structure. Molecular dynamics simulations, within the framework of the Born-Oppenheimer approximation, require the definition of a force field. The ability to calculate the forces on the nuclei in bio-systems when autoionization takes place seems to rely on an understanding of radiative damages in RNA and DNA arising from the release of slow moving electrons which have long de Broglie wavelengths. This work addresses calculation of the real forces on the nuclei moving on the CPES. By using the transformation of the time-dependent Schrödinger equation, previously used by Madelung, we proved that the classical forces on nuclei moving on the CPES correlated with the gradient of the real part of the CPES. It was proved that the force on the nuclei of the metastable molecules is time independent although the probability to detect metastable molecules exponentially decays. The classical force is obtained from the transformed Schrödinger equation when ℏ=0 and the Schrödinger equation is reduced to the classical (Newtonian) equations of motion. The forces on the nuclei regardless on what potential energy surface they move (parent CPES or product real PESs) vary in time due to the autoionization process.

  5. Molecular understanding of mutagenicity using potential energy methods

    SciTech Connect

    Broyde, S.; Shapiro, R.

    1992-07-01

    Our objective, has been to elucidate on a molecular level, at atomic resolution, the structures of DNAs modified by 2-aminofluorene and its N-acetyl derivative, 2-acetylaminofluorene (AAF). The underlying hypothesis is that DNA replicates with reduced fidelity when its normal right-handed B-structure is altered, and one result is a higher mutation rate. This change in structure may occur normally at a low incidence, for example by the formation of hairpin loops in appropriate sequences, but it may be enhanced greatly after covalent modification by a mutagenic substance. We use computational methods and have been able to incorporate the first data from NMR studies in our calculations. Computational approaches are important because x-ray and spectroscopic studies have not succeeded in producing atomic resolution views of mutagen and carcinogen-oligonucleotide adducts. The specific methods that we employ are minimized potential energy calculations using the torsion angle space molecular mechanics program DUPLEX to yield static views. Molecular dynamics simulations, with full solvent and salt, of the important static structures are carried out with the program AMBER; this yields mobile views in a medium that mimics the natural aqueous environment of the cell as well as can be done with current available computing resources.

  6. Photon Upconversion and Molecular Solar Energy Storage by Maximizing the Potential of Molecular Self-Assembly.

    PubMed

    Kimizuka, Nobuo; Yanai, Nobuhiro; Morikawa, Masa-Aki

    2016-11-29

    The self-assembly of functional molecules into ordered molecular assemblies and the fulfillment of potentials unique to their nanotomesoscopic structures have been one of the central challenges in chemistry. This Feature Article provides an overview of recent progress in the field of molecular self-assembly with the focus on the triplet-triplet annihilation-based photon upconversion (TTA-UC) and supramolecular storage of photon energy. On the basis of the integration of molecular self-assembly and photon energy harvesting, triplet energy migration-based TTA-UC has been achieved in varied molecular systems. Interestingly, some molecular self-assemblies dispersed in solution or organogels revealed oxygen barrier properties, which allowed TTA-UC even under aerated conditions. The elements of molecular self-assembly were also introduced to the field of molecular solar thermal fuel, where reversible photoliquefaction of ionic crystals to ionic liquids was found to double the molecular storage capacity with the simultaneous pursuit of switching ionic conductivity. A future prospect in terms of innovating molecular self-assembly toward molecular systems chemistry is also discussed.

  7. Footprinting molecular electrostatic potential surfaces for calculation of solvation energies.

    PubMed

    Calero, Christian Solis; Farwer, Jochen; Gardiner, Eleanor J; Hunter, Christopher A; Mackey, Mark; Scuderi, Serena; Thompson, Stuart; Vinter, Jeremy G

    2013-11-07

    A liquid is composed of an ensemble of molecules that populate a large number of different states, so calculation of the solvation energy of a molecule in solution requires a method for summing the interactions with the environment over all of these states. The surface site interaction model for the properties of liquids at equilibrium (SSIMPLE) simplifies the surface of a molecule to a discrete number of specific interaction sites (SSIPs). The thermodynamic properties of these interaction sites can be characterised experimentally, for example, through measurement of association constants for the formation of simple complexes that feature a single H-bonding interaction. Correlation of experimentally determined solution phase H-bond parameters with gas phase ab initio calculations of maxima and minima on molecular electrostatic potential surfaces (MEPS) provides a method for converting gas phase calculations on isolated molecules to parameters that can be used to estimate solution phase interaction free energies. This approach has been generalised using a footprinting technique that converts an MEPS into a discrete set of SSIPs (each described by a polar interaction parameter, εi). These SSIPs represent the molecular recognition properties of the entire surface of the molecule. For example, water is described by four SSIPs, two H-bond donor sites and two H-bond acceptor sites. A liquid mixture is described as an ensemble of SSIPs that represent the components of the mixture at appropriate concentrations. Individual SSIPs are assumed to be independent, so speciation of SSIP contacts can be calculated based on properties of the individual SSIP interactions, which are given by the sum of a polar (εiεj) and a non-polar (E(vdW)) interaction term. Results are presented for calculation the free energies of transfer of a range of organic molecules from the pure liquid into water, from the pure liquid into n-hexadecane, from n-hexadecane into water, from n-octanol into

  8. Electronic structure, molecular bonding and potential energy surfaces

    SciTech Connect

    Ruedenberg, K.

    1993-12-01

    By virtue of the universal validity of the generalized Born-Oppenheimer separation, potential energy surfaces (PES`) represent the central conceptual as well as quantitative entities of chemical physics and provide the basis for the understanding of most physicochemical phenomena in many diverse fields. The research in this group deals with the elucidation of general properties of PES` as well as with the quantitative determination of PES` for concrete systems, in particular pertaining to reactions involving carbon, oxygen, nitrogen and hydrogen molecules.

  9. Foraging on the potential energy surface: A swarm intelligence-based optimizer for molecular geometry

    NASA Astrophysics Data System (ADS)

    Wehmeyer, Christoph; Falk von Rudorff, Guido; Wolf, Sebastian; Kabbe, Gabriel; Schärf, Daniel; Kühne, Thomas D.; Sebastiani, Daniel

    2012-11-01

    We present a stochastic, swarm intelligence-based optimization algorithm for the prediction of global minima on potential energy surfaces of molecular cluster structures. Our optimization approach is a modification of the artificial bee colony (ABC) algorithm which is inspired by the foraging behavior of honey bees. We apply our modified ABC algorithm to the problem of global geometry optimization of molecular cluster structures and show its performance for clusters with 2-57 particles and different interatomic interaction potentials.

  10. Ab initio potential energy and dipole moment surfaces for CS2: determination of molecular vibrational energies.

    PubMed

    Pradhan, Ekadashi; Carreón-Macedo, José-Luis; Cuervo, Javier E; Schröder, Markus; Brown, Alex

    2013-08-15

    The ground state potential energy and dipole moment surfaces for CS2 have been determined at the CASPT2/C:cc-pVTZ,S:aug-cc-pV(T+d)Z level of theory. The potential energy surface has been fit to a sum-of-products form using the neural network method with exponential neurons. A generic interface between neural network potential energy surface fitting and the Heidelberg MCTDH software package is demonstrated. The potential energy surface has also been fit using the potfit procedure in MCTDH. For fits to the low-energy regions of the potential, the neural network method requires fewer parameters than potfit to achieve high accuracy; global fits are comparable between the two methods. Using these potential energy surfaces, the vibrational energies have been computed for the four most abundant CS2 isotopomers. These results are compared to experimental and previous theoretical data. The current potential energy surfaces are shown to accurately reproduce the low-lying vibrational energies within a few wavenumbers. Hence, the potential energy and dipole moments surfaces will be useful for future study on the control of quantum dynamics in CS2.

  11. Hierarchical particle swarm optimizer for minimizing the non-convex potential energy of molecular structure.

    PubMed

    Cheung, Ngaam J; Shen, Hong-Bin

    2014-11-01

    The stable conformation of a molecule is greatly important to uncover the secret of its properties and functions. Generally, the conformation of a molecule will be the most stable when it is of the minimum potential energy. Accordingly, the determination of the conformation can be solved in the optimization framework. It is, however, not an easy task to achieve the only conformation with the lowest energy among all the potential ones because of the high complexity of the energy landscape and the exponential computation increasing with molecular size. In this paper, we develop a hierarchical and heterogeneous particle swarm optimizer (HHPSO) to deal with the problem in the minimization of the potential energy. The proposed method is evaluated over a scalable simplified molecular potential energy function with up to 200 degrees of freedom and a realistic energy function of pseudo-ethane molecule. The experimental results are compared with other six PSO variants and four genetic algorithms. The results show HHPSO is significantly better than the compared PSOs with p-value less than 0.01277 over molecular potential energy function.

  12. Phosphorescent Molecular Butterflies with Controlled Potential-Energy Surfaces and Their Application as Luminescent Viscosity Sensor.

    PubMed

    Zhou, Chenkun; Yuan, Lin; Yuan, Zhao; Doyle, Nicholas Kelly; Dilbeck, Tristan; Bahadur, Divya; Ramakrishnan, Subramanian; Dearden, Albert; Huang, Chen; Ma, Biwu

    2016-09-06

    We report precise manipulation of the potential-energy surfaces (PESs) of a series of butterfly-like pyrazolate-bridged platinum binuclear complexes, by synthetic control of the electronic structure of the cyclometallating ligand and the steric bulkiness of the pyrazolate bridging ligand. Color tuning of dual emission from blue/red, to green/red and red/deep red were achieved for these phosphorescent molecular butterflies, which have two well-controlled energy minima on the PESs. The environmentally dependent photoluminescence of these molecular butterflies enabled their application as self-referenced luminescent viscosity sensor.

  13. The molecular potential energy surface and vibrational energy levels of methyl fluoride. Part II.

    PubMed

    Manson, Steven A; Law, Mark M; Atkinson, Ian A; Thomson, Grant A

    2006-06-28

    New analytical bending and stretching, ground electronic state, potential energy surfaces for CH(3)F are reported. The surfaces are expressed in bond-length, bond-angle internal coordinates. The four-dimensional stretching surface is an accurate, least squares fit to over 2000 symmetrically unique ab initio points calculated at the CCSD(T) level. Similarly, the five-dimensional bending surface is a fit to over 1200 symmetrically unique ab initio points. This is an important first stage towards a full nine-dimensional potential energy surface for the prototype CH(3)F molecule. Using these surfaces, highly excited stretching and (separately) bending vibrational energy levels of CH(3)F are calculated variationally using a finite basis representation method. The method uses the exact vibrational kinetic energy operator derived for XY(3)Z systems by Manson and Law (preceding paper, Part I, Phys. Chem. Chem. Phys., 2006, 8, DOI: 10.1039/b603106d). We use the full C(3v) symmetry and the computer codes are designed to use an arbitrary potential energy function. Ultimately, these results will be used to design a compact basis for fully coupled stretch-bend calculations of the vibrational energy levels of the CH(3)F system.

  14. New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations.

    PubMed

    Gapsys, Vytautas; Seeliger, Daniel; de Groot, Bert L

    2012-07-10

    The fields of rational drug design and protein engineering benefit from accurate free energy calculations based on molecular dynamics simulations. A thermodynamic integration scheme is often used to calculate changes in the free energy of a system by integrating the change of the system's Hamiltonian with respect to a coupling parameter. These methods exploit nonphysical pathways over thermodynamic cycles involving particle introduction and annihilation. Such alchemical transitions require the modification of the classical nonbonded potential energy terms by applying soft-core potential functions to avoid singularity points. In this work, we propose a novel formulation for a soft-core potential to be applied in nonequilibrium free energy calculations that alleviates singularities, numerical instabilities, and additional minima in the potential energy for all combinations of nonbonded interactions at all intermediate alchemical states. The method was validated by application to (a) the free energy calculations of a closed thermodynamic cycle, (b) the mutation influence on protein thermostability, (c) calculations of small ligand solvation free energies, and (d) the estimation of binding free energies of trypsin inhibitors. The results show that the novel soft-core function provides a robust and accurate general purpose solution to alchemical free energy calculations.

  15. Diabatic Molecular Orbitals, Potential Energies, and Potential Energy Surface Couplings by the 4-fold Way for Photodissociation of Phenol.

    PubMed

    Xu, Xuefei; Yang, Ke R; Truhlar, Donald G

    2013-08-13

    Complete-active-space self-consistent-field (CASSCF) calculations provide useful reference wave functions for configuration interaction or perturbation theory calculations of excited-state potential energy surfaces including dynamical electron correlation. However, the canonical molecular orbitals (MOs) of CASSCF calculations usually have mixed character in regions of strong interaction of two or more electronic states; therefore, they are unsuitable for diabatization using the configurational uniformity approach. Here, CASSCF diabatic MOs for phenol have been obtained by the 4-fold way, and comparison to the CASSCF canonical MOs shows that they are much smoother. Using these smooth CASSCF diabatic MOs, we performed direct diabatization calculations for the three low-lying states ((1)ππ, (1)ππ*, and (1)πσ*) and their diabatic (scalar) couplings at the dynamically correlated multiconfiguration quasidegenerate perturbation theory (MC-QDPT) level. We present calculations along the O-H stretching and C-C-O-H torsion coordinates for the nonadiabatic photodissociation of phenol to the phenoxyl radical and hydrogen atom. The seams of (1)ππ*/(1)πσ* and (1)ππ/(1)πσ* diabatic crossings are plotted as functions of these coordinates. We also present diabatization calculations for displacements along the out-of-plane ring distortion modes 16a and 16b of the phenyl group. The dominant coupling modes of the two conical intersections ((1)ππ*/(1)πσ* and (1)ππ/(1)πσ*) are discussed. The present diabatization method is confirmed to be valid even for significantly distorted ring structures by diabatization calculations along a reaction path connecting the planar equilibrium geometry of phenol to its strongly distorted prefulvenic form. The present work provides insight into the mode specificity of phenol photodissociation and shows that diabatization at the MC-QDPT level employing CASSCF diabatic MOs can be a good starting point for multidimensional dynamics

  16. Quantitative analysis of molecular surfaces: areas, volumes, electrostatic potentials and average local ionization energies.

    PubMed

    Bulat, Felipe A; Toro-Labbé, Alejandro; Brinck, Tore; Murray, Jane S; Politzer, Peter

    2010-11-01

    We describe a procedure for performing quantitative analyses of fields f(r) on molecular surfaces, including statistical quantities and locating and evaluating their local extrema. Our approach avoids the need for explicit mathematical representation of the surface and can be implemented easily in existing graphical software, as it is based on the very popular representation of a surface as collection of polygons. We discuss applications involving the volumes, surface areas and molecular surface electrostatic potentials, and local ionization energies of a group of 11 molecules.

  17. Molecular potential energies in dodecahedron cell of methane hydrate and dispersion correction for DFT.

    PubMed

    Du, Qi-Shi; Li, Da-Peng; Liu, Peng-Jun; Huang, Ri-Bo

    2008-09-01

    The interaction potential energies of water-water and water-methane in structure-I unit cell of methane hydrate are calculated from 2.1 to 8.0A using density functional theory (DFT) B3LYP/TZVP. The curves of potential energies are corrected for basis set superposition error (BSSE) and dispersion interaction using a 4-term L-J (4,6-8,12) correction equation, which is derived from CCSD(T)/cc-pVTZ calculations of water-water and water-methane molecular pairs, using least squares curve-fitting. The methane hydrate unit cell is a regular water dodecahedron cell consisting of 20 water molecules with a methane molecule in the center. The geometries of water and methane are optimized at CCSD(T)/cc-pVTZ level. The BSSE-corrections are calculated for water-water and water-methane interaction energies as functions of the side length, l, of the dodecahedron cell at B3LYP/TZVP level in the range from 2.1 to 8.0A. The BSSE CP-corrected and dispersion-corrected potential energy surfaces (PES) of water-water and water-methane are useful for molecular dynamics simulation of gas clathrate-hydrates.

  18. Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations

    SciTech Connect

    Kandel, Saugat; Salomon-Ferrer, Romelia; Larsen, Adrien B.; Vaidehi, Nagarajan; Jain, Abhinandan

    2016-01-28

    The Internal Coordinate Molecular Dynamics (ICMD) method is an attractive molecular dynamics (MD) method for studying the dynamics of bonded systems such as proteins and polymers. It offers a simple venue for coarsening the dynamics model of a system at multiple hierarchical levels. For example, large scale protein dynamics can be studied using torsional dynamics, where large domains or helical structures can be treated as rigid bodies and the loops connecting them as flexible torsions. ICMD with such a dynamic model of the protein, combined with enhanced conformational sampling method such as temperature replica exchange, allows the sampling of large scale domain motion involving high energy barrier transitions. Once these large scale conformational transitions are sampled, all-torsion, or even all-atom, MD simulations can be carried out for the low energy conformations sampled via coarse grained ICMD to calculate the energetics of distinct conformations. Such hierarchical MD simulations can be carried out with standard all-atom forcefields without the need for compromising on the accuracy of the forces. Using constraints to treat bond lengths and bond angles as rigid can, however, distort the potential energy landscape of the system and reduce the number of dihedral transitions as well as conformational sampling. We present here a two-part solution to overcome such distortions of the potential energy landscape with ICMD models. To alleviate the intrinsic distortion that stems from the reduced phase space in torsional MD, we use the Fixman compensating potential. To additionally alleviate the extrinsic distortion that arises from the coupling between the dihedral angles and bond angles within a force field, we propose a hybrid ICMD method that allows the selective relaxing of bond angles. This hybrid ICMD method bridges the gap between all-atom MD and torsional MD. We demonstrate with examples that these methods together offer a solution to eliminate the potential

  19. Spectroscopic studies, potential energy surface and molecular orbital calculations of pramipexole

    NASA Astrophysics Data System (ADS)

    Muthu, S.; Uma Maheswari, J.; Srinivasan, S.; Isac paulraj, E.

    2013-11-01

    A systematic vibrational spectroscopic assignment and analysis of pramipexole [(S)-N6-propyl-4,5,6,7-tetrahydro-1,3-benzothiazole-2,6-diamine] has been carried out using FT-IR and FT-Raman spectral data. The vibrational analysis was aided by an electronic structure calculation based on the hybrid density functional method B3LYP using a 6-311G(d, p) and cc-pVTZ basis sets. Molecular equilibrium geometries, electronic energies, IR and Raman intensities, harmonic vibrational frequencies have been computed. The assignments are based on the experimental IR and Raman spectra, and a complete assignment of the observed spectra has been proposed. The UV-visible spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies and the maximum absorption λmax were determined by time-dependent DFT (TD-DFT) method. The geometrical parameters, vibrational frequencies and absorption wavelengths were compared with the experimental data. The complete vibrational assignments are performed on the basis of the potential energy distributions (PEDs) of the vibrational modes in terms of natural internal coordinates. The simulated FT-IR, FT-Raman, and UV spectra of the title compound have been constructed. In addition, the potential energy surface, HOMO and LUMO energies, the molecular electrostatic potential and the first-order hyperpolarizability have been computed. The magnitude of the first-order hyperpolarizability is 5 times larger than that of urea and the title compound may be a potential applicant for the development of NLO materials.

  20. Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations

    PubMed Central

    Kandel, Saugat; Salomon-Ferrer, Romelia; Larsen, Adrien B.; Jain, Abhinandan; Vaidehi, Nagarajan

    2016-01-01

    The Internal Coordinate Molecular Dynamics (ICMD) method is an attractive molecular dynamics (MD) method for studying the dynamics of bonded systems such as proteins and polymers. It offers a simple venue for coarsening the dynamics model of a system at multiple hierarchical levels. For example, large scale protein dynamics can be studied using torsional dynamics, where large domains or helical structures can be treated as rigid bodies and the loops connecting them as flexible torsions. ICMD with such a dynamic model of the protein, combined with enhanced conformational sampling method such as temperature replica exchange, allows the sampling of large scale domain motion involving high energy barrier transitions. Once these large scale conformational transitions are sampled, all-torsion, or even all-atom, MD simulations can be carried out for the low energy conformations sampled via coarse grained ICMD to calculate the energetics of distinct conformations. Such hierarchical MD simulations can be carried out with standard all-atom forcefields without the need for compromising on the accuracy of the forces. Using constraints to treat bond lengths and bond angles as rigid can, however, distort the potential energy landscape of the system and reduce the number of dihedral transitions as well as conformational sampling. We present here a two-part solution to overcome such distortions of the potential energy landscape with ICMD models. To alleviate the intrinsic distortion that stems from the reduced phase space in torsional MD, we use the Fixman compensating potential. To additionally alleviate the extrinsic distortion that arises from the coupling between the dihedral angles and bond angles within a force field, we propose a hybrid ICMD method that allows the selective relaxing of bond angles. This hybrid ICMD method bridges the gap between all-atom MD and torsional MD. We demonstrate with examples that these methods together offer a solution to eliminate the potential

  1. Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Kandel, Saugat; Salomon-Ferrer, Romelia; Larsen, Adrien B.; Jain, Abhinandan; Vaidehi, Nagarajan

    2016-01-01

    The Internal Coordinate Molecular Dynamics (ICMD) method is an attractive molecular dynamics (MD) method for studying the dynamics of bonded systems such as proteins and polymers. It offers a simple venue for coarsening the dynamics model of a system at multiple hierarchical levels. For example, large scale protein dynamics can be studied using torsional dynamics, where large domains or helical structures can be treated as rigid bodies and the loops connecting them as flexible torsions. ICMD with such a dynamic model of the protein, combined with enhanced conformational sampling method such as temperature replica exchange, allows the sampling of large scale domain motion involving high energy barrier transitions. Once these large scale conformational transitions are sampled, all-torsion, or even all-atom, MD simulations can be carried out for the low energy conformations sampled via coarse grained ICMD to calculate the energetics of distinct conformations. Such hierarchical MD simulations can be carried out with standard all-atom forcefields without the need for compromising on the accuracy of the forces. Using constraints to treat bond lengths and bond angles as rigid can, however, distort the potential energy landscape of the system and reduce the number of dihedral transitions as well as conformational sampling. We present here a two-part solution to overcome such distortions of the potential energy landscape with ICMD models. To alleviate the intrinsic distortion that stems from the reduced phase space in torsional MD, we use the Fixman compensating potential. To additionally alleviate the extrinsic distortion that arises from the coupling between the dihedral angles and bond angles within a force field, we propose a hybrid ICMD method that allows the selective relaxing of bond angles. This hybrid ICMD method bridges the gap between all-atom MD and torsional MD. We demonstrate with examples that these methods together offer a solution to eliminate the potential

  2. Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations.

    PubMed

    Kandel, Saugat; Salomon-Ferrer, Romelia; Larsen, Adrien B; Jain, Abhinandan; Vaidehi, Nagarajan

    2016-01-28

    The Internal Coordinate Molecular Dynamics (ICMD) method is an attractive molecular dynamics (MD) method for studying the dynamics of bonded systems such as proteins and polymers. It offers a simple venue for coarsening the dynamics model of a system at multiple hierarchical levels. For example, large scale protein dynamics can be studied using torsional dynamics, where large domains or helical structures can be treated as rigid bodies and the loops connecting them as flexible torsions. ICMD with such a dynamic model of the protein, combined with enhanced conformational sampling method such as temperature replica exchange, allows the sampling of large scale domain motion involving high energy barrier transitions. Once these large scale conformational transitions are sampled, all-torsion, or even all-atom, MD simulations can be carried out for the low energy conformations sampled via coarse grained ICMD to calculate the energetics of distinct conformations. Such hierarchical MD simulations can be carried out with standard all-atom forcefields without the need for compromising on the accuracy of the forces. Using constraints to treat bond lengths and bond angles as rigid can, however, distort the potential energy landscape of the system and reduce the number of dihedral transitions as well as conformational sampling. We present here a two-part solution to overcome such distortions of the potential energy landscape with ICMD models. To alleviate the intrinsic distortion that stems from the reduced phase space in torsional MD, we use the Fixman compensating potential. To additionally alleviate the extrinsic distortion that arises from the coupling between the dihedral angles and bond angles within a force field, we propose a hybrid ICMD method that allows the selective relaxing of bond angles. This hybrid ICMD method bridges the gap between all-atom MD and torsional MD. We demonstrate with examples that these methods together offer a solution to eliminate the potential

  3. Direct molecular simulation of nitrogen dissociation based on an ab initio potential energy surface

    SciTech Connect

    Valentini, Paolo Schwartzentruber, Thomas E. Bender, Jason D. Nompelis, Ioannis Candler, Graham V.

    2015-08-15

    The direct molecular simulation (DMS) approach is used to predict the internal energy relaxation and dissociation dynamics of high-temperature nitrogen. An ab initio potential energy surface (PES) is used to calculate the dynamics of two interacting nitrogen molecules by providing forces between the four atoms. In the near-equilibrium limit, it is shown that DMS reproduces the results obtained from well-established quasiclassical trajectory (QCT) analysis, verifying the validity of the approach. DMS is used to predict the vibrational relaxation time constant for N{sub 2}–N{sub 2} collisions and its temperature dependence, which are in close agreement with existing experiments and theory. Using both QCT and DMS with the same PES, we find that dissociation significantly depletes the upper vibrational energy levels. As a result, across a wide temperature range, the dissociation rate is found to be approximately 4–5 times lower compared to the rates computed using QCT with Boltzmann energy distributions. DMS calculations predict a quasi-steady-state distribution of rotational and vibrational energies in which the rate of depletion of high-energy states due to dissociation is balanced by their rate of repopulation due to collisional processes. The DMS approach simulates the evolution of internal energy distributions and their coupling to dissociation without the need to precompute rates or cross sections for all possible energy transitions. These benchmark results could be used to develop new computational fluid dynamics models for high-enthalpy flow applications.

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

    PubMed

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

    2016-07-13

    Almost 50 years have passed from the first computer simulations of water, and a large number of molecular models have been proposed since then to elucidate the unique behavior of water across different phases. In this article, we review the recent progress in the development of analytical potential energy functions that aim at correctly representing many-body effects. Starting from the many-body expansion of the interaction energy, specific focus is on different classes of potential energy functions built upon a hierarchy of approximations and on their ability to accurately reproduce reference data obtained from state-of-the-art electronic structure calculations and experimental measurements. We show that most recent potential energy functions, which include explicit short-range representations of two-body and three-body effects along with a physically correct description of many-body effects at all distances, predict the properties of water from the gas to the condensed phase with unprecedented accuracy, thus opening the door to the long-sought "universal model" capable of describing the behavior of water under different conditions and in different environments.

  5. Molecular structure and analytical potential energy function of SeCO

    NASA Astrophysics Data System (ADS)

    Zhang, Heng; Tian, Duan-Liang; Yan, Shi-Ying

    2014-09-01

    The density functional method (B3P86/6-311G) is used for calculating the possible structures of SeC, SeO, and SeCO molecules. The result shows that the ground state of the SeC molecule is 1Σ, the equilibrium nuclear distance is RSeC = 0.1699 nm, and the dissociation energy is De = 8.7246 eV. The ground state of the SeO molecule is 3Σ, with equilibrium nuclear distance RSeO = 0.1707 nm and dissociation energy De = 7.0917 eV. There are two structures for the ground state of the SeCO molecule: Se=C=O and Se=O=C. The linear Se=C=O is 1Σ. Its equilibrium nuclear distances and dissociation energy are RSeC = 0.1715 nm, RCO = 0.1176 nm and 18.8492 eV, respectively. The other structure Se=O=C is 1Σ. Its equilibrium nuclear distances and dissociation energy are RCO = 0.1168 nm, RSeO = 0.1963 nm and 15.5275 eV, respectively. The possible dissociative limit of the SeCO molecule is analyzed. The potential energy function for the SeCO molecule has been obtained from the many-body expansion theory. The contour of the potential energy curve describes the structure characters of the SeCO molecule. Furthermore, contours of the molecular stretching vibration based on this potential energy function are discussed.

  6. Molecular understanding of mutagenicity using potential energy methods. Progress report, July 1, 1992--September 30, 1993

    SciTech Connect

    Broyde, S.; Shapiro, R.

    1993-09-01

    Our objective has been to elucidate on a molecular level, at atomic resolution, the structures of DNAs modified by highly mutagenic aromatic amines and hydrocarbons. The underlying hypothesis is that DNA replicates with reduced fidelity when its normal right-handed B-structure is altered, and one result is a higher mutation rate. This change in structure may occur normally at a low incidence but it may be enhanced greatly after covalent modification by a mutagenic substance. The methods that we use to elucidate structures are computational, but we keep in close contact with experimental developments, and we incorporate data from NMR studies in our calculations when they are available. X-ray and low resolution spectroscopic studies have not succeeded in producing atomic resolution views of mutagen and carcinogen-oligonucleotide adducts. Even the high resolution NMR method cannot alone yield molecular views, though it does so in combination with our computations. The specific methods that we employ are minimized potential energy calculations using the torsion angle space molecular mechanics program DUPLEX to yield static views. Molecular dynamics simulations of static structures with solvent and salt can be carried out with the program AMBER; this yields mobile views in a medium that mimics aspects of the natural aqueous environment of the cell.

  7. Spin Dynamics and Low Energy Vibrations: Insights from Vanadyl-Based Potential Molecular Qubits.

    PubMed

    Atzori, Matteo; Tesi, Lorenzo; Benci, Stefano; Lunghi, Alessandro; Righini, Roberto; Taschin, Andrea; Torre, Renato; Sorace, Lorenzo; Sessoli, Roberta

    2017-03-15

    Here we report the investigation of the magnetization dynamics of a vanadyl complex with diethyldithiocarbamate (Et2dtc(-)) ligands, namely [VO(Et2dtc)2] (1), in both solid-state and frozen solution. This showed an anomalous and unprecedentedly observed field dependence of the relaxation time, which was modeled with three contributions to the relaxation mechanism. The temperature dependence of the weight of the two processes dominating at low fields was found to well correlate with the low energy vibrations as determined by THz spectroscopy. This detailed experimental comparative study represents a fundamental step to understand the spin dynamics of potential molecular quantum bits, and enriches the guidelines to design molecule-based systems with enhanced quantum coherence.

  8. Tapping the Molecular Potential of Microalgae to Produce Biomass (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema

    Sayre, Richard [LANL

    2016-07-12

    Richard Sayre, from Los Alamos National Laboratory, presents a talk titled "Tapping the Molecular Potential of Microalgae to Produce Biomass" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  9. Molecular vibrational energy flow

    NASA Astrophysics Data System (ADS)

    Gruebele, M.; Bigwood, R.

    This article reviews some recent work in molecular vibrational energy flow (IVR), with emphasis on our own computational and experimental studies. We consider the problem in various representations, and use these to develop a family of simple models which combine specific molecular properties (e.g. size, vibrational frequencies) with statistical properties of the potential energy surface and wavefunctions. This marriage of molecular detail and statistical simplification captures trends of IVR mechanisms and survival probabilities beyond the abilities of purely statistical models or the computational limitations of full ab initio approaches. Of particular interest is IVR in the intermediate time regime, where heavy-atom skeletal modes take over the IVR process from hydrogenic motions even upon X H bond excitation. Experiments and calculations on prototype heavy-atom systems show that intermediate time IVR differs in many aspects from the early stages of hydrogenic mode IVR. As a result, IVR can be coherently frozen, with potential applications to selective chemistry.

  10. Path integral molecular dynamics calculations of the H6+ and D6+ clusters on an ab initio potential energy surface

    NASA Astrophysics Data System (ADS)

    Kakizaki, Akira; Takayanagi, Toshiyuki; Shiga, Motoyuki

    2007-11-01

    Path integral molecular dynamics simulations for the H6+ and D6+ cluster cations have been carried out in order to understand the floppy nature of their molecular structure due to quantum-mechanical fluctuation. A full-dimensional analytical potential energy surface for the ground electronic state of H6+ has been developed on the basis of accurate ab initio electronic structure calculations at the CCSD(T)/cc-pVTZ level. It is found that the outer H 2(D 2) nuclei rotate almost freely and that the probability density distributions of the central H 2(D 2) nuclei show strong spatial delocalization.

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

    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.

  12. Fully Relativistic Calculations on the Potential Energy Surfaces of the Lowest 23 States of Molecular Chlorine

    SciTech Connect

    Luiz Guilherme M. de Macedo; de Jong, Wibe A.

    2008-01-24

    The electronic structure and spectroscopic properties (Re, ωexe, βe, Te ) of the ground state and the 22 lowest excited states of chlorine molecule were studied within a four component relativistic framework using the MOLFDIR program package. The potential energy curves of all possible 23 covalent states were calculated using relativistic complete open shell configuration interaction (COSCI) approach. In addition, four component multi-reference configuration interaction with singles and doubles excitations (MRCISD) calculations were performed in order to infer the effects due to dynamical correlation in vertical excitations. The calculated properties are in good agreement with the available experimental data.

  13. Free energy profiles of cocaine esterase-cocaine binding process by molecular dynamics and potential of mean force simulations.

    PubMed

    Zhang, Yuxin; Huang, Xiaoqin; Han, Keli; Zheng, Fang; Zhan, Chang-Guo

    2016-11-25

    The combined molecular dynamics (MD) and potential of mean force (PMF) simulations have been performed to determine the free energy profile of the CocE)-(+)-cocaine binding process in comparison with that of the corresponding CocE-(-)-cocaine binding process. According to the MD simulations, the equilibrium CocE-(+)-cocaine binding mode is similar to the CocE-(-)-cocaine binding mode. However, based on the simulated free energy profiles, a significant free energy barrier (∼5 kcal/mol) exists in the CocE-(+)-cocaine binding process whereas no obvious free energy barrier exists in the CocE-(-)-cocaine binding process, although the free energy barrier of ∼5 kcal/mol is not high enough to really slow down the CocE-(+)-cocaine binding process. In addition, the obtained free energy profiles also demonstrate that (+)-cocaine and (-)-cocaine have very close binding free energies with CocE, with a negligible difference (∼0.2 kcal/mol), which is qualitatively consistent with the nearly same experimental KM values of the CocE enzyme for (+)-cocaine and (-)-cocaine. The consistency between the computational results and available experimental data suggests that the mechanistic insights obtained from this study are reasonable.

  14. CEPA Calculations of potential energy surfaces for open-shell systems. II. The reaction of C + Ions with molecular hydrogen

    NASA Astrophysics Data System (ADS)

    Jaquet, Ralph; Staemmler, Volker

    1982-07-01

    Ab initio calculations including electron correlation effects (mainly on CEPA-PNO level) have been performed for the potential energy surface (PES) of the reaction of 2P carbon ions with molecular hydrogen. For the collinear abstraction reactions (C ∞v symmetry: 2σ +, 2Π-2) the minimum energy paths have been determined. The vertical insertion reaction (C 2v; 2A 1,B 1, 2B 2) has been investigated with particular emphasis (minimum energy path, barrier heights, intersystem crossing). The influence of the size of the orbital basis and of electron correlation has been studied in some detail. The interaction of the 2A 1, and 2B 2 surfaces has been analyzed, leading to the conclusion that close to C 2v symmetry a low energy path exists by which CH 2+( 2A 1)can be easily formed, with a barrier ( 2B 2 → 2A 1) ≈ 18 kcal/mol below the asymptote. The analysis of electron correlation effects reveals that it is compulsory to correlate the whole valence shell if one wants to obtain reliable surfaces. The influence of singly excited configurations for getting the correct behaviour of the PES is generally small.

  15. College Chemistry Students' Understanding of Potential Energy in the Context of Atomic-Molecular Interactions

    ERIC Educational Resources Information Center

    Becker, Nicole M.; Cooper, Melanie M.

    2014-01-01

    Understanding the energy changes that occur as atoms and molecules interact forms the foundation for understanding the macroscopic energy changes that accompany chemical processes. In order to identify ways to scaffold students' understanding of the connections between atomic-molecular and macroscopic energy perspectives, we conducted a…

  16. Molecular structural property and potential energy dependence on nonequilibrium-thermodynamic state point of liquid n-hexadecane under shear

    NASA Astrophysics Data System (ADS)

    Tseng, Huan-Chang; Chang, Rong-Yeu; Wu, Jiann-Shing

    2011-01-01

    Extensive computer experiments have been conducted in order to shed light on the macroscopic shear flow behavior of liquid n-hexadecane fluid under isobaric-isothermal conditions through the nonequilibrium molecular dynamic methodology. With respect to shear rates, the accompanying variations in structural properties of the fluid span the microscopic range of understanding from the intrinsic to extrinsic characteristics. As drawn from the average value of bond length and bond angle, the distribution of dihedral angle, and the radius distribution function of intramolecular and intermolecular van der Waals distances, these intrinsic structures change with hardness, except in the situation of extreme shear rates. The shear-induced variation of thermodynamic state curve along with the shear rate studied is shown to consist of both the quasiequilibrium state plateau and the nonequilibrium-thermodynamic state slope. Significantly, the occurrence of nonequilibrium-thermodynamic state behavior is attributed to variations in molecular potential energies, which include bond stretching, bond bending, bond torsion, and intra- and intermolecular van der Waals interactions. To unfold the physical representation of extrinsic structural deformation, under the aggressive influence of a shear flow field, the molecular dimension and appearance can be directly described via the squared radius of gyration and the sphericity angle, Rg2 and φ, respectively. In addition, a specific orientational order Sx defines the alignment of the molecules with the flow direction of the x-axis. As a result, at low shear rates, the overall molecules are slightly stretched and shaped in a manner that is increasingly ellipsoidal. Simultaneously, there is an obvious enhancement in the order. In contrast to high shear rates, the molecules spontaneously shrink themselves with a decreased value of Rg2, while their shape and order barely vary with an infinite value of φ and Sx. It is important to note that

  17. Exploring the potential of fulvalene dimetals as platforms for molecular solar thermal energy storage: computations, syntheses, structures, kinetics, and catalysis.

    PubMed

    Börjesson, Karl; Ćoso, Dušan; Gray, Victor; Grossman, Jeffrey C; Guan, Jingqi; Harris, Charles B; Hertkorn, Norbert; Hou, Zongrui; Kanai, Yosuke; Lee, Donghwa; Lomont, Justin P; Majumdar, Arun; Meier, Steven K; Moth-Poulsen, Kasper; Myrabo, Randy L; Nguyen, Son C; Segalman, Rachel A; Srinivasan, Varadharajan; Tolman, Willam B; Vinokurov, Nikolai; Vollhardt, K Peter C; Weidman, Timothy W

    2014-11-17

    A study of the scope and limitations of varying the ligand framework around the dinuclear core of FvRu2 in its function as a molecular solar thermal energy storage framework is presented. It includes DFT calculations probing the effect of substituents, other metals, and CO exchange for other ligands on ΔHstorage . Experimentally, the system is shown to be robust in as much as it tolerates a number of variations, except for the identity of the metal and certain substitution patterns. Failures include 1,1',3,3'-tetra-tert-butyl (4), 1,2,2',3'-tetraphenyl (9), diiron (28), diosmium (24), mixed iron-ruthenium (27), dimolybdenum (29), and ditungsten (30) derivatives. An extensive screen of potential catalysts for the thermal reversal identified AgNO3 -SiO2 as a good candidate, although catalyst decomposition remains a challenge.

  18. Exploring the Potential of Fulvalene Dimetals as Platforms for Molecular Solar Thermal Energy Storage: Computations, Syntheses, Structures, Kinetics, and Catalysis

    SciTech Connect

    Borjesson, K; Coso, D; Gray, V; Grossman, JC; Guan, JQ; Harris, CB; Hertkorn, N; Hou, ZR; Kanai, Y; Lee, D; Lomont, JP; Majumdar, A; Meier, SK; Moth-Poulsen, K; Myrabo, RL; Nguyen, SC; Segalman, RA; Srinivasan, V; Tolman, WB; Vinokurov, N; Vollhardt, KPC; Weidman, TW

    2014-10-03

    A study of the scope and limitations of varying the ligand framework around the dinuclear core of FvRu(2) in its function as a molecular solar thermal energy storage framework is presented. It includes DFT calculations probing the effect of substituents, other metals, and CO exchange for other ligands on Delta H-storage. Experimentally, the system is shown to be robust in as much as it tolerates a number of variations, except for the identity of the metal and certain substitution patterns. Failures include 1,1',3,3'-tetra-tert-butyl (4), 1,2,2',3'-tetraphenyl (9), diiron (28), diosmium (24), mixed iron-ruthenium (27), dimolybdenum (29), and di-tungsten (30) derivatives. An extensive screen of potential catalysts for the thermal reversal identified AgNO3-SiO2 as a good candidate, although catalyst decomposition remains a challenge.

  19. Relative contribution of combined kinetic and exchange energy terms vs the electronic component of molecular electrostatic potential in hardness potential derivatives.

    PubMed

    Bhattacharjee, Rituparna; Roy, Ram Kinkar

    2013-11-14

    The relative contribution of the sum of kinetic [(10/9)CFρ(r)2/3] and exchange energy [(4/9)CXρ(r)1/3] terms to that of the electronic part of the molecular electrostatic potential [Vel(r)] in the variants of hardness potential is investigated to assess the proposed definition of Δ+h(k) = −[VelN+1(k) – VelN(k)] and Δ–h(k) = −[VelN(k) – VelN–1(k)] (Saha; et al. J. Comput. Chem. 2013, 34, 662). Some substituted benzenes and polycyclic aromatic hydrocarbons (PAHs) (undergoing electrophilic aromatic substitution), carboxylic acids, and their derivatives are chosen to carry out the theoretical investigation as stated above. Intra- and intermolecular reactivity trends generated by Δ+h(k) and Δ–h(k) are found to be satisfactory and are correlated reasonably well with experimental results.

  20. Identification of potential CCR5 inhibitors through pharmacophore-based virtual screening, molecular dynamics simulation and binding free energy analysis.

    PubMed

    Wang, Juan; Shu, Mao; Wang, Yuanqiang; Hu, Yong; Wang, Yuanliang; Luo, Yanfeng; Lin, Zhihua

    2016-10-18

    CC chemokine receptor 5 (CCR5), a member of G protein-coupled receptors (GPCRs), plays a vital role in inflammatory responses to infection. Alterations in the expression of CCR5 have been correlated with disease progression in many types of cancers. The idea of using CCR5 as a target for therapeutic intervention has been demonstrated to prevent disease progression. To date, only a few compounds have been reported as CCR5 inhibitors. In this study, a series of CCR5 antagonists were used to construct pharmacophore models. Then the optimal model was utilized as a 3D query to identify novel chemical entities from structural databases. After refinement by molecular docking, drug-likeness analysis, molecular dynamics simulations (MDS) and binding free energy analysis, three potential inhibitors (25, 29 and 45) were identified. MD simulations suggested that the screened compounds retained the important common binding mode known for CCR5 inhibitors (maraviroc and nifeviroc), which occupied the bottom of a pocket and stabilized the conformation of CCR5. During the binding process, van der Waals interactions provided the substantial driving force. The most favorable contributions were from Tyr37, Trp86, Tyr89, Tyr108, Phe109, Phe112, Gln194, Thr195, Ile198, Trp248, Tyr251, Leu255, Thr259, Met279, Glu283 and Met287. The above results suggest that the hybrid strategy would provide a basis for rational drug design.

  1. Locating gravitational potential energy

    NASA Astrophysics Data System (ADS)

    Keeports, David

    2017-01-01

    Where does gravitational potential energy reside when a ball is in the air? The perfectly correct answer is that it is located in the ball-Earth system. Still, mechanical energy conservation problems are routinely solved by assigning a potential energy to the ball alone. Provided here is a proof that such an assignment introduces only an entirely undetectable error.

  2. Relativistic four-component potential energy curves for the lowest 23 covalent states of molecular bromine (Br2).

    PubMed

    Gomes, José da Silva; Gargano, Ricardo; Martins, João B L; M de Macedo, Luiz Guilherme

    2014-08-07

    The covalent excited states and ground state of the Br2 molecule has been investigated by using four-component relativistic COSCI and MRCISD methods. These methods were performed for all covalent states in the representation Ω((±)). Calculated potential energy curves (PECs) were obtained at the four-component COSCI level, and spectroscopic constants (R(e), D(e), D0, ω(e), ω(e)x(e), ω(e)y(e), B(e), α(e), γ(e), Te, Dv) for bounded states are reported. The vertical excitations for all covalent states are reported at COSCI, MRCISD, and MRCISD+Q levels. We also present spectroscopic constants for two weakly bounded states (A':(1)2u and B':(1)0(-)u) not yet reported in the literature, as well as accurate analytical curves for all five relativistic molecular bounded sates [the ground state X:0 g(+) and the excited states A:(1)1(u), B:(1)0(u)(+), C:(2)1(u), and B':(1)0(u)(-)] found in this work.

  3. CALCULATED MOLECULAR STRUCTURES AND POTENTIAL ENERGY FUNCTIONS OF PAHS WITH METHYL CROWDING IN THE BAY REGION AND THEIR METABOLITES: COMPARISON TO EXPERIMENTAL STRUCTURES

    EPA Science Inventory

    Abstract Title: Calculated molecular structures and potential energy functions of P AHs with methyl crowding in the bay region and their metabolites: Comparison to experimental structures.

    Abstract:
    PAHs with methyl group substitution near a bay region represent a cl...

  4. CALCULATED MOLECULAR STRUCTURES AND POTENTIAL ENERGY FUNCTIONS OF PAHS WITH METHYL CROWDING IN THE BAY REGION AND THEIR METABOLITES: COMPARISON TO EXPERIMENTAL STRUCTURES

    EPA Science Inventory

    Calculated molecular structures and potential energy functions ofP AHs with methyl crowding in the bay region and their metabolites: Comparison to experimental structures

    PAHs with methyl group substitution near a bay region represent a class of chemicals associated with ...

  5. The /A 1 Sigma +/ - /X 1 Sigma +/ system of the isotopic lithium hydrides - The molecular constants, potential energy curves, and their adiabatic corrections

    NASA Technical Reports Server (NTRS)

    Vidal, C. R.; Stwalley, W. C.

    1982-01-01

    The molecular constants and their adiabatic corrections have been determined for the (A 1 Sigma +) - (X 1 Sigma +) system of the isotopic lithium hydrides: (Li-6)H, (Li-7)H, (Li-6)D, and (Li-7)D. Using a fully quantum mechanical variational method, the potential energy curves (IPA potentials) are determined. Extending the variational method, we have obtained for the first time adiabatic corrections of potential energy curves from isotopic spectroscopic data. A significant difference between the potential energy curves of the lithium hydrides and the lithium deuterides has been observed. When Li-6 was replaced by Li-7, a significant difference was only observed for the (A 1 Sigma +) state, but not for the (X 1 Sigma +) state.

  6. Path-integral molecular dynamics simulations of hydrated hydrogen chloride cluster HCl(H 2O) 4 on a semiempirical potential energy surface

    NASA Astrophysics Data System (ADS)

    Takayanagi, Toshiyuki; Takahashi, Kenta; Kakizaki, Akira; Shiga, Motoyuki; Tachikawa, Masanori

    2009-04-01

    Path-integral molecular dynamics simulations for the HCl(H 2O) 4 cluster have been performed on the ground-state potential energy surface directly obtained on-the-fly from semiempirical PM3-MAIS molecular orbital calculations. It is found that the HCl(H 2O) 4 cluster has structural rearrangement above the temperature of 300 K showing a liquid-like behavior. Quantum mechanical fluctuation of hydrogen nuclei plays a significant role in structural arrangement processes in this cluster.

  7. Getting the Right Answers for the Right Reasons: Toward Predictive Molecular Simulations of Water with Many-Body Potential Energy Functions.

    PubMed

    Paesani, Francesco

    2016-09-20

    The central role played by water in fundamental processes relevant to different disciplines, including chemistry, physics, biology, materials science, geology, and climate research, cannot be overemphasized. It is thus not surprising that, since the pioneering work by Stillinger and Rahman, many theoretical and computational studies have attempted to develop a microscopic description of the unique properties of water under different thermodynamic conditions. Consequently, numerous molecular models based on either molecular mechanics or ab initio approaches have been proposed over the years. However, despite continued progress, the correct prediction of the properties of water from small gas-phase clusters to the liquid phase and ice through a single molecular model remains challenging. To large extent, this is due to the difficulties encountered in the accurate modeling of the underlying hydrogen-bond network in which both number and strength of the hydrogen bonds vary continuously as a result of a subtle interplay between energetic, entropic, and nuclear quantum effects. In the past decade, the development of efficient algorithms for correlated electronic structure calculations of small molecular complexes, accompanied by tremendous progress in the analytical representation of multidimensional potential energy surfaces, opened the doors to the design of highly accurate potential energy functions built upon rigorous representations of the many-body expansion (MBE) of the interaction energies. This Account provides a critical overview of the performance of the MB-pol many-body potential energy function through a systematic analysis of energetic, structural, thermodynamic, and dynamical properties as well as of vibrational spectra of water from the gas to the condensed phase. It is shown that MB-pol achieves unprecedented accuracy across all phases of water through a quantitative description of each individual term of the MBE, with a physically correct representation

  8. Free-energy calculations using classical molecular simulation: application to the determination of the melting point and chemical potential of a flexible RDX model.

    PubMed

    Sellers, Michael S; Lísal, Martin; Brennan, John K

    2016-03-21

    We present an extension of various free-energy methodologies to determine the chemical potential of the solid and liquid phases of a fully-flexible molecule using classical simulation. The methods are applied to the Smith-Bharadwaj atomistic potential representation of cyclotrimethylene trinitramine (RDX), a well-studied energetic material, to accurately determine the solid and liquid phase Gibbs free energies, and the melting point (Tm). We outline an efficient technique to find the absolute chemical potential and melting point of a fully-flexible molecule using one set of simulations to compute the solid absolute chemical potential and one set of simulations to compute the solid-liquid free energy difference. With this combination, only a handful of simulations are needed, whereby the absolute quantities of the chemical potentials are obtained, for use in other property calculations, such as the characterization of crystal polymorphs or the determination of the entropy. Using the LAMMPS molecular simulator, the Frenkel and Ladd and pseudo-supercritical path techniques are adapted to generate 3rd order fits of the solid and liquid chemical potentials. Results yield the thermodynamic melting point Tm = 488.75 K at 1.0 atm. We also validate these calculations and compare this melting point to one obtained from a typical superheated simulation technique.

  9. A full-dimension intra- and inter-molecular ab initio potential energy surface and predicted infrared spectra for H2O-He

    NASA Astrophysics Data System (ADS)

    Hou, Dan; Ma, Yong-Tao; Zhang, Xiao-Long; Li, Hui

    2016-12-01

    A full-dimension intra- and inter-molecular ab initio potential energy surface (PES) for H2O-He, which explicitly incorporates dependence on the intra-molecular (Q1,Q2,Q3) normal-mode coordinates of the H2O monomer has been calculated in this work. In addition, three analytic vibrational-quantum-state-specific PESs are obtained by least-squares fitting vibrationally averaged interaction energies for the (v1,v2,v3) = (0, 0, 0), (0, 0, 1) and (0, 1, 0) states of H2O to the three-dimensional Morse/long-range potential function. Each vibrationally averaged PES fitted to 578 points has root-mean-square (rms) deviation smaller than 0.1 cm-1, and required only 53 parameters. With the 3D PESs of the H2O-He dimer system, we employed the combined radial discrete variable representation/angular finite basis representation method and Lanczos algorithm to calculate rovibrational energy levels. The rovibrational spectra and their relative intensities for the H2O-He complex have been predicted for the first time.

  10. Molecular dynamics investigations of the dissociation of SiO2 on an ab initio potential energy surface obtained using neural network methods.

    PubMed

    Agrawal, Paras M; Raff, Lionel M; Hagan, Martin T; Komanduri, Ranga

    2006-04-07

    The neural network (NN) procedure to interpolate ab initio data for the purpose of molecular dynamics (MD) simulations has been tested on the SiO(2) system. Unlike other similar NN studies, here, we studied the dissociation of SiO(2) without the initial use of any empirical potential. During the dissociation of SiO(2) into Si+O or Si+O(2), the spin multiplicity of the system changes from singlet to triplet in the first reaction and from singlet to pentet in the second. This paper employs four potential surfaces. The first is a NN fit [NN(STP)] to a database comprising the lowest of the singlet, triplet, and pentet energies obtained from density functional calculations in 6673 nuclear configurations. The other three potential surfaces are obtained from NN fits to the singlet, triplet, and pentet-state energies. The dissociation dynamics on the singlet-state and NN(STP) surfaces are reported. The results obtained using the singlet surface correspond to those expected if the reaction were to occur adiabatically. The dynamics on the NN(STP) surface represent those expected if the reaction follows a minimum-energy pathway. This study on a small system demonstrates the application of NNs for MD studies using ab initio data when the spin multiplicity of the system changes during the dissociation process.

  11. Molecular dynamics investigations of the dissociation of SiO2 on an ab initio potential energy surface obtained using neural network methods

    NASA Astrophysics Data System (ADS)

    Agrawal, Paras M.; Raff, Lionel M.; Hagan, Martin T.; Komanduri, Ranga

    2006-04-01

    The neural network (NN) procedure to interpolate ab initio data for the purpose of molecular dynamics (MD) simulations has been tested on the SiO2 system. Unlike other similar NN studies, here, we studied the dissociation of SiO2 without the initial use of any empirical potential. During the dissociation of SiO2 into Si +O or Si +O2, the spin multiplicity of the system changes from singlet to triplet in the first reaction and from singlet to pentet in the second. This paper employs four potential surfaces. The first is a NN fit [NN(STP)] to a database comprising the lowest of the singlet, triplet, and pentet energies obtained from density functional calculations in 6673 nuclear configurations. The other three potential surfaces are obtained from NN fits to the singlet, triplet, and pentet-state energies. The dissociation dynamics on the singlet-state and NN(STP) surfaces are reported. The results obtained using the singlet surface correspond to those expected if the reaction were to occur adiabatically. The dynamics on the NN(STP) surface represent those expected if the reaction follows a minimum-energy pathway. This study on a small system demonstrates the application of NNs for MD studies using ab initio data when the spin multiplicity of the system changes during the dissociation process.

  12. The Origins of - and Inter-Molecular Vibrational Couplings: a Case Study of H_2O-Ar on Full and Reduced-Dimensional Potential Energy Surface

    NASA Astrophysics Data System (ADS)

    Hou, Dan; Ma, Yong-Tao; Zhang, Xiao-Long; Li, Hui

    2016-06-01

    The origin and strength of intra- and inter-molecular vibrational coupling is difficult to probe by direct experimental observations. However, explicitly including or not including some specific intramolecular vibrational modes to study intermolecular interaction provides a precise theoretical way to examine the effects of anharmonic coupling between modes. In this work, a full-dimension intra- and inter-molecular ab initio potential energy surface (PES) for H_2O-Ar, which explicitly incorporates interdependence on the intramolecular normal-mode coordinates of the H_2O monomer, has been calculated. In addition, four analytic vibrational-quantum-state-specific PESs are obtained by least-squares fitting vibrationally averaged interaction energies for the (νb{1},νb{2},νb{3})=(0,0,0),(0,0,1),(1,0,0),(0,1,0) states of H_2O to the three-dimensional Morse/long-range potential function. The resulting vibrationally averaged PESs provide good representations of the experimental infrared data, with RMS discrepancies smaller than 0.02 wn for all three rotational branches of the asymmetric stretch fundamental transitions. The infrared band origin shifts associated with three fundamental bands of H_2O in H_2O-Ar complex are predicted for the first time and are found to be in good agreement with the (extrapolated) experimental values. Upon introduction of additional intramolecular degrees of freedom into the intermolecular potential energy surface, there is clear spectroscopic evidence of intra- and intermolecular vibrational couplings. J. Chem. Phys., 144, 014301 (2016)

  13. An ab initio molecular orbital study of potential energy surface of the NH2+NO2 reaction

    NASA Astrophysics Data System (ADS)

    Mebel, A. M.; Hsu, C.-C.; Lin, M. C.; Morokuma, K.

    1995-10-01

    Potential energy surface of the reaction of NH2 with NO2 has been studied at the QCISD(T)/6-311G(d,p)//MP2/6-311G(d,p)+ZPC[MP2/6-311G(d,p)] and GAUSSIAN-2 (G2) levels of calculation. The reaction is shown to give three different groups of products. H2NO+NO can be produced by two different channels: (i) the barrierless association of the reactants to form H2NNO2 1, followed by the nitro-nitrite rearrangement into H2NONO 3 and the ON bond scission and (ii) the association of H2N with ONO directly forming 3 without barrier, followed by the dissociation 3. The barrier for the nitro-nitrite rearrangement at the transition state (TS) 2, 31.2 kcal/mol with respect to 1, is 20.8 kcal/mol lower than the reactants at the best G2 level. The TS 2 is found to lie significantly lower and to have much tighter structure than those previously reported. The thermodynamically most stable N2O+H2O products can be formed from 1 by the complex mechanism (iii), involving 1,3-hydrogen shift from nitrogen to oxygen, rotation of the OH bond, H shift from one oxygen to another and migration of the second H atom from N to O leading to elimination of H2O. The rate-determining step is the 1,3-H shift at TS 4 which is 12.5 kcal/mol lower than NH2+NO2, but 8.3 kcal/mol higher than the barrier for the nitro-nitrite isomerization at TS 2 at the G2 level. N2+H2O2 cannot be formed in the reaction, but several channels are shown to produce N2+2OH. All of them have as the rate-determining step the second 1,3-hydrogen shift from nitrogen to oxygen at TS 11 or 16, lying by 6.9 kcal/mol higher than NH2+NO2, and are not expected to compete with the reaction mechanisms producing H2NO+NO and N2O+H2O.

  14. Alaska's renewable energy potential.

    SciTech Connect

    Not Available

    2009-02-01

    This paper delivers a brief survey of renewable energy technologies applicable to Alaska's climate, latitude, geography, and geology. We first identify Alaska's natural renewable energy resources and which renewable energy technologies would be most productive. e survey the current state of renewable energy technologies and research efforts within the U.S. and, where appropriate, internationally. We also present information on the current state of Alaska's renewable energy assets, incentives, and commercial enterprises. Finally, we escribe places where research efforts at Sandia National Laboratories could assist the state of Alaska with its renewable energy technology investment efforts.

  15. Molecular associations from ab initio pair potentials

    NASA Astrophysics Data System (ADS)

    Iglesias, E.; Sordo, T. L.; Sordo, J. A.

    1991-12-01

    A method of building up stable molecular associations by using pair potentials from ab initio calculations is presented. The Matsuoka-Clementi-Yoshimine potential has been chosen to emulate the water-water interactions while 1-6-12 potentials are used to compute both solute-solvent and solute-solute interactions. Parameters for neutral-amino-acid-water and neutral- amino-acid-neutral-amino-acid interactions are provided by the program. Supermolecules are constructed by minimization of the interaction energy of the molecules involved. Both steepest-decent and Fletcher-Powell algorithms are available to carry out such a minimization.

  16. Monte Carlo simulations on atropisomerism of thienotriazolodiazepines applicable to slow transition phenomena using potential energy surfaces by ab initio molecular orbital calculations.

    PubMed

    Morikami, Kenji; Itezono, Yoshiko; Nishimoto, Masahiro; Ohta, Masateru

    2014-01-01

    Compounds with a medium-sized flexible ring often show atropisomerism that is caused by the high-energy barriers between long-lived conformers that can be isolated and often have different biological properties to each other. In this study, the frequency of the transition between the two stable conformers, aS and aR, of thienotriazolodiazepine compounds with flexible 7-membered rings was estimated computationally by Monte Carlo (MC) simulations and validated experimentally by NMR experiments. To estimate the energy barriers for transitions as precisely as possible, the potential energy (PE) surfaces used in the MC simulations were calculated by molecular orbital (MO) methods. To accomplish the MC simulations with the MO-based PE surfaces in a practical central processing unit (CPU) time, the MO-based PE of each conformer was pre-calculated and stored before the MC simulations, and then only referred to during the MC simulations. The activation energies for transitions calculated by the MC simulations agreed well with the experimental ΔG determined by the NMR experiments. The analysis of the transition trajectories of the MC simulations revealed that the transition occurred not only through the transition states, but also through many different transition paths. Our computational methods gave us quantitative estimates of atropisomerism of the thienotriazolodiazepine compounds in a practical period of time, and the method could be applicable for other slow-dynamics phenomena that cannot be investigated by other atomistic simulations.

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

    PubMed

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

    2011-10-13

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

  18. Quantum Tunneling in Testosterone 6β-Hydroxylation by Cytochrome P450: Reaction Dynamics Calculations Employing Multiconfiguration Molecular-Mechanical Potential Energy Surfaces

    NASA Astrophysics Data System (ADS)

    Zhang, Yan; Lin, Hai

    2009-05-01

    Testosterone hydroxylation is a prototypical reaction of human cytochrome P450 3A4, which metabolizes about 50% of oral drugs on the market. Reaction dynamics calculations were carried out for the testosterone 6β-hydrogen abstraction and the 6β-d1-testosterone 6β-duterium abstraction employing a model that consists of the substrate and the active oxidant compound I. The calculations were performed at the level of canonical variational transition state theory with multidimensional tunneling and were based on a semiglobal full-dimensional potential energy surface generated by the multiconfiguration molecular mechanics technique. The tunneling coefficients were found to be around 3, indicating substantial contributions by quantum tunneling. However, the tunneling made only modest contributions to the kinetic isotope effects. The kinetic isotope effects were computed to be about 2 in the doublet spin state and about 5 in the quartet spin state.

  19. Coupled wave-packets for non-adiabatic molecular dynamics: a generalization of Gaussian wave-packet dynamics to multiple potential energy surfaces

    SciTech Connect

    White, Alexander James; Tretiak, Sergei; Mozyrsky, Dima V.

    2016-04-25

    Accurate simulation of the non-adiabatic dynamics of molecules in excited electronic states is key to understanding molecular photo-physical processes. Here we present a novel method, based on a semiclassical approximation, that is as efficient as the commonly used mean field Ehrenfest or ad hoc surface hopping methods and properly accounts for interference and decoherence effects. This novel method is an extension of Heller's thawed Gaussian wave-packet dynamics that includes coupling between potential energy surfaces. By studying several standard test problems we demonstrate that the accuracy of the method can be systematically improved while maintaining high efficiency. The method is suitable for investigating the role of quantum coherence in the non-adiabatic dynamics of many-atom molecules.

  20. Coupled wave-packets for non-adiabatic molecular dynamics: a generalization of Gaussian wave-packet dynamics to multiple potential energy surfaces

    DOE PAGES

    White, Alexander James; Tretiak, Sergei; Mozyrsky, Dima V.

    2016-04-25

    Accurate simulation of the non-adiabatic dynamics of molecules in excited electronic states is key to understanding molecular photo-physical processes. Here we present a novel method, based on a semiclassical approximation, that is as efficient as the commonly used mean field Ehrenfest or ad hoc surface hopping methods and properly accounts for interference and decoherence effects. This novel method is an extension of Heller's thawed Gaussian wave-packet dynamics that includes coupling between potential energy surfaces. By studying several standard test problems we demonstrate that the accuracy of the method can be systematically improved while maintaining high efficiency. The method is suitablemore » for investigating the role of quantum coherence in the non-adiabatic dynamics of many-atom molecules.« less

  1. Energy Ordering of Molecular Orbitals

    PubMed Central

    2016-01-01

    Orbitals are invaluable in providing a model of bonding in molecules or between molecules and surfaces. Most present-day methods in computational chemistry begin by calculating the molecular orbitals of the system. To what extent have these mathematical objects analogues in the real world? To shed light on this intriguing question, we employ a photoemission tomography study on monolayers of 3,4,9,10-perylene-tetracarboxylic acid dianhydride (PTCDA) grown on three Ag surfaces. The characteristic photoelectron angular distribution enables us to assign individual molecular orbitals to the emission features. When comparing the resulting energy positions to density functional calculations, we observe deviations in the energy ordering. By performing complete active space calculations (CASSCF), we can explain the experimentally observed orbital ordering, suggesting the importance of static electron correlation beyond a (semi)local approximation. On the other hand, our results also show reality and robustness of the orbital concept, thereby making molecular orbitals accessible to experimental observations. PMID:27935313

  2. Vanishing rainbows near orbiting and the energy dependence of rainbow scattering - Relation to properties of the potential. [molecular beam scattering cross sections

    NASA Technical Reports Server (NTRS)

    Greene, E. F.; Hall, R. B.; Mason, E. A.

    1975-01-01

    The energy threshold behavior of elastic rainbow scattering near the transition to orbiting is derived. Analysis of the energy dependence of the rainbow angle shows that the full range from high energies down to orbiting can be fitted with two parameters. Thus, measurements of the rainbow angle can give essentially only two pieces of information about the potential. For potentials of common shapes, such measurements are sensitive to regions of the potential just beyond the minimum and give information about the shape of the potential in this range. However, neither a minimum nor a point of inflection in the potential is necessary for rainbow scattering.

  3. Potential molecular wires and molecular alligator clips

    NASA Astrophysics Data System (ADS)

    Schumm, Jeffry S.; Pearson, Darren L.; Jones, LeRoy, II; Hara, Ryuichiro; Tour, James M.

    1996-12-01

    The synthesis of oligo(2-ethylphenylene-ethynylene)s, oligo(2-(0957-4484/7/4/023/img1-ethylheptyl)phenylene-ethynylene)s, and oligo(3-ethylthiophene-ethynylene)s is described via an iterative divergent convergent approach. Synthesized were the monomer, dimer, tetramer, octamer and 16-mer of the oligo(3-ethylthiophene-ethynylene)s and oligo(2-0957-4484/7/4/023/img1-ethylheptyl)phenylene-ethynylene)s. The 16-mers are 100 Å and 128 Å long, respectively. At each stage in the iteration, the length of the framework doubles. Only three sets of reaction conditions are needed for the entire iterative synthetic sequence; an iodination, a protodesilylation, and a Pd/Cu-catalyzed cross coupling. The oligomers were characterized spectroscopically and by mass spectrometry. The optical properties are presented which show the stage of optical absorbance saturation. The size exclusion chromatography values for the number average weights, relative to polystyrene, illustrate the tremendous differences in the hydrodynamic volume of these rigid rod oligomers versus the random coils of polystyrene. These differences become quite apparent at the octamer stage. The preparation of thiol-protected end groups is described. These may serve as molecular alligator clips for adhesion to gold surfaces. These oligomers may act as molecular wires in molecular electronic devices and they also serve as useful models for understanding related bulk polymers.

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

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  6. TheoReTS - An information system for theoretical spectra based on variational predictions from molecular potential energy and dipole moment surfaces

    NASA Astrophysics Data System (ADS)

    Rey, Michaël; Nikitin, Andrei V.; Babikov, Yurii L.; Tyuterev, Vladimir G.

    2016-09-01

    Knowledge of intensities of rovibrational transitions of various molecules and theirs isotopic species in wide spectral and temperature ranges is essential for the modeling of optical properties of planetary atmospheres, brown dwarfs and for other astrophysical applications. TheoReTS ("Theoretical Reims-Tomsk Spectral data") is an Internet accessible information system devoted to ab initio based rotationally resolved spectra predictions for some relevant molecular species. All data were generated from potential energy and dipole moment surfaces computed via high-level electronic structure calculations using variational methods for vibration-rotation energy levels and transitions. When available, empirical corrections to band centers were applied, all line intensities remaining purely ab initio. The current TheoReTS implementation contains information on four-to-six atomic molecules, including phosphine, methane, ethylene, silane, methyl-fluoride, and their isotopic species 13CH4 , 12CH3D , 12CH2D2 , 12CD4 , 13C2H4, … . Predicted hot methane line lists up to T = 2000 K are included. The information system provides the associated software for spectra simulation including absorption coefficient, absorption and emission cross-sections, transmittance and radiance. The simulations allow Lorentz, Gauss and Voight line shapes. Rectangular, triangular, Lorentzian, Gaussian, sinc and sinc squared apparatus function can be used with user-defined specifications for broadening parameters and spectral resolution. All information is organized as a relational database with the user-friendly graphical interface according to Model-View-Controller architectural tools. The full-featured web application is written on PHP using Yii framework and C++ software modules. In case of very large high-temperature line lists, a data compression is implemented for fast interactive spectra simulations of a quasi-continual absorption due to big line density. Applications for the TheoReTS may

  7. LHC Physics Potential versus Energy

    SciTech Connect

    Quigg, Chris; /Fermilab

    2009-08-01

    Parton luminosities are convenient for estimating how the physics potential of Large Hadron Collider experiments depends on the energy of the proton beams. I present parton luminosities, ratios of parton luminosities, and contours of fixed parton luminosity for gg, u{bar d}, and qq interactions over the energy range relevant to the Large Hadron Collider, along with example analyses for specific processes.

  8. An ab initio method for locating potential energy minima

    SciTech Connect

    Bock, Nicolas; Peery, Travis; Venneri, Giulia; Chisolm, Eric; Wallace, Duane; Lizarraga, Raquel; Holmstrom, Erik

    2009-01-01

    We study the potential energy landscape underlying the motion of monatomic liquids by quenching from random initial configurations (stochastic configurations) to the nearest local minimum of the potential energy. We show that this procedure reveals the underlying potential energy surface directly. This is in contrast to the common technique of quenching from a molecular dynamics trajectory which does not allow a direct view of the underlying potential energy surface, but needs to be corrected for thermodynamic weighting factors.

  9. Energy restriction and potential energy restriction mimetics.

    PubMed

    Nikolai, Sibylle; Pallauf, Kathrin; Huebbe, Patricia; Rimbach, Gerald

    2015-12-01

    Energy restriction (ER; also known as caloric restriction) is the only nutritional intervention that has repeatedly been shown to increase lifespan in model organisms and may delay ageing in humans. In the present review we discuss current scientific literature on ER and its molecular, metabolic and hormonal effects. Moreover, criteria for the classification of substances that might induce positive ER-like changes without having to reduce energy intake are summarised. Additionally, the putative ER mimetics (ERM) 2-deoxy-d-glucose, metformin, rapamycin, resveratrol, spermidine and lipoic acid and their suggested molecular targets are discussed. While there are reports on these ERM candidates that describe lifespan extension in model organisms, data on longevity-inducing effects in higher organisms such as mice remain controversial or are missing. Furthermore, some of these candidates produce detrimental side effects such as immunosuppression or lactic acidosis, or have not been tested for safety in long-term studies. Up to now, there are no known ERM that could be recommended without limitations for use in humans.

  10. Relativity, potential energy, and mass

    NASA Astrophysics Data System (ADS)

    Hecht, Eugene

    2016-11-01

    This paper is an exploration of the concept of energy, illuminated by the transformative insights of the special theory of relativity. Focusing on potential energy (PE), it will be shown that PE as presently defined is in conflict with the tenets of special relativity. Even though PE remains an indispensable theoretical device its actual physicality is questionable. Moreover its ontological status is quite different from that of both kinetic energy and mass, a significant point that is not widely appreciated. We will establish that PE is a theoretical concept as opposed to an empirical one; it is a descriptor of mass-energy without a detectable physical presence of its own. PE is a measure of energy stored, it is not the energy stored.

  11. Molecularly Engineered Energy Materials, an Energy Frontier Research Center

    SciTech Connect

    Ozolins, Vidvuds

    2016-09-28

    Molecularly Engineered Energy Materials (MEEM) was established as an interdisciplinary cutting-edge UCLA-based research center uniquely equipped to attack the challenge of rationally designing, synthesizing and testing revolutionary new energy materials. Our mission was to achieve transformational improvements in the performance of materials via controlling the nano-and mesoscale structure using selectively designed, earth-abundant, inexpensive molecular building blocks. MEEM has focused on materials that are inherently abundant, can be easily assembled from intelligently designed building blocks (molecules, nanoparticles), and have the potential to deliver transformative economic benefits in comparison with the current crystalline-and polycrystalline-based energy technologies. MEEM addressed basic science issues related to the fundamental mechanisms of carrier generation, energy conversion, as well as transport and storage of charge and mass in tunable, architectonically complex materials. Fundamental understanding of these processes will enable rational design, efficient synthesis and effective deployment of novel three-dimensional material architectures for energy applications. Three interrelated research directions were initially identified where these novel architectures hold great promise for high-reward research: solar energy generation, electrochemical energy storage, and materials for CO2 capture. Of these, the first two remained throughout the project performance period, while carbon capture was been phased out in consultation and with approval from BES program manager.

  12. Learning molecular energies using localized graph kernels

    NASA Astrophysics Data System (ADS)

    Ferré, Grégoire; Haut, Terry; Barros, Kipton

    2017-03-01

    Recent machine learning methods make it possible to model potential energy of atomic configurations with chemical-level accuracy (as calculated from ab initio calculations) and at speeds suitable for molecular dynamics simulation. Best performance is achieved when the known physical constraints are encoded in the machine learning models. For example, the atomic energy is invariant under global translations and rotations; it is also invariant to permutations of same-species atoms. Although simple to state, these symmetries are complicated to encode into machine learning algorithms. In this paper, we present a machine learning approach based on graph theory that naturally incorporates translation, rotation, and permutation symmetries. Specifically, we use a random walk graph kernel to measure the similarity of two adjacency matrices, each of which represents a local atomic environment. This Graph Approximated Energy (GRAPE) approach is flexible and admits many possible extensions. We benchmark a simple version of GRAPE by predicting atomization energies on a standard dataset of organic molecules.

  13. Assessment of Triton Potential Energy

    NASA Astrophysics Data System (ADS)

    Friar, J. L.; Payne, G. L.

    1995-12-01

    An assessment is made of the dominant features contributing to the triton potential energy, with the objective of understanding qualitatively their origins and sensitivities. Relativistic effects, short-range repulsion, and OPEP dominance are discussed. A determination of the importance of various regions of nucleon-nucleon separation is made numerically.

  14. Analysis of Potential Energy Surfaces.

    ERIC Educational Resources Information Center

    Fernandez, G. M.; And Others

    1988-01-01

    Introduces different methodological strategies in analyzing potential energy surfaces (PES) used in chemical reactivity studies. Discusses the theory of PES and gives examples to be used for student work. Provides procedures for calculating normal coordinates and vibrational properties of an activated complex. (ML)

  15. Energies of Screened Coulomb Potentials.

    ERIC Educational Resources Information Center

    Lai, C. S.

    1979-01-01

    This article shows that, by applying the Hellman-Feynman theorem alone to screened Coulomb potentials, the first four coefficients in the energy series in powers of the perturbation parameter can be obtained from the unperturbed Coulomb system. (Author/HM)

  16. Development of Molecular Electrocatalysts for Energy Storage

    SciTech Connect

    DuBois, Daniel L.

    2014-02-20

    Molecular electrocatalysts can play an important role in energy storage and utilization reactions needed for intermittent renewable energy sources. This manuscript describes three general themes that our laboratories have found useful in the development of molecular electrocatalysts for reduction of CO2 to CO and for H2 oxidation and production. The first theme involves a conceptual partitioning of catalysts into first, second, and outer coordination spheres. This is illustrated with the design of electrocatalysts for CO2 reduction to CO using first and second coordination spheres and for H2 production catalysts using all three coordination spheres. The second theme focuses on the development of thermodynamic models that can be used to design catalysts to avoid high energy and low energy intermediates. In this research, new approaches to the measurement of thermodynamic hydride donor and acceptor abilities of transition metal complexes were developed. Combining this information with other thermodynamic information such as pKa values and redox potentials led to more complete thermodynamic descriptions of transition metal hydride, dihydride, and related species. Relationships extracted from this information were then used to develop models that are powerful tools for predicting and understanding the relative free energies of intermediates in catalytic reactions. The third theme is the control of proton movement during electrochemical fuel generation and utilization reactions. This research involves the incorporation of pendant amines in the second coordination sphere that can facilitate H-H bond heterolysis and heteroformation, intramolecular and intermolecular proton transfer steps, and the coupling of proton and electron transfer steps. Studies also indicate an important role for outer coordination sphere in the delivery of protons to the second coordination sphere. Understanding these proton transfer reactions and their

  17. An exchange-Coulomb model potential energy surface for the Ne-CO interaction. II. Molecular beam scattering and bulk gas phenomena in Ne-CO mixtures.

    PubMed

    Dham, Ashok K; McBane, George C; McCourt, Frederick R W; Meath, William J

    2010-01-14

    Four potential energy surfaces are of current interest for the Ne-CO interaction. Two are high-level fully ab initio surfaces obtained a decade ago using symmetry-adapted perturbation theory and supermolecule coupled-cluster methods. The other two are very recent exchange-Coulomb (XC) model potential energy surfaces constructed by using ab initio Heitler-London interaction energies and literature long range dispersion and induction energies, followed by the determination of a small number of adjustable parameters to reproduce a selected subset of pure rotational transition frequencies for the (20)Ne-(12)C(16)O van der Waals cluster. Testing of the four potential energy surfaces against a wide range of available experimental microwave, millimeter-wave, and mid-infrared Ne-CO transition frequencies indicated that the XC potential energy surfaces gave results that were generally far superior to the earlier fully ab initio surfaces. In this paper, two XC model surfaces and the two fully ab initio surfaces are tested for their abilities to reproduce experiment for a wide range of nonspectroscopic Ne-CO gas mixture properties. The properties considered here are relative integral cross sections and the angle dependence of rotational state-to-state differential cross sections, rotational relaxation rate constants for CO(v=2) in Ne-CO mixtures at T=296 K, pressure broadening of two pure rotational lines and of the rovibrational lines in the CO fundamental and first overtone transitions at 300 K, and the temperature and, where appropriate, mole fraction dependencies of the interaction second virial coefficient, the binary diffusion coefficient, the interaction viscosity, the mixture shear viscosity and thermal conductivity coefficients, and the thermal diffusion factor. The XC model potential energy surfaces give results that lie within or very nearly within the experimental uncertainties for all properties considered, while the coupled-cluster ab initio surface gives

  18. California Industrial Energy Efficiency Potential

    SciTech Connect

    Coito, Fred; Worrell, Ernst; Price, Lynn; Masanet, Eric; RafaelFriedmann; Rufo, Mike

    2005-06-01

    This paper presents an overview of the modeling approach andhighlights key findings of a California industrial energy efficiencypotential study. In addition to providing estimates of technical andeconomic potential, the study examines achievable program potential undervarious program-funding scenarios. The focus is on electricity andnatural gas savings for manufacturing in the service territories ofCalifornia's investor-owned utilities (IOUs). The assessment is conductedby industry type and by end use. Both crosscutting technologies andindustry-specific process measures are examined. Measure penetration intothe marketplace is modeled as a function of customer awareness, measurecost effectiveness, and perceived market barriers. Data for the studycomes from a variety of sources, including: utility billing records, theEnergy Information Association (EIA) Manufacturing Energy ConsumptionSurvey (MECS), state-sponsored avoided cost studies, energy efficiencyprogram filings, and technology savings and cost data developed throughLawrence Berkeley National Laboratory (LBNL). The study identifies 1,706GWh and 47 Mth (million therms) per year of achievable potential over thenext twelve years under recent levels of program expenditures, accountingfor 5.2 percent of industrial electricity consumption and 1.3 percent ofindustrial natural gas consumption. These estimates grow to 2,748 GWh and192 Mth per year if all cost-effective and achievable opportunities arepursued. Key industrial electricity end uses, in terms of energy savingspotential, include compressed air and pumping systems that combine toaccount for about half of the total achievable potential estimates. Fornatural gas, savings are concentrated in the boiler and process heatingend uses, accounting for over 99 percent to total achievablepotential.

  19. Effects of molecular potential and geometry on atomic core-level photoemission over an extended energy range - the case study of CO molecule

    NASA Astrophysics Data System (ADS)

    Kukk, E.; Ayuso, D.; Thomas, T. D.; Decleva, P.; Patanen, M.; Argenti, L.; Plésiat, E.; Palacios, A.; Kooser, K.; Travnikova, O.; Mondal, S.; Kimura, M.; Sakai, K.; Miron, C.; Martín, F.; Ueda, K.

    2014-04-01

    We report an experimental and theoretical study of single-molecule inner-shell photoemission over an extended range of photon energies. The vibrational ratios v=1/v=0 from the C 1s photoelectron spectra, although mostly determined by the bond length change, are shown to be affected also by photoelectron recoil and scattering on the neighboring oxygen atom. Density functional theory is used to encompass all these effect in unified treatment. It is also demonstrated that the DFT calculations can be used as a means to extract dynamic and static molecular geometry values.

  20. The potential of renewable energy

    SciTech Connect

    Not Available

    1990-03-01

    On June 27 and 28, 1989, the US Department of Energy (DOE) national laboratories were convened to discuss plans for the development of a National Energy Strategy (NES) and, in particular, the analytic needs in support of NES that could be addressed by the laboratories. As a result of that meeting, interlaboratory teams were formed to produce analytic white papers on key topics, and a lead laboratory was designated for each core laboratory team. The broad-ranging renewables assignment is summarized by the following issue statement from the Office of Policy, Planning and Analysis: to what extent can renewable energy technologies contribute to diversifying sources of energy supply What are the major barriers to greater renewable energy use and what is the potential timing of widespread commercialization for various categories of applications This report presents the results of the intensive activity initiated by the June 1989 meeting to produce a white paper on renewable energy. Scores of scientists, analysts, and engineers in the five core laboratories gave generously of their time over the past eight months to produce this document. Their generous, constructive efforts are hereby gratefully acknowledged. 126 refs., 44 figs., 32 tabs.

  1. Molecular electrostatic potential as a graph.

    PubMed

    Daza, Edgar E; Maza, Julio; Torres, Raul

    2013-06-01

    We present several procedures to represent molecular electrostatic potential as a graph, based on the pattern of critical points and their neighborhood relations. This representation is used for the molecular electrostatic comparison, which is reduced to a comparison of tree-type graphs. Several methods to compare trees are also presented. The applications of this algorithm to compare and classify molecules through their electrostatic potential are illustrated.

  2. Combined valence bond-molecular mechanics potential-energy surface and direct dynamics study of rate constants and kinetic isotope effects for the H + C2H6 reaction.

    PubMed

    Chakraborty, Arindam; Zhao, Yan; Lin, Hai; Truhlar, Donald G

    2006-01-28

    This article presents a multifaceted study of the reaction H+C(2)H(6)-->H(2)+C(2)H(5) and three of its deuterium-substituted isotopologs. First we present high-level electronic structure calculations by the W1, G3SX, MCG3-MPWB, CBS-APNO, and MC-QCISD/3 methods that lead to a best estimate of the barrier height of 11.8+/-0.5 kcal/mol. Then we obtain a specific reaction parameter for the MPW density functional in order that it reproduces the best estimate of the barrier height; this yields the MPW54 functional. The MPW54 functional, as well as the MPW60 functional that was previously parametrized for the H+CH(4) reaction, is used with canonical variational theory with small-curvature tunneling to calculate the rate constants for all four ethane reactions from 200 to 2000 K. The final MPW54 calculations are based on curvilinear-coordinate generalized-normal-mode analysis along the reaction path, and they include scaled frequencies and an anharmonic C-C bond torsion. They agree with experiment within 31% for 467-826 K except for a 38% deviation at 748 K; the results for the isotopologs are predictions since these rate constants have never been measured. The kinetic isotope effects (KIEs) are analyzed to reveal the contributions from subsets of vibrational partition functions and from tunneling, which conspire to yield a nonmonotonic temperature dependence for one of the KIEs. The stationary points and reaction-path potential of the MPW54 potential-energy surface are then used to parametrize a new kind of analytical potential-energy surface that combines a semiempirical valence bond formalism for the reactive part of the molecule with a standard molecular mechanics force field for the rest; this may be considered to be either an extension of molecular mechanics to treat a reactive potential-energy surface or a new kind of combined quantum-mechanical/molecular mechanical (QM/MM) method in which the QM part is semiempirical valence bond theory; that is, the new potential-energy

  3. Combined valence bond-molecular mechanics potential-energy surface and direct dynamics study of rate constants and kinetic isotope effects for the H +C2H6 reaction

    NASA Astrophysics Data System (ADS)

    Chakraborty, Arindam; Zhao, Yan; Lin, Hai; Truhlar, Donald G.

    2006-01-01

    This article presents a multifaceted study of the reaction H +C2H6→H2+C2H5 and three of its deuterium-substituted isotopologs. First we present high-level electronic structure calculations by the W1, G3SX, MCG3-MPWB, CBS-APNO, and MC-QCISD/3 methods that lead to a best estimate of the barrier height of 11.8±0.5kcal/mol. Then we obtain a specific reaction parameter for the MPW density functional in order that it reproduces the best estimate of the barrier height; this yields the MPW54 functional. The MPW54 functional, as well as the MPW60 functional that was previously parametrized for the H +CH4 reaction, is used with canonical variational theory with small-curvature tunneling to calculate the rate constants for all four ethane reactions from 200 to 2000 K. The final MPW54 calculations are based on curvilinear-coordinate generalized-normal-mode analysis along the reaction path, and they include scaled frequencies and an anharmonic C-C bond torsion. They agree with experiment within 31% for 467-826 K except for a 38% deviation at 748 K; the results for the isotopologs are predictions since these rate constants have never been measured. The kinetic isotope effects (KIEs) are analyzed to reveal the contributions from subsets of vibrational partition functions and from tunneling, which conspire to yield a nonmonotonic temperature dependence for one of the KIEs. The stationary points and reaction-path potential of the MPW54 potential-energy surface are then used to parametrize a new kind of analytical potential-energy surface that combines a semiempirical valence bond formalism for the reactive part of the molecule with a standard molecular mechanics force field for the rest; this may be considered to be either an extension of molecular mechanics to treat a reactive potential-energy surface or a new kind of combined quantum-mechanical/molecular mechanical (QM/MM) method in which the QM part is semiempirical valence bond theory; that is, the new potential-energy

  4. Effects of molecular potential and geometry on atomic core-level photoemission over an extended energy range: The case study of the CO molecule

    NASA Astrophysics Data System (ADS)

    Kukk, E.; Ayuso, D.; Thomas, T. D.; Decleva, P.; Patanen, M.; Argenti, L.; Plésiat, E.; Palacios, A.; Kooser, K.; Travnikova, O.; Mondal, S.; Kimura, M.; Sakai, K.; Miron, C.; Martín, F.; Ueda, K.

    2013-09-01

    We report an experimental and theoretical study of single-molecule inner-shell photoemission measured over an extended range of photon energies. The vibrational intensity ratios I(ν=1)/I(ν=0) from the C 1s photoelectron spectra of carbon monoxide, although mostly determined by the bond length change upon ionization, are shown to be affected also by photoelectron recoil and by scattering from the neighboring oxygen atom. Static-exchange density functional theory (DFT) is used to encompass all these effects in a unified theoretical treatment. The ab initio calculations show that the vibrational ratio as a function of the photoelectron momentum is sensitive to both the ground-state internuclear distance and its contraction upon photoionization. We present a proof-of-principle application of DFT calculations as a quantitative structural analysis tool for extracting the dynamic and static molecular geometry parameters simultaneously.

  5. Potential energy surface of cyclooctatetraene

    NASA Astrophysics Data System (ADS)

    Andrés, José L.; Castaño, Obis; Morreale, Antonio; Palmeiro, Raul; Gomperts, Roberto

    1998-01-01

    We present a theoretical study of the cyclooctatetraene (COT) molecule. Seven COT structures are located on the singlet ground state potential energy surface. Four of them, which present D2d (tub), Cs (bicyclo[4.2.0]octa-2,4,7-triene or BOT), C2h (chair) and D4 (crown) symmetries are stable species, and the other three are transition state structures showing Cs, D4h, and D8h symmetry. We discuss the symmetry of wave functions for these stationary points. Geometries, energies, and harmonic vibrational frequencies of these structures, and energy gaps between singlet-triplet states and low-lying singlets are presented. For the planar D4h and D8h structures, Jahn-Teller and tunneling effects have also been discussed. Ring inversion, bond shifting and valence isomerization reactive channels from the tub COT conformer are discussed from the point of view of the corresponding transition state structures. Where possible, in order to lend support to this theoretical information comparisons with recent transition state spectroscopy data are made.

  6. Communication: Rate coefficients of the H + CH{sub 4} → H{sub 2} + CH{sub 3} reaction from ring polymer molecular dynamics on a highly accurate potential energy surface

    SciTech Connect

    Meng, Qingyong Chen, Jun Zhang, Dong H.

    2015-09-14

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

  7. Benchmark Calculations with Correlated Molecular Wave Functions. XIII. Potential Energy Curves for He-2, Ne-2, and Ar-2 Using Correlation Consistent Basis Sets Through Augmented Sextuple Zeta.

    SciTech Connect

    Mourik, Van Tonja; Wilson, Angela K.; Dunning, Thomas H.

    1999-02-20

    The potential energy curves of the rare gas dimers He2, Ne2, and Ar2 have been computed using correlation consistent basis sets ranging from singly augmented aug-cc-pVDZ sets through triply augmented t-aug-cc-pV6Z sets, with the augmented sextuple basis sets being reported herein. Several methods for including electron correlation were investigated, namely Moller Plesset perturbation theory (MP2, MP3 and MP4) and coupled cluster theory [CCSD and CCSD(T)].

  8. Molecular dynamics investigation of the bimolecular reaction BeH + H(2) --> BeH(2) + H on an ab initio potential-energy surface obtained using neural network methods with both potential and gradient accuracy determination.

    PubMed

    Le, Hung M; Raff, Lionel M

    2010-01-14

    The classical reaction dynamics of a four-body, bimolecular reaction on a neural network (NN) potential-energy surface (PES) fitted to a database obtained solely from ab initio MP2/6-311G(d,p) calculations are reported. The present work represents the first reported application of ab initio NN methods to a four-body, bimolecular, gas-phase reaction where bond extensions reach 8.1 A for the BeH + H(2) --> BeH(2) + H reaction. A modified, iterative novelty sampling method is used to select data points based on classical trajectories computed on temporary NN surfaces. After seven iterations, the sampling process is found to converge after selecting 9604 configurations. Incorporation of symmetry increases this to 19 208 BeH(3) configurations. The analytic PES for the system is obtained from the ensemble average of a five-member (6-60-1) NN committee. The mean absolute error (MAE) for the committee is 0.0046 eV (0.44 kJ mol(-1)). The total energy range of the BeH(3) database is 147.0 kJ mol(-1). Therefore, this MAE represents a percent energy error of 0.30%. Since it is the gradient of the PES that constitutes the most important quantity in molecular dynamics simulations, the paper also reports mean absolute error for the gradient. This result is 0.026 eV A(-1) (2.51 kJ mol(-1) A(-1)). Since the gradient magnitudes span a range of 15.32 eV A(-1) over the configuration space tested, this mean absolute gradient error represents a percent error of 0.17%. The mean percent absolute relative gradient error is 4.67%. The classically computed reaction cross sections generally increase with total energy. They vary from 0.007 to 0.030 A(2) when H(2) is at ground state, and from 0.05 to 0.10 A(2) when H(2) is in the first excited state. Trajectory integration is very fast using the five-member NN PES. The average trajectory integration time is 1.07 s on a CPU with a clock speed of 2.4 GHz. Zero angular momentum collisions are also investigated and compared with previously reported

  9. Mean excitation energies for molecular ions

    NASA Astrophysics Data System (ADS)

    Jensen, Phillip W. K.; Sauer, Stephan P. A.; Oddershede, Jens; Sabin, John R.

    2017-03-01

    The essential material constant that determines the bulk of the stopping power of high energy projectiles, the mean excitation energy, is calculated for a range of smaller molecular ions using the RPA method. It is demonstrated that the mean excitation energy of both molecules and atoms increase with ionic charge. However, while the mean excitation energies of atoms also increase with atomic number, the opposite is the case for mean excitation energies for molecules and molecular ions. The origin of these effects is explained by considering the spectral representation of the excited state contributing to the mean excitation energy.

  10. Geothermal Energy: Tapping the Potential

    ERIC Educational Resources Information Center

    Johnson, Bill

    2008-01-01

    Ground source geothermal energy enables one to tap into the earth's stored renewable energy for heating and cooling facilities. Proper application of ground-source geothermal technology can have a dramatic impact on the efficiency and financial performance of building energy utilization (30%+). At the same time, using this alternative energy…

  11. Morphing ab initio potential energy curve of beryllium monohydride

    NASA Astrophysics Data System (ADS)

    Špirko, Vladimír

    2016-12-01

    Effective (mass-dependent) potential energy curves of the ground electronic states of 9BeH, 9BeD, and 9BeT are constructed by morphing a very accurate MR-ACPF ab initio potential of Koput (2011) within the framework of the reduced potential energy curve approach of Jenč (1983). The morphing is performed by fitting the RPC parameters to available experimental ro-vibrational data. The resulting potential energy curves provide a fairly quantitative reproduction of the fitted data. This allows for a reliable prediction of the so-far unobserved molecular states in terms of only a small number of fitting parameters.

  12. Molecular dynamics simulation of threshold displacement energies in zircon

    SciTech Connect

    Moreira, Pedro A.; Devanathan, Ramaswami; Yu, Jianguo; Weber, William J.

    2009-10-15

    Molecular-dynamics simulations were used to examine the displacement threshold energy (Ed) surface for Zr, Si and O in zircon using two different interatomic potentials. For each sublattice, the simulation was repeated from different initial conditions to estimate the uncertainty in the calculated value of Ed. The displacement threshold energies vary considerably with crystallographic direction and sublattice. The average displacement energy calculated with a recently developed transferable potential is about 120 and 60 eV for cations and anions, respectively. The oxygen displacement energy shows good agreement with experimental estimates in ceramics.

  13. Nonintuitive Diabatic Potential Energy Surfaces for Thioanisole.

    PubMed

    Li, Shaohong L; Xu, Xuefei; Hoyer, Chad E; Truhlar, Donald G

    2015-09-03

    Diabatization of potential energy surfaces is a technique that enables convenient molecular dynamics simulations of electronically nonadiabatic processes, but diabatization itself is nonunique and can be inconvenient; the best methods to achieve diabatization are still under study. Here, we present the diabatization of two electronic states of thioanisole in the S-CH3 bond stretching and C-C-S-C torsion two-dimensional nuclear coordinate space containing a conical intersection. We use two systematic methods: the (orbital-dependent) 4-fold way and the (orbital-free) Boys localization diabatization method. These very different methods yield strikingly similar diabatic potential energy surfaces that cross at geometries where the adiabatic surfaces are well separated and do not exhibit avoided crossings, and the contours of the diabatic gap and diabatic coupling are similar for the two methods. The validity of the diabatization is supported by comparing the nonadiabatic couplings calculated from the diabatic matrix elements to those calculated by direct differentiation of the adiabatic states.

  14. Hydration Free Energies of Molecular Ions from Theory and Simulation.

    PubMed

    Misin, Maksim; Fedorov, Maxim V; Palmer, David S

    2016-02-11

    We present a theoretical/computational framework for accurate calculation of hydration free energies of ionized molecular species. The method is based on a molecular theory, 3D-RISM, combined with a recently developed pressure correction (PC+). The 3D-RISM/PC+ model can provide ∼3 kcal/mol hydration free energy accuracy for a large variety of ionic compounds, provided that the Galvani potential of water is taken into account. The results are compared with direct atomistic simulations. Several methodological aspects of hydration free energy calculations for charged species are discussed.

  15. Potential of renewable and alternative energy sources

    NASA Astrophysics Data System (ADS)

    Konovalov, V.; Pogharnitskaya, O.; Rostovshchikova, A.; Matveenko, I.

    2015-11-01

    The article deals with application potential of clean alternative renewable energy sources. By means of system analysis the forecast for consumption of electrical energy in Tomsk Oblast as well as main energy sources of existing energy system have been studied up to 2018. Engineering potential of renewable and alternative energy sources is evaluated. Besides, ranking in the order of their efficiency descending is performed. It is concluded that Tomsk Oblast has high potential of alternative and renewable energy sources, among which the most promising development perspective is implementation of gasification stations to save fuel consumed by diesel power stations as well as building wind-power plants.

  16. Molecular Motion and Energy Migration in Polymers.

    DTIC Science & Technology

    1985-06-01

    A EDUUNI MAR 8 STOK ISEXHASTED " LOAN, 0 - LO 00 MOLECULAR MOTION AND ENERGY MIGRATION IN POLYMERS Professor David Phillips June 1985 US Army...and Energy Migration in Final Technical Report Polymers 6. PERFORMING ORG. REPORT NUMBER 7. AUTHOR(s) 8. CONTRACT OR GRANT NUMBER(s) Professor David...acenaphthylene, poly(diacetylenes),4h,4’ - diphenylene diphenyl vinylene, energy transfer, migration, segmental motion, rotational relaxation. 20. ABSTRACT

  17. Zero-point Energy is Needed in Molecular Dynamics Calculations to Access the Saddle Point for H+HCN→H2CN* and cis/trans-HCNH* on a New Potential Energy Surface.

    PubMed

    Wang, Xiaohong; Bowman, Joel M

    2013-02-12

    We calculate the probabilities for the association reactions H+HCN→H2CN* and cis/trans-HCNH*, using quasiclassical trajectory (QCT) and classical trajectory (CT) calculations, on a new global ab initio potential energy surface (PES) for H2CN including the reaction channels. The surface is a linear least-squares fit of roughly 60 000 CCSD(T)-F12b/aug-cc-pVDZ electronic energies, using a permutationally invariant basis with Morse-type variables. The reaction probabilities are obtained at a variety of collision energies and impact parameters. Large differences in the threshold energies in the two types of dynamics calculations are traced to the absence of zero-point energy in the CT calculations. We argue that the QCT threshold energy is the realistic one. In addition, trajectories find a direct pathway to trans-HCNH, even though there is no obvious transition state (TS) for this pathway. Instead the saddle point (SP) for the addition to cis-HCNH is evidently also the TS for direct formation of trans-HCNH.

  18. Guide for Conducting Energy Efficiency Potential Studies

    EPA Pesticide Factsheets

    The Guide for Conducting Energy Efficiency Potential Studies is provided to assist state officials, regulators, legislators, and others in implementing the recommendations of the National Action Plan for Energy Efficiency.

  19. Energy potential of modern landfills

    SciTech Connect

    Bogner, J.E.

    1990-01-01

    Methane produced by refuse decomposition in a sanitary landfill can be recovered for commercial use. Landfill methane is currently under-utilized, with commercial recovery at only a small percentage of US landfills. New federal regulations mandating control of landfill gas migration and atmospheric emissions are providing impetus to methane recovery schemes as a means of recovering costs for increased environmental control. The benefits of landfill methane recovery include utilization of an inexpensive renewable energy resource, removal of explosive gas mixtures from the subsurface, and mitigation of observed historic increases in atmospheric methane. Increased commercial interest in landfill methane recovery is dependent on the final form of Clean Air Act amendments pertaining to gaseous emissions from landfills; market shifts in natural gas prices; financial incentives for development of renewable energy resources; and support for applied research and development to develop techniques for increased control of the gas generation process in situ. This paper will discuss the controls on methane generation in landfills. In addition, it will address how landfill regulations affect landfill design and site management practices which, in turn, influence decomposition rates. Finally, future trends in landfilling, and their relationship to gas production, will be examined. 19 refs., 2 figs., 3 tabs.

  20. Molecular origins of the zeta potential

    DOE PAGES

    Predota, Milan; Machesky, Michael L.; Wesolowski, David J.

    2016-09-19

    The zeta potential (ZP) is an oft-reported measure of the macroscopic charge state of solid surfaces and colloidal particles in contact with solvents. However, the origin of this readily measurable parameter has remained divorced from the molecular-level processes governing the underlying electrokinetic phenomena, which limits its usefulness. Here, we connect the macroscopic measure to the microscopic realm through nonequilibrium molecular dynamics simulations of electroosmotic flow between parallel slabs of the hydroxylated (110) rutile (TiO2) surface. These simulations provided streaming mobilities, which were converted to ZP via the commonly used Helmholtz-Smoluchowski equation. A range of rutile surface charge densities (0.1 tomore » –0.4 C/m2), corresponding to pH values between about 2.8 and 9.4, in RbCl, NaCl, and SrCl2 aqueous solutions, were modeled and compared to experimental ZPs for TiO2 particle suspensions. Simulated ZPs qualitatively agree with experiment and show that “anomalous” ZP values and inequalities between the point of zero charge derived from electrokinetic versus pH titration measurements both arise from differing co- and counterion sorption affinities. We show that at the molecular level the ZP arises from the delicate interplay of spatially varying dynamics, structure, and electrostatics in a narrow interfacial region within about 15 Å of the surface, even in dilute salt solutions. This contrasts fundamentally with continuum descriptions of such interfaces, which predict the ZP response region to be inversely related to ionic strength. In reality the properties of this interfacial region are dominated by relatively immobile and structured water. Furthermore, viscosity values are substantially greater than in the bulk, and electrostatic potential profiles are oscillatory in nature.« less

  1. Molecular origins of the zeta potential

    SciTech Connect

    Predota, Milan; Machesky, Michael L.; Wesolowski, David J.

    2016-09-19

    The zeta potential (ZP) is an oft-reported measure of the macroscopic charge state of solid surfaces and colloidal particles in contact with solvents. However, the origin of this readily measurable parameter has remained divorced from the molecular-level processes governing the underlying electrokinetic phenomena, which limits its usefulness. Here, we connect the macroscopic measure to the microscopic realm through nonequilibrium molecular dynamics simulations of electroosmotic flow between parallel slabs of the hydroxylated (110) rutile (TiO2) surface. These simulations provided streaming mobilities, which were converted to ZP via the commonly used Helmholtz-Smoluchowski equation. A range of rutile surface charge densities (0.1 to –0.4 C/m2), corresponding to pH values between about 2.8 and 9.4, in RbCl, NaCl, and SrCl2 aqueous solutions, were modeled and compared to experimental ZPs for TiO2 particle suspensions. Simulated ZPs qualitatively agree with experiment and show that “anomalous” ZP values and inequalities between the point of zero charge derived from electrokinetic versus pH titration measurements both arise from differing co- and counterion sorption affinities. We show that at the molecular level the ZP arises from the delicate interplay of spatially varying dynamics, structure, and electrostatics in a narrow interfacial region within about 15 Å of the surface, even in dilute salt solutions. This contrasts fundamentally with continuum descriptions of such interfaces, which predict the ZP response region to be inversely related to ionic strength. In reality the properties of this interfacial region are dominated by relatively immobile and structured water. Furthermore, viscosity values are substantially greater than in the bulk, and electrostatic potential profiles are oscillatory in nature.

  2. Path-integral molecular dynamics simulations of glycine·(H 2O) n ( n = 1-7) clusters on semi-empirical PM6 potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Yoshikawa, Takehiro; Motegi, Haruki; Kakizaki, Akira; Takayanagi, Toshiyuki; Shiga, Motoyuki; Tachikawa, Masanori

    2009-11-01

    Path-integral molecular dynamics simulations for the hydrogen-bonded glycine·(H 2O) n ( n = 1-7) clusters have been carried out using an on-the-fly direct dynamics technique at the semi-empirical PM6 level of theory. In the case of smaller clusters with n = 1-3, the simulations show that the cluster structure takes exclusively the hydrogen-bonded complex between a canonical neutral glycine and a water cluster moiety. In contrast, it was found that proton-exchange processes effectively occur between the COOH carboxylic group and water cluster moiety for n = 4-6 clusters although the overall structures are the complex between a neutral glycine and water clusters. In the case of the n = 7 cluster, glycine preferentially takes a zwitterionic form having NH3+ and COO - functional groups.

  3. Vibrational energy transfer in shocked molecular crystals.

    PubMed

    Hooper, Joe

    2010-01-07

    We consider the process of establishing thermal equilibrium behind an ideal shock front in molecular crystals and its possible role in initiating chemical reaction at high shock pressures. A new theory of equilibration via multiphonon energy transfer is developed to treat the scattering of shock-induced phonons into internal molecular vibrations. Simple analytic forms are derived for the change in this energy transfer at different Hugoniot end states following shock compression. The total time required for thermal equilibration is found to be an order of magnitude or faster than proposed in previous work; in materials representative of explosive molecular crystals, equilibration is predicted to occur within a few picoseconds following the passage of an ideal shock wave. Recent molecular dynamics calculations are consistent with these time scales. The possibility of defect-induced temperature localization due purely to nonequilibrium phonon processes is studied by means of a simple model of the strain field around an inhomogeneity. The specific case of immobile straight dislocations is studied, and a region of enhanced energy transfer on the order of 5 nm is found. Due to the rapid establishment of thermal equilibrium, these regions are unrelated to the shock sensitivity of a material but may allow temperature localization at high shock pressures. Results also suggest that if any decomposition due to molecular collisions is occurring within the shock front itself, these collisions are not enhanced by any nonequilibrium thermal state.

  4. Computer experiments on aqueous solutions. VI. Potential energy function for tert-butyl alcohol dimer and molecular dynamics calculation of 3 mol % aqueous solution of tert-butyl alcohol

    NASA Astrophysics Data System (ADS)

    Tanaka, Hideki; Nakanishi, Koichiro; Touhara, Hidekazu

    1984-11-01

    Molecular dynamics (MD) calculation has been carried out for a dilute aqueous solution of tert-butyl alcohol (TBA) at 298.15 K and with experimental density value by the use of constant temperature technique developed previously. The total number of molecule is 216, seven of which are TBA. The mole fraction of TBA is thus 0.032. For water-water and TBA-water interactions, the MCY (Matsuoka-Clementi-Yoshimine) potential and previously reported potential determined by MO calculation are used. A new potential for TBA-TBA is determined by ab initio LCAO SCF calculations for more than 500 different configurations with an STO-3G basis set and subsequent multiparameter fitting of the MO data to a 12-6-3-1 type potential energy function. The MD calculation is extended up to 84 000 time steps (26 ps) and final 60 000 time steps are used to calculate both static and dynamic properties of the system. Both hydrophobic hydration and interaction due to TBA molecules are proved to be stronger than those of methanol studied previously. Structural promotion of water is clearly observed in radial distribution functions and trajectories of each molecule. The configuration and trajectory of all the molecules in solution indicate clearly the association of TBA molecules. It is also found from pair interaction distribution functions that no hydrogen bonding interaction occurs between two TBA molecules. The self-diffusion coefficient of water in the solution is appreciably smaller than that in pure water.

  5. The origins of intra- and inter-molecular vibrational couplings: A case study of H{sub 2}O-Ar on full and reduced-dimensional potential energy surface

    SciTech Connect

    Hou, Dan; Ma, Yong-Tao; Zhang, Xiao-Long; Li, Hui

    2016-01-07

    The origin and strength of intra- and inter-molecular vibrational coupling is difficult to probe by direct experimental observations. However, explicitly including or not including some specific intramolecular vibrational modes to study intermolecular interaction provides a precise theoretical way to examine the effects of anharmonic coupling between modes. In this work, a full-dimension intra- and inter-molecular ab initio potential energy surface (PES) for H{sub 2}O–Ar, which explicitly incorporates interdependence on the intramolecular (Q{sub 1},  Q{sub 2},  Q{sub 3}) normal-mode coordinates of the H{sub 2}O monomer, has been calculated. In addition, four analytic vibrational-quantum-state-specific PESs are obtained by least-squares fitting vibrationally averaged interaction energies for the (v{sub 1},  v{sub 2},  v{sub 3}) =  (0,  0,  0), (0,  0,  1), (1,  0,  0), (0,  1,  0) states of H{sub 2}O to the three-dimensional Morse/long-range potential function. Each vibrationally averaged PES fitted to 442 points has root-mean-square (rms) deviation smaller than 0.15 cm{sup −1}, and required only 58 parameters. With the 3D PESs of H{sub 2}O–Ar dimer system, we employed the combined radial discrete variable representation/angular finite basis representation method and Lanczos algorithm to calculate rovibrational energy levels. This showed that the resulting vibrationally averaged PESs provide good representations of the experimental infrared data, with rms discrepancies smaller than 0.02 cm{sup −1} for all three rotational branches of the asymmetric stretch fundamental transitions. The infrared band origin shifts associated with three fundamental bands of H{sub 2}O in H{sub 2}O–Ar complex are predicted for the first time and are found to be in good agreement with the (extrapolated) experimental values. Upon introduction of additional intramolecular degrees of freedom into the intermolecular potential energy surface, there is clear

  6. Geothermal Energy Potential in Western United States

    ERIC Educational Resources Information Center

    Pryde, Philip R.

    1977-01-01

    Reviews types of geothermal energy sources in the western states, including hot brine systems and dry steam systems. Conversion to electrical energy is a major potential use of geothermal energy, although it creates environmental disruptions such as noise, corrosion, and scaling of equipment. (AV)

  7. Potential Energy Surface Database of Group II Dimer

    National Institute of Standards and Technology Data Gateway

    SRD 143 NIST Potential Energy Surface Database of Group II Dimer (Web, free access)   This database provides critical atomic and molecular data needed in order to evaluate the feasibility of using laser cooled and trapped Group II atomic species (Mg, Ca, Sr, and Ba) for ultra-precise optical clocks or quantum information processing devices.

  8. Communication: Fitting potential energy surfaces with fundamental invariant neural network

    NASA Astrophysics Data System (ADS)

    Shao, Kejie; Chen, Jun; Zhao, Zhiqiang; Zhang, Dong H.

    2016-08-01

    A more flexible neural network (NN) method using the fundamental invariants (FIs) as the input vector is proposed in the construction of potential energy surfaces for molecular systems involving identical atoms. Mathematically, FIs finitely generate the permutation invariant polynomial (PIP) ring. In combination with NN, fundamental invariant neural network (FI-NN) can approximate any function to arbitrary accuracy. Because FI-NN minimizes the size of input permutation invariant polynomials, it can efficiently reduce the evaluation time of potential energy, in particular for polyatomic systems. In this work, we provide the FIs for all possible molecular systems up to five atoms. Potential energy surfaces for OH3 and CH4 were constructed with FI-NN, with the accuracy confirmed by full-dimensional quantum dynamic scattering and bound state calculations.

  9. Wave Energy Potential in the Latvian EEZ

    NASA Astrophysics Data System (ADS)

    Beriņš, J.; Beriņš, J.; Kalnačs, J.; Kalnačs, A.

    2016-06-01

    The present article deals with one of the alternative forms of energy - sea wave energy potential in the Latvian Exclusice Economic Zone (EEZ). Results have been achieved using a new method - VEVPP. Calculations have been performed using the data on wave parameters over the past five years (2010-2014). We have also considered wave energy potential in the Gulf of Riga. The conclusions have been drawn on the recommended methodology for the sea wave potential and power calculations for wave-power plant pre-design stage.

  10. Computational investigation of the binding mode of bis(hydroxylphenyl)arenes in 17β-HSD1: molecular dynamics simulations, MM-PBSA free energy calculations, and molecular electrostatic potential maps

    NASA Astrophysics Data System (ADS)

    Negri, Matthias; Recanatini, Maurizio; Hartmann, Rolf W.

    2011-09-01

    17β-Hydroxysteroid dehydrogenase type 1 (17β-HSD1) catalyzes the last step of the estrogen biosynthesis, namely the reduction of estrone to the biologically potent estradiol. As such it is a potentially attractive drug target for the treatment of estrogen-dependent diseases like breast cancer and endometriosis. 17β-HSD1 belongs to the bisubstrate enzymes and exists as an ensemble of conformations. These principally differ in the region of the βFαG'-loop, suggesting a prominent role in substrate and inhibitor binding. Although several classes of potent non-steroidal 17β-HSD1 inhibitors currently exist, their binding mode is still unclear. We aimed to elucidate the binding mode of bis(hydroxyphenyl)arenes, a highly potent class of 17β-HSD1 inhibitors, and to rank these compounds correctly with respect to their inhibitory potency, two essential aspects in drug design. Ensemble docking experiments resulted in a steroidal binding mode for the closed enzyme conformations and in an alternative mode for the opened and occluded conformers with the inhibitors placed below the NADPH interacting with it synergically via π-π stacking and H-bond formation. Both binding modes were investigated by MD simulations and MM-PBSA binding free energy estimations using as representative member for this class compound 1 (50 nM). Notably, only the alternative binding mode proved stable and was energetically more favorable, while when simulated in the steroidal binding mode compound 1 was displaced from the active site. In parallel, ab initio studies of small NADPH-inhibitor complexes were performed, which supported the importance of the synergistic interaction between inhibitors and cofactor.

  11. Wind energy in China: Estimating the potential

    NASA Astrophysics Data System (ADS)

    Yuan, Jiahai

    2016-07-01

    Persistent and significant curtailment has cast concern over the prospects of wind power in China. A comprehensive assessment of the production of energy from wind has identified grid-integrated wind generation potential at 11.9-14% of China's projected energy demand by 2030.

  12. Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: Sequential sampling and optimization on the potential of mean force surface

    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

  13. Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: Sequential sampling and optimization on the potential of mean force surface

    SciTech Connect

    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

  14. Economic Energy Savings Potential in Federal Buildings

    SciTech Connect

    Brown, Daryl R.; Dirks, James A.; Hunt, Diane M.

    2000-09-04

    The primary objective of this study was to estimate the current life-cycle cost-effective (i.e., economic) energy savings potential in Federal buildings and the corresponding capital investment required to achieve these savings, with Federal financing. Estimates were developed for major categories of energy efficiency measures such as building envelope, heating system, cooling system, and lighting. The analysis was based on conditions (building stock and characteristics, retrofit technologies, interest rates, energy prices, etc.) existing in the late 1990s. The potential impact of changes to any of these factors in the future was not considered.

  15. Applying supersymmetry to energy dependent potentials

    SciTech Connect

    Yekken, R.; Lassaut, M.; Lombard, R.J.

    2013-11-15

    We investigate the supersymmetry properties of energy dependent potentials in the D=1 dimensional space. We show the main aspects of supersymmetry to be preserved, namely the factorization of the Hamiltonian, the connections between eigenvalues and wave functions of the partner Hamiltonians. Two methods are proposed. The first one requires the extension of the usual rules via the concept of local equivalent potential. In this case, the superpotential becomes depending on the state. The second method, applicable when the potential depends linearly on the energy, is similar to what has been already achieved by means of the Darboux transform. -- Highlights: •Supersymmetry extended to energy dependent potentials. •Generalization of the concept of superpotential. •An alternative method used for linear E-dependence leads to the same results as Darboux transform.

  16. A molecularly based theory for electron transfer reorganization energy.

    PubMed

    Zhuang, Bilin; Wang, Zhen-Gang

    2015-12-14

    Using field-theoretic techniques, we develop a molecularly based dipolar self-consistent-field theory (DSCFT) for charge solvation in pure solvents under equilibrium and nonequilibrium conditions and apply it to the reorganization energy of electron transfer reactions. The DSCFT uses a set of molecular parameters, such as the solvent molecule's permanent dipole moment and polarizability, thus avoiding approximations that are inherent in treating the solvent as a linear dielectric medium. A simple, analytical expression for the free energy is obtained in terms of the equilibrium and nonequilibrium electrostatic potential profiles and electric susceptibilities, which are obtained by solving a set of self-consistent equations. With no adjustable parameters, the DSCFT predicts activation energies and reorganization energies in good agreement with previous experiments and calculations for the electron transfer between metallic ions. Because the DSCFT is able to describe the properties of the solvent in the immediate vicinity of the charges, it is unnecessary to distinguish between the inner-sphere and outer-sphere solvent molecules in the calculation of the reorganization energy as in previous work. Furthermore, examining the nonequilibrium free energy surfaces of electron transfer, we find that the nonequilibrium free energy is well approximated by a double parabola for self-exchange reactions, but the curvature of the nonequilibrium free energy surface depends on the charges of the electron-transferring species, contrary to the prediction by the linear dielectric theory.

  17. A molecularly based theory for electron transfer reorganization energy

    SciTech Connect

    Zhuang, Bilin; Wang, Zhen-Gang

    2015-12-14

    Using field-theoretic techniques, we develop a molecularly based dipolar self-consistent-field theory (DSCFT) for charge solvation in pure solvents under equilibrium and nonequilibrium conditions and apply it to the reorganization energy of electron transfer reactions. The DSCFT uses a set of molecular parameters, such as the solvent molecule’s permanent dipole moment and polarizability, thus avoiding approximations that are inherent in treating the solvent as a linear dielectric medium. A simple, analytical expression for the free energy is obtained in terms of the equilibrium and nonequilibrium electrostatic potential profiles and electric susceptibilities, which are obtained by solving a set of self-consistent equations. With no adjustable parameters, the DSCFT predicts activation energies and reorganization energies in good agreement with previous experiments and calculations for the electron transfer between metallic ions. Because the DSCFT is able to describe the properties of the solvent in the immediate vicinity of the charges, it is unnecessary to distinguish between the inner-sphere and outer-sphere solvent molecules in the calculation of the reorganization energy as in previous work. Furthermore, examining the nonequilibrium free energy surfaces of electron transfer, we find that the nonequilibrium free energy is well approximated by a double parabola for self-exchange reactions, but the curvature of the nonequilibrium free energy surface depends on the charges of the electron-transferring species, contrary to the prediction by the linear dielectric theory.

  18. Molecular dynamics simulations of solutions at constant chemical potential

    NASA Astrophysics Data System (ADS)

    Perego, C.; Salvalaglio, M.; Parrinello, M.

    2015-04-01

    Molecular dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, which influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a grand-canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work, we propose the Constant Chemical Potential Molecular Dynamics (CμMD) method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the CμMD method to the paradigmatic case of urea crystallization in aqueous solution. As a result, we have been able to study crystal growth dynamics under constant supersaturation conditions and to extract growth rates and free-energy barriers.

  19. Biomass resource potential using energy crops

    SciTech Connect

    Wright, L.L.; Cushman, J.H.; Martin, S.A.

    1993-09-01

    Biomass energy crops can provide a significant and environmentally beneficial source of renewable energy feedstocks for the future. They can revitalize the agricultural sector of the US economy by providing profitable uses for marginal cropland. Energy crops include fast-growing trees, perennial grasses, and annual grasses, all capable of collecting solar energy and storing it as cellulosic compounds for several months to several years. Once solar energy is thus captured, it can be converted by means of currently available technologies to a wide variety of energy products such as electricity, heat, liquid transportation fuels, and gases. Experimental results from field trials have generated optimism that selected and improved energy crops, established on cropland with moderate limitations for crop production, have the potential for producing high yields. Both trees and grasses, under very good growing conditions, have produced average annual yields of 20 to 40 dry Mg ha{sup {minus}1} year{sup {minus}1}. Sorghum has shown especially high yields in the Midwest. Hybrids between sugar cane and its wild relatives, called energy cane, have yielded as much as 50 dry Mg ha{sup {minus}1} year{sup {minus}1} in Florida. These experimental results demonstrate that some species have the genetic potential for very rapid growth rates. New wood energy crop systems developed by the Department of Energy`s Biofuels Feedstock Development Program offer, at a minimum, a 100% increase in biomass production rates over the 2 to 4 Mg ha{sup {minus}1} year{sup {minus}1} of dry leafless woody biomass produced by most natural forest systems. Experimental data indicate that short rotation wood crops established on cropland with moderate limitations are capable of producing biomass yields of 8--20 dry Mg ha{sup {minus}1} year{sup {minus}1} with a present average about 11 dry Mg ha{sup {minus}1} year{sup {minus}1} on typical cropland sites.

  20. Potential energy surfaces for cluster emitting nuclei

    SciTech Connect

    Poenaru, Dorin N.; Gherghescu, Radu A.; Greiner, Walter

    2006-01-15

    Potential energy surfaces are calculated by use of the most advanced asymmetric two-center shell model that allows us to obtain shell-and-pairing corrections that are added to the Yukawa-plus-exponential model deformation energy. Shell effects are of crucial importance for the experimental observation of spontaneous disintegration by heavy-ion emission. Results for {sup 222}Ra, {sup 232}U, {sup 236}Pu, and {sup 242}Cm illustrate the main ideas and show for the first time, for a cluster emitter, a potential barrier obtained by use of the macroscopic-microscopic method.

  1. Potential energy function for the hydroperoxyl radical

    SciTech Connect

    Lemon, W.J.; Hase, W.L.

    1987-03-12

    A switching function formalism is used to derive an analytic potential energy surface for the O + OH in equilibrium HO/sub 2/ in equilibrium H + O/sub 2/ reactive system. Both experimental and ab initio data are used to derive parameters for the potential energy surface. Trajectory calculations for highly excited HO/sub 2/ are performed on this surface. From these trajectories quasi-periodic eigentrajectories are found for vibrational levels near the HO/sub 2/ dissociation threshold with small amounts of quanta in the OH stretch mode and large amounts of quanta in the OO stretch mode.

  2. Scalable Quantum Simulation of Molecular Energies

    NASA Astrophysics Data System (ADS)

    O'Malley, P. J. J.; Babbush, R.; Kivlichan, I. D.; Romero, J.; McClean, J. R.; Barends, R.; Kelly, J.; Roushan, P.; Tranter, A.; Ding, N.; Campbell, B.; Chen, Y.; Chen, Z.; Chiaro, B.; Dunsworth, A.; Fowler, A. G.; Jeffrey, E.; Lucero, E.; Megrant, A.; Mutus, J. Y.; Neeley, M.; Neill, C.; Quintana, C.; Sank, D.; Vainsencher, A.; Wenner, J.; White, T. C.; Coveney, P. V.; Love, P. J.; Neven, H.; Aspuru-Guzik, A.; Martinis, J. M.

    2016-07-01

    We report the first electronic structure calculation performed on a quantum computer without exponentially costly precompilation. We use a programmable array of superconducting qubits to compute the energy surface of molecular hydrogen using two distinct quantum algorithms. First, we experimentally execute the unitary coupled cluster method using the variational quantum eigensolver. Our efficient implementation predicts the correct dissociation energy to within chemical accuracy of the numerically exact result. Second, we experimentally demonstrate the canonical quantum algorithm for chemistry, which consists of Trotterization and quantum phase estimation. We compare the experimental performance of these approaches to show clear evidence that the variational quantum eigensolver is robust to certain errors. This error tolerance inspires hope that variational quantum simulations of classically intractable molecules may be viable in the near future.

  3. Potential function and dissociation energy of alkali halide

    NASA Astrophysics Data System (ADS)

    Srivastava, Abhay P.; Pandey, Anjani K.; Pandey, Brijesh K.

    2016-05-01

    Dissociation energy of some alkali halides have been calculated by using different interaction potential function such as Born-Mayer, Varshani-Shukla and L5 potential model. The theoretical calculation is compared with experimental values. The Result shows that the values of dissociation energy as calculated by using different potential models have an equal amount of deviation with experimental values. The above said deviation with experimental values can be explained by consideration of rotational-vibrational coupling between the constituents of molecules in the limelight of molecular spectroscopy. Findings of present work suggest that the existing potential model need to be reviewed in view of the correction factors solely depending on the rotational, vibrational and electronic coupling between the constituents of molecules.

  4. Potential energy sputtering of EUVL materials

    SciTech Connect

    Pomeroy, J M; Ratliff, L P; Gillaspy, J D; Bajt, S

    2004-07-02

    Of the many candidates employed for understanding the erosion of critical Extreme Ultraviolet Lithography (EUVL) components, potential energy damage remains relatively uninvestigated. Unlike the familiar kinetic energy sputtering, which is a consequence of the momentum transferred by an ion to atoms in the target, potential energy sputtering occurs when an ion rapidly collects charge from the target as it neutralizes. Since the neutralization energy of a singly charged ion is typically on the order of 10 eV, potential energy effects are generally neglected for low charge state ions, and hence the bulk of the sputtering literature. As an ion's charge state is increased, the potential energy (PE) increases rapidly, e.g. PE(Xe{sup 1+})= 11 eV, PE(Xe{sup 10+}) = 810 eV, PE(Xe{sup 20+}) = 4.6 keV, etc. By comparison, the binding energy of a single atom on a surface is typically about 5 eV, so even relatively inefficient energy transfer mechanisms can lead to large quantities of material being removed, e.g. 25% efficiency for Xe{sup 10+} corresponds to {approx} 40 atoms/ion. By comparison, singly charged xenon ions with {approx} 20 keV of kinetic energy sputter only about 5 atoms/ion at normal incidence, and less than 1 atom/ion at typical EUV source energies. EUV light sources are optimized for producing approximately 10{sup 16} xenon ions per shot with an average charge state of q=10 in the core plasma. At operational rates of {approx}10 kHz, the number of ions produced per second becomes a whopping 10{sup 20}. Even if only one in a billion ions reaches the collector, erosion rates could reach {approx}10{sup 12} atoms per second, severely reducing the collector lifetime (for an average yield of 10 atoms/ion). In addition, efforts to reduce contamination effects may contribute to reduced neutralization and even larger potential energy damages rates (discussed further below). In order to provide accurate estimates for collector lifetimes and to develop mitigation schemes

  5. Collision Induced Dissociation and Energy Transfer in Molecular Hydroge

    NASA Astrophysics Data System (ADS)

    Mandy, Margot E.

    2006-06-01

    Molecular hydrogen is a significant constituent in giant molecular clouds in the interstellar medium. Shocks in these clouds are associated with star formation. The cooling of the shocks is governed by competition of collisional energy transfer and dissociation with radiative cooling by quadrupole emission. Thus a detailed understanding of collisional behaviour of molecular hydrogen is needed. Work in this group has examined energy transfer and dissociation in molecular energy transfer as the result of collisions with H, D, He, and H2. Using quasiclassical trajectories and chemically accurate ab initio potentials state-to-state rate coefficients have been determined. The uncertainties of the cross sections are propagated rigourously to give uncertainties of the rate coefficients and the rate coefficients are parameterized as a function of temperature. Comparisons with quantum calculations are discussed and the proposed website is described.This work was supported by a grant from the Natural Sciences and Engineering Research Council of Canada. The calculations were carried out using the high performance computing facility jointly supported by the Canadian Foundation for Innovation, the British Columbia Knowledge Development Fund, and Silicon Graphics at the University of Northern British Columbia.

  6. Nondynamical correlation energy in model molecular systems

    NASA Astrophysics Data System (ADS)

    Chojnacki, Henryk

    The hypersurfaces for the deprotonation processes have been studied at the nonempirical level for H3O+, NH+4, PH+4, and H3S+ cations within their correlation consistent basis set. The potential energy curves were calculated and nondynamical correlation energies analyzed. We have found that the restricted Hartree-Fock wavefunction leads to the improper dissociation limit and, in the three latest cases requires multireference description. We conclude that these systems may be treated as a good models for interpretation of the proton transfer mechanism as well as for testing one-determinantal or multireference cases.

  7. Free-energy coarse-grained potential for C{sub 60}

    SciTech Connect

    Edmunds, D. M. Tangney, P.; Vvedensky, D. D.; Foulkes, W. M. C.

    2015-10-28

    We propose a new deformable free energy method for generating a free-energy coarse-graining potential for C{sub 60}. Potentials generated from this approach exhibit a strong temperature dependence and produce excellent agreement with benchmark fully atomistic molecular dynamics simulations. Parameter sets for analytical fits to this potential are provided at four different temperatures.

  8. Ridge-based bias potentials to accelerate molecular dynamics

    NASA Astrophysics Data System (ADS)

    Xiao, Penghao; Duncan, Juliana; Zhang, Liang; Henkelman, Graeme

    2015-12-01

    An effective way to accelerate rare events in molecular dynamics simulations is to apply a bias potential which destabilizes minima without biasing the transitions between stable states. This approach, called hyperdynamics, is limited by our ability to construct general bias potentials without having to understand the reaction mechanisms available to the system, a priori. Current bias potentials are typically constructed in terms of a metric which quantifies the distance that a trajectory deviates from the reactant state minimum. Such metrics include detection of negative curvatures of the potential, an energy increase, or deviations in bond lengths from the minimum. When one of these properties exceeds a critical value, the bias potentials are constructed to approach zero. A problem common to each of these schemes is that their effectiveness decreases rapidly with system size. We attribute this problem to a diminishing volume defined by the metrics around a reactant minimum as compared to the total volume of the reactant state basin. In this work, we mitigate the dimensionality scaling problem by constructing bias potentials that are based upon the distance to the boundary of the reactant basin. This distance is quantified in two ways: (i) by following the minimum mode direction to the reactant boundary and (ii) by training a machine learning algorithm to give an analytic expression for the boundary to which the distance can be calculated. Both of these ridge-based bias potentials are demonstrated to scale qualitatively better with dimensionality than the existing methods. We attribute this improvement to a greater filling fraction of the reactant state using the ridge-based bias potentials as compared to the standard potentials.

  9. Determination of a PAF antagonist pharmacophore using combined Molecular Electrostatic Potential and Molecular Lipophilicity Potential.

    PubMed

    Le Solleu, H; Langlois, M H; Kummer, E; Dubost, J P

    1994-11-01

    PAF is a potent lipid mediator involved in many pathological disorders, such as platelet aggregation, immuno-inflammatory reactions, vascular disorders, septic shock and bronchoconstriction. We chose to study the electronic and lipophilic properties of eleven PAF antagonists, comprising five tetrahydrofuran derivatives, four hetrazepines, the ginkgolide BN-52021 and the pyrrolo-thiazole derivative RP-59227. A Molecular Electrostatic Potential (MEP) contour drawn at -25 kCal/Mol shows three electronegative areas in most compounds. Two areas can be considered as analogous to those described in the so-called "Cache-Oreille" (Earmuff) Model. Molecular Lipophilicity Potential (MLP) analysis allows us to characterise one hydrophilic area, localised at the same place as one of the electronegative areas, and two lipophilic areas, of which the biggest draws a typical "sock" contour. These three areas represent the minimal requirements for a high affinity to the PAF receptor. MEP and MLP results are here combined to propose a pharmacophore for PAF antagonists, including two lipophilic areas, two hydrophilic and electronegative areas and an electronegative zone with no particular hydrophilic behaviour.

  10. Equiparatition of energy for turbulent astrophysical fluids: Accounting for the unseen energy in molecular clouds

    NASA Technical Reports Server (NTRS)

    Zweibel, Ellen G.; Mckee, Christopher F.

    1995-01-01

    Molecular clouds are observed to be partially supported by turbulent pressure. The kinetic energy of the turbulence is directly measurable, but the potential energy, which consists of magnetic, thermal, and gravitational potential energy, is largly unseen. We have extended previous results on equipartition between kinetic and potential energy to show that it is likely to be a very good approximation in molecular clouds. We have used two separate approaches to demonstrate this result: For small-amplitude perturbations of a static equilibrium, we have used the energy principle analysis of Bernstein et al. (1958); this derivation applies to perturbations of arbitary wavelength. To treat perturbations of a nonstatic equilibrium, we have used the Lagrangian analysis of Dewar (1970); this analysis applies only to short-wavelength perturbations. Both analysis assume conservation of energy. Wave damping has only a small effect on equipartition if the wave frequency is small compared to the neutral-ion collision frequency; for the particular case we considered, radiative losses have no effect on equipartition. These results are then incorporated in a simple way into analyses of cloud equilibrium and global stability. We discuss the effect of Alfvenic turbulence on the Jeans mass and show that it has little effect on the magnetic critical mass.

  11. Potential Energy Cost Savings from Increased Commercial Energy Code Compliance

    SciTech Connect

    Rosenberg, Michael I.; Hart, Philip R.; Athalye, Rahul A.; Zhang, Jian; Cohan, David F.

    2016-08-22

    An important question for commercial energy code compliance is: “How much energy cost savings can better compliance achieve?” This question is in sharp contrast to prior efforts that used a checklist of code requirements, each of which was graded pass or fail. Percent compliance for any given building was simply the percent of individual requirements that passed. A field investigation method is being developed that goes beyond the binary approach to determine how much energy cost savings is not realized. Prototype building simulations were used to estimate the energy cost impact of varying levels of non-compliance for newly constructed office buildings in climate zone 4C. Field data collected from actual buildings on specific conditions relative to code requirements was then applied to the simulation results to find the potential lost energy savings for a single building or for a sample of buildings. This new methodology was tested on nine office buildings in climate zone 4C. The amount of additional energy cost savings they could have achieved had they complied fully with the 2012 International Energy Conservation Code is determined. This paper will present the results of the test, lessons learned, describe follow-on research that is needed to verify that the methodology is both accurate and practical, and discuss the benefits that might accrue if the method were widely adopted.

  12. Energy transformation in molecular electronic systems

    SciTech Connect

    Kasha, M.

    1985-07-25

    Our new optical pumping spectroscopy (steady state, and double-laser pulse) allows the production and study of the unstable rare tautomer in its ground and excited states, including picosecond dynamic studies. Molecules under study here included 7-azaindole (model for biological purines), 3-hydroxyflavone (model for plant flavones), lumichrome, and other heterocyclics. New detailed molecular mechanisms for proton transfer are derived, especially with catalytic assisting molecules. A new proton-transfer laser of extraordinary efficiency has become a side dividend, possibly worth of industrial development. The excited and highly reactive singlet molecular oxygen species /sup 1/..delta../sub g/) has proven to be ubiquitous in chemical peroxide systems and in physically excited sensitizer-oxygen systems. Hyperbaric oxygen mechanisms in biology probably involve singlet oxygen. We have undertaken a spectroscopic study of tris - dibenzoylmethane chelates of Al, Gd, Eu, and Yb trivalent ions. These chelates offer a variety of electronic behaviors, from Z-effects on ..pi..-electron spin-orbital coupling (Al, Gd) to Weissman intramolecular energy transfer to 4f mestable levels (Eu, Gd). Elegant new spectroscopic resolution at 77K permits separation of tautomeric, parasitic self-absorption, dissociation, and cage effects to be resolved. 18 refs., 4 figs.

  13. Energy transformation in molecular electronic systems

    NASA Astrophysics Data System (ADS)

    Kasha, M.

    1985-07-01

    Our new optical pumping spectroscopy allows the production and study of the unstable rate tautomer in its ground and excited states, including picosecond dynamic studies. Molecules under study here included 7-azaindole 3-hydroxyflavone, lumichrome, and other heterocyclics. New detailed molecular mechanisms for proton transfer are derived, especially with catalytic assisting molecules. A new proton-transfer laser of extraordinary efficiency has become a side dividend, possibly worthy of industrial development. The excited and highly reactive singlet molecular oxygen species (1) DELTA sub g has proven to be ubiquitous in chemical peroxide systems and in physically excited sensitizer-oxygen systems. Hyperbaric oxygen mechanisms in biology probably involve singlet oxygen. We have undertaken a spectroscopic study of trisdibenzoylmethane chelates of Al, Gd, Eu, and Yb trivalent ions. These chelates offer a variety of electronic behaviors, from Z-effects on (PI)--electron spin-orbital coupling (Al, Gd) to Weissman intramolecular energy transfer to 4f mestable levels (Eu, Gd). Elegant new spectroscopic resolution at 77K permits separation of tautomeric, parasitic self-absorption, dissociation, and cage effects to be resolved.

  14. Divacancy binding energy, formation energy and surface energy of BCC transition metals using MEAM potentials

    NASA Astrophysics Data System (ADS)

    Uniyal, Shweta; Chand, Manesh; Joshi, Subodh; Semalty, P. D.

    2016-05-01

    The modified embedded atom method (MEAM) potential parameters have been employed to calculate the unrelaxed divacancy formation energy, binding energy and surface energies for low index planes in bcc transition metals. The calculated results of divacancy binding energy and vacancy formation energy compare well with experimental and other available calculated results.

  15. Spectroscopic investigations, molecular interactions, and molecular docking studies on the potential inhibitor "thiophene-2-carboxylicacid"

    NASA Astrophysics Data System (ADS)

    Karthick, T.; Balachandran, V.; Perumal, S.

    2015-04-01

    Thiophene derivatives have been focused in the past decades due to their remarkable biological and pharmacological activities. In connection with that the conformational stability, spectroscopic characterization, molecular (inter- and intra-) interactions, and molecular docking studies on thiophene-2-carboxylicacid have been performed in this work by experimental FT-IR and theoretical quantum chemical computations. Experimentally recorded FT-IR spectrum in the region 4000-400 cm-1 has been compared with the scaled theoretical spectrum and the spectral peaks have been assigned on the basis of potential energy distribution results obtained from MOLVIB program package. The conformational stability of monomer and dimer conformers has been examined. The presence of inter- and intramolecular interactions in the monomer and dimer conformers have been explained by natural bond orbital analysis. The UV-Vis spectra of the sample in different solvents have been simulated and solvent effects were predicted by polarisable continuum model with TD-DFT/B3LYP/6-31+G(d,p) method. To test the biological activity of the sample, molecular docking (ligand-protein) simulations have been performed using SWISSDOCK web server. The full fitness (FF) score and binding affinity values revealed that thiophene-2-carboxylicacid can act as potential inhibitor against inflammation.

  16. Computed potential energy surfaces for chemical reactions

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.

    1994-01-01

    Quantum mechanical methods have been used to compute potential energy surfaces for chemical reactions. The reactions studied were among those believed to be important to the NASP and HSR programs and included the recombination of two H atoms with several different third bodies; the reactions in the thermal Zeldovich mechanism; the reactions of H atom with O2, N2, and NO; reactions involved in the thermal De-NO(x) process; and the reaction of CH(squared Pi) with N2 (leading to 'prompt NO'). These potential energy surfaces have been used to compute reaction rate constants and rates of unimolecular decomposition. An additional application was the calculation of transport properties of gases using a semiclassical approximation (and in the case of interactions involving hydrogen inclusion of quantum mechanical effects).

  17. Computed potential energy surfaces for chemical reactions

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.

    1990-01-01

    The objective was to obtain accurate potential energy surfaces (PES's) for a number of reactions which are important in the H/N/O combustion process. The interest in this is centered around the design of the SCRAM jet engine for the National Aerospace Plane (NASP), which was envisioned as an air-breathing hydrogen-burning vehicle capable of reaching velocities as large as Mach 25. Preliminary studies indicated that the supersonic flow in the combustor region of the scram jet engine required accurate reaction rate data for reactions in the H/N/O system, some of which was not readily available from experiment. The most important class of combustion reactions from the standpoint of the NASP project are radical recombinaton reactions, since these reactions result in most of the heat release in the combustion process. Theoretical characterizations of the potential energy surfaces for these reactions are presented and discussed.

  18. Convective Available Potential Energy of World Ocean

    NASA Astrophysics Data System (ADS)

    Su, Z.; Ingersoll, A. P.; Thompson, A. F.

    2012-12-01

    Here, for the first time, we propose the concept of Ocean Convective Available Potential Energy (OCAPE), which is the maximum kinetic energy (KE) per unit seawater mass achievable by ocean convection. OCAPE occurs through a different mechanism from atmospheric CAPE, and involves the interplay of temperature and salinity on the equation of state of seawater. The thermobaric effect, which arises because the thermal coefficient of expansion increases with depth, is an important ingredient of OCAPE. We develop an accurate algorithm to calculate the OCAPE for a given temperature and salinity profile. We then validate our calculation of OCAPE by comparing it with the conversion of OCAPE to KE in a 2-D numerical model. We propose that OCAPE is an important energy source of ocean deep convection and contributes to deep water formation. OCAPE, like Atmospheric CAPE, can help predict deep convection and may also provide a useful constraint for modelling deep convection in ocean GCMs. We plot the global distribution of OCAPE using data from the World Ocean Atlas 2009 (WOA09) and see many important features. These include large values of OCAPE in the Labrador, Greenland, Weddell and Mediterranean Seas, which are consistent with our present observations and understanding, but also identify some new features like the OCAPE pattern in the Antarctic Circumpolar Current (ACC). We propose that the diagnosis of OCAPE can improve our understanding of global patterns of ocean convection and deep water formation as well as ocean stratification, the meridional overturning circulation and mixed layer processes. The background of this work is briefly introduced as below. Open-ocean deep convection can significantly modify water properties both at the ocean surface and throughout the water column (Gordon 1982). Open-ocean convection is also an important mechanism for Ocean Deep Water formation and the transport of heat, freshwater and nutrient (Marshall and Schott 1999). Open

  19. Contact potential difference measurements of doped organic molecular thin films

    NASA Astrophysics Data System (ADS)

    Chan, Calvin; Gao, Weiying; Kahn, Antoine

    2004-07-01

    The possibility of nonequilibrium conditions in doped organic molecular thin films is investigated using a combination of ultraviolet photoemission spectroscopy (UPS) and contact potential difference measurements. Surface or interface photovoltage is of particular concern in materials with large band gap and appreciable band (or energy level) bending at interfaces. We investigate here zinc phthalocyanine (ZnPc) and N,N'-diphenyl-N,N'-bis(1-naphthyl)-1,1'biphenyl-4,4'' diamine (α-NPD) p-doped with the acceptor molecule, tetrafluorotetracyanoquinodimethane (F4-TCNQ). In both cases, we observe an upward movement of the vacuum level away from the metal interface with respect to the Fermi level, consistent with the formation of a depletion region. We show that photovoltage is not a significant factor in these doped films, under ultraviolet illumination during UPS. We suggest that the carrier recombination rate in organic films is sufficiently fast to exclude any photovoltage effects at room temperature. .

  20. Potential Energy Curves of Hydrogen Fluoride

    NASA Technical Reports Server (NTRS)

    Fallon, Robert J.; Vanderslice, Joseph T.; Mason, Edward A.

    1960-01-01

    Potential energy curves for the X(sup 1)sigma+ and V(sup 1)sigma+ states of HF and DF have been calculated by the Rydberg-Klein-Rees method. The results calculated from the different sets of data for HF and DF are found to be in very good agreement. The theoretical results of Karo are compared to the experimental results obtained here.

  1. Energy Savings Potential of Radiative Cooling Technologies

    SciTech Connect

    Fernandez, Nicholas; Wang, Weimin; Alvine, Kyle J.; Katipamula, Srinivas

    2015-11-30

    Pacific Northwest National Laboratory (PNNL), with funding from the U.S. Department of Energy’s (DOE’s) Building Technologies Program (BTP), conducted a study to estimate, through simulation, the potential cooling energy savings that could be achieved through novel approaches to capturing free radiative cooling in buildings, particularly photonic ‘selective emittance’ materials. This report documents the results of that study.

  2. Potential energy landscapes of tetragonal pyramid molecules

    NASA Astrophysics Data System (ADS)

    Yoshida, Yuichiro; Sato, Hirofumi; Morgan, John W. R.; Wales, David J.

    2016-11-01

    Hiraoka et al. have developed a self-assembling system referred to as a nanocube (Hiraoka et al., 2008). In the present contribution a coarse-grained model for this system is analysed, focusing on how the potential energy landscape for self-assembly is related to the geometry of the building blocks. We find that six molecules assemble to form various clusters, with cubic and sheet structures the most stable. The relative stability is determined by the geometry of the building blocks.

  3. Potential energy surfaces of Polonium isotopes

    NASA Astrophysics Data System (ADS)

    Nerlo-Pomorska, B.; Pomorski, K.; Schmitt, C.; Bartel, J.

    2015-11-01

    The evolution of the potential energy landscape is analysed in detail for ten even-even polonium isotopes in the mass range 188\\lt A\\lt 220 as obtained within the macroscopic-microscopic approach, relying on the Lublin-Strasbourg drop model and the Yukawa-folded single-particle energies for calculating the microscopic shell and pairing corrections. A variant of the modified Funny-Hills nuclear shape parametrization is used to efficiently map possible fission paths. The approach explains the main features of the fragment partition as measured in low-energy fission along the polonium chain. The latter lies in a transitional region of the nuclear chart, and will be essential to consistently understand the evolution of fission properties from neutron-deficient mercury to heavy actinides. The ability of our method to predict fission observables over such an extended region looks promising.

  4. The Wind Energy Potential of Iceland

    NASA Astrophysics Data System (ADS)

    Nawri, Nikolai; Nína Petersen, Guðrún; Bjornsson, Halldór; Hahmann, Andrea N.; Jónasson, Kristján; Bay Hasager, Charlotte; Clausen, Niels-Erik

    2014-05-01

    While Iceland has an abundant wind energy resource, its use for electrical power production has so far been limited. Electricity in Iceland is generated primarily from hydro- and geothermal sources, and adding wind energy has so far not been considered practical or even necessary. However, wind energy is becoming a more viable option, as opportunities for new hydro- or geothermal power installations become limited. In order to obtain an estimate of the wind energy potential of Iceland, a wind atlas has been developed as part of the joint Nordic project 'Improved Forecast of Wind, Waves and Icing' (IceWind). Downscaling simulations performed with the Weather Research and Forecasting (WRF) model were used to determine the large-scale wind energy potential of Iceland. Local wind speed distributions are represented by Weibull statistics. The shape parameter across Iceland varies between 1.2 and 3.6, with the lowest values indicative of near-exponential distributions at sheltered locations, and the highest values indicative of normal distributions at exposed locations in winter. Compared with summer, average power density in winter is increased throughout Iceland by a factor of 2.0 - 5.5. In any season, there are also considerable spatial differences in average wind power density. Relative to the average value within 10 km of the coast, power density across Iceland varies between 50 - 250%, excluding glaciers, or between 300 - 1500 W m-2 at 50 m above ground level in winter. At intermediate elevations of 500 - 1000 m above mean sea level, power density is independent of the distance to the coast. In addition to seasonal and spatial variability, differences in average wind speed and power density also exist for different wind directions. Along the coast in winter, power density of onshore winds is higher by 100 - 700 W m-2 than that of offshore winds. The regions with the highest average wind speeds are impractical for wind farms, due to the distances from road

  5. Gaq proteins: molecular pharmacology and therapeutic potential.

    PubMed

    Kamato, Danielle; Mitra, Partha; Davis, Felicity; Osman, Narin; Chaplin, Rebecca; Cabot, Peter J; Afroz, Rizwana; Thomas, Walter; Zheng, Wenhua; Kaur, Harveen; Brimble, Margaret; Little, Peter J

    2017-04-01

    Seven transmembrane G protein-coupled receptors (GPCRs) have gained much interest in recent years as it is the largest class among cell surface receptors. G proteins lie in the heart of GPCRs signalling and therefore can be therapeutically targeted to overcome complexities in GPCR responses and signalling. G proteins are classified into four families (Gi, Gs, G12/13 and Gq); Gq is further subdivided into four classes. Among them Gαq and Gαq/11 isoforms are most crucial and ubiquitously expressed; these isoforms are almost 88% similar at their amino acid sequence but may exhibit functional divergences. However, uncertainties often arise about Gαq and Gαq/11 inhibitors, these G proteins might also have suitability to the invention of novel-specific inhibitors for each isoforms. YM-254890 and UBO-QIC are discovered as potent inhibitors of Gαq functions and also investigated in thrombin protease-activated receptor (PAR)-1 inhibitors and platelet aggregation inhibition. The most likely G protein involved in PAR-1 stimulates responses is one of the Gαq family isoforms. In this review, we highlight the molecular structures and pharmacological responses of Gαq family which may reflect the biochemical and molecular role of Gαq and Gαq/11. The advanced understanding of Gαq and Gαq/11 role in GPCR signalling may shed light on our understanding on cell biology, cellular physiology and pathophysiology and also lead to the development of novel therapeutic agents for a number of diseases.

  6. Pseudospectral Gaussian quantum dynamics: Efficient sampling of potential energy surfaces.

    PubMed

    Heaps, Charles W; Mazziotti, David A

    2016-04-28

    Trajectory-based Gaussian basis sets have been tremendously successful in describing high-dimensional quantum molecular dynamics. In this paper, we introduce a pseudospectral Gaussian-based method that achieves accurate quantum dynamics using efficient, real-space sampling of the time-dependent basis set. As in other Gaussian basis methods, we begin with a basis set expansion using time-dependent Gaussian basis functions guided by classical mechanics. Unlike other Gaussian methods but characteristic of the pseudospectral and collocation methods, the basis set is tested with N Dirac delta functions, where N is the number of basis functions, rather than using the basis function as test functions. As a result, the integration for matrix elements is reduced to function evaluation. Pseudospectral Gaussian dynamics only requires O(N) potential energy calculations, in contrast to O(N(2)) evaluations in a variational calculation. The classical trajectories allow small basis sets to sample high-dimensional potentials. Applications are made to diatomic oscillations in a Morse potential and a generalized version of the Henon-Heiles potential in two, four, and six dimensions. Comparisons are drawn to full analytical evaluation of potential energy integrals (variational) and the bra-ket averaged Taylor (BAT) expansion, an O(N) approximation used in Gaussian-based dynamics. In all cases, the pseudospectral Gaussian method is competitive with full variational calculations that require a global, analytical, and integrable potential energy surface. Additionally, the BAT breaks down when quantum mechanical coherence is particularly strong (i.e., barrier reflection in the Morse oscillator). The ability to obtain variational accuracy using only the potential energy at discrete points makes the pseudospectral Gaussian method a promising avenue for on-the-fly dynamics, where electronic structure calculations become computationally significant.

  7. Theoretical studies of potential energy surfaces

    SciTech Connect

    Harding, L.B.

    1993-12-01

    The goal of this program is to calculate accurate potential energy surfaces (PES) for both reactive and nonreactive systems. To do this the electronic Schrodinger equation must be solved. Our approach to this problem starts with multiconfiguration self-consistent field (MCSCF) reference wavefunctions. These reference wavefunctions are designed to be sufficiently flexible to accurately describe changes in electronic structure over a broad range of geometries. Electron correlation effects are included via multireference, singles and doubles configuration interaction (MRSDCI) calculations. With this approach, the authors are able to provide useful predictions of the energetics for a broad range of systems.

  8. Energy conservation in molecular dynamics simulations of classical systems.

    PubMed

    Toxvaerd, Søren; Heilmann, Ole J; Dyre, Jeppe C

    2012-06-14

    Classical Newtonian dynamics is analytic and the energy of an isolated system is conserved. The energy of such a system, obtained by the discrete "Verlet" algorithm commonly used in molecular dynamics simulations, fluctuates but is conserved in the mean. This is explained by the existence of a "shadow Hamiltonian" H [S. Toxvaerd, Phys. Rev. E 50, 2271 (1994)], i.e., a Hamiltonian close to the original H with the property that the discrete positions of the Verlet algorithm for H lie on the analytic trajectories of H. The shadow Hamiltonian can be obtained from H by an asymptotic expansion in the time step length. Here we use the first non-trivial term in this expansion to obtain an improved estimate of the discrete values of the energy. The investigation is performed for a representative system with Lennard-Jones pair interactions. The simulations show that inclusion of this term reduces the standard deviation of the energy fluctuations by a factor of 100 for typical values of the time step length. Simulations further show that the energy is conserved for at least one hundred million time steps provided the potential and its first four derivatives are continuous at the cutoff. Finally, we show analytically as well as numerically that energy conservation is not sensitive to round-off errors.

  9. Computed potential energy surfaces for chemical reactions

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.; Levin, Eugene

    1993-01-01

    A new global potential energy surface (PES) is being generated for O(P-3) + H2 yields OH + H. This surface is being fit using the rotated Morse oscillator method, which was used to fit the previous POL-CI surface. The new surface is expected to be more accurate and also includes a much more complete sampling of bent geometries. A new study has been undertaken of the reaction N + O2 yields NO + O. The new studies have focused on the region of the surface near a possible minimum corresponding to the peroxy form of NOO. A large portion of the PES for this second reaction has been mapped out. Since state to state cross sections for the reaction are important in the chemistry of high temperature air, these studies will probably be extended to permit generation of a new global potential for reaction.

  10. Assessment of wind energy potential in Poland

    NASA Astrophysics Data System (ADS)

    Starosta, Katarzyna; Linkowska, Joanna; Mazur, Andrzej

    2014-05-01

    The aim of the presentation is to show the suitability of using numerical model wind speed forecasts for the wind power industry applications in Poland. In accordance with the guidelines of the European Union, the consumption of wind energy in Poland is rapidly increasing. According to the report of Energy Regulatory Office from 30 March 2013, the installed capacity of wind power in Poland was 2807MW from 765 wind power stations. Wind energy is strongly dependent on the meteorological conditions. Based on the climatological wind speed data, potential energy zones within the area of Poland have been developed (H. Lorenc). They are the first criterion for assessing the location of the wind farm. However, for exact monitoring of a given wind farm location the prognostic data from numerical model forecasts are necessary. For the practical interpretation and further post-processing, the verification of the model data is very important. Polish Institute Meteorology and Water Management - National Research Institute (IMWM-NRI) runs an operational model COSMO (Consortium for Small-scale Modelling, version 4.8) using two nested domains at horizontal resolutions of 7 km and 2.8 km. The model produces 36 hour and 78 hour forecasts from 00 UTC, for 2.8 km and 7 km domain resolutions respectively. Numerical forecasts were compared with the observation of 60 SYNOP and 3 TEMP stations in Poland, using VERSUS2 (Unified System Verification Survey 2) and R package. For every zone the set of statistical indices (ME, MAE, RMSE) was calculated. Forecast errors for aerological profiles are shown for Polish TEMP stations at Wrocław, Legionowo and Łeba. The current studies are connected with a topic of the COST ES1002 WIRE-Weather Intelligence for Renewable Energies.

  11. Theoretical studies of potential energy surfaces and computational methods

    SciTech Connect

    Shepard, R.

    1993-12-01

    This project involves the development, implementation, and application of theoretical methods for the calculation and characterization of potential energy surfaces involving molecular species that occur in hydrocarbon combustion. These potential energy surfaces require an accurate and balanced treatment of reactants, intermediates, and products. This difficult challenge is met with general multiconfiguration self-consistent-field (MCSCF) and multireference single- and double-excitation configuration interaction (MRSDCI) methods. In contrast to the more common single-reference electronic structure methods, this approach is capable of describing accurately molecular systems that are highly distorted away from their equilibrium geometries, including reactant, fragment, and transition-state geometries, and of describing regions of the potential surface that are associated with electronic wave functions of widely varying nature. The MCSCF reference wave functions are designed to be sufficiently flexible to describe qualitatively the changes in the electronic structure over the broad range of geometries of interest. The necessary mixing of ionic, covalent, and Rydberg contributions, along with the appropriate treatment of the different electron-spin components (e.g. closed shell, high-spin open-shell, low-spin open shell, radical, diradical, etc.) of the wave functions, are treated correctly at this level. Further treatment of electron correlation effects is included using large scale multireference CI wave functions, particularly including the single and double excitations relative to the MCSCF reference space. This leads to the most flexible and accurate large-scale MRSDCI wave functions that have been used to date in global PES studies.

  12. Triton Binding Energy of Kharkov Potential

    NASA Astrophysics Data System (ADS)

    Kamada, H.; Shebeko, O.; Arslanaliev, A.

    2017-03-01

    The Kharkov potential is a recent field theoretical model of nucleon-nucleon (NN) interaction that has been built up in the framework of the instant form of relativistic dynamics starting with the total Hamiltonian of interacting meson and nucleon fields and using the method of unitary clothing transformations. The latter connect the representation of "bare" particles and the representation of "clothed" particles, i.e., the particles with physical properties. Unlike many available NN potentials each of which is the kernel of the corresponding nonrelativistic Lippmann-Schwinger (LS) equation this potential being dependent in momentum space on the Feynman-like propagators and covariant cutoff factors at the meson-nucleon vertices is the kernel of relativistic integral equations for the NN bound and scattering states. Therefore we do not need to invent any transform of a given nonrelativistic potential to its relativistic counterpart. As a feasible study, we have started with the so-called 5ch Faddeev calculation for three-nucleon bound state (triton) and obtained a reasonable value of its binding energy (-7.42 MeV).

  13. A test of H2-He potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Thibault, Franck; Wcisło, Piotr; Ciuryło, Roman

    2016-11-01

    The close-coupling method is used to calculate purely rotational relaxation rates and pressure broadening and shifting coefficients for H2-He collisions, in order to test various potential energy surfaces. Downward rate coefficients k3→1(T) and k2→0(T) are compared with experimental data, but the subtle differences in the potential energy surfaces are hardly reflected in these rates. Helium pressure broadening and shifting generalized cross sections for the isotropic Raman Q(1) lines of the fundamental bands of D2 and H2 as well as the purely rotational Stokes S0(1) line of H2 are therefore also considered. While these spectroscopic characteristics are much more sensitive to the precise form of the interaction potential, a proper validation cannot be performed without taking into account the influence of the translational motion on the molecular line shapes. After including this, it is found that the potential energy surface of Bakr, Smith and Patkowski [B.W. Bakr, D.G.A. Smith, K. Patkowski, J. Chem. Phys. 139, 144305 (2013)] allows the best reproduction of the experimental data.

  14. Potential energy surfaces of superheavy nuclei

    SciTech Connect

    Bender, M.; Rutz, K.; Maruhn, J.A.; Greiner, W.; Reinhard, P.-G. Rutz, K.; Maruhn, J.A.; Greiner, W.

    1998-10-01

    We investigate the structure of the potential energy surfaces of the superheavy nuclei {sub 158}{sup 258}Fm{sub 100}, {sub 156}{sup 264}Hs{sub 108}, {sub 166}{sup 278}112, {sub 184}{sup 298}114, and {sub 172}{sup 292}120 within the framework of self-consistent nuclear models, i.e., the Skyrme-Hartree-Fock approach and the relativistic mean-field model. We compare results obtained with one representative parametrization of each model which is successful in describing superheavy nuclei. We find systematic changes as compared to the potential energy surfaces of heavy nuclei in the uranium region: there is no sufficiently stable fission isomer any more, the importance of triaxial configurations to lower the first barrier fades away, and asymmetric fission paths compete down to rather small deformation. Comparing the two models, it turns out that the relativistic mean-field model gives generally smaller fission barriers. {copyright} {ital 1998} {ital The American Physical Society}

  15. Orbital Energy Levels in Molecular Hydrogen. A Simple Approach.

    ERIC Educational Resources Information Center

    Willis, Christopher J.

    1988-01-01

    Described are the energetics involved in the formation of molecular hydrogen using concepts that should be familiar to students beginning the study of molecular orbital theory. Emphasized are experimental data on ionization energies. Included are two-electron atomic and molecular systems. (CW)

  16. Quantum mechanics/molecular mechanics dual Hamiltonian free energy perturbation

    NASA Astrophysics Data System (ADS)

    Polyak, Iakov; Benighaus, Tobias; Boulanger, Eliot; Thiel, Walter

    2013-08-01

    The dual Hamiltonian free energy perturbation (DH-FEP) method is designed for accurate and efficient evaluation of the free energy profile of chemical reactions in quantum mechanical/molecular mechanical (QM/MM) calculations. In contrast to existing QM/MM FEP variants, the QM region is not kept frozen during sampling, but all degrees of freedom except for the reaction coordinate are sampled. In the DH-FEP scheme, the sampling is done by semiempirical QM/MM molecular dynamics (MD), while the perturbation energy differences are evaluated from high-level QM/MM single-point calculations at regular intervals, skipping a pre-defined number of MD sampling steps. After validating our method using an analytic model potential with an exactly known solution, we report a QM/MM DH-FEP study of the enzymatic reaction catalyzed by chorismate mutase. We suggest guidelines for QM/MM DH-FEP calculations and default values for the required computational parameters. In the case of chorismate mutase, we apply the DH-FEP approach in combination with a single one-dimensional reaction coordinate and with a two-dimensional collective coordinate (two individual distances), with superior results for the latter choice.

  17. Molecular Imaging with MRI: Potential Application in Pancreatic Cancer

    PubMed Central

    Chen, Chen; Wu, Chang Qiang; Chen, Tian Wu; Tang, Meng Yue; Zhang, Xiao Ming

    2015-01-01

    Despite the variety of approaches that have been improved to achieve a good understanding of pancreatic cancer (PC), the prognosis of PC remains poor, and the survival rates are dismal. The lack of early detection and effective interventions is the main reason. Therefore, considerable ongoing efforts aimed at identifying early PC are currently being pursued using a variety of methods. In recent years, the development of molecular imaging has made the specific targeting of PC in the early stage possible. Molecular imaging seeks to directly visualize, characterize, and measure biological processes at the molecular and cellular levels. Among different imaging technologies, the magnetic resonance (MR) molecular imaging has potential in this regard because it facilitates noninvasive, target-specific imaging of PC. This topic is reviewed in terms of the contrast agents for MR molecular imaging, the biomarkers related to PC, targeted molecular probes for MRI, and the application of MRI in the diagnosis of PC. PMID:26579537

  18. Potential energy surface and rovibrational energy levels of the H2-CS van der Waals complex.

    PubMed

    Denis-Alpizar, Otoniel; Stoecklin, Thierry; Halvick, Philippe; Dubernet, Marie-Lise; Marinakis, Sarantos

    2012-12-21

    Owing to its large dipole, astrophysicists use carbon monosulfide (CS) as a tracer of molecular gas in the interstellar medium, often in regions where H(2) is the most abundant collider. Predictions of the rovibrational energy levels of the weakly bound complex CS-H(2) (not yet observed) and also of rate coefficients for rotational transitions of CS in collision with H(2) should help to interpret the observed spectra. This paper deals with the first goal, i.e., the calculation of the rovibrational energy levels. A new four-dimensional intermolecular potential energy surface for the H(2)-CS complex is presented. Ab initio potential energy calculations were carried out at the coupled-cluster level with single and double excitations and a perturbative treatment of triple excitations, using a quadruple-zeta basis set and midbond functions. The potential energy surface was obtained by an analytic fit of the ab initio data. The equilibrium structure of the H(2)-CS complex is found to be linear with the carbon pointing toward H(2) at the intermolecular separation of 8.6 a(o). The corresponding well depth is -173 cm(-1). The potential was used to calculate the rovibrational energy levels of the para-H(2)-CS and ortho-H(2)-CS complexes. The present work provides the first theoretical predictions of these levels. The calculated dissociation energies are found to be 35.9 cm(-1) and 49.9 cm(-1), respectively, for the para and ortho complexes. The second virial coefficient for the H(2)-CS pair has also been calculated for a large range of temperature. These results could be used to assign future experimental spectra and to check the accuracy of the potential energy surface.

  19. Ab initio effective core potentials for molecular calculations. Potentials for main group elements Na to Bi

    SciTech Connect

    Wadt, W.R.; Hay, P.J.

    1985-01-01

    A consistent set of ab initio effective core potentials (ECP) has been generated for the main group elements from Na to Bi using the procedure originally developed by Kahn. The ECP's are derived from all-electron numerical Hartree--Fock atomic wave functions and fit to analytical representations for use in molecular calculations. For Rb to Bi the ECP's are generated from the relativistic Hartree--Fock atomic wave functions of Cowan which incorporate the Darwin and mass--velocity terms. Energy-optimized valence basis sets of (3s3p) primitive Gaussians are presented for use with the ECP's. Comparisons between all-electron and valence-electron ECP calculations are presented for NaF, NaCl, Cl/sub 2/, Cl/sub 2//sup -/, Br/sub 2/, Br/sub 2//sup -/, and Xe/sub 2//sup +/. The results show that the average errors introduced by the ECP's are generally only a few percent.

  20. Computed potential energy surfaces for chemical reactions

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.

    1988-01-01

    The minimum energy path for the addition of a hydrogen atom to N2 is characterized in CASSCF/CCI calculations using the (4s3p2d1f/3s2p1d) basis set, with additional single point calculations at the stationary points of the potential energy surface using the (5s4p3d2f/4s3p2d) basis set. These calculations represent the most extensive set of ab initio calculations completed to date, yielding a zero point corrected barrier for HN2 dissociation of approx. 8.5 kcal mol/1. The lifetime of the HN2 species is estimated from the calculated geometries and energetics using both conventional Transition State Theory and a method which utilizes an Eckart barrier to compute one dimensional quantum mechanical tunneling effects. It is concluded that the lifetime of the HN2 species is very short, greatly limiting its role in both termolecular recombination reactions and combustion processes.

  1. Thermophotovoltaic energy conversion: Technology and market potential

    SciTech Connect

    Ostrowski, L.J.; Pernisz, U.C.; Fraas, L.M.

    1996-02-01

    This report contains material displayed on poster panels during the Conference. The purpose of the contribution was to present a summary of the business overview of thermophotovoltaic generation of electricity and its market potential. The market analysis has shown that the TPV market, while currently still in an early nucleation phase, is evolving into a range of small niche markets out of which larger-size opportunities can emerge. Early commercial applications on yachts and recreational vehicles which require a quiet and emission-free compact electrical generator fit the current TPV technology and economics. Follow-on residential applications are attractive since they can combine generation of electricity with space and hot water heating in a co-generation system. Development of future markets in transportation, both private and communal or industrial, will be driven by legislation requiring emission-free vehicles, and by a reduction in TPV systems cost. As a result of {open_quote}{open_quote}moving down the learning curve,{close_quote}{close_quote} growing power and consumer markets are predicted to come into reach of TPV systems, a development favored by high overall energy conversion efficiency due to high radiation energy density and to high electric conversion efficiency available with photovoltaic cells. {copyright} {ital 1996 American Institute of Physics.}

  2. The Wind Energy Potential of Kurdistan, Iran.

    PubMed

    Arefi, Farzad; Moshtagh, Jamal; Moradi, Mohammad

    2014-01-01

    In the current work by using statistical methods and available software, the wind energy assessment of prone regions for installation of wind turbines in, Qorveh, has been investigated. Information was obtained from weather stations of Baneh, Bijar, Zarina, Saqez, Sanandaj, Qorveh, and Marivan. The monthly average and maximum of wind speed were investigated between the years 2000-2010 and the related curves were drawn. The Golobad curve (direction and percentage of dominant wind and calm wind as monthly rate) between the years 1997-2000 was analyzed and drawn with plot software. The ten-minute speed (at 10, 30, and 60 m height) and direction (at 37.5 and 10 m height) wind data were collected from weather stations of Iranian new energy organization. The wind speed distribution during one year was evaluated by using Weibull probability density function (two-parametrical), and the Weibull curve histograms were drawn by MATLAB software. According to the average wind speed of stations and technical specifications of the types of turbines, the suitable wind turbine for the station was selected. Finally, the Divandareh and Qorveh sites with favorable potential were considered for installation of wind turbines and construction of wind farms.

  3. Thermophotovoltaic energy conversion: Technology and market potential

    NASA Astrophysics Data System (ADS)

    Ostrowski, Leon J.; Pernisz, Udo C.; Fraas, Lewis M.

    1996-02-01

    This report contains material displayed on poster panels during the Conference. The purpose of the contribution was to present a summary of the business overview of thermophotovoltaic generation of electricity and its market potential. The market analysis has shown that the TPV market, while currently still in an early nucleation phase, is evolving into a range of small niche markets out of which larger-size opportunities can emerge. Early commercial applications on yachts and recreational vehicles which require a quiet and emission-free compact electrical generator fit the current TPV technology and economics. Follow-on residential applications are attractive since they can combine generation of electricity with space and hot water heating in a co-generation system. Development of future markets in transportation, both private and communal or industrial, will be driven by legislation requiring emission-free vehicles, and by a reduction in TPV systems cost. As a result of ``moving down the learning curve,'' growing power and consumer markets are predicted to come into reach of TPV systems, a development favored by high overall energy conversion efficiency due to high radiation energy density and to high electric conversion efficiency available with photovoltaic cells.

  4. The Wind Energy Potential of Kurdistan, Iran

    PubMed Central

    Arefi, Farzad; Moshtagh, Jamal; Moradi, Mohammad

    2014-01-01

    In the current work by using statistical methods and available software, the wind energy assessment of prone regions for installation of wind turbines in, Qorveh, has been investigated. Information was obtained from weather stations of Baneh, Bijar, Zarina, Saqez, Sanandaj, Qorveh, and Marivan. The monthly average and maximum of wind speed were investigated between the years 2000–2010 and the related curves were drawn. The Golobad curve (direction and percentage of dominant wind and calm wind as monthly rate) between the years 1997–2000 was analyzed and drawn with plot software. The ten-minute speed (at 10, 30, and 60 m height) and direction (at 37.5 and 10 m height) wind data were collected from weather stations of Iranian new energy organization. The wind speed distribution during one year was evaluated by using Weibull probability density function (two-parametrical), and the Weibull curve histograms were drawn by MATLAB software. According to the average wind speed of stations and technical specifications of the types of turbines, the suitable wind turbine for the station was selected. Finally, the Divandareh and Qorveh sites with favorable potential were considered for installation of wind turbines and construction of wind farms. PMID:27355042

  5. Inhomogeneous dark states of atomic-molecular Bose-Einstein condensates in trapping potentials

    SciTech Connect

    Cruz, H. A.; Konotop, V. V.

    2011-03-15

    We investigate possibilities of existence of inhomogeneous dark states of atomic-molecular Bose-Einstein condensates loaded in trap potentials. The system is described by three-coupled equations of the Gross-Pitaevskii type, which account for contributions of the kinetic energy, two-body interactions, and an external potential, and which govern the conversion between atoms and molecules in the stimulated Raman adiabatic passage. We report a class of trapping potentials allowing for the existence of localized stable dark states. The respective atomic and molecular distributions are computed, and their stability and dynamics are discussed.

  6. Ab initio molecular dynamics calculations of ion hydration free energies.

    PubMed

    Leung, Kevin; Rempe, Susan B; von Lilienfeld, O Anatole

    2009-05-28

    We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or "lambda-path" technique to compute the intrinsic hydration free energies of Li(+), Cl(-), and Ag(+) ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential (phi) contributions, we obtain absolute AIMD hydration free energies (DeltaG(hyd)) within a few kcal/mol, or better than 4%, of Tissandier et al.'s [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model phi predictions. The sums of Li(+)/Cl(-) and Ag(+)/Cl(-) AIMD DeltaG(hyd), which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag(+)+Ni(+)-->Ag+Ni(2+) in water. The predictions for this reaction suggest that existing estimates of DeltaG(hyd) for unstable radiolysis intermediates such as Ni(+) may need to be extensively revised.

  7. Energy resource potential of natural gas hydrates

    USGS Publications Warehouse

    Collett, T.S.

    2002-01-01

    The discovery of large gas hydrate accumulations in terrestrial permafrost regions of the Arctic and beneath the sea along the outer continental margins of the world's oceans has heightened interest in gas hydrates as a possible energy resource. However, significant to potentially insurmountable technical issues must be resolved before gas hydrates can be considered a viable option for affordable supplies of natural gas. The combined information from Arctic gas hydrate studies shows that, in permafrost regions, gas hydrates may exist at subsurface depths ranging from about 130 to 2000 m. The presence of gas hydrates in offshore continental margins has been inferred mainly from anomalous seismic reflectors, known as bottom-simulating reflectors, that have been mapped at depths below the sea floor ranging from about 100 to 1100 m. Current estimates of the amount of gas in the world's marine and permafrost gas hydrate accumulations are in rough accord at about 20,000 trillion m3. Disagreements over fundamental issues such as the volume of gas stored within delineated gas hydrate accumulations and the concentration of gas hydrates within hydrate-bearing strata have demonstrated that we know little about gas hydrates. Recently, however, several countries, including Japan, India, and the United States, have launched ambitious national projects to further examine the resource potential of gas hydrates. These projects may help answer key questions dealing with the properties of gas hydrate reservoirs, the design of production systems, and, most important, the costs and economics of gas hydrate production.

  8. Potential energy curves and collision integrals of air components

    NASA Technical Reports Server (NTRS)

    Partridge, Harry; Stallcop, James R.; 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 with an emphasis on the accuracy that is obtainable. Results for interactions, e.g. N+N, N+O, O+O, and H+N2 will be reviewed and their application to the determination of transport properties, such as diffusion and viscosity coefficients, will be examined.

  9. Molecular sonography with targeted microbubbles: current investigations and potential applications.

    PubMed

    Hwang, Misun; Lyshchik, Andrej; Fleischer, Arthur C

    2010-06-01

    Sonography using targeted microbubbles affords a variety of diagnostic and potentially therapeutic clinical applications. It provides a whole new world of functional information at the cellular and molecular level. This information can then be used to diagnose and possibly prevent diseases at early stages as well as devise therapeutic strategies at the molecular level. It is also useful in monitoring tumor response to therapy and devising treatment timing and plans based on the molecular state of an individual's health. Moreover, targeted microbubble-enhanced sonography has several advantages over other imaging modalities, including widespread availability, low cost, fast acquisition times, and lack of radiation risk. These traits are likely to advance it as one of the imaging methods of choice in future clinical trials examining the impact of molecular imaging on treatment outcome. This review describes the fundamental concepts of targeted microbubble-enhanced sonography as well as its potential clinical applications.

  10. Nucleation of carbon nanostructures: Molecular dynamics with reactive potentials

    NASA Astrophysics Data System (ADS)

    Galiullina, G. M.; Orekhov, N. D.; Stegailov, V. V.

    2016-11-01

    In this paper, we present our first results in the study of the details of nucleation in the homogeneous carbon gas phase using computer calculations with molecular dynamics methods. Direct and controlled molecular-dynamics approaches are used and two reactive potentials (ReaxFF and AIREBO) are compared. The calculations have shown that the nucleation process in the AIREBO model is going more actively than in the ReaxFF one.

  11. Transportation Energy Use and Conservation Potential

    ERIC Educational Resources Information Center

    Hirst, Eric

    1973-01-01

    Analyzes transportation energy consumption and energy intensiveness for inter-city freight and passenger traffic and urban passenger traffic with the definition of energy intensiveness as Btu per ton-mile or per passenger-mile. Indicates that public education is one of three ways to achieve the goals of energy conservation. (CC)

  12. Calculations of Solvation Free Energy through Energy Reweighting from Molecular Mechanics to Quantum Mechanics.

    PubMed

    Jia, Xiangyu; Wang, Meiting; Shao, Yihan; König, Gerhard; Brooks, Bernard R; Zhang, John Z H; Mei, Ye

    2016-02-09

    In this work, the solvation free energies of 20 organic molecules from the 4th Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL4) have been calculated. The sampling of phase space is carried out at a molecular mechanical level, and the associated free energy changes are estimated using the Bennett Acceptance Ratio (BAR). Then the quantum mechanical (QM) corrections are computed through the indirect Non-Boltzmann Bennett's acceptance ratio (NBB) or the thermodynamics perturbation (TP) method. We show that BAR+TP gives a minimum analytic variance for the calculated solvation free energy at the Gaussian limit and performs slightly better than NBB in practice. Furthermore, the expense of the QM calculations in TP is only half of that in NBB. We also show that defining the biasing potential as the difference of the solute-solvent interaction energy, instead of the total energy, can converge the calculated solvation free energies much faster but possibly to different values. Based on the experimental solvation free energies which have been published before, it is discovered in this study that BLYP yields better results than MP2 and some other later functionals such as B3LYP, M06-2X, and ωB97X-D.

  13. Resonance energies, lifetimes and complex energy potential curves from standard wave-packet calculations

    NASA Astrophysics Data System (ADS)

    Goldzak, Tamar; Gilary, Ido; Moiseyev, Nimrod

    2012-05-01

    We show here for a simple model system that the wavepacket dynamics in the interaction region can be described by a superposition of the non-Hermitian exponential divergent eigenfunctions of the physical Hamiltonian. We demonstrate how it is possible to obtain the complex eigenvalues and also the corresponding resonance eigenfunctions from the propagation of the wavepacket within the framework of the standard formalism of quantum mechanics. The general results demonstrated here for a simple model can lead to two different types of computational applications: (i) for systems where one can obtain the resonance energies and lifetimes as well as their corresponding eigenfunctions it is possible to study the evolution of the physical properties solely based on the initially populated resonance states without the need to propagate the wavepacket; (ii) for molecular systems where it is quite difficult to solve the non-Hermitian time-independent Schrödinger equation and obtain molecular resonance energies and functions. For this type of problem, the methods presented here enable one to evaluate the topology of complex potential energy surfaces from the wavepacket propagation and facilitate the study of the nuclear dynamics of ionizing molecular systems.

  14. IPPP-CLOPPA Analysis of the Influence of the Methylation on the Potential Energy and the Molecular Polarizability of the Hydrogen Bonds in the Cytosine-Guanine Base Pair.

    PubMed

    Giribet, Claudia G; Ruiz de Azua, Martin C

    2017-03-28

    The IPPP-CLOPPA method is applied to investigate the influence of a methyl group on the energy of the hydrogen bonds and the potential energy curve of the bridge protons in model compounds which mimic the methylated and unmethylated cytosine guanine base pairs. On the same grounds, this influence on the polarizability of the intermolecular hydrogen bonds of these compounds is also addressed, in order to determine if this linear response property provides a significant proof of the electronic mechanisms that affect the stabilization of the hydrogen bonds. Results obtained show that the methyl electronic system delocalizes on the hydrogen bond region, and changes of these intermolecular hydrogen bonds are due to this effect of delocalization.

  15. Renewable Energy Potential for New Mexico

    EPA Pesticide Factsheets

    RE-Powering America's Land: Renewable Energy on Contaminated Land and Mining Sites was presented by Penelope McDaniel, during the 2008 Brown to Green: Make the Connection to Renewable Energy workshop.

  16. Molecular Slater Integrals for Electronic Energy Calculations

    DTIC Science & Technology

    2010-10-15

    Facultad de Ciencias . Departamento de Quı́mica Fı́sica Aplicada. C-XIV. Abstract The algorithms for computing molecular integrals with Slater functions...and propulsion sciences research programs. This extension requires a thorough revision on the performance of the algorithms currently available and

  17. Localization of energy on the molecular scale

    SciTech Connect

    Lindenberg, K.; Brown, D.W.

    1997-12-31

    We discuss the spontaneous localization of vibrational energy in translationally invariant anharmonic chains at finite temperatures. In addition to the familiar energy-driven coherent mechanisms, which are rapidly degraded by thermal fluctuations, we identify the entropy-driven phenomenon we call {open_quotes}stochastic localization{close_quotes}, within which we include a number of characteristics of soft anharmonic oscillators in thermal equilibrium. Principal among these are a tendency for soft oscillators to spend more time at higher energies than comparable harmonic oscillators, and for high-energy fluctuations in soft oscillators to persist for longer times than lower-energy fluctuations, leading to a tendency for energy fluctuations to be organized into {open_quotes}bursts{close_quotes} separated by intervals of relative quiet. We illustrate the effects of stochastic localization on a bistable impurity embedded in a chain of soft oscillators by comparing it to an impurity embedded in a harmonic chain. Effects on transition rates at a given system energy can be quite dramatic.

  18. Molecular approaches to solar energy conversion: the energetic cost of charge separation from molecular-excited states.

    PubMed

    Durrant, James R

    2013-08-13

    This review starts with a brief overview of the technological potential of molecular-based solar cell technologies. It then goes on to focus on the core scientific challenge associated with using molecular light-absorbing materials for solar energy conversion, namely the separation of short-lived, molecular-excited states into sufficiently long-lived, energetic, separated charges capable of generating an external photocurrent. Comparisons are made between different molecular-based solar cell technologies, with particular focus on the function of dye-sensitized photoelectrochemical solar cells as well as parallels with the function of photosynthetic reaction centres. The core theme of this review is that generating charge carriers with sufficient lifetime and a high quantum yield from molecular-excited states comes at a significant energetic cost-such that the energy stored in these charge-separated states is typically substantially less than the energy of the initially generated excited state. The role of this energetic loss in limiting the efficiency of solar energy conversion by such devices is emphasized, and strategies to minimize this energy loss are compared and contrasted.

  19. MOLECULAR ANALYSIS OF HUMAN SPERMATOZOA: POTENTIAL FOR INFERTILITY RESEARCH

    EPA Science Inventory

    Gordon Research Conference: Mammalian Gametogenesis and Embryogenesis
    New London, CT, July 1-6, 2000

    Molecular Analysis of Human Spermatozoa:
    Potential for Infertility Research

    David Miller 1, David Dix2, Robert Reid 3, Stephen A Krawetz 3
    1Reproductive ...

  20. The potential impact of hydrogen energy use on the atmosphere

    NASA Astrophysics Data System (ADS)

    van Ruijven, B. J.; Lamarque, J. F.; van Vuuren, D. P.; Kram, T.; Eerens, H.

    2009-04-01

    ., Hess, P. G., Collins, W. D., Emmons, L. K., Ginoux, P., Luo, C. and Tie, X. X. (2005). "Response of a coupled chemistry-climate model to changes in aerosol emissions: Global impact on the hydrological cycle and the tropospheric burdens of OH, ozone and NOx." Geophysical Research Letters 32(16). Lamarque, J.-F., Kinnison, D. E., Hess, P. G. and Vitt, F. (2008). "Simulated lower stratospheric trends between 1970 and 2005: identifying the role of climate and composition changes." Journal of Geophysical Research 113(D12301). Price, H., Jaegle, L., Rice, A., Quay, P., Novelli, P. C. and Gammon, R. (2007). "Global budget of molecular hydrogen and its deuterium content: constraints from ground station, cruise, and aircraft observations." Journal of Geophysical Research 112(D22108). Sanderson, M. G., Collins, W. J., Derwent, R. G. and Johnson, C. E. (2003). "Simulation of Global Hydrogen Levels Using a Lagrangian Three-Dimensional Model." Journal of Atmospheric Chemistry 46(1): 15-28. Schultz, M. G., Diehl, T., Brasseur, G. P. and Zittel, W. (2003). "Air Pollution and Climate-Forcing Impacts of a Global Hydrogen Economy." Science 302(5645): 624-627. Tromp, T. K., Shia, R. L., Allen, M., Eiler, J. M. and Yung, Y. L. (2003). "Potential environmental impact of a hydrogen economy on the stratosphere." Science 300(5626): 1740-1742. van Ruijven, B., Hari, L., van Vuuren, D. P. and de Vries, B. (2008). "The potential role of hydrogen in India and Western Europe." Energy Policy 36(5): 1649-1665. van Ruijven, B., van Vuuren, D. P. and de Vries, B. (2007). "The potential role of hydrogen in energy systems with and without climate policy." International Journal of Hydrogen Energy 32(12): 1655-1672. van Vuuren, D. P. (2007). Energy systems and climate policy. Dept. of Science, Technology and Society, Faculty of Science. Utrecht, Utrecht University: 326.

  1. Accurate ab initio potential energy computations for the H sub 4 system: Tests of some analytic potential energy surfaces

    SciTech Connect

    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.

  2. Structural and energy properties of interstitial molecular hydrogen in single-crystal silicon

    SciTech Connect

    Melnikov, V. V.

    2015-06-15

    The structural and energy characteristics of interstitial molecular hydrogen in single-crystal silicon are theoretically studied. The dependence of the potential energy of the system on the position and orientation of the interstitial defect is investigated, and the mechanism of interaction of a hydrogen molecule with a silicon crystal is considered. A three-dimensional model is employed to calculate the energy spectrum of H{sub 2} in Si, and the obtained dispersion law is analyzed.

  3. Molecular Biology of Gallbladder Cancer: Potential Clinical Implications

    PubMed Central

    Andrén-Sandberg, Åke

    2012-01-01

    Gallbladder cancer (GBC) is a common malignancy of the biliary tract and involves the changes in multiple oncogenes and multiple genetic genes. Since over the past decade there has been an advance in the knowledge of the genetic basis of cancer, mainly as a result of the rapid progression of molecular technology; however, conventional therapeutic approaches have not had much impact on the course of this aggressive neoplasm. Knowledge of the molecular biology of GBC is rapidly growing. Genetic alterations in GBC include adenosine triphosphate-binding cassette transporter ABCG8, membrane-bound enzyme ADAM-17 of multi-functional gene family, and other genes including p53, COX2, XPC, and RASSF1A. The advances in molecular biology have potential implications for the detection of this disease, using Synuclein-gamma, Syndecan-1, glycoprotein 72 (TAG-72), tumor endothelial marker 8 protein (TEM8) and TNF-alpha. The use of these molecular diagnostic methods is of clinical importance for the gene replacement therapy, genetic prodrug activation therapy, and antisense immunology technology for the treatment of malignancy. The author reviewed recent publications on PubMed, and summarized molecular biology of GBC, with an emphasis on features of potential clinical implications for diagnosis and management. PMID:23112962

  4. Surface Immobilization of Molecular Electrocatalysts for Energy Conversions.

    PubMed

    Bullock, Morris; Das, Atanu K; Appel, Aaron M

    2017-02-08

    Electrocatalysts are critically important for a secure energy future, as they facilitate the conversion between electrical and chemical energy. Molecular catalysts offer precise control of structure that enables understanding of structure-reactivity relationships, which can be difficult to achieve with heterogeneous catalysts. Molecular electrocatalysts can be immobilized on surfaces by covalent bonds or through non-covalent interactions. Advantages of surface immobilization include the need for less catalyst, avoidance of bimolecular decomposition pathways, and easier determination of catalyst lifetime. This mini-review highlights surface immobilization of molecular electrocatalysts for reduction of O2, oxidation of H2O, production of H2, and reduction of CO2.

  5. Energy conservation potential of surface modification technologies

    SciTech Connect

    Le, H.K.; Horne, D.M.; Silberglitt, R.S.

    1985-09-01

    This report assesses the energy conservation impact of surface modification technologies on the metalworking industries. The energy conservation impact of surface modification technologies on the metalworking industries is assessed by estimating their friction and wear tribological sinks and the subsequent reduction in these sinks when surface modified tools are used. Ion implantation, coatings, and laser and electron beam surface modifications are considered.

  6. The Potential Energy of an Autoencoder.

    PubMed

    Kamyshanska, Hanna; Memisevic, Roland

    2015-06-01

    Autoencoders are popular feature learning models, that are conceptually simple, easy to train and allow for efficient inference. Recent work has shown how certain autoencoders can be associated with an energy landscape, akin to negative log-probability in a probabilistic model, which measures how well the autoencoder can represent regions in the input space. The energy landscape has been commonly inferred heuristically, by using a training criterion that relates the autoencoder to a probabilistic model such as a Restricted Boltzmann Machine (RBM). In this paper we show how most common autoencoders are naturally associated with an energy function, independent of the training procedure, and that the energy landscape can be inferred analytically by integrating the reconstruction function of the autoencoder. For autoencoders with sigmoid hidden units, the energy function is identical to the free energy of an RBM, which helps shed light onto the relationship between these two types of model. We also show that the autoencoder energy function allows us to explain common regularization procedures, such as contractive training, from the perspective of dynamical systems. As a practical application of the energy function, a generative classifier based on class-specific autoencoders is presented.

  7. Energy in America: Progress and Potential.

    ERIC Educational Resources Information Center

    American Petroleum Inst., Washington, DC.

    An overview of America's energy situation is presented with emphasis on recent progress, the risk of depending upon foreign oil, and policy choices. Section one reviews the energy problems of the 1970s, issues of the 1980s, concerns for the future, and choices that if made today could alleviate future problems. Section two examines past problems,…

  8. Potential Advantages of Reusing Potentially Contaminated Land for Renewable Energy Fact Sheet

    EPA Pesticide Factsheets

    EPA promotes the reuse of potentially contaminated lands and landfills for renewable energy. This strategy creates new markets for potentially contaminated lands, while providing a sustainable land development strategy for renewable energy.

  9. Molecular Beam Studies of Low Energy Reactions.

    DTIC Science & Technology

    1983-03-31

    COMPLETING PORN . REPORT NUMBER 1 2. GOVT ACCESSION NO. S. RECIPIENT’S CATALOG NUMBER A D A Oaq J- 4. TITLE (And Subtitle) . TYPE OF REPORT & PERIOD COVERED...Gatlinburg, Tenn . in 1981. 2+ c) Studies were made of the charge transfer reaction Ar + Ar 4 2+ Ar + Ar at relative energies from 2 to 1000 eV. Reasons for

  10. Potential energy curves crossing and low-energy charge transfer dynamics in (BeH2O)2+ complex

    NASA Astrophysics Data System (ADS)

    Sun, QiXiang; Yan, Bing

    2012-07-01

    The singlet rigid Be—O dissociation potential energy curves correlating to the first four molecular limits of (BeH2O)2+ complex were calculated using the multi-reference single and double excitation configuration interaction theory. The radial couplings of three low-lying 1A1 states were calculated and combined with adiabatic potential energy curves to investigate and charge-transfer collision dynamics by using quantum-mechanical molecular orbital close-coupling methods. It is found that the total charge-transfer cross sections are dominated by the Be+(2S)+H2O+(Ã2A1) channel. The rate coefficients in the range of 10-17-10-12 cm3/s are very sensitive to temperature below 1000 K. The complexation energy without charge-transfer was determined to be 143.6 kcal/mol, including zero-point vibration energy corrections. This is in good agreement with the previous results.

  11. Sampling the potential energy surface of a DNA duplex damaged by a food carcinogen: Force field parameterization by ab initio quantum calculations and conformational searching using molecular mechanics computations

    NASA Astrophysics Data System (ADS)

    Wu, Xiangyang

    1999-07-01

    The heterocyclic amine 2-amino-3-methylimidazo (4, 5-f) quinoline (IQ) is one of a number of carcinogens found in barbecued meat and fish. It induces tumors in mammals and is probably involved in human carcinogenesis, because of great exposure to such food carcinogens. IQ is biochemically activated to a derivative which reacts with DNA to form a covalent adduct. This adduct may deform the DNA and consequently cause a mutation. which may initiate carcinogenesis. To understand this cancer initiating event, it is necessary to obtain atomic resolution structures of the damaged DNA. No such structures are available experimentally due to synthesis difficulties. Therefore, we employ extensive molecular mechanics and dynamics calculations for this purpose. The major IQ-DNA adduct in the specific DNA sequence d(5'G1G2C G3CCA3') - d(5'TGGCGCC3') with IQ modified at G3 is studied. The d(5'G1G2C G3CC3') sequence has recently been shown to be a hot-spot for mutations when IQ modification is at G3. Although this sequence is prone to -2 deletions via a ``slippage mechanism'' even when unmodified, a key question is why IQ increases the mutation frequency of the unmodified DNA by about 104 fold. Is there a structural feature imposed by IQ that is responsible? The molecular mechanics and dynamics program AMBER for nucleic acids with the latest force field was chosen for this work. This force field has been demonstrated to reproduce well the B-DNA structure. However, some parameters, the partial charges, bond lengths and angles, dihedral parameters of the modified residue, are not available in the AMBER database. We parameterized the force field using high level ab initio quantum calculations. We created 800 starting conformations which uniformly sampled in combination at 18° intervals three torsion angles that govern the IQ-DNA orientations, and energy minimized them. The most important structures are abnormal; the IQ damaged guanine is rotated out of its standard B

  12. Energy Transformation in Molecular Electronic Systems

    SciTech Connect

    Kasha, Michael

    1999-05-17

    This laboratory has developed many new ideas and methods in the electronic spectroscopy of molecules. This report covers the contract period 1993-1995. A number of the projects were completed in 1996, and those papers are included in the report. The DOE contract was terminated at the end of 1995 owing to a reorganizational change eliminating nationally the projects under the Office of Health and Environmental Research, U. S. Department of Energy.

  13. Diagnosis of inflammatory bowel disease: Potential role of molecular biometrics.

    PubMed

    M'Koma, Amosy E

    2014-11-27

    Accurate diagnosis of predominantly colonic inflammatory bowel disease (IBD) is not possible in 30% of patients. For decades, scientists have worked to find a solution to improve diagnostic accuracy for IBD, encompassing Crohn's colitis and ulcerative colitis. Evaluating protein patterns in surgical pathology colectomy specimens of colonic mucosal and submucosal compartments, individually, has potential for diagnostic medicine by identifying integrally independent, phenotype-specific cellular and molecular characteristics. Mass spectrometry (MS) and imaging (I) MS are analytical technologies that directly measure molecular species in clinical specimens, contributing to the in-depth understanding of biological molecules. The biometric-system complexity and functional diversity is well suited to proteomic and diagnostic studies. The direct analysis of cells and tissues by Matrix-Assisted-Laser Desorption/Ionization (MALDI) MS/IMS has relevant medical diagnostic potential. MALDI-MS/IMS detection generates molecular signatures obtained from specific cell types within tissue sections. Herein discussed is a perspective on the use of MALDI-MS/IMS and bioinformatics technologies for detection of molecular-biometric patterns and identification of differentiating proteins. I also discuss a perspective on the global challenge of transferring technologies to clinical laboratories dealing with IBD issues. The significance of serologic-immunometric advances is also discussed.

  14. Zoonotic potential and molecular epidemiology of Giardia species and giardiasis.

    PubMed

    Feng, Yaoyu; Xiao, Lihua

    2011-01-01

    Molecular diagnostic tools have been used recently in assessing the taxonomy, zoonotic potential, and transmission of Giardia species and giardiasis in humans and animals. The results of these studies have firmly established giardiasis as a zoonotic disease, although host adaptation at the genotype and subtype levels has reduced the likelihood of zoonotic transmission. These studies have also identified variations in the distribution of Giardia duodenalis genotypes among geographic areas and between domestic and wild ruminants and differences in clinical manifestations and outbreak potentials of assemblages A and B. Nevertheless, our efforts in characterizing the molecular epidemiology of giardiasis and the roles of various animals in the transmission of human giardiasis are compromised by the lack of case-control and longitudinal cohort studies and the sampling and testing of humans and animals living in the same community, the frequent occurrence of infections with mixed genotypes and subtypes, and the apparent heterozygosity at some genetic loci for some G. duodenalis genotypes. With the increased usage of multilocus genotyping tools, the development of next-generation subtyping tools, the integration of molecular analysis in epidemiological studies, and an improved understanding of the population genetics of G. duodenalis in humans and animals, we should soon have a better appreciation of the molecular epidemiology of giardiasis, the disease burden of zoonotic transmission, the taxonomy status and virulences of various G. duodenalis genotypes, and the ecology of environmental contamination.

  15. Automatic search for maximum similarity between molecular electrostatic potential distributions

    NASA Astrophysics Data System (ADS)

    Manaut, Francesc; Sanz, Ferran; José, Jaume; Milesi, Massimo

    1991-08-01

    A new computer program has been developed to automatically obtain the relative position of two molecules in which the similarity between molecular electrostatic-potential distributions is greatest. These distributions are considered in a volume around the molecules, and the similarity is measured by the Spearman rank coefficient. The program has been tested using several pairs of molecules: water vs. water; phenylethylamine and phenylpropylamine vs. benzylamine; and methotrexate vs. dihydrofolic acid.

  16. EFFECT OF STRAIN FIELD ON THRESHOLD DISPLACEMENT ENERGY OF TUNGSTEN STUDIED BY MOLECULAR DYNAMICS SIMULATION

    SciTech Connect

    Wang, D.; Gao, Ning; Setyawan, Wahyu; Kurtz, Richard J.; Gao, X.; He, W. H.

    2016-03-31

    The influence of hydrostatic strain on point defect formation energy and threshold displacement energy (Ed) in body-centered cubic (BCC) tungsten was studied with molecular dynamics simulations. Two different tungsten potentials (Fikar and Juslin) were used. The minimum Ed direction calculated with the Fikar-potential was <100>, but with the Juslin-potential it was <111>. The most stable self-interstitial (SIA) configuration was a <111>-crowdion for both potentials. The stable SIA configuration did not change with applied strain. Varying the strain from compression to tension increased the vacancy formation energy but decreased the SIA formation energy. The SIA formation energy changed more significantly than for a vacancy such that Ed decreased with applied strain from compression to tension.

  17. Bohm's Quantum Potential and the Visualization of Molecular Structure

    NASA Technical Reports Server (NTRS)

    Levit, Creon; Chancellor, Marisa K. (Technical Monitor)

    1997-01-01

    David Bohm's ontological interpretation of quantum theory can shed light on otherwise counter-intuitive quantum mechanical phenomena including chemical bonding. In the field of quantum chemistry, Richard Bader has shown that the topology of the Laplacian of the electronic charge density characterizes many features of molecular structure and reactivity. Visual and computational examination suggests that the Laplacian of Bader and the quantum potential of Bohm are morphologically equivalent. It appears that Bohmian mechanics and the quantum potential can make chemistry as clear as they makes physics.

  18. Low Molecular Weight Norbornadiene Derivatives for Molecular Solar-Thermal Energy Storage.

    PubMed

    Quant, Maria; Lennartson, Anders; Dreos, Ambra; Kuisma, Mikael; Erhart, Paul; Börjesson, Karl; Moth-Poulsen, Kasper

    2016-09-05

    Molecular solar-thermal energy storage systems are based on molecular switches that reversibly convert solar energy into chemical energy. Herein, we report the synthesis, characterization, and computational evaluation of a series of low molecular weight (193-260 g mol(-1) ) norbornadiene-quadricyclane systems. The molecules feature cyano acceptor and ethynyl-substituted aromatic donor groups, leading to a good match with solar irradiation, quantitative photo-thermal conversion between the norbornadiene and quadricyclane, as well as high energy storage densities (396-629 kJ kg(-1) ). The spectroscopic properties and energy storage capability have been further evaluated through density functional theory calculations, which indicate that the ethynyl moiety plays a critical role in obtaining the high oscillator strengths seen for these molecules.

  19. Low Molecular Weight Norbornadiene Derivatives for Molecular Solar‐Thermal Energy Storage

    PubMed Central

    Quant, Maria; Lennartson, Anders; Dreos, Ambra; Kuisma, Mikael; Erhart, Paul; Börjesson, Karl

    2016-01-01

    Abstract Molecular solar‐thermal energy storage systems are based on molecular switches that reversibly convert solar energy into chemical energy. Herein, we report the synthesis, characterization, and computational evaluation of a series of low molecular weight (193–260 g mol−1) norbornadiene–quadricyclane systems. The molecules feature cyano acceptor and ethynyl‐substituted aromatic donor groups, leading to a good match with solar irradiation, quantitative photo‐thermal conversion between the norbornadiene and quadricyclane, as well as high energy storage densities (396–629 kJ kg−1). The spectroscopic properties and energy storage capability have been further evaluated through density functional theory calculations, which indicate that the ethynyl moiety plays a critical role in obtaining the high oscillator strengths seen for these molecules. PMID:27492997

  20. How the Reorganization Free Energy Affects the Reduction Potential of Structurally Homologous Cytochromes.

    PubMed

    Daidone, Isabella; Amadei, Andrea; Zaccanti, Francesco; Borsari, Marco; Bortolotti, Carlo Augusto

    2014-05-01

    Differences in the reduction potential E(0) among structurally similar metalloproteins cannot always be fully explained on the basis of their 3-D structures. We investigate the molecular determinants to E(0) using the mixed quantum mechanics/molecular mechanics approach named perturbed matrix method (PMM); after comparison with experimental values to assess the reliability of our calculations, we investigate the relationship between the change in free energy upon reduction ΔA(0) and the reorganization energy. We find that the reduction potential of cytochromes can be regarded as the result of the sum of two terms, one being mostly dependent on the energy fluctuations within a limited range around the mean transition energy and the second being mostly dependent linearly on the difference Δλ = λred - λox of the reorganization free energies for the ox → red (λred) and for the red → ox (λox) relaxations.

  1. Energy Aspects of Thermal Molecular Switching: Molecular Thermal Hysteresis of Helicene Oligomers.

    PubMed

    Shigeno, Masanori; Kushida, Yo; Yamaguchi, Masahiko

    2015-07-20

    Molecular switching is a phenomenon by which a molecule reversibly changes its structure and state in response to external stimuli or energy. Herein, molecular switching is discussed from thermodynamic and kinetic aspects in terms of energy supply with an emphasis on the thermal switching exhibited by helicene oligomers. It includes the inversion of relative thermodynamic stability induced by temperature changes and molecular thermal hysteresis in a closed system. The thermal phenomenon associated with the oligomers involves population/concentration changes between metastable states under nonequilibrium thermodynamic control.

  2. Up and away in the potential landscape of diatomic molecule potential energy curves

    NASA Astrophysics Data System (ADS)

    Stwalley, William C.

    2016-12-01

    The understanding of the potential curves of a given molecule has expanded in many ways during my last 52 years as an experimental and theoretical molecular chemist/physicist in graduate school in Chemistry at Harvard and in both the Chemistry and Physics Departments at University of Iowa and University of Connecticut. This expansion has been up in energy and vibrational and rotational quantum numbers and away from Re to long range as well. It is clear that Prof. Robert Le Roy, who I have known since the late 1960s, has made many important and greatly appreciated contributions to the landscape I describe below from my personal perspective, especially with regard to long range molecules and solution of the radial Schrödinger equations and related calculations.

  3. Energy Consumption and Renewable Energy Development Potential on Indian Lands

    EIA Publications

    2000-01-01

    Includes information on the electricity use and needs of Indian households and tribes, the comparative electricity rates that Indian households are paying, and the potential for renewable resources development of Indian lands.

  4. Framework for State-Level Renewable Energy Market Potential Studies

    EPA Pesticide Factsheets

    This document provides a framework and next steps for state officials who require estimates of renewable energy market potential. The report gives insight into how to conduct a market potential study.

  5. Energy Savings Potential and Research & Development Opportunities for Commercial Refrigeration

    SciTech Connect

    none,

    2009-09-01

    This study documents the energy consumption of commercial refrigeration equipment (CRE) in the U.S. and evaluated the energy savings potential of various technologies and energy efficiency measures that could be applied to such equipment. The study provided an overview of CRE applications, assessed the energy-savings potential of CRE in the U.S., outline key barriers to adoption of energy-savings technologies, and recommended opportunities for advanced energy saving technology research. The study was modeled after an earlier 1996 report by Arthur D. Little, Inc., and updated key information, examined more equipment types, and outlined long-term research and development opportunities.

  6. Energy dissipation in an adaptive molecular circuit

    NASA Astrophysics Data System (ADS)

    Wang, Shou-Wen; Lan, Yueheng; Tang, Lei-Han

    2015-07-01

    The ability to monitor nutrient and other environmental conditions with high sensitivity is crucial for cell growth and survival. Sensory adaptation allows a cell to recover its sensitivity after a transient response to a shift in the strength of extracellular stimulus. The working principles of adaptation have been established previously based on rate equations which do not consider fluctuations in a thermal environment. Recently, Lan et al (2012 Nat. Phys. 8 422-8) performed a detailed analysis of a stochastic model for the Escherichia coli sensory network. They showed that accurate adaptation is possible only when the system operates in a nonequilibrium steady-state (NESS). They further proposed an energy-speed-accuracy (ESA) trade-off relation. We present here analytic results on the NESS of the model through a mapping to a one-dimensional birth-death process. An exact expression for the entropy production rate is also derived. Based on these results, we are able to discuss the ESA relation in a more general setting. Our study suggests that the adaptation error can be reduced exponentially as the methylation range increases. Finally, we show that a nonequilibrium phase transition exists in the infinite methylation range limit, despite the fact that the model contains only two discrete variables.

  7. Potential Energy Sources Pose Mining Problem

    ERIC Educational Resources Information Center

    Chemical and Engineering News, 1974

    1974-01-01

    Summarizes the discussions of a Division of Industrial and Engineering Chemistry symposium on solids handling for synthetic fuels production. Included is a description of technical difficulties with the use of coal seams and deposits of oil shale and oil sand as potential sources of fuel. (CC)

  8. Bandwidth Study on Energy Use and Potential Energy Saving Opportunities in U.S. Chemical Manufacturing

    SciTech Connect

    Sabine Brueske, Caroline Kramer, Aaron Fisher

    2015-06-01

    Energy bandwidth studies of U.S. manufacturing sectors can serve as foundational references in framing the range (or bandwidth) of potential energy savings opportunities. This bandwidth study examines energy consumption and potential energy savings opportunities in U.S. chemical manufacturing. The study relies on multiple sources to estimate the energy used in the production of 74 individual chemicals, representing 57% of sector-wide energy consumption. Energy savings opportunities for individual chemicals and for 15 subsectors of chemicals manufacturing are based on technologies currently in use or under development; these potential savings are then extrapolated to estimate sector-wide energy savings opportunity.

  9. Bandwidth Study on Energy Use and Potential Energy Savings Opportunities in U.S. Petroleum Refining

    SciTech Connect

    Sabine Brueske, Caroline Kramer, Aaron Fisher

    2015-06-01

    Energy bandwidth studies of U.S. manufacturing sectors can serve as foundational references in framing the range (or bandwidth) of potential energy savings opportunities. This bandwidth study examines energy consumption and potential energy savings opportunities in U.S. petroleum refining. The study relies on multiple sources to estimate the energy used in nine individual process areas, representing 68% of sector-wide energy consumption. Energy savings opportunities for individual processes are based on technologies currently in use or under development; these potential savings are then extrapolated to estimate sector-wide energy savings opportunity.

  10. Infinite swapping replica exchange molecular dynamics leads to a simple simulation patch using mixture potentials.

    PubMed

    Lu, Jianfeng; Vanden-Eijnden, Eric

    2013-02-28

    Replica exchange molecular dynamics (REMD) becomes more efficient as the frequency of swap between the temperatures is increased. Recently Plattner et al. [J. Chem. Phys. 135, 134111 (2011)] proposed a method to implement infinite swapping REMD in practice. Here we introduce a natural modification of this method that involves molecular dynamics simulations over a mixture potential. This modification is both simple to implement in practice and provides a better, energy based understanding of how to choose the temperatures in REMD to optimize efficiency. It also has implications for generalizations of REMD in which the swaps involve other parameters than the temperature.

  11. Potential production of energy cane for fuel in the Caribbean

    SciTech Connect

    Samuels, G.

    1984-12-01

    Sugarcane presents a tremendous potential as a renewable energy source for the non-oil producing countries of the Caribbean. The energy cane concept is sugarcane managed for maximum dry matter (total fermentable solids for alcohol fuel and combustible solids for electricity) rather than sucrose. The use of sugarcane as a renewable energy source can provide a solution, either partial or total, to the Caribbean energy problem. Sugar cane production and the use of this crop as a renewable energy source are described.

  12. Study on Properties of Energy Spectra of the Molecular Crystals

    NASA Astrophysics Data System (ADS)

    Pang, Xiao-Feng; Chen, Xiang-Rong

    The energy-spectra of nonlinear vibration of molecular crystals such as acetanilide have been calculated by using discrete nonlinear Schrödinger equation appropriate to the systems, containing various interactions. The energy levels including higher excited states are basically consistent with experimental values obtained by infrared absorption and Raman scattering in acetanilide. We further give the features of distribution of the energy-spectra for the acetanilide. Using the energy spectra we also explained well experimental results obtained by Careri et al..

  13. Electron energy-loss spectra in molecular fluorine

    NASA Technical Reports Server (NTRS)

    Nishimura, H.; Cartwright, D. C.; Trajmar, S.

    1979-01-01

    Electron energy-loss spectra in molecular fluorine, for energy losses from 0 to 17.0 eV, have been taken at incident electron energies of 30, 50, and 90 eV and scattering angles from 5 to 140 deg. Features in the spectra above 11.5 eV energy loss agree well with the assignments recently made from optical spectroscopy. Excitations of many of the eleven repulsive valence excited electronic states are observed and their location correlates reasonably well with recent theoretical results. Several of these excitations have been observed for the first time and four features, for which there are no identifications, appear in the spectra.

  14. State-to-state dynamics of molecular energy transfer

    SciTech Connect

    Gentry, W.R.; Giese, C.F.

    1993-12-01

    The goal of this research program is to elucidate the elementary dynamical mechanisms of vibrational and rotational energy transfer between molecules, at a quantum-state resolved level of detail. Molecular beam techniques are used to isolate individual molecular collisions, and to control the kinetic energy of collision. Lasers are used both to prepare specific quantum states prior to collision by stimulated-emission pumping (SEP), and to measure the distribution of quantum states in the collision products by laser-induced fluorescence (LIF). The results are interpreted in terms of dynamical models, which may be cast in a classical, semiclassical or quantum mechanical framework, as appropriate.

  15. Molecular Diagnosis of Diarrhea: Current Status and Future Potential

    PubMed Central

    Platts-Mills, James A; Operario, Darwin J

    2011-01-01

    Determining the microbiologic etiology of enteric infection remains an elusive goal. Conventional approaches, including culture, microscopy, and antigen-based tests have significant limitations such as limit of detection and the need for multiple procedures. Molecular diagnostics, especially PCR based tests, are rapidly changing research and practice in infectious diseases. Diarrheal disease, with its broad range of potential infectious etiologies, is well suited for multiplex molecular testing. This review highlights examples of currently employed molecular tests, as well as ways in which these tests can be applied in the future. The absence of a gold standard for the microbiologic cause of diarrhea means that the clinical significance of detected organisms may not always be clear. Conventional wisdom is that there should be one main pathogen causing diarrhea, however our thinking is challenged by increased detection of mixed infections. Thus, the successful incorporation of molecular diagnostics for diarrheal disease into practice will require both a careful understanding of the technical aspects and research to define their clinical utility. PMID:22116640

  16. Development of a "First Principles" Water Potential with Flexible Monomers: Dimer Potential Energy Surface, VRT Spectrum, and Second Virial Coefficient.

    PubMed

    Babin, Volodymyr; Leforestier, Claude; Paesani, Francesco

    2013-12-10

    The development of a "first principles" water potential with flexible monomers (MB-pol) for molecular simulations of water systems from gas to condensed phases is described. MB-pol is built upon the many-body expansion of the intermolecular interactions, and the specific focus of this study is on the two-body term (V2B) representing the full-dimensional intermolecular part of the water dimer potential energy surface. V2B is constructed by fitting 40,000 dimer energies calculated at the CCSD(T)/CBS level of theory and imposing the correct asymptotic behavior at long-range as predicted from "first principles". The comparison of the calculated vibration-rotation tunneling (VRT) spectrum and second virial coefficient with the corresponding experimental results demonstrates the accuracy of the MB-pol dimer potential energy surface.

  17. Development of Ultra Small Shock Tube for High Energy Molecular Beam Source

    SciTech Connect

    Miyoshi, Nobuya; Nagata, Shuhei; Kinefuchi, Ikuya; Shimizu, Kazuya; Matsumoto, Yoichiro; Takagi, Shu

    2008-12-31

    A molecular beam source exploiting a small shock tube is described for potential generation of high energy beam in a range of 1-5 eV without any undesirable impurities. The performance of a non-diaphragm type shock tube with an inner diameter of 2 mm was evaluated by measuring the acceleration and attenuation process of shock waves. With this shock tube installed in a molecular beam source, we measured the time-of-flight distributions of shock-heated beams, which demonstrated the ability of controlling the beam energy with the initial pressure ratio of the shock tube.

  18. Geothermal energy potential in the San Luis Valley, Colorado

    SciTech Connect

    Coe, B.A.

    1980-01-01

    The background of the area itself is investigated considering the geography, population, economy, attitudes of residents, and energy demands of the area. The requirements for geothermal energy development are considered, including socio-economic, institutional, and environmental conditions as well as some technical aspects. The current, proposed, and potential geothermal energy developments are described. The summary, conclusions, and methodology are included. (MHR)

  19. A new approach to the method of source-sink potentials for molecular conduction

    SciTech Connect

    Pickup, Barry T. E-mail: P.W.Fowler@sheffield.ac.uk; Fowler, Patrick W. E-mail: P.W.Fowler@sheffield.ac.uk; Borg, Martha; Sciriha, Irene

    2015-11-21

    We re-derive the tight-binding source-sink potential (SSP) equations for ballistic conduction through conjugated molecular structures in a form that avoids singularities. This enables derivation of new results for families of molecular devices in terms of eigenvectors and eigenvalues of the adjacency matrix of the molecular graph. In particular, we define the transmission of electrons through individual molecular orbitals (MO) and through MO shells. We make explicit the behaviour of the total current and individual MO and shell currents at molecular eigenvalues. A rich variety of behaviour is found. A SSP device has specific insulation or conduction at an eigenvalue of the molecular graph (a root of the characteristic polynomial) according to the multiplicities of that value in the spectra of four defined device polynomials. Conduction near eigenvalues is dominated by the transmission curves of nearby shells. A shell may be inert or active. An inert shell does not conduct at any energy, not even at its own eigenvalue. Conduction may occur at the eigenvalue of an inert shell, but is then carried entirely by other shells. If a shell is active, it carries all conduction at its own eigenvalue. For bipartite molecular graphs (alternant molecules), orbital conduction properties are governed by a pairing theorem. Inertness of shells for families such as chains and rings is predicted by selection rules based on node counting and degeneracy.

  20. A new approach to the method of source-sink potentials for molecular conduction

    NASA Astrophysics Data System (ADS)

    Pickup, Barry T.; Fowler, Patrick W.; Borg, Martha; Sciriha, Irene

    2015-11-01

    We re-derive the tight-binding source-sink potential (SSP) equations for ballistic conduction through conjugated molecular structures in a form that avoids singularities. This enables derivation of new results for families of molecular devices in terms of eigenvectors and eigenvalues of the adjacency matrix of the molecular graph. In particular, we define the transmission of electrons through individual molecular orbitals (MO) and through MO shells. We make explicit the behaviour of the total current and individual MO and shell currents at molecular eigenvalues. A rich variety of behaviour is found. A SSP device has specific insulation or conduction at an eigenvalue of the molecular graph (a root of the characteristic polynomial) according to the multiplicities of that value in the spectra of four defined device polynomials. Conduction near eigenvalues is dominated by the transmission curves of nearby shells. A shell may be inert or active. An inert shell does not conduct at any energy, not even at its own eigenvalue. Conduction may occur at the eigenvalue of an inert shell, but is then carried entirely by other shells. If a shell is active, it carries all conduction at its own eigenvalue. For bipartite molecular graphs (alternant molecules), orbital conduction properties are governed by a pairing theorem. Inertness of shells for families such as chains and rings is predicted by selection rules based on node counting and degeneracy.

  1. Photoswitchable Molecular Rings for Solar-Thermal Energy Storage.

    PubMed

    Durgun, E; Grossman, Jeffrey C

    2013-03-21

    Solar-thermal fuels reversibly store solar energy in the chemical bonds of molecules by photoconversion, and can release this stored energy in the form of heat upon activation. Many conventional photoswichable molecules could be considered as solar thermal fuels, although they suffer from low energy density or short lifetime in the photoinduced high-energy metastable state, rendering their practical use unfeasible. We present a new approach to the design of chemistries for solar thermal fuel applications, wherein well-known photoswitchable molecules are connected by different linker agents to form molecular rings. This approach allows for a significant increase in both the amount of stored energy per molecule and the stability of the fuels. Our results suggest a range of possibilities for tuning the energy density and thermal stability as a function of the type of the photoswitchable molecule, the ring size, or the type of linkers.

  2. Potential environmental problems of photovoltaic energy technology

    SciTech Connect

    Hendrey, G.R.; Moskowitz, P.D.; Patten, D.; Berry, W.; Conway, H.L.

    1980-01-01

    Separate abstracts were prepared for the ten papers of this proceedings of a workshop held at Brookhaven National Laboratory in 1980. The purposes of this proceedings are to provide a preliminary identificaton and assessment of environmental hazards which might be realistically associated with growth of the photovoltaic industry, and to provide a reference for environmental considerations by obtaining a 1980 state-of-the-art assessment of growth anticipated for the industry. Currently the industry is considered to be in the early stages of development and several possible technological options are available for large-scale manufacturing as the industry grows. Estimates of the industrial emissions of materials considered to be potentially harmful in the environment were obtained by several different analytical methods. (KRM)

  3. Molecular dynamics simulations of intergranular fracture in UO2 with nine empirical interatomic potentials

    SciTech Connect

    Yongfeng Zhang; Paul C Millett; Michael R Tonks; Xian-Ming Bai; S Bulent Biner

    2014-09-01

    The intergranular fracture behavior of UO2 was studied using molecular dynamics simulations with a bicrystal model. The anisotropic fracture behavior due to the different grain boundary characters was investigated with the View the MathML source symmetrical tilt S5 and the View the MathML source symmetrical tilt S3 ({1 1 1} twin) grain boundaries. Nine interatomic potentials, seven rigid-ion plus two core–shell ones, were utilized to elucidate possible potential dependence. Initiating from a notch, crack propagation along grain boundaries was observed for most potentials. The S3 boundary was found to be more prone to fracture than the S5 one, indicated by a lower energy release rate associated with the former. However, some potential dependence was identified on the existence of transient plastic deformation at crack tips, and the results were discussed regarding the relevant material properties including the excess energies of metastable phases and the critical energy release rate for intergranular fracture. In general, local plasticity at crack tips was observed in fracture simulations with potentials that predict low excess energies for metastable phases and high critical energy release rates for intergranular fracture.

  4. Potential for energy recovery from solid wastes

    SciTech Connect

    Velzy, C.O.

    1983-01-01

    This paper discusses the technologies, opportunities, and problems of energy-from-refuse systems. Topics considered include the direct combustion of as-received refuse, the mass-burn systems, the combustion of refuse-derived fuel, and the production of methane gas from the organic and cellulosic fraction of solid waste. A DOE-sponsored methane plant operated by Waste Management is now being evaluated at Pompano Beach, Florida. The Europeans have moved ahead so rapidly in the beneficial use of heat from the combustion of their solid waste because of the availability of a ready market for the heat in municipal facilities and/or town district heating systems. It is suggested that the use of the heat from the combustion of solid waste should be broadened to include district heating and cooling, complementary municipal functions (e.g. the disposal of sludges from wastewater treatment), integration in power generation facilities in uses other than direct production of power (e.g. boiler feedwater heating), and in industrial processing.

  5. Molecular ion sources for low energy semiconductor ion implantation (invited)

    NASA Astrophysics Data System (ADS)

    Hershcovitch, A.; Gushenets, V. I.; Seleznev, D. N.; Bugaev, A. S.; Dugin, S.; Oks, E. M.; Kulevoy, T. V.; Alexeyenko, O.; Kozlov, A.; Kropachev, G. N.; Kuibeda, R. P.; Minaev, S.; Vizir, A.; Yushkov, G. Yu.

    2016-02-01

    Smaller semiconductors require shallow, low energy ion implantation, resulting space charge effects, which reduced beam currents and production rates. To increase production rates, molecular ions are used. Boron and phosphorous (or arsenic) implantation is needed for P-type and N-type semiconductors, respectively. Carborane, which is the most stable molecular boron ion leaves unacceptable carbon residue on extraction grids. A self-cleaning carborane acid compound (C4H12B10O4) was synthesized and utilized in the ITEP Bernas ion source resulting in large carborane ion output, without carbon residue. Pure gaseous processes are desired to enable rapid switch among ion species. Molecular phosphorous was generated by introducing phosphine in dissociators via 4PH3 = P4 + 6H2; generated molecular phosphorous in a pure gaseous process was then injected into the HCEI Calutron-Bernas ion source, from which P4+ ion beams were extracted. Results from devices and some additional concepts are described.

  6. Molecular ion sources for low energy semiconductor ion implantation (invited).

    PubMed

    Hershcovitch, A; Gushenets, V I; Seleznev, D N; Bugaev, A S; Dugin, S; Oks, E M; Kulevoy, T V; Alexeyenko, O; Kozlov, A; Kropachev, G N; Kuibeda, R P; Minaev, S; Vizir, A; Yushkov, G Yu

    2016-02-01

    Smaller semiconductors require shallow, low energy ion implantation, resulting space charge effects, which reduced beam currents and production rates. To increase production rates, molecular ions are used. Boron and phosphorous (or arsenic) implantation is needed for P-type and N-type semiconductors, respectively. Carborane, which is the most stable molecular boron ion leaves unacceptable carbon residue on extraction grids. A self-cleaning carborane acid compound (C4H12B10O4) was synthesized and utilized in the ITEP Bernas ion source resulting in large carborane ion output, without carbon residue. Pure gaseous processes are desired to enable rapid switch among ion species. Molecular phosphorous was generated by introducing phosphine in dissociators via 4PH3 = P4 + 6H2; generated molecular phosphorous in a pure gaseous process was then injected into the HCEI Calutron-Bernas ion source, from which P4(+) ion beams were extracted. Results from devices and some additional concepts are described.

  7. Preliminary evaluation of wind energy potential: Cook Inlet area, Alaska

    SciTech Connect

    Hiester, T.R.

    1980-06-01

    This report summarizes work on a project performed under contract to the Alaska Power Administration (APA). The objective of this research was to make a preliminary assessment of the wind energy potential for interconnection with the Cook Inlet area electric power transmission and distribution systems, to identify the most likely candidate regions (25 to 100 square miles each) for energy potential, and to recommend a monitoring program sufficient to quantify the potential.

  8. High level predictions on the potential energy hypersurface of the nitric oxide dimer

    SciTech Connect

    Huang, Q.; Magers, D.H.; Leszczynski, J.

    1994-12-31

    The potential energy hypersurface of the NO dimer is investigated at the SCF and MP2 levels of theory using three spit-valence basis sets: 6-31G(d), 6-311G(2d), 6-311G(3df). Seven minimum energy conformers are identified. Their molecular structures, energetics, and harmonic vibrational frequencies are discussed and compared to available experimental data.

  9. Molecular Mechanisms of Diabetic Retinopathy: Potential Therapeutic Targets

    PubMed Central

    Coucha, Maha; Elshaer, Sally L.; Eldahshan, Wael S.; Mysona, Barbara A.; El-Remessy, Azza B.

    2015-01-01

    Diabetic retinopathy (DR) is the leading cause of blindness in working-age adults in United States. Research indicates an association between oxidative stress and the development of diabetes complications. However, clinical trials with general antioxidants have failed to prove effective in diabetic patients. Mounting evidence from experimental studies that continue to elucidate the damaging effects of oxidative stress and inflammation in both vascular and neural retina suggest its critical role in the pathogenesis of DR. This review will outline the current management of DR as well as present potential experimental therapeutic interventions, focusing on molecules that link oxidative stress to inflammation to provide potential therapeutic targets for treatment or prevention of DR. Understanding the biochemical changes and the molecular events under diabetic conditions could provide new effective therapeutic tools to combat the disease. PMID:25949069

  10. Are two-station biased random walkers always potential molecular motors?

    PubMed

    Bakalis, Evangelos; Zerbetto, Francesco

    2015-01-12

    The short answer to the title question is no. Despite their tremendous complexity, many nanomachines are simply one-dimensional systems undergoing a biased, that is, unidirectional, walk on a two-minima potential energy curve. The initially prepared state, or station, is higher in energy than the final equilibrium state that is reached after overcoming an energy barrier. All chemical reactions comply with this scheme, which does not necessarily imply that a generic chemical reaction is a potential molecular motor. If the barrier is low, the system may walk back and the motion will have a large purely Brownian component. Alternatively, a large distance from the barrier of either of the two stations may introduce a Brownian component. Starting from a general inequality that leverages on the idea that the amount of heat dissipated along the potential energy curve is a good indication of the effectiveness of the biased walk, we provide guidelines for the selection of the features of artificial molecular motors.

  11. Vitamin D in Autoimmunity: Molecular Mechanisms and Therapeutic Potential

    PubMed Central

    Dankers, Wendy; Colin, Edgar M.; van Hamburg, Jan Piet; Lubberts, Erik

    2017-01-01

    Over the last three decades, it has become clear that the role of vitamin D goes beyond the regulation of calcium homeostasis and bone health. An important extraskeletal effect of vitamin D is the modulation of the immune system. In the context of autoimmune diseases, this is illustrated by correlations of vitamin D status and genetic polymorphisms in the vitamin D receptor with the incidence and severity of the disease. These correlations warrant investigation into the potential use of vitamin D in the treatment of patients with autoimmune diseases. In recent years, several clinical trials have been performed to investigate the therapeutic value of vitamin D in multiple sclerosis, rheumatoid arthritis, Crohn’s disease, type I diabetes, and systemic lupus erythematosus. Additionally, a second angle of investigation has focused on unraveling the molecular pathways used by vitamin D in order to find new potential therapeutic targets. This review will not only provide an overview of the clinical trials that have been performed but also discuss the current knowledge about the molecular mechanisms underlying the immunomodulatory effects of vitamin D and how these advances can be used in the treatment of autoimmune diseases. PMID:28163705

  12. Development of energy plants and their potential to withstand various extreme environments.

    PubMed

    Saibi, Walid; Brini, Faiçal; Hanin, Moez; Masmoudi, Khaled

    2013-04-01

    Biomass utilization is increasingly considered as a practical way for sustainable energy supply and long-term environment care around the world. In concerns with food security, starch or sugar-based bioethanol and edible-oilderived biodiesel are severely restricted for large scale production. Alternatively, conversion of lignocellulosic residues from food crops could be considered, but due to its recalcitrance, the current biomass process is unacceptably expensive. In this context, genetic breeding of energy crops appears as a promising solution. To fulfil the global world need as both food and biofuel sources, energy crops are expected to be produced with higher yields and especially in marginal lands. This review focus on recent progress and patents dealing with energy plants and the challenges associated with bioenergy development. We also discuss the potential use of molecular approaches including genome sequencing, molecular markers, and genetic transformation for improving specific traits or generating new cultivars of energy plants.

  13. Quantum mechanics/molecular mechanics restrained electrostatic potential fitting.

    PubMed

    Burger, Steven K; Schofield, Jeremy; Ayers, Paul W

    2013-12-05

    We present a quantum mechanics/molecular mechanics (QM/MM) method to evaluate the partial charges of amino acid residues for use in MM potentials based on their protein environment. For each residue of interest, the nearby residues are included in the QM system while the rest of the protein is treated at the MM level of theory. After a short structural optimization, the partial charges of the central residue are fit to the electrostatic potential using the restrained electrostatic potential (RESP) method. The resulting charges and electrostatic potential account for the individual environment of the residue, although they lack the transferable nature of library partial charges. To evaluate the quality of the QM/MM RESP charges, thermodynamic integration is used to measure the pKa shift of the aspartic acid residues in three different proteins, turkey egg lysozyme, beta-cryptogein, and Thioredoxin. Compared to the AMBER ff99SB library values, the QM/MM RESP charges show better agreement between the calculated and experimental pK(a) values for almost all of the residues considered.

  14. Molecular trophic markers in marine food webs and their potential use for coral ecology.

    PubMed

    Leal, Miguel Costa; Ferrier-Pagès, Christine

    2016-10-01

    Notable advances in ecological genomics have been driven by high-throughput sequencing technology and taxonomically broad sequence repositories that allow us to accurately assess species interactions with great taxonomic resolution. The use of DNA as a marker for ingested food is particularly relevant to address predator-prey interactions and disentangle complex marine food webs. DNA-based methods benefit from reductionist molecular approaches to address ecosystem scale processes, such as community structure and energy flow across trophic levels, among others. Here we review how molecular trophic markers have been used to better understand trophic interactions in the marine environment and their advantages and limitations. We focus on animal groups where research has been focused, such as marine mammals, seabirds, fishes, pelagic invertebrates and benthic invertebrates, and use case studies to illustrate how DNA-based methods unraveled food-web interactions. The potential of molecular trophic markers for disentangling the complex trophic ecology of corals is also discussed.

  15. Ground state potential energy surfaces around selected atoms from resonant inelastic x-ray scattering

    NASA Astrophysics Data System (ADS)

    Schreck, Simon; Pietzsch, Annette; Kennedy, Brian; Såthe, Conny; Miedema, Piter S.; Techert, Simone; Strocov, Vladimir N.; Schmitt, Thorsten; Hennies, Franz; Rubensson, Jan-Erik; Föhlisch, Alexander

    2016-01-01

    Thermally driven chemistry as well as materials’ functionality are determined by the potential energy surface of a systems electronic ground state. This makes the potential energy surface a central and powerful concept in physics, chemistry and materials science. However, direct experimental access to the potential energy surface locally around atomic centers and to its long-range structure are lacking. Here we demonstrate how sub-natural linewidth resonant inelastic soft x-ray scattering at vibrational resolution is utilized to determine ground state potential energy surfaces locally and detect long-range changes of the potentials that are driven by local modifications. We show how the general concept is applicable not only to small isolated molecules such as O2 but also to strongly interacting systems such as the hydrogen bond network in liquid water. The weak perturbation to the potential energy surface through hydrogen bonding is observed as a trend towards softening of the ground state potential around the coordinating atom. The instrumental developments in high resolution resonant inelastic soft x-ray scattering are currently accelerating and will enable broad application of the presented approach. With this multidimensional potential energy surfaces that characterize collective phenomena such as (bio)molecular function or high-temperature superconductivity will become accessible in near future.

  16. Ground state potential energy surfaces around selected atoms from resonant inelastic x-ray scattering.

    PubMed

    Schreck, Simon; Pietzsch, Annette; Kennedy, Brian; Såthe, Conny; Miedema, Piter S; Techert, Simone; Strocov, Vladimir N; Schmitt, Thorsten; Hennies, Franz; Rubensson, Jan-Erik; Föhlisch, Alexander

    2016-01-29

    Thermally driven chemistry as well as materials' functionality are determined by the potential energy surface of a systems electronic ground state. This makes the potential energy surface a central and powerful concept in physics, chemistry and materials science. However, direct experimental access to the potential energy surface locally around atomic centers and to its long-range structure are lacking. Here we demonstrate how sub-natural linewidth resonant inelastic soft x-ray scattering at vibrational resolution is utilized to determine ground state potential energy surfaces locally and detect long-range changes of the potentials that are driven by local modifications. We show how the general concept is applicable not only to small isolated molecules such as O2 but also to strongly interacting systems such as the hydrogen bond network in liquid water. The weak perturbation to the potential energy surface through hydrogen bonding is observed as a trend towards softening of the ground state potential around the coordinating atom. The instrumental developments in high resolution resonant inelastic soft x-ray scattering are currently accelerating and will enable broad application of the presented approach. With this multidimensional potential energy surfaces that characterize collective phenomena such as (bio)molecular function or high-temperature superconductivity will become accessible in near future.

  17. Ground state potential energy surfaces around selected atoms from resonant inelastic x-ray scattering

    PubMed Central

    Schreck, Simon; Pietzsch, Annette; Kennedy, Brian; Såthe, Conny; Miedema, Piter S.; Techert, Simone; Strocov, Vladimir N.; Schmitt, Thorsten; Hennies, Franz; Rubensson, Jan-Erik; Föhlisch, Alexander

    2016-01-01

    Thermally driven chemistry as well as materials’ functionality are determined by the potential energy surface of a systems electronic ground state. This makes the potential energy surface a central and powerful concept in physics, chemistry and materials science. However, direct experimental access to the potential energy surface locally around atomic centers and to its long-range structure are lacking. Here we demonstrate how sub-natural linewidth resonant inelastic soft x-ray scattering at vibrational resolution is utilized to determine ground state potential energy surfaces locally and detect long-range changes of the potentials that are driven by local modifications. We show how the general concept is applicable not only to small isolated molecules such as O2 but also to strongly interacting systems such as the hydrogen bond network in liquid water. The weak perturbation to the potential energy surface through hydrogen bonding is observed as a trend towards softening of the ground state potential around the coordinating atom. The instrumental developments in high resolution resonant inelastic soft x-ray scattering are currently accelerating and will enable broad application of the presented approach. With this multidimensional potential energy surfaces that characterize collective phenomena such as (bio)molecular function or high-temperature superconductivity will become accessible in near future. PMID:26821751

  18. Energy conserving, linear scaling Born-Oppenheimer molecular dynamics.

    PubMed

    Cawkwell, M J; Niklasson, Anders M N

    2012-10-07

    Born-Oppenheimer molecular dynamics simulations with long-term conservation of the total energy and a computational cost that scales linearly with system size have been obtained simultaneously. Linear scaling with a low pre-factor is achieved using density matrix purification with sparse matrix algebra and a numerical threshold on matrix elements. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] yields microcanonical trajectories with the approximate forces obtained from the linear scaling method that exhibit no systematic drift over hundreds of picoseconds and which are indistinguishable from trajectories computed using exact forces.

  19. Intermolecular potential energy surface for CS2 dimer.

    PubMed

    Farrokhpour, Hossein; Mombeini, Zainab; Namazian, Mansoor; Coote, Michelle L

    2011-04-15

    A new four-dimensional intermolecular potential energy surface for CS(2) dimer is obtained by ab initio calculation of the interaction energies for a range of configurations and center-of-mass separation distances for the first time. The calculations were performed using the supermolecular approach at the Møller-Plesset second-order perturbation (MP2) level of theory with the augmented correlation consistent basis sets (aug-cc-pVxZ, x = D, T) and corrected for the basis-set superposition error using the full counterpoise correction method. A two-point extrapolation method was used to extrapolate the calculated energy points to the complete basis set limit. The effect of using the higher levels of theory, quadratic configuration interaction containing single, double, and perturbative triple excitations QCISD(T) and coupled cluster singles, doubles and perturbative triples excitations CCSD(T), on the shape of potential energy surface was investigated. It is shown that the MP2 level of theory apparently performs extremely poorly for describing the intermolecular potential energy surface, overestimating the total energy by a factor of nearly 1.73 in comparison with the QCISD(T) and CCSD(T) values. The value of isotropic dipole-dipole dispersion coefficient (C(6) ) of CS(2) fluid was obtained from the extrapolated MP2 potential energy surface. The MP2 extrapolated energy points were fitted to well-known analytical potential functions using two different methods to represent the potential energy surface analytically. The most stable configuration of the dimer was determined at R = 6.23 au, α = 90°, β = 90°, and γ = 90°, with a well depth of 3.980 kcal mol(-1) at the MP2 level of theory. Finally, the calculated second virial coefficients were compared with experimental values to test the quality of the presented potential energy surface.

  20. Biomass energy: the scale of the potential resource.

    PubMed

    Field, Christopher B; Campbell, J Elliott; Lobell, David B

    2008-02-01

    Increased production of biomass for energy has the potential to offset substantial use of fossil fuels, but it also has the potential to threaten conservation areas, pollute water resources and decrease food security. The net effect of biomass energy agriculture on climate could be either cooling or warming, depending on the crop, the technology for converting biomass into useable energy, and the difference in carbon stocks and reflectance of solar radiation between the biomass crop and the pre-existing vegetation. The area with the greatest potential for yielding biomass energy that reduces net warming and avoids competition with food production is land that was previously used for agriculture or pasture but that has been abandoned and not converted to forest or urban areas. At the global scale, potential above-ground plant growth on these abandoned lands has an energy content representing approximately 5% of world primary energy consumption in 2006. The global potential for biomass energy production is large in absolute terms, but it is not enough to replace more than a few percent of current fossil fuel usage. Increasing biomass energy production beyond this level would probably reduce food security and exacerbate forcing of climate change.

  1. Exploring the vibrational fingerprint of the electronic excitation energy via molecular dynamics

    SciTech Connect

    Deyne, Andy Van Yperen-De; Pauwels, Ewald; Ghysels, An; Waroquier, Michel; Van Speybroeck, Veronique; Hemelsoet, Karen; De Meyer, Thierry; De Clerck, Karen

    2014-04-07

    A Fourier-based method is presented to relate changes of the molecular structure during a molecular dynamics simulation with fluctuations in the electronic excitation energy. The method implies sampling of the ground state potential energy surface. Subsequently, the power spectrum of the velocities is compared with the power spectrum of the excitation energy computed using time-dependent density functional theory. Peaks in both spectra are compared, and motions exhibiting a linear or quadratic behavior can be distinguished. The quadratically active motions are mainly responsible for the changes in the excitation energy and hence cause shifts between the dynamic and static values of the spectral property. Moreover, information about the potential energy surface of various excited states can be obtained. The procedure is illustrated with three case studies. The first electronic excitation is explored in detail and dominant vibrational motions responsible for changes in the excitation energy are identified for ethylene, biphenyl, and hexamethylbenzene. The proposed method is also extended to other low-energy excitations. Finally, the vibrational fingerprint of the excitation energy of a more complex molecule, in particular the azo dye ethyl orange in a water environment, is analyzed.

  2. Potential production of energy cane for fuel in the Caribbean

    SciTech Connect

    Samuels, G.

    1984-08-01

    Sugarcane grown as energy cane presents a new potential to the Caribbean countries to provide their own energy needs and to reduce or eliminate fuel oil imports. The use of proper agronomic techniques can convert conventional sugarcane growing to a crop capable of giving energy feedstocks in the form of fiber for boiler fuel for electricity and fermentable solids for alcohol for motor fuel. Sugarcane can still be obtained from the energy cane for domestic consumption and export if desired. The aerable land now devoted to sugarcane can utilized for energy-cane production without causing any serious imbalance in food crop production.

  3. Ab initio Potential Energy Surface for H-H2

    NASA Technical Reports Server (NTRS)

    Partridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene

    1993-01-01

    Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- (mu)E(sub h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(sub 0) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.

  4. Representing Global Reactive Potential Energy Surfaces Using Gaussian Processes.

    PubMed

    Kolb, Brian; Marshall, Paul; Zhao, Bin; Jiang, Bin; Guo, Hua

    2017-03-23

    Representation of multidimensional global potential energy surfaces suitable for spectral and dynamical calculations from high-level ab initio calculations remains a challenge. Here, we present a detailed study on constructing potential energy surfaces using a machine learning method, namely, Gaussian process regression. Tests for the (3)A″ state of SH2, which facilitates the SH + H ↔ S((3)P) + H2 abstraction reaction and the SH + H' ↔ SH' + H exchange reaction, suggest that the Gaussian process is capable of providing a reasonable potential energy surface with a small number (∼1 × 10(2)) of ab initio points, but it needs substantially more points (∼1 × 10(3)) to converge reaction probabilities. The implications of these observations for construction of potential energy surfaces are discussed.

  5. Saint Paul Energy Park: the potential for district heating

    SciTech Connect

    Lee, C.; Kron, R.; Davis, H.

    1980-03-01

    The results of ANL's study of the energy and economic aspects of using district heating in the St. Paul Energy Park are summarized. The Energy Park is a 6 million ft/sup 2/ residential, commercial office, and light industrial complex to be built in the midway area of St. Paul, Minnesota. Space heating and cooling design loads for the park were calculated assuming that the ASHRAE's 90-75 energy-conserving construction standards would be used in constructing the park's buildings. Based in part on this assumption, ANL estimated the costs and energy use characteristics of six possible energy system options for supplying Energy Park's space heating, space cooling, and domestic hot water heating needs. The results indicate that in today's economy, a central heating and cooling plant with natural gas boilers and electrically driven centrifugal chillers with thermal storage has good potential for energy and economic savings and clearly merits further consideration.

  6. Molecularly-imprinted polymer sensors: realising their potential.

    PubMed

    Uzun, Lokman; Turner, Anthony P F

    2016-02-15

    In parallel with recent developments in communications, nanotechnology and materials sciences, there has been extraordinary growth in the area of biosensors, with almost half of the total number of papers ever published (1962-2015) appearing in the last five-years (2010-2015). Molecular imprinting offers a route to the creation of specific and selective cavities in a 3D-polymeric network, which are complementary not only to the size and shape of a target species, but also provide interaction points and a coordination sphere around the template molecule. Given the challenges facing biosensor technologists, it is natural that this approach to create potentially highly stable synthetic ligands as an alternative to, or to compliment natural receptors, should emerge as a key line of interdisciplinary research. Despite the profuse amount of recent literature on molecularly-imprinted polymers (MIPs) and some limited commercial activity, these promising materials still need to overcome some limitations before taking their place in analytical market. In this review, we have focused on the most promising advances in MIP-based biosensors to illustrate how close to market they really are. We present our material under five main sections covering computational design, polymerisation strategies, material combinations, recent sensor designs and manufacturing issues. Each section provides technical details and evaluates the effect on sensor performance.

  7. Possible explanation of the atmospheric kinetic and potential energy spectra.

    PubMed

    Vallgren, Andreas; Deusebio, Enrico; Lindborg, Erik

    2011-12-23

    We hypothesize that the observed wave number spectra of kinetic and potential energy in the atmosphere can be explained by assuming that there are two related cascade processes emanating from the same large-scale energy source, a downscale cascade of potential enstrophy, giving rise to the k(-3) spectrum at synoptic scales and a downscale energy cascade giving rise to the k(-5/3) spectrum at mesoscales. The amount of energy which is going into the downscale energy cascade is determined by the rate of system rotation, with negligible energy going downscale in the limit of very fast rotation. We present a set of simulations of a system with strong rotation and stratification, supporting these hypotheses and showing good agreement with observations.

  8. Gravitational potential as a source of earthquake energy

    USGS Publications Warehouse

    Barrows, L.; Langer, C.J.

    1981-01-01

    Some degree of tectonic stress within the earth originates from gravity acting upon density structures. The work performed by this "gravitational tectonics stress" must have formerly existed as gravitational potential energy contained in the stress-causing density structure. According to the elastic rebound theory (Reid, 1910), the energy of earthquakes comes from an elastic strain field built up by fairly continuous elastic deformation in the period between events. For earthquakes resulting from gravitational tectonic stress, the elastic rebound theory requires the transfer of energy from the gravitational potential of the density structures into an elastic strain field prior to the event. An alternate theory involves partial gravitational collapse of the stress-causing density structures. The earthquake energy comes directly from a net decrease in gravitational potential energy. The gravitational potential energy released at the time of the earthquake is split between the energy released by the earthquake, including work done in the fault zone and an increase in stored elastic strain energy. The stress associated with this elastic strain field should oppose further fault slip. ?? 1981.

  9. Geospatial Analysis of Renewable Energy Technical Potential on Tribal Lands

    SciTech Connect

    Doris, E.; Lopez, A.; Beckley, D.

    2013-02-01

    This technical report uses an established geospatial methodology to estimate the technical potential for renewable energy on tribal lands for the purpose of allowing Tribes to prioritize the development of renewable energy resources either for community scale on-tribal land use or for revenue generating electricity sales.

  10. Waste to Energy Potential - A High Concentration Anaerobic Bioreactor

    DTIC Science & Technology

    2012-05-23

    output • Uses the organic portion of solid waste (such as food waste , paper products, and agricultural waste ) to fuel an anaerobic digestion ...Sustainability Symposium & Exhibition Anaerobic Digestion • What does it do? • Offers sustainability by addressing renewable energy, waste ... Waste to Energy Potential – A High Concentration Anaerobic Bioreactor Presenter: Scott Murphy & Rebecca Robbennolt ARCADIS/Malcolm Pirnie Date

  11. Energy potential of municipal solid waste is limited

    SciTech Connect

    1994-09-01

    Energy recovery from municipal solid waste has the potential for making only a limited contribution to the nation`s overall energy production. Although the current contribution of waste-derived energy production is less than one-half of 1 percent of the nation`s total energy Supply, DOE has set a goal for energy from waste at 2 percent of the total supply by 2010. The industry`s estimates show a smaller role for waste as an energy source in the future. The energy potential from waste is limited not only by the volume and energy content of the waste itself, but also by the factors affecting the use of waste disposal options, including public opposition and the availability of financing. Energy production from waste combustors and from landfill gases generates pollutants, although these are reduced through current regulations that require the use of emissions control technology and define operational criteria for the facilities. Although DOE estimates that one-third of the energy available from waste is available in the form of energy savings through the recycling of materials, the Department`s research in this area is ongoing.

  12. Free energy landscape and molecular pathways of gas hydrate nucleation

    NASA Astrophysics Data System (ADS)

    Bi, Yuanfei; Porras, Anna; Li, Tianshu

    2016-12-01

    Despite the significance of gas hydrates in diverse areas, a quantitative knowledge of hydrate formation at a molecular level is missing. The impediment to acquiring this understanding is primarily attributed to the stochastic nature and ultra-fine scales of nucleation events, posing a great challenge for both experiment and simulation to explore hydrate nucleation. Here we employ advanced molecular simulation methods, including forward flux sampling (FFS), pB histogram analysis, and backward flux sampling, to overcome the limit of direct molecular simulation for exploring both the free energy landscape and molecular pathways of hydrate nucleation. First we test the half-cage order parameter (H-COP) which we developed for driving FFS, through conducting the pB histogram analysis. Our results indeed show that H-COP describes well the reaction coordinates of hydrate nucleation. Through the verified order parameter, we then directly compute the free energy landscape for hydrate nucleation by combining both forward and backward flux sampling. The calculated stationary distribution density, which is obtained independently of nucleation theory, is found to fit well against the classical nucleation theory (CNT). Subsequent analysis of the obtained large ensemble of hydrate nucleation trajectories show that although on average, hydrate formation is facilitated by a two-step like mechanism involving a gradual transition from an amorphous to a crystalline structure, there also exist nucleation pathways where hydrate crystallizes directly, without going through the amorphous stage. The CNT-like free energy profile and the structural diversity suggest the existence of multiple active transition pathways for hydrate nucleation, and possibly also imply the near degeneracy in their free energy profiles among different pathways. Our results thus bring a new perspective to the long standing question of how hydrates crystallize.

  13. Fluorescence Molecular Tomography: Principles and Potential for Pharmaceutical Research

    PubMed Central

    Stuker, Florian; Ripoll, Jorge; Rudin, Markus

    2011-01-01

    Fluorescence microscopic imaging is widely used in biomedical research to study molecular and cellular processes in cell culture or tissue samples. This is motivated by the high inherent sensitivity of fluorescence techniques, the spatial resolution that compares favorably with cellular dimensions, the stability of the fluorescent labels used and the sophisticated labeling strategies that have been developed for selectively labeling target molecules. More recently, two and three-dimensional optical imaging methods have also been applied to monitor biological processes in intact biological organisms such as animals or even humans. These whole body optical imaging approaches have to cope with the fact that biological tissue is a highly scattering and absorbing medium. As a consequence, light propagation in tissue is well described by a diffusion approximation and accurate reconstruction of spatial information is demanding. While in vivo optical imaging is a highly sensitive method, the signal is strongly surface weighted, i.e., the signal detected from the same light source will become weaker the deeper it is embedded in tissue, and strongly depends on the optical properties of the surrounding tissue. Derivation of quantitative information, therefore, requires tomographic techniques such as fluorescence molecular tomography (FMT), which maps the three-dimensional distribution of a fluorescent probe or protein concentration. The combination of FMT with a structural imaging method such as X-ray computed tomography (CT) or Magnetic Resonance Imaging (MRI) will allow mapping molecular information on a high definition anatomical reference and enable the use of prior information on tissue's optical properties to enhance both resolution and sensitivity. Today many of the fluorescent assays originally developed for studies in cellular systems have been successfully translated for experimental studies in animals. The opportunity of monitoring molecular processes non

  14. Path Integral Computation of Quantum Free Energy Differences Due to Alchemical Transformations Involving Mass and Potential.

    PubMed

    Pérez, Alejandro; von Lilienfeld, O Anatole

    2011-08-09

    Thermodynamic integration, perturbation theory, and λ-dynamics methods were applied to path integral molecular dynamics calculations to investigate free energy differences due to "alchemical" transformations. Several estimators were formulated to compute free energy differences in solvable model systems undergoing changes in mass and/or potential. Linear and nonlinear alchemical interpolations were used for the thermodynamic integration. We find improved convergence for the virial estimators, as well as for the thermodynamic integration over nonlinear interpolation paths. Numerical results for the perturbative treatment of changes in mass and electric field strength in model systems are presented. We used thermodynamic integration in ab initio path integral molecular dynamics to compute the quantum free energy difference of the isotope transformation in the Zundel cation. The performance of different free energy methods is discussed.

  15. Free energy calculations: an efficient adaptive biasing potential method.

    PubMed

    Dickson, Bradley M; Legoll, Frédéric; Lelièvre, Tony; Stoltz, Gabriel; Fleurat-Lessard, Paul

    2010-05-06

    We develop an efficient sampling and free energy calculation technique within the adaptive biasing potential (ABP) framework. By mollifying the density of states we obtain an approximate free energy and an adaptive bias potential that is computed directly from the population along the coordinates of the free energy. Because of the mollifier, the bias potential is "nonlocal", and its gradient admits a simple analytic expression. A single observation of the reaction coordinate can thus be used to update the approximate free energy at every point within a neighborhood of the observation. This greatly reduces the equilibration time of the adaptive bias potential. This approximation introduces two parameters: strength of mollification and the zero of energy of the bias potential. While we observe that the approximate free energy is a very good estimate of the actual free energy for a large range of mollification strength, we demonstrate that the errors associated with the mollification may be removed via deconvolution. The zero of energy of the bias potential, which is easy to choose, influences the speed of convergence but not the limiting accuracy. This method is simple to apply to free energy or mean force computation in multiple dimensions and does not involve second derivatives of the reaction coordinates, matrix manipulations nor on-the-fly adaptation of parameters. For the alanine dipeptide test case, the new method is found to gain as much as a factor of 10 in efficiency as compared to two basic implementations of the adaptive biasing force methods, and it is shown to be as efficient as well-tempered metadynamics with the postprocess deconvolution giving a clear advantage to the mollified density of states method.

  16. Separable representation of energy-dependent optical potentials

    NASA Astrophysics Data System (ADS)

    Hlophe, L.; Elster, Ch.

    2016-03-01

    Background: One important ingredient for many applications of nuclear physics to astrophysics, nuclear energy, and stockpile stewardship are cross sections for reactions of neutrons with rare isotopes. Since direct measurements are often not feasible, indirect methods, e.g., (d ,p ) reactions, should be used. Those (d ,p ) reactions may be viewed as three-body reactions and described with Faddeev techniques. Purpose: Faddeev equations in momentum space have a long tradition of utilizing separable interactions in order to arrive at sets of coupled integral equations in one variable. Optical potentials representing the effective interactions in the neutron (proton) nucleus subsystem are usually non-Hermitian as well as energy dependent. Potential matrix elements as well as transition matrix elements calculated with them must fulfill the reciprocity theorem. The purpose of this paper is to introduce a separable, energy-dependent representation of complex, energy-dependent optical potentials that fulfill reciprocity exactly. Methods: Momentum space Lippmann-Schwinger integral equations are solved with standard techniques to obtain the form factors for the separable representation. Results: Starting from a separable, energy-independent representation of global optical potentials based on a generalization of the Ernst-Shakin-Thaler (EST) scheme, a further generalization is needed to take into account the energy dependence. Applications to n +48Ca ,n +208Pb , and p +208Pb are investigated for energies from 0 to 50 MeV with special emphasis on fulfilling reciprocity. Conclusions: We find that the energy-dependent separable representation of complex, energy-dependent phenomenological optical potentials fulfills reciprocity exactly. In addition, taking into account the explicit energy dependence slightly improves the description of the S matrix elements.

  17. Investigating Energy-Saving Potentials in the Cloud

    PubMed Central

    Lee, Da-Sheng

    2014-01-01

    Collecting webpage messages can serve as a sensor for investigating the energy-saving potential of buildings. Focusing on stores, a cloud sensor system is developed to collect data and determine their energy-saving potential. The owner of a store under investigation must register online, report the store address, area, and the customer ID number on the electric meter. The cloud sensor system automatically surveys the energy usage records by connecting to the power company website and calculating the energy use index (EUI) of the store. Other data includes the chain store check, company capital, location price, and the influence of weather conditions on the store; even the exposure frequency of store under investigation may impact the energy usage collected online. After collecting data from numerous stores, a multi-dimensional data array is constructed to determine energy-saving potential by identifying stores with similarity conditions. Similarity conditions refer to analyzed results that indicate that two stores have similar capital, business scale, weather conditions, and exposure frequency on web. Calculating the EUI difference or pure technical efficiency of stores, the energy-saving potential is determined. In this study, a real case study is performed. An 8-dimensional (8D) data array is constructed by surveying web data related to 67 stores. Then, this study investigated the savings potential of the 33 stores, using a site visit, and employed the cloud sensor system to determine the saving potential. The case study results show good agreement between the data obtained by the site visit and the cloud investigation, with errors within 4.17%. Among 33 the samples, eight stores have low saving potentials of less than 5%. The developed sensor on the cloud successfully identifies them as having low saving potential and avoids wasting money on the site visit. PMID:24561405

  18. A triangular element based on generalized potential energy concepts

    NASA Technical Reports Server (NTRS)

    Thomas, G. R.; Gallagher, R. H.

    1976-01-01

    Stiffness equations are formulated for a doubly-curved triangular thin shell finite element. The strain energy component of the potential energy is first expressed in terms of displacements and displacement gradients with the aid of consistent deep shell strain-displacement equations. The element in-plane and normal displacement fields are approximated by complete cubic polynomials. These functions do not satisfy the interelement displacement admissibility conditions. Satisfaction is forced by the imposition of constraint conditions on the interelement boundaries; the constraints represent the modification of the potential energy. Some numerical results for a pinched cylinder, a cylindrical sphere, and a pinched sphere are examined.

  19. Redox potentials and pKa for benzoquinone from density functional theory based molecular dynamics.

    PubMed

    Cheng, Jun; Sulpizi, Marialore; Sprik, Michiel

    2009-10-21

    The density functional theory based molecular dynamics (DFTMD) method for the computation of redox free energies presented in previous publications and the more recent modification for computation of acidity constants are reviewed. The method uses a half reaction scheme based on reversible insertion/removal of electrons and protons. The proton insertion is assisted by restraining potentials acting as chaperones. The procedure for relating the calculated deprotonation free energies to Brønsted acidities (pK(a)) and the oxidation free energies to electrode potentials with respect to the normal hydrogen electrode is discussed in some detail. The method is validated in an application to the reduction of aqueous 1,4-benzoquinone. The conversion of hydroquinone to quinone can take place via a number of alternative pathways consisting of combinations of acid dissociations, oxidations, or dehydrogenations. The free energy changes of all elementary steps (ten in total) are computed. The accuracy of the calculations is assessed by comparing the energies of different pathways for the same reaction (Hess's law) and by comparison to experiment. This two-sided test enables us to separate the errors related with the restrictions on length and time scales accessible to DFTMD from the errors introduced by the DFT approximation. It is found that the DFT approximation is the main source of error for oxidation free energies.

  20. Accelerating ab initio path integral molecular dynamics with multilevel sampling of potential surface

    SciTech Connect

    Geng, Hua Y.

    2015-02-15

    A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model—the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of r{sub s}=0.912.

  1. Accelerating ab initio path integral molecular dynamics with multilevel sampling of potential surface

    NASA Astrophysics Data System (ADS)

    Geng, Hua Y.

    2015-02-01

    A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model-the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of rs = 0.912.

  2. Scenarios of energy demand and efficiency potential for Bulgaria

    SciTech Connect

    Tzvetanov, P.; Ruicheva, M.; Denisiev, M.

    1996-12-31

    The paper presents aggregated results on macroeconomic and final energy demand scenarios developed within the Bulgarian Country Study on Greenhouse Gas Emissions Mitigation, supported by US Country Studies Program. The studies in this area cover 5 main stages: (1) {open_quotes}Baseline{close_quotes} and {open_quotes}Energy Efficiency{close_quotes} socioeconomic and energy policy philosophy; (2) Modeling of macroeconomic and sectoral development till 2020; (3) Expert assessments on the technological options for energy efficiency increase and GHG mitigation in the Production, Transport and Households and Services Sectors; (4) Bottom-up modeling of final energy demand; and (5) Sectoral and overall energy efficiency potential and policy. Within the Bulgarian Country Study, the presented results have served as a basis for the final integration stage {open_quotes}Assessment of the Mitigation Policy and Measures in the Energy System of Bulgaria{close_quotes}.

  3. Solar energy in California industry - Applications, characteristics and potential

    NASA Technical Reports Server (NTRS)

    Barbieri, R. H.; Pivirotto, D. S.

    1978-01-01

    Results of a survey to determine the potential applicability of solar thermal energy to industrial processes in California are presented. It is found that if the heat for all industrial processes at temperatures below 212 F were supplied by solar energy, total state energy consumption could be reduced by 100 trillion Btus (2%), while the use of solar energy in processes between 212 and 350 F could displace 500 trillion Btus. The issues and problems with which solar energy must contend are illustrated by a description of fluid milk processing operations. Solar energy application is found to be technically feasible for processes with thermal energy requirements below 212 F, with design, and degree of technical, economic and management feasibility being site specific. It is recommended that the state provide support for federal and industrial research, development and demonstration programs in order to stimulate acceptance of solar process heat application by industry.

  4. Savings potential of ENERGY STAR (registered trademark) voluntary labeling programs

    SciTech Connect

    Webber, Carrie A.; Brown, Richard E.

    1998-06-19

    In 1993 the U.S. Environmental Protection Agency (EPA) introduced ENERGY STAR (registered trademark), a voluntary labeling program designed to identify and promote energy-efficient products. Since then EPA, now in partnership with the U.S. Department of Energy (DOE), has introduced programs for more than twenty products, spanning office equipment, residential heating and cooling equipment, new homes, commercial and residential lighting, home electronics, and major appliances. We present potential energy, dollar and carbon savings forecasts for these programs for the period 1998 to 2010. Our target market penetration case represents our best estimate of future ENERGY STAR savings. It is based on realistic market penetration goals for each of the products. We also provide results under the assumption of 100% market penetration; that is, we assume that all purchasers buy ENERGY STAR-compliant products instead of standard efficiency products throughout the analysis period. Finally, we assess the sensitivity of our target penetration case forecasts to greater or lesser marketing success by EPA and DOE, lower-than-expected future energy prices, and higher or lower rates of carbon emission by electricity generators. The potential savings of ENERGY STAR are substantial. If all purchasers chose Energy Star-compliant products instead of standard efficiency products over the next 15 years, they would save more than $100 billion on their energy bills during those 15 years. (Bill savings are in 1995 dollars, discounted at a 4% real discount rate.)

  5. Kappa distribution in the presence of a potential energy

    NASA Astrophysics Data System (ADS)

    Livadiotis, George

    2015-02-01

    The present paper develops the theory and formulations of the kappa distributions that describe particle systems characterized by a nonzero potential energy. As yet, kappa distributions were used for the statistical description of the velocity or kinetic energy of particles but not of the potential energy. With the results provided here, it is straightforward to use the developed kappa distributions to describe any particle population of space plasmas subject to a nonnegligible potential energy. Starting from the kappa distribution of the Hamiltonian function, we develop the distributions that describe either the complete phase space or the marginal spaces of positions and velocities. The study shows, among others: (a) The kappa distributions of velocities that describe space plasmas can be vastly different from the standard formulation of the kappa distribution, because of the presence of a potential energy; the correct formulation should be given by the marginal kappa distribution of velocities by integrating the distribution of the Hamiltonian over the potential energy. (b) The long-standing problem of the divergence of the Boltzmannian exponential distribution for bounded radial potentials is solved using kappa distributions of negative kappa index. (c) Anisotropic distributions of velocities can exist in the presence of a velocity-dependent potential. (d) A variety of applications, including derivations/verifications of the following: (i) the Jeans', the most frequent, and the maximum radii in spherical/linear gravitational potentials; (ii) the Virial theorem for power law potentials; (iii) the generalized barometric formula, (iv) the plasma density profiles in Saturnian magnetosphere, and (v) the average electron magnetic moment in Earth's magnetotail.

  6. An ab initio molecular dynamics analysis of lignin as a potential antioxidant for hydrocarbons.

    PubMed

    Pan, Tongyan; Cheng, Cheng

    2015-11-01

    Lignins are complex phenolic polymers with limited industrial uses. To identify new applications of lignins, this study aims to evaluate the conifer alcohol lignin as a potential antioxidant for hydrocarbons, using the petroleum asphalt as an example. Using the ab initio molecular dynamics (AIMD) method, the evaluation is accomplished by tracking the generation of critical species in a lignin-asphalt mixture under a simulated oxidative condition. The generation of new species was detected using nuclear magnetic resonance and four analytical methods including density of states analysis, highest occupied molecular orbital and lowest unoccupied molecular orbital analyses, bonding and energy level analysis, and electrostatic potential energy analysis. Results of the analyses show that the chemical radicals of carbon, nitrogen and sulfur generated in the oxidation process could enhance the agglomeration and/or decomposition tendency of asphalt. The effectiveness of lignins as an antioxidant depends on their chemical compositions. Lignins with a HOMO-LUMO gap larger than the HOMO-LUMO gap of the hydrocarbon system to be protected, such as the conifer alcohol lignin to protect petroleum asphalt as was studied in this work, do not demonstrate beneficial anti-oxidation capacity. Lignins, however, may be effective oxidants for hydrocarbon systems with a larger HOMO-LUMO gap. In addition, lignins may contain more polar sites than the hydrocarbons to be protected; thus the lignins' hydrophobicity and compatibility with the host hydrocarbons need to be well evaluated. The developed AIMD model provides a useful tool for developing antioxidants for generic hydrocarbons.

  7. Fusion at deep subbarrier energies: potential inversion revisited

    SciTech Connect

    Hagino, K.; Rowley, N.

    2009-03-04

    For a single potential barrier, the barrier penetrability can be inverted based on the WKB approximation to yield the barrier thickness. We apply this method to heavy-ion fusion reactions at energies well below the Coulomb barrier and directly determine the inter-nucleus potential between the colliding nuclei. To this end, we assume that fusion cross sections at deep subbarrier energies are governed by the lowest barrier in the barrier distribution. The inverted inter-nucleus potentials for the {sup 16}O+{sup 144}Sm and {sup 16}O+{sup 208}Pb reactions show that they are much thicker than phenomenological potentials. We discuss a consequence of such thick potential by fitting the inverted potentials with the Bass function.

  8. New Methods for Exploring QM:MM Potential Energy Landscapes

    NASA Astrophysics Data System (ADS)

    Hratchian, Hrant P.

    2010-06-01

    In recent years, the applicability of quantum chemical methods for large system studies has been greatly enhanced by the development of hybrid QM:MM techniques. Despite these advancements, exploring the associated potential energy surfaces continues to present two key challenges. First, the QM energy and derivative evaluations may be too costly for simulations; and second, the system size for many QM:MM cases are too large to effectively store or use second-order information, an approach often used in QM studies to allow for larger integration steps and fewer QM evaluations of the potential energy surface. Our most recent work is focused on overcoming both computational bottlenecks. Using surface fitting models together with direct Hessian-vector and diagonalization algorithms, we are developing models that can accurately and efficiently explore QM:MM potential energy landscapes for very large systems. Our current development status and results from initial applications will be described.

  9. Communication: Separable potential energy surfaces from multiplicative artificial neural networks

    SciTech Connect

    Koch, Werner Zhang, Dong H.

    2014-07-14

    We present a potential energy surface fitting scheme based on multiplicative artificial neural networks. It has the sum of products form required for efficient computation of the dynamics of multidimensional quantum systems with the multi configuration time dependent Hartree method. Moreover, it results in analytic potential energy matrix elements when combined with quantum dynamics methods using Gaussian basis functions, eliminating the need for a local harmonic approximation. Scaling behavior with respect to the complexity of the potential as well as the requested accuracy is discussed.

  10. Framework for State-Level Renewable Energy Market Potential Studies

    SciTech Connect

    Kreycik, C.; Vimmerstedt, L.; Doris, E.

    2010-01-01

    State-level policymakers are relying on estimates of the market potential for renewable energy resources as they set goals and develop policies to accelerate the development of these resources. Therefore, accuracy of such estimates should be understood and possibly improved to appropriately support these decisions. This document provides a framework and next steps for state officials who require estimates of renewable energy market potential. The report gives insight into how to conduct a market potential study, including what supporting data are needed and what types of assumptions need to be made. The report distinguishes between goal-oriented studies and other types of studies, and explains the benefits of each.

  11. Molecular Imaging in Breast Cancer – Potential Future Aspects

    PubMed Central

    Pinker, Katja; Bogner, Wolfgang; Gruber, Stephan; Brader, Peter; Trattnig, Siegfried; Karanikas, Georgios; Helbich, Thomas H.

    2011-01-01

    Summary Molecular imaging aims to visualize and quantify biological, physiological, and pathological processes at cellular and molecular levels. Recently, molecular imaging has been introduced into breast cancer imaging. In this review, we will present a survey of the molecular imaging techniques that are either clinically available or are being introduced into clinical imaging. We will discuss nuclear imaging and multiparametric magnetic resonance imaging as well as the combined application of molecular imaging in the assessment of breast lesions. In addition, we will briefly discuss other evolving molecular imaging techniques, such as phosphorus magnetic resonance spectroscopic imaging and sodium imaging. PMID:21673821

  12. Energy versus free-energy conservation in first-principles molecular dynamics

    NASA Astrophysics Data System (ADS)

    Wentzcovitch, Renata M.; Martins, José Luís; Allen, Philip B.

    1992-05-01

    In applying first-principles molecular dynamics to metals, a fictitious temperature is usefully assigned to the electronic (Fermi-Dirac) occupation functions. This avoids instabilities associated with fluctuations in these occupations during the minimization of the energy density functional. Because these occupations vary with the ionic motion, they give rise to an extra contribution in addition to the usual Hellmann-Feynman forces. If this extra force is omitted, energy is not conserved. We point out, however, that ionic kinetic energy plus electronic free energy is conserved, and argue that this yields a sensible and realistic conservative dynamics.

  13. Potential for energy conservation in the glass industry

    SciTech Connect

    Garrett-Price, B.A.; Fassbender, A.G.; Bruno, G.A.

    1986-06-01

    While the glass industry (flat glass, container glass, pressed and blown glass, and insulation fiber glass) has reduced its specific energy use (Btu/ton) by almost 30% since 1972, significant potential for further reduction still remains. State-of-the-art technologies are available which could lead to incremental improvements in glass industry energy productivity; however, these technologies must compete for capital with projects undertaken for other reasons (e.g., capacity expansion, equipment rebuild, labor cost reduction, product quality improvement, or compliance with environmental, health or safety regulations). Narrowing profit margins in the large tonnage segments of the glass industry in recent years and the fact that energy costs represent less than 25% of the value added in glass manufacture have combined to impede the widespread adoption of many state-of-the-art conservation technologies. Savings in energy costs alone have not provided the incentive to justify the capital expenditures required to realize the energy savings. Beyond implementation of state-of-the-art technologies, significant potential energy savings could accrue from advanced technologies which represent a radical departure from current glass making technology. Long-term research and development (R and D) programs, which address the technical and economic barriers associated with advanced, energy-conserving technologies, offer the opportunity to realize this energy-saving potential.

  14. Molecular dynamics algorithm enforcing energy conservation for microcanonical simulations.

    PubMed

    Salueña, Clara; Avalos, Josep Bonet

    2014-05-01

    A reversible algorithm [enforced energy conservation (EEC)] that enforces total energy conservation for microcanonical simulations is presented. The key point is the introduction of the discrete-gradient method to define the forces from the conservative potentials, instead of the direct use of the force field at the actual position of the particle. We have studied the performance and accuracy of the EEC in two cases, namely Lennard-Jones fluid and a simple electrolyte model. Truncated potentials that usually induce inaccuracies in energy conservation are used. In particular, the reaction field approach is used in the latter. The EEC is able to preserve energy conservation for a long time, and, in addition, it performs better than the Verlet algorithm for these kinds of simulations.

  15. Monte Carlo simulation of energy deposition by low-energy electrons in molecular hydrogen

    NASA Technical Reports Server (NTRS)

    Heaps, M. G.; Furman, D. R.; Green, A. E. S.

    1975-01-01

    A set of detailed atomic cross sections has been used to obtain the spatial deposition of energy by 1-20-eV electrons in molecular hydrogen by a Monte Carlo simulation of the actual trajectories. The energy deposition curve (energy per distance traversed) is quite peaked in the forward direction about the entry point for electrons with energies above the threshold of the electronic states, but the peak decreases and broadens noticeably as the electron energy decreases below 10 eV (threshold for the lowest excitable electronic state of H2). The curve also assumes a very symmetrical shape for energies below 10 eV, indicating the increasing importance of elastic collisions in determining the shape of the curve, although not the mode of energy deposition.

  16. Effect of Strain Field on Threshold Displacement Energy of Tungsten Studied by Molecular Dynamics Simulation

    SciTech Connect

    Wang, Dong; Gao, Ning; Setyawan, W.; Kurtz, R. J.; Wang, Zhi-Guang; Gao, Xing; He, Wen-Hao; Pang, Li-Long

    2016-09-01

    The influence of strain field on defect formation energy and threshold displacement energy (Ed) in body-centered cubic (BCC) tungsten (W) has been studied with molecular dynamics simulations. Two different W potentials (Fikar and Juslin) were compared and the results indicate that the connection distance and selected function linking the short-range and long-range portions of the potentials affects the threshold displacement energy and its direction-specific values. The minimum Ed direction calculated with the Fikar-potential is <100> and with the Juslin-potential is <111>. Nevertheless, the most stable self-interstitial configuration is found to be a <111>-crowdion for both potentials. This stable configuration does not change with applied strain. Varying the strain from compression to tension increases the vacancy formation energy but decreases the self-interstitial formation energy. The formation energy of a self-interstitial changes more significantly than a vacancy such that Ed decreases with applied hydrostatic strain from compression to tension.

  17. Energy life cycle assessment of rice straw bio-energy derived from potential gasification technologies.

    PubMed

    Shie, Je-Lueng; Chang, Ching-Yuan; Chen, Ci-Syuan; Shaw, Dai-Gee; Chen, Yi-Hung; Kuan, Wen-Hui; Ma, Hsiao-Kan

    2011-06-01

    To be a viable alternative, a biofuel should provide a net energy gain and be capable of being produced in large quantities without reducing food supplies. Amounts of agricultural waste are produced and require treatment, with rice straw contributing the greatest source of such potential bio-fuel in Taiwan. Through life-cycle accounting, several energy indicators and four potential gasification technologies (PGT) were evaluated. The input energy steps for the energy life cycle assessment (ELCA) include collection, generator, torrefaction, crushing, briquetting, transportation, energy production, condensation, air pollution control and distribution of biofuels to the point of end use. Every PGT has a positive energy benefit. The input of energy required for the transportation and pre-treatment are major steps in the ELCA. On-site briquetting of refused-derived fuel (RDF) provides an alternative means of reducing transportation energy requirements. Bio-energy sources, such as waste rice straw, provide an ideal material for the bio-fuel plant.

  18. Designing molecular complexes using free-energy derivatives from liquid-state integral equation theory

    NASA Astrophysics Data System (ADS)

    Mrugalla, Florian; Kast, Stefan M.

    2016-09-01

    Complex formation between molecules in solution is the key process by which molecular interactions are translated into functional systems. These processes are governed by the binding or free energy of association which depends on both direct molecular interactions and the solvation contribution. A design goal frequently addressed in pharmaceutical sciences is the optimization of chemical properties of the complex partners in the sense of minimizing their binding free energy with respect to a change in chemical structure. Here, we demonstrate that liquid-state theory in the form of the solute-solute equation of the reference interaction site model provides all necessary information for such a task with high efficiency. In particular, computing derivatives of the potential of mean force (PMF), which defines the free-energy surface of complex formation, with respect to potential parameters can be viewed as a means to define a direction in chemical space toward better binders. We illustrate the methodology in the benchmark case of alkali ion binding to the crown ether 18-crown-6 in aqueous solution. In order to examine the validity of the underlying solute-solute theory, we first compare PMFs computed by different approaches, including explicit free-energy molecular dynamics simulations as a reference. Predictions of an optimally binding ion radius based on free-energy derivatives are then shown to yield consistent results for different ion parameter sets and to compare well with earlier, orders-of-magnitude more costly explicit simulation results. This proof-of-principle study, therefore, demonstrates the potential of liquid-state theory for molecular design problems.

  19. Designing molecular complexes using free-energy derivatives from liquid-state integral equation theory.

    PubMed

    Mrugalla, Florian; Kast, Stefan M

    2016-09-01

    Complex formation between molecules in solution is the key process by which molecular interactions are translated into functional systems. These processes are governed by the binding or free energy of association which depends on both direct molecular interactions and the solvation contribution. A design goal frequently addressed in pharmaceutical sciences is the optimization of chemical properties of the complex partners in the sense of minimizing their binding free energy with respect to a change in chemical structure. Here, we demonstrate that liquid-state theory in the form of the solute-solute equation of the reference interaction site model provides all necessary information for such a task with high efficiency. In particular, computing derivatives of the potential of mean force (PMF), which defines the free-energy surface of complex formation, with respect to potential parameters can be viewed as a means to define a direction in chemical space toward better binders. We illustrate the methodology in the benchmark case of alkali ion binding to the crown ether 18-crown-6 in aqueous solution. In order to examine the validity of the underlying solute-solute theory, we first compare PMFs computed by different approaches, including explicit free-energy molecular dynamics simulations as a reference. Predictions of an optimally binding ion radius based on free-energy derivatives are then shown to yield consistent results for different ion parameter sets and to compare well with earlier, orders-of-magnitude more costly explicit simulation results. This proof-of-principle study, therefore, demonstrates the potential of liquid-state theory for molecular design problems.

  20. Representing potential energy surfaces by high-dimensional neural network potentials.

    PubMed

    Behler, J

    2014-05-07

    The development of interatomic potentials employing artificial neural networks has seen tremendous progress in recent years. While until recently the applicability of neural network potentials (NNPs) has been restricted to low-dimensional systems, this limitation has now been overcome and high-dimensional NNPs can be used in large-scale molecular dynamics simulations of thousands of atoms. NNPs are constructed by adjusting a set of parameters using data from electronic structure calculations, and in many cases energies and forces can be obtained with very high accuracy. Therefore, NNP-based simulation results are often very close to those gained by a direct application of first-principles methods. In this review, the basic methodology of high-dimensional NNPs will be presented with a special focus on the scope and the remaining limitations of this approach. The development of NNPs requires substantial computational effort as typically thousands of reference calculations are required. Still, if the problem to be studied involves very large systems or long simulation times this overhead is regained quickly. Further, the method is still limited to systems containing about three or four chemical elements due to the rapidly increasing complexity of the configuration space, although many atoms of each species can be present. Due to the ability of NNPs to describe even extremely complex atomic configurations with excellent accuracy irrespective of the nature of the atomic interactions, they represent a general and therefore widely applicable technique, e.g. for addressing problems in materials science, for investigating properties of interfaces, and for studying solvation processes.

  1. Technical Potential of Solar Energy to Address Energy Poverty and Avoid GHG Emissions in Africa

    SciTech Connect

    Cowlin, S. C.; Heimiller, D.; Bilello, D.; Renne, D.

    2008-01-01

    This analysis explores the technical potential of photovoltaics (PV) or concentrating solar power (CSP) to address energy poverty in Africa through a geographic information system (GIS) screening of solar resource data developed by the U.S. Department of Energy's National Renewable Energy Laboratory (NREL).

  2. Selective excitation, relaxation, and energy channeling in molecular systems

    SciTech Connect

    Rhodes, W.C.

    1993-08-01

    Research involves theoretical studies of response, relaxation, and correlated motion in time-dependent behavior of large molecular systems ranging from polyatomic molecules to protein molecules in their natural environment. Underlying theme is subsystem modulation dynamics. Main idea is that quantum mechanical correlations between components of a system develop with time, playing a major role in determining the balance between coherent and dissipative forces. Central theme is interplay of coherence and dissipation in determining the nature of dynamic structuring and energy flow in molecular transformation mechanisms. Subsystem equations of motion are being developed to show how nonlinear, dissipative dynamics of a particular subsystem arise from correlated interactions with the rest of the system (substituent groups, solvent, lattice modes, etc.); one consequence is resonance structures and networks. Quantum dynamics and thermodynamics are being applied to understand control and energy transfer mechanisms in biological functions of protein molecules; these mechanisms are both global and local. Besides the above theory, the research deals with phenomenological aspects of molecular systems.

  3. Ab Initio Potential Energy Surface for H-H2

    NASA Technical Reports Server (NTRS)

    Patridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene

    1993-01-01

    Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- 3 micro E(h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces (25-70 kcal/mol above the H-H2 asymptote) at small interatomic separations; the Boothroyd, Keogh, Martin, and Peterson (BKMP) potential energy surface is found to agree with results of the present calculations within the expected uncertainty (+/- 1 kcal/mol) of the fit. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(0)) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.

  4. Wind energy potential analysis in Al-Fattaih-Darnah

    NASA Astrophysics Data System (ADS)

    Tjahjana, Dominicus Danardono Dwi Prija; Salem, Abdelkarim Ali; Himawanto, Dwi Aries

    2016-03-01

    In this paper the wind energy potential in Al-Fattaih-Darnah, Libya, had been studied. Wind energy is very attractive because it can provide a clean and renewable energy. Due mostly to the uncertainty caused by the chaotic characteristics of wind near the earth's surface, wind energy characteristic need to be investigated carefully in order to get consistent power generation. This investigation was based on one year wind data measured in 2003. As a result of the analysis, wind speed profile and wind energy potential have been developed. The wind energy potential of the location is looked very promising to generate electricity. The annual wind speed of the site is 8.21 m/s and the wind speed carrying maximum energy is 7.97 m/s. The annual power density of the site is classified into class 3. The Polaris P50-500 wind turbine can produce 768.39 M Wh/year and has capacity factor of 17.54%.

  5. Warm body temperature facilitates energy efficient cortical action potentials.

    PubMed

    Yu, Yuguo; Hill, Adam P; McCormick, David A

    2012-01-01

    The energy efficiency of neural signal transmission is important not only as a limiting factor in brain architecture, but it also influences the interpretation of functional brain imaging signals. Action potential generation in mammalian, versus invertebrate, axons is remarkably energy efficient. Here we demonstrate that this increase in energy efficiency is due largely to a warmer body temperature. Increases in temperature result in an exponential increase in energy efficiency for single action potentials by increasing the rate of Na(+) channel inactivation, resulting in a marked reduction in overlap of the inward Na(+), and outward K(+), currents and a shortening of action potential duration. This increase in single spike efficiency is, however, counterbalanced by a temperature-dependent decrease in the amplitude and duration of the spike afterhyperpolarization, resulting in a nonlinear increase in the spike firing rate, particularly at temperatures above approximately 35°C. Interestingly, the total energy cost, as measured by the multiplication of total Na(+) entry per spike and average firing rate in response to a constant input, reaches a global minimum between 37-42°C. Our results indicate that increases in temperature result in an unexpected increase in energy efficiency, especially near normal body temperature, thus allowing the brain to utilize an energy efficient neural code.

  6. Bound state solutions of the Schrödinger equation for modified Kratzer's molecular potential

    NASA Astrophysics Data System (ADS)

    Berkdemir, Cüneyt; Berkdemir, Ayşe; Han, Jiaguang

    2006-01-01

    We present the arbitrary angular momentum solutions of the Schrödinger equation for a diatomic molecule with the modified Kratzer potential De[( r - re)/ r] 2. The bound state energy eigenvalues and the corresponding eigenfunctions are obtained by the use of the Nikiforov-Uvarov (NU) method which is related to the solutions in terms of Jacobi polynomials. The bound states are calculated for various values of ℓ with n ⩽ 5 and applied to several diatomic molecules. All of these calculations present an effective and methodological procedure under the NU method to investigate the Kratzer's molecular systems.

  7. RKRV potential energy curves and dissociation energies of NH and PH

    NASA Astrophysics Data System (ADS)

    Reddy, R. R.; Viswanath, R.

    1989-05-01

    The turning points of the potential energy curves for the ground states of NH and PH molecules were calculated using the approach of Rydberg-Klein-Rees modified by Vanderslice et al. (1960), together with the energy values obtained from the Lippincott potential function. These values were compared with those obtained by Jarmain (1960). The values of the dissociation energies of the NH and PH were estimated to be about 3.45 and 3.16, respectively.

  8. Solubility curves and nucleation rates from molecular dynamics for polymorph prediction - moving beyond lattice energy minimization.

    PubMed

    Parks, Conor; Koswara, Andy; DeVilbiss, Frank; Tung, Hsien-Hsin; Nere, Nandkishor K; Bordawekar, Shailendra; Nagy, Zoltan K; Ramkrishna, Doraiswami

    2017-02-15

    Current polymorph prediction methods, known as lattice energy minimization, seek to determine the crystal lattice with the lowest potential energy, rendering it unable to predict solvent dependent metastable form crystallization. Facilitated by embarrassingly parallel, multiple replica, large-scale molecular dynamics simulations, we report on a new method concerned with predicting crystal structures using the kinetics and solubility of the low energy polymorphs predicted by lattice energy minimization. The proposed molecular dynamics simulation methodology provides several new predictions to the field of crystallization. (1) The methodology is shown to correctly predict the kinetic preference for β-glycine nucleation in water relative to α- and γ-glycine. (2) Analysis of nanocrystal melting temperatures show γ- nanocrystals have melting temperatures up to 20 K lower than either α- or β-glycine. This provides a striking explanation of how an energetically unstable classical nucleation theory (CNT) transition state complex leads to kinetic inaccessibility of γ-glycine in water, despite being the thermodynamically preferred polymorph predicted by lattice energy minimization. (3) The methodology also predicts polymorph-specific solubility curves, where the α-glycine solubility curve is reproduced to within 19% error, over a 45 K temperature range, using nothing but atomistic-level information provided from nucleation simulations. (4) Finally, the methodology produces the correct solubility ranking of β- > α-glycine. In this work, we demonstrate how the methodology supplements lattice energy minimization with molecular dynamics nucleation simulations to give the correct polymorph prediction, at different length scales, when lattice energy minimization alone would incorrectly predict the formation of γ-glycine in water from the ranking of lattice energies. Thus, lattice energy minimization optimization algorithms are supplemented with the necessary solvent

  9. Molecular ion sources for low energy semiconductor ion implantation (invited)

    SciTech Connect

    Hershcovitch, A.; Gushenets, V. I.; Bugaev, A. S.; Oks, E. M.; Vizir, A.; Yushkov, G. Yu.; Seleznev, D. N.; Kulevoy, T. V.; Kozlov, A.; Kropachev, G. N.; Kuibeda, R. P.; Minaev, S.; Dugin, S.; Alexeyenko, O.

    2016-02-15

    Smaller semiconductors require shallow, low energy ion implantation, resulting space charge effects, which reduced beam currents and production rates. To increase production rates, molecular ions are used. Boron and phosphorous (or arsenic) implantation is needed for P-type and N-type semiconductors, respectively. Carborane, which is the most stable molecular boron ion leaves unacceptable carbon residue on extraction grids. A self-cleaning carborane acid compound (C{sub 4}H{sub 12}B{sub 10}O{sub 4}) was synthesized and utilized in the ITEP Bernas ion source resulting in large carborane ion output, without carbon residue. Pure gaseous processes are desired to enable rapid switch among ion species. Molecular phosphorous was generated by introducing phosphine in dissociators via 4PH{sub 3} = P{sub 4} + 6H{sub 2}; generated molecular phosphorous in a pure gaseous process was then injected into the HCEI Calutron-Bernas ion source, from which P{sub 4}{sup +} ion beams were extracted. Results from devices and some additional concepts are described.

  10. Polarizable interaction potential for water from coupled cluster calculations. I. Analysis of dimer 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.

  11. Low-energy K- optical potentials: deep or shallow?

    NASA Astrophysics Data System (ADS)

    Cieplý, A.; Friedman, E.; Gal, A.; Mareš, J.

    2001-12-01

    The K- optical potential in the nuclear medium is evaluated self consistently from a free-space K-Nt matrix constructed within a coupled-channel chiral approach. The fit of model parameters gives a good description of the low-energy data plus the available K- atomic data. The resulting optical potential is relatively `shallow' in contradiction to the potentials obtained from phenomenological analysis. The calculated (Kstop-,π) hypernuclear production rates are very sensitive to the details of kaonic bound state wave function. The (Kstop-,π) reaction could thus serve as a suitable tool to distinguish between shallow and deep K- optical potentials.

  12. Electric potential invariants and ions-in-molecules effective potentials for molecular Rydberg states

    NASA Astrophysics Data System (ADS)

    Coy, Stephen L.; Grimes, David D.; Zhou, Yan; Field, Robert W.; Wong, Bryan M.

    2016-12-01

    The dependence of multipole moments and polarizabilities on external fields appears in many applications including biomolecular molecular mechanics, optical non-linearity, nanomaterial calculations, and the perturbation of spectroscopic signatures in atomic clocks. Over a wide range of distances, distributed multipole and polarizability potentials can be applied to obtain the variation of atom-centered atoms-in-molecules electric properties like bonding-quenched polarizability. For cylindrically symmetric charge distributions, we examine single-center and atom-centered effective polarization potentials in a non-relativistic approximation for Rydberg states. For ions, the multipole expansion is strongly origin-dependent, but we note that origin-independent invariants can be defined. The several families of invariants correspond to optimized representations differing by origin and number of terms. Among them, a representation at the center of dipole polarizability optimizes the accuracy of the potential with terms through 1/r4. We formulate the single-center expansion in terms of polarization-modified effective multipole moments, defining a form related to the source-multipole expansion of Brink and Satchler. Atom-centered potentials are an origin independent alternative but are limited both by the properties allowed at each center and by the neglected effects like bond polarizability and charge flow. To enable comparisons between single-center effective potentials in Cartesian or spherical form and two-center effective potentials with differing levels of mutual induction between atomic centers, we give analytical expressions for the bond-length and origin-dependence of multipole and polarizability terms projected in the multipole and polarizability expansion of Buckingham. The atom-centered potentials can then be used with experimental data and ab initio calculations to estimate atoms-in-molecules properties. Some results are given for BaF+ and HF showing the

  13. Electric potential invariants and ions-in-molecules effective potentials for molecular Rydberg states.

    PubMed

    Coy, Stephen L; Grimes, David D; Zhou, Yan; Field, Robert W; Wong, Bryan M

    2016-12-21

    The dependence of multipole moments and polarizabilities on external fields appears in many applications including biomolecular molecular mechanics, optical non-linearity, nanomaterial calculations, and the perturbation of spectroscopic signatures in atomic clocks. Over a wide range of distances, distributed multipole and polarizability potentials can be applied to obtain the variation of atom-centered atoms-in-molecules electric properties like bonding-quenched polarizability. For cylindrically symmetric charge distributions, we examine single-center and atom-centered effective polarization potentials in a non-relativistic approximation for Rydberg states. For ions, the multipole expansion is strongly origin-dependent, but we note that origin-independent invariants can be defined. The several families of invariants correspond to optimized representations differing by origin and number of terms. Among them, a representation at the center of dipole polarizability optimizes the accuracy of the potential with terms through 1/r(4). We formulate the single-center expansion in terms of polarization-modified effective multipole moments, defining a form related to the source-multipole expansion of Brink and Satchler. Atom-centered potentials are an origin independent alternative but are limited both by the properties allowed at each center and by the neglected effects like bond polarizability and charge flow. To enable comparisons between single-center effective potentials in Cartesian or spherical form and two-center effective potentials with differing levels of mutual induction between atomic centers, we give analytical expressions for the bond-length and origin-dependence of multipole and polarizability terms projected in the multipole and polarizability expansion of Buckingham. The atom-centered potentials can then be used with experimental data and ab initio calculations to estimate atoms-in-molecules properties. Some results are given for BaF(+) and HF showing the

  14. Molecular dynamics study on microstructures of diblock copolymer melts with soft potential and potential recovery

    NASA Astrophysics Data System (ADS)

    Ryu, Ji Ho; Wee, Han Sol; Lee, Won Bo

    2016-09-01

    Various microstructures are obtained through the self-assembly of block copolymers on the basis of the compositional fractions and repulsive interactions among different types of beads. The inhomogeneity of block copolymers can be studied by molecular dynamics. However, preparing initial configurations of various self-assembled structures directly by molecular dynamics requires extensive computational time because of topological constraints. Furthermore, manual preparation often becomes a complicated and time-consuming procedure even for the simplest structures, such as a lamellar phase, not to mention three-dimensional bicontinuous cubic phases such as a gyroid phase. In this paper, this difficulty is overcome by using a soft potential, which allows the system to reach a self-assembled state quickly (within 3 τd ). Once a self-assembled microstructure is obtained, the normal potential is restored and equilibration steps are performed to enable the calculation of various properties of the microstructures. Various equilibrated phase structures—including S (spherical), H (hexagonal), G (gyroid), and L (lamellar) phases—are obtained by this approach. To verify our method, static and dynamic properties of the lamellar phase are examined and compared with previous results.

  15. Photochemical energy conversion: from molecular dyads to solar cells.

    PubMed

    Durrant, James R; Haque, Saif A; Palomares, Emilio

    2006-08-21

    Photochemical approaches to solar energy conversion are currently making rapid progress, increasing not only academic but also commercial interest in molecular-based photovoltaic solar cells. This progress has been achieved not only by increased understanding of the physics and physical chemistry of device function but also through advances in chemical and materials synthesis and processing, which now allows the design and fabrication of increasingly sophisticated device structures organised on the nanometer length scale. In this feature article, we review some progress in this field, focusing in particular upon the electron-transfer dynamics which underlie the function of dye-sensitised, nanocrystalline solar cells. The article starts by building upon the parallels between the function of such devices and the function of simple donor/acceptor molecular systems in solution. We then go on to discuss the optimisation of device function, and in particular the use of self-assembly-based strategies to control interfacial electron-transfer kinetics.

  16. Renewable energy technologies adoption in Kazakhstan: potentials, barriers and solutions

    NASA Astrophysics Data System (ADS)

    Karatayev, Marat; Marazza, Diego; Contin, Andrea

    2015-04-01

    The growth in environmental pollution alongside an increasing demand for electricity in Kazakhstan calls for a higher level of renewable energy penetration into national power systems. Kazakhstan has great potential for renewable energies from wind, solar, hydro and biomass resources that can be exploited for electricity production. In 2013, the Kazakhstani Ministry of Energy initiated a new power development plan, which aims to bring the share of renewable energy to 3% by 2020 rising to 30% by 2030 and 50% by 2050. The current contribution of renewable energy resources in the national electricity mix, however, is less than 1%. As a developing country, Kazakhstan has faced a number of barriers to increase renewable energy use, which have to be analysed and translated into a comprehensive renewable energy policy framework. This study presents an overview of the current conditions of renewable energy development in Kazakhstan. Secondly, it identifies and describes the main barriers that prevent diffusion of renewable energy technologies in Kazakhstan. Finally, the paper provides solutions to overcome specific barriers in order to successfully develop a renewable energy technology sector in Kazakhstan.

  17. Electronic excitation of molecular hydrogen by low-energy electrons

    NASA Astrophysics Data System (ADS)

    Hargreaves, Leigh

    2016-09-01

    Molecular hydrogen is the most abundant element in the universe, particularly in interstellar plasmas such as atmospheres of gas giant planets and stars. Electron collision data for hydrogen is critical to interpreting the spectroscopy of interstellar objects, as well as being of applied value for modelling technological plasmas. Hydrogen is also fundamentally interesting, as while highly accurate wave functions for this simple molecule are available, providing an accurate, ab initio, treatment the collision dynamics has proven challenging, on account of the need to have a complete description of channel coupling and polarization effects. To date, no single theoretical approach has been able to replicate experimental results across all transitions and incident energies, while the experimental database that is available is far from complete and not all available measurements are in satisfactory agreement. In this talk, we present differential and integral cross section measurements for electronic excitation cross sections for molecular hydrogen by low-energy electron impact. The data were measured at incident energies below 20eV, using a well-tested crossed beam apparatus and employing a moveable gas source approach to ensure that background contributions to the scattering are accurately accounted for. These measurements are compared with new theoretical results employing the convergent close coupling approach.

  18. Calculating Free Energies Using Scaled-Force Molecular Dynamics Algorithm

    NASA Technical Reports Server (NTRS)

    Darve, Eric; Wilson, Micahel A.; Pohorille, Andrew

    2000-01-01

    One common objective of molecular simulations in chemistry and biology is to calculate the free energy difference between different states of the system of interest. Examples of problems that have such an objective are calculations of receptor-ligand or protein-drug interactions, associations of molecules in response to hydrophobic, and electrostatic interactions or partition of molecules between immiscible liquids. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), 'native' state. Perhaps the best example of such a problem is folding of proteins or short RNA molecules. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to 'quasi non-ergodicity', whereby a part of phase space is inaccessible on timescales of the simulation. A host of strategies has been developed to improve efficiency of sampling the phase space. For example, some Monte Carlo techniques involve large steps which move the system between low-energy regions in phase space without the need for sampling the configurations corresponding to energy barriers (J-walking). Most strategies, however, rely on modifying probabilities of sampling low and high-energy regions in phase space such that transitions between states of interest are encouraged. Perhaps the simplest implementation of this strategy is to increase the temperature of the system. This approach was successfully used to identify denaturation pathways in several proteins, but it is clearly not applicable to protein folding. It is also not a successful method for determining free energy differences. Finally, the approach is likely to fail for systems with co-existing phases, such as water-membrane systems, because it may lead to spontaneous

  19. Saturation wind power potential and its implications for wind energy

    PubMed Central

    Jacobson, Mark Z.; Archer, Cristina L.

    2012-01-01

    Wind turbines convert kinetic to electrical energy, which returns to the atmosphere as heat to regenerate some potential and kinetic energy. As the number of wind turbines increases over large geographic regions, power extraction first increases linearly, but then converges to a saturation potential not identified previously from physical principles or turbine properties. These saturation potentials are >250 terawatts (TW) at 100 m globally, approximately 80 TW at 100 m over land plus coastal ocean outside Antarctica, and approximately 380 TW at 10 km in the jet streams. Thus, there is no fundamental barrier to obtaining half (approximately 5.75 TW) or several times the world’s all-purpose power from wind in a 2030 clean-energy economy. PMID:23019353

  20. Saturation wind power potential and its implications for wind energy.

    PubMed

    Jacobson, Mark Z; Archer, Cristina L

    2012-09-25

    Wind turbines convert kinetic to electrical energy, which returns to the atmosphere as heat to regenerate some potential and kinetic energy. As the number of wind turbines increases over large geographic regions, power extraction first increases linearly, but then converges to a saturation potential not identified previously from physical principles or turbine properties. These saturation potentials are >250 terawatts (TW) at 100 m globally, approximately 80 TW at 100 m over land plus coastal ocean outside Antarctica, and approximately 380 TW at 10 km in the jet streams. Thus, there is no fundamental barrier to obtaining half (approximately 5.75 TW) or several times the world's all-purpose power from wind in a 2030 clean-energy economy.

  1. Collisionless Plasma Modeling in an Arbitrary Potential Energy Distribution

    NASA Technical Reports Server (NTRS)

    Liemohn, M. W.; Khazanov, G. V.

    1997-01-01

    A new technique for calculating a collisionless plasma along a field line is presented. The primary feature of the new model is that it can handle an arbitrary (including nonmonotonic) potential energy distribution. This was one of the limiting constraints on the existing models in this class, and these constraints are generalized for an arbitrary potential energy composition. The formulation for relating current density to the field-aligned potential as well as formulas for density, temperature and energy flux calculations are presented for several distribution functions, ranging from a bi-Lorentzian with a loss cone to an isotropic Maxwellian. A comparison of these results with previous models shows that the formulation reduces.to the earlier models under similar assumptions.

  2. Molecular Spectrum Capture by Tuning the Chemical Potential of Graphene

    PubMed Central

    Cheng, Yue; Yang, Jingjing; Lu, Qiannan; Tang, Hao; Huang, Ming

    2016-01-01

    Due to its adjustable electronic properties and effective excitation of surface plasmons in the infrared and terahertz frequency range, research on graphene has attracted a great deal of attention. Here, we demonstrate that plasmon modes in graphene-coated dielectric nanowire (GNW) waveguides can be excited by a monolayer graphene ribbon. What is more the transverse resonant frequency spectrum of the GNW can be flexibly tuned by adjusting the chemical potential of graphene, and amplitude of the resonance peak varies linearly with the imaginary part of the analyte permittivity. As a consequence, the GNW works as a probe for capturing the molecular spectrum. Broadband sensing of toluene, ethanol and sulfurous anhydride thin layers is demonstrated by calculating the changes in spectral intensity of the propagating mode and the results show that the intensity spectra correspond exactly to the infrared spectra of these molecules. This may open an effective avenue to design sensors for detecting nanometric-size molecules in the terahertz and infrared regimes. PMID:27240372

  3. Luminescent chiral lanthanide(III) complexes as potential molecular probes

    PubMed Central

    Muller, Gilles

    2009-01-01

    This perspective gives an introduction into the design of luminescent lanthanide(III)-containing complexes possessing chiral properties and used to probe biological materials. The first part briefly describes general principles, focusing on the optical aspect (i.e. lanthanide luminescence, sensitization processes) of the most emissive trivalent lanthanide ions, europium and terbium, incorporated into molecular luminescent edifices. This is followed by a short discussion on the importance of chirality in the biological and pharmaceutical fields. The second part is devoted to the assessment of the chiroptical spectroscopic tools available (typically circular dichroism and circularly polarized luminescence) and the strategies used to introduce a chiral feature into luminescent lanthanide(III) complexes (chiral structure resulting from a chiral arrangement of the ligand molecules surrounding the luminescent center or presence of chiral centers in the ligand molecules). Finally, the last part illustrates these fundamental principles with recent selected examples of such chiral luminescent lanthanide-based compounds used as potential probes of biomolecular substrates. PMID:19885510

  4. Potential structural material problems in a hydrogen energy system

    NASA Technical Reports Server (NTRS)

    Gray, H. R.; Nelson, H. G.; Johnson, R. E.; Mcpherson, B.; Howard, F. S.; Swisher, J. H.

    1975-01-01

    Potential structural material problems that may be encountered in the three components of a hydrogen energy system - production, transmission/storage, and utilization - were identified. Hydrogen embrittlement, corrosion, oxidation, and erosion may occur during the production of hydrogen. Hydrogen embrittlement is of major concern during both transmission and utilization of hydrogen. Specific materials research and development programs necessary to support a hydrogen energy system are described.

  5. Reaction Path Optimization with Holonomic Constraints and Kinetic Energy Potentials

    SciTech Connect

    Brokaw, Jason B.; Haas, Kevin R.; Chu, Jhih-wei

    2009-08-11

    Two methods are developed to enhance the stability, efficiency, and robustness of reaction path optimization using a chain of replicas. First, distances between replicas are kept equal during path optimization via holonomic constraints. Finding a reaction path is, thus, transformed into a constrained optimization problem. This approach avoids force projections for finding minimum energy paths (MEPs), and fast-converging schemes such as quasi-Newton methods can be readily applied. Second, we define a new objective function - the total Hamiltonian - for reaction path optimization, by combining the kinetic energy potential of each replica with its potential energy function. Minimizing the total Hamiltonian of a chain determines a minimum Hamiltonian path (MHP). If the distances between replicas are kept equal and a consistent force constant is used, then the kinetic energy potentials of all replicas have the same value. The MHP in this case is the most probable isokinetic path. Our results indicate that low-temperature kinetic energy potentials (<5 K) can be used to prevent the development of kinks during path optimization and can significantly reduce the required steps of minimization by 2-3 times without causing noticeable differences between a MHP and MEP. These methods are applied to three test cases, the C₇eq-to-Cax isomerization of an alanine dipeptide, the ⁴C₁- to-¹C₄ transition of an α-D-glucopyranose, and the helix-to-sheet transition of a GNNQQNY heptapeptide. By applying the methods developed in this work, convergence of reaction path optimization can be achieved for these complex transitions, involving full atomic details and a large number of replicas (>100). For the case of helix-to-sheet transition, we identify pathways whose energy barriers are consistent with experimental measurements. Further, we develop a method based on the work energy theorem to quantify the accuracy of reaction paths and to determine whether the atoms used to define a

  6. Reaction Path Optimization with Holonomic Constraints and Kinetic Energy Potentials.

    PubMed

    Brokaw, Jason B; Haas, Kevin R; Chu, Jhih-Wei

    2009-08-11

    Two methods are developed to enhance the stability, efficiency, and robustness of reaction path optimization using a chain of replicas. First, distances between replicas are kept equal during path optimization via holonomic constraints. Finding a reaction path is, thus, transformed into a constrained optimization problem. This approach avoids force projections for finding minimum energy paths (MEPs), and fast-converging schemes such as quasi-Newton methods can be readily applied. Second, we define a new objective function - the total Hamiltonian - for reaction path optimization, by combining the kinetic energy potential of each replica with its potential energy function. Minimizing the total Hamiltonian of a chain determines a minimum Hamiltonian path (MHP). If the distances between replicas are kept equal and a consistent force constant is used, then the kinetic energy potentials of all replicas have the same value. The MHP in this case is the most probable isokinetic path. Our results indicate that low-temperature kinetic energy potentials (<5 K) can be used to prevent the development of kinks during path optimization and can significantly reduce the required steps of minimization by 2-3 times without causing noticeable differences between a MHP and MEP. These methods are applied to three test cases, the C7eq-to-Cax isomerization of an alanine dipeptide, the (4)C1-to-(1)C4 transition of an α-d-glucopyranose, and the helix-to-sheet transition of a GNNQQNY heptapeptide. By applying the methods developed in this work, convergence of reaction path optimization can be achieved for these complex transitions, involving full atomic details and a large number of replicas (>100). For the case of helix-to-sheet transition, we identify pathways whose energy barriers are consistent with experimental measurements. Further, we develop a method based on the work energy theorem to quantify the accuracy of reaction paths and to determine whether the atoms used to define a path

  7. Reference pressure changes and available potential energy in isobaric coordinates

    NASA Technical Reports Server (NTRS)

    Robertson, F. R.

    1985-01-01

    A formulation of the available potential energy (APE) equation in isobaric coordinates which alleviates the need for computing temporal derivatives of reference pressure and describes how work done relates to changes in the APE of a limited region is presented. The APE budget equation possesses terms analogous to those in Johnson's (1970) isentropic version. It is shown that APE changes result from either mechanical work inside the domain or an exchange of energy via boundary processes with the surrounding environment.

  8. Finding reaction paths using the potential energy as reaction coordinate.

    PubMed

    Aguilar-Mogas, Antoni; Giménez, Xavier; Bofill, Josep Maria

    2008-03-14

    The intrinsic reaction coordinate curve (IRC), normally proposed as a representation of a reaction path, is parametrized as a function of the potential energy rather than the arc-length. This change in the parametrization of the curve implies that the values of the energy of the potential energy surface points, where the IRC curve is located, play the role of reaction coordinate. We use Caratheodory's relation to derive in a rigorous manner the proposed parametrization of the IRC path. Since this Caratheodory's relation is the basis of the theory of calculus of variations, then this fact permits to reformulate the IRC model from this mathematical theory. In this mathematical theory, the character of the variational solution (either maximum or minimum) is given through the Weierstrass E-function. As proposed by Crehuet and Bofill [J. Chem. Phys. 122, 234105 (2005)], we use the minimization of the Weierstrass E-function, as a function of the potential energy, to locate an IRC path between two minima from an arbitrary curve on the potential energy surface, and then join these two minima. We also prove, from the analysis of the Weierstrass E-function, the mathematical bases for the algorithms proposed to locate the IRC path. The proposed algorithm is applied to a set of examples. Finally, the algorithm is used to locate a discontinuous, or broken, IRC path, namely, when the path connects two first order saddle points through a valley-ridged inflection point.

  9. Molecular dynamics simulations for mechanical properties of borophene: parameterization of valence force field model and Stillinger-Weber potential

    PubMed Central

    Zhou, Yu-Ping; Jiang, Jin-Wu

    2017-01-01

    While most existing theoretical studies on the borophene are based on first-principles calculations, the present work presents molecular dynamics simulations for the lattice dynamical and mechanical properties in borophene. The obtained mechanical quantities are in good agreement with previous first-principles calculations. The key ingredients for these molecular dynamics simulations are the two efficient empirical potentials developed in the present work for the interaction of borophene with low-energy triangular structure. The first one is the valence force field model, which is developed with the assistance of the phonon dispersion of borophene. The valence force field model is a linear potential, so it is rather efficient for the calculation of linear quantities in borophene. The second one is the Stillinger-Weber potential, whose parameters are derived based on the valence force field model. The Stillinger-Weber potential is applicable in molecular dynamics simulations of nonlinear physical or mechanical quantities in borophene. PMID:28349983

  10. Calculating vibrational spectra using modified Shepard interpolated potential energy surfaces.

    PubMed

    Evenhuis, Christian R; Manthe, Uwe

    2008-07-14

    A potential energy interpolation approach based on modified Shepard interpolation and specifically designed for calculation of vibrational states is presented. The importance of the choice of coordinates for the rate of convergence is demonstrated. Studying the vibrational states of the water molecule as a test case, a coordinate system comprised of inverse bond distances and trigonometric functions of the bond angle is found to be particularly efficient. Different sampling schemes used to locate the reference points in the modified Shepard interpolation are investigated. A final scheme is recommended, which allows the construction of potential energy surfaces to sub-wave-number accuracy.

  11. Molecular dynamics simulation of vapour-liquid nucleation of water with constant energy

    NASA Astrophysics Data System (ADS)

    Duška, Michal; Němec, Tomáš; Hrubý, Jan; Vinš, Václav; Planková, Barbora

    2015-05-01

    The paper describes molecular dynamics study of nucleation of water in NVE ensemble. The numerical simulation was performed with the DL_POLY. The metastable steam consisting of 10976 water molecules with TIP4P/2005 potential was driven on the desired energy level by a simulation at constant temperature, and then the nucleation at constant energy was studied for several tens of nanoseconds, which was sufficient for clusters to evolve at hundred molecules size. The results were compared with the previously published results and the classical nucleation theory predictions.

  12. Energy savings potential in air conditioners and chiller systems

    SciTech Connect

    Kaya, Durmus; Alidrisi, Hisham

    2014-01-22

    In the current paper we quantified and evaluated the energy saving potential in air conditioners and chiller systems. Here, we also showed how to reduce the cost of air conditioners and chiller systems in existing facilities on the basis of payback periods. Among the measures investigated were: (1) installing higher efficiency air conditioners, (2) installing higher efficiency chillers, (3) duty cycling air conditioning units, and (4) utilizing existing economizers on air conditioning units. For each method, examples were provided from Arizona, USA. In these examples, the amount of saved energy, the financial evaluation of this energy, and the investment cost and pay back periods were calculated.

  13. LHC Physics Potential vs. Energy: Considerations for the 2011 Run

    SciTech Connect

    Quigg, Chris; /Fermilab /CERN

    2011-02-01

    Parton luminosities are convenient for estimating how the physics potential of Large Hadron Collider experiments depends on the energy of the proton beams. I quantify the advantage of increasing the beam energy from 3.5 TeV to 4 TeV. I present parton luminosities, ratios of parton luminosities, and contours of fixed parton luminosity for gg, u {bar d}, qq, and gq interactions over the energy range relevant to the Large Hadron Collider, along with example analyses for specific processes. This note extends the analysis presented in Ref. [1]. Full-size figures are available as pdf files at lutece.fnal.gov/PartonLum11/.

  14. Energy savings potential in air conditioners and chiller systems

    DOE PAGES

    Kaya, Durmus; Alidrisi, Hisham

    2014-01-22

    In the current paper we quantified and evaluated the energy saving potential in air conditioners and chiller systems. Here, we also showed how to reduce the cost of air conditioners and chiller systems in existing facilities on the basis of payback periods. Among the measures investigated were: (1) installing higher efficiency air conditioners, (2) installing higher efficiency chillers, (3) duty cycling air conditioning units, and (4) utilizing existing economizers on air conditioning units. For each method, examples were provided from Arizona, USA. In these examples, the amount of saved energy, the financial evaluation of this energy, and the investment costmore » and pay back periods were calculated.« less

  15. Efficient Radioisotope Energy Transfer by Gold Nanoclusters for Molecular Imaging.

    PubMed

    Volotskova, Olga; Sun, Conroy; Stafford, Jason H; Koh, Ai Leen; Ma, Xiaowei; Cheng, Zhen; Cui, Bianxiao; Pratx, Guillem; Xing, Lei

    2015-08-26

    Beta-emitting isotopes Fluorine-18 and Yttrium-90 are tested for their potential to stimulate gold nanoclusters conjugated with blood serum proteins (AuNCs). AuNCs excited by either medical radioisotope are found to be highly effective ionizing radiation energy transfer mediators, suitable for in vivo optical imaging. AuNCs synthesized with protein templates convert beta-decaying radioisotope energy into tissue-penetrating optical signals between 620 and 800 nm. Optical signals are not detected from AuNCs incubated with Technetium-99m, a pure gamma emitter that is used as a control. Optical emission from AuNCs is not proportional to Cerenkov radiation, indicating that the energy transfer between the radionuclide and AuNC is only partially mediated by Cerenkov photons. A direct Coulombic interaction is proposed as a novel and significant mechanism of energy transfer between decaying radionuclides and AuNCs.

  16. Potentials and policy implications of energy and material efficiency improvement

    SciTech Connect

    Worrell, Ernst; Levine, Mark; Price, Lynn; Martin, Nathan; van den Broek, Richard; Block, Kornelis

    1997-01-01

    There is a growing awareness of the serious problems associated with the provision of sufficient energy to meet human needs and to fuel economic growth world-wide. This has pointed to the need for energy and material efficiency, which would reduce air, water and thermal pollution, as well as waste production. Increasing energy and material efficiency also have the benefits of increased employment, improved balance of imports and exports, increased security of energy supply, and adopting environmentally advantageous energy supply. A large potential exists for energy savings through energy and material efficiency improvements. Technologies are not now, nor will they be, in the foreseeable future, the limiting factors with regard to continuing energy efficiency improvements. There are serious barriers to energy efficiency improvement, including unwillingness to invest, lack of available and accessible information, economic disincentives and organizational barriers. A wide range of policy instruments, as well as innovative approaches have been tried in some countries in order to achieve the desired energy efficiency approaches. These include: regulation and guidelines; economic instruments and incentives; voluntary agreements and actions, information, education and training; and research, development and demonstration. An area that requires particular attention is that of improved international co-operation to develop policy instruments and technologies to meet the needs of developing countries. Material efficiency has not received the attention that it deserves. Consequently, there is a dearth of data on the qualities and quantities for final consumption, thus, making it difficult to formulate policies. Available data, however, suggest that there is a large potential for improved use of many materials in industrialized countries.

  17. Advances in molecular electronics: Synthesis and testing of potential molecular electronic devices

    NASA Astrophysics Data System (ADS)

    Price, David Wilson, Jr.

    New potential molecular electronics devices have been synthesized based on our knowledge of previous systems that have come out of our group. Previous studies and current studies have shown that simple molecular systems demonstrate negative differential resistance (NDR) and memory characteristics. The new systems rely primarily on the redox properties of the compounds to improve upon the solid state properties already observed. Most of these new organic compounds use thiol-based "alligator clips" for attachment to metal surfaces. Some of the compounds, however, contain different "alligator clips," primarily isonitriles, for attachment to metal substrates. It is our hope that these new "alligator clips" will offer lower conductivity barriers (higher current density). Electrochemical tests have been performed in order to evaluate those redox properties and in the hope of using those electrochemical results as a predictive tool to evaluate the usefulness of those compounds. Also, organic structures with polymerizable functionalities have been synthesized in order to cross-link the molecules once they are a part of a self-assembled monolayer (SAM). This has been shown to enable the electrochemical growth of polypyrrole from a SAM in a controllable manner.

  18. The pDynamo Program for Molecular Simulations using Hybrid Quantum Chemical and Molecular Mechanical Potentials.

    PubMed

    Field, Martin J

    2008-07-01

    The pDynamo program has been developed for the simulation of molecular systems using hybrid quantum chemical (QC) and molecular mechanical (MM) potentials. pDynamo is written in a mixture of the computer languages Python and C and is a successor to the previous version of Dynamo, now denoted fDynamo, that was written in Fortran 90 (J. Comput. Chem. 2000, 21, 1088). The current version of Dynamo has a similar range of functionality to the older one but extends it in some significant ways, including the addition of a density functional theory QC capability. This paper gives a general description of pDynamo and outlines some of the advantages and disadvantages that have been encountered in switching computer languages. Some technical aspects of the implementation of pDynamo's algorithms are also discussed and illustrated with the results of example calculations. pDynamo is available on the Web at the address http://www.pdynamo.org and is released under the CeCILL license which is equivalent to the GNU general public license but conforms to the principles of French law.

  19. Global Potential of Energy Efficiency Standards and Labeling Programs

    SciTech Connect

    McNeil, Michael A; McNeil, Michael A.; Letschert, Virginie; de la Rue du Can, Stephane

    2008-06-15

    This report estimates the global potential reductions in greenhouse gas emissions by 2030 for energy efficiency improvements associated with equipment (appliances, lighting, and HVAC) in buildings by means of energy efficiency standards and labels (EES&L). A consensus has emerged among the world's scientists and many corporate and political leaders regarding the need to address the threat of climate change through emissions mitigation and adaptation. A further consensus has emerged that a central component of these strategies must be focused around energy, which is the primary generator of greenhouse gas emissions. Two important questions result from this consensus: 'what kinds of policies encourage the appropriate transformation to energy efficiency' and 'how much impact can these policies have'? This report aims to contribute to the dialogue surrounding these issues by considering the potential impacts of a single policy type, applied on a global scale. The policy addressed in this report is Energy Efficient Standards and Labeling (EES&L) for energy-consuming equipment, which has now been implemented in over 60 countries. Mandatory energy performance standards are important because they contribute positively to a nation's economy and provide relative certainty about the outcome (both timing and magnitudes). Labels also contribute positively to a nation's economy and importantly increase the awareness of the energy-consuming public. Other policies not analyzed here (utility incentives, tax credits) are complimentary to standards and labels and also contribute in significant ways to reducing greenhouse gas emissions. We believe the analysis reported here to be the first systematic attempt to evaluate the potential of savings from EES&L for all countries and for such a large set of products. The goal of the analysis is to provide an assessment that is sufficiently well-quantified and accurate to allow comparison and integration with other strategies under

  20. Bioinspired molecular electrets: bottom-up approach to energy materials and applications

    NASA Astrophysics Data System (ADS)

    Larsen, Jillian M.; Espinoza, Eli M.; Vullev, Valentine I.

    2015-01-01

    The diversity of life on Earth is made possible through an immense variety of proteins that stems from less than a couple of dozen native amino acids. Is it possible to achieve similar engineering freedom and precision to design electronic materials? What if a handful of non-native residues with a wide range of characteristics could be rationally placed in sequences to form organic macromolecules with specifically targeted properties and functionalities? Referred to as molecular electrets, dipolar oligomers and polymers composed of non-native aromatic beta-amino acids, anthranilamides (Aa) provide venues for pursuing such possibilities. The electret molecular dipoles play a crucial role in rectifying charge transfer, e.g., enhancing charge separation and suppressing undesired charge recombination, which is essential for photovoltaics, photocatalysis, and other solar-energy applications. A set of a few Aa residues can serve as building blocks for molecular electrets with widely diverse electronic properties, presenting venues for bottom-up designs. We demonstrate how three substituents and structural permutations within an Aa residue widely alter its reduction potential. Paradigms of diversity in electronic properties, originating from a few changes within a basic molecular structure, illustrate the promising potentials of biological inspiration for energy science and engineering.

  1. Organic surfaces excited by low-energy ions: atomic collisions, molecular desorption and buckminsterfullerenes.

    PubMed

    Delcorte, Arnaud

    2005-10-07

    This article reviews the recent progress in the understanding of kiloelectronvolt particle interactions with organic solids, including atomic displacements in a light organic medium, vibrational excitation and desorption of fragments and entire molecules. This new insight is the result of a combination of theoretical and experimental approaches, essentially molecular dynamics (MD) simulations and secondary ion mass spectrometry (SIMS). Classical MD simulations provide us with a detailed microscopic view of the processes occurring in the bombarded target, from the collision cascade specifics to the scenarios of molecular emission. Time-of-flight SIMS measures the mass and energy distributions of sputtered ionized fragments and molecular species, a precious source of information concerning their formation, desorption, ionization and delayed unimolecular dissociation in the gas phase. The mechanisms of energy transfer and sputtering are compared for bulk molecular solids, organic overlayers on metal and large molecules embedded in a low-molecular weight matrix. These comparisons help understand some of the beneficial effects of metal substrates and matrices for the analysis of molecules by SIMS. In parallel, I briefly describe the distinct ionization channels of molecules sputtered from organic solids and overlayers. The specific processes induced by polyatomic projectile bombardment, especially fullerenes, are discussed on the basis of new measurements and calculations. Finally, the perspective addresses the state-of-the-art and potential developments in the fields of surface modification and analysis of organic materials by kiloelectronvolt ion beams.

  2. Molecular markers: a potential resource for ginger genetic diversity studies.

    PubMed

    Ismail, Nor Asiah; Rafii, M Y; Mahmud, T M M; Hanafi, M M; Miah, Gous

    2016-12-01

    Ginger is an economically important and valuable plant around the world. Ginger is used as a food, spice, condiment, medicine and ornament. There is available information on biochemical aspects of ginger, but few studies have been reported on its molecular aspects. The main objective of this review is to accumulate the available molecular marker information and its application in diverse ginger studies. This review article was prepared by combing material from published articles and our own research. Molecular markers allow the identification and characterization of plant genotypes through direct access to hereditary material. In crop species, molecular markers are applied in different aspects and are useful in breeding programs. In ginger, molecular markers are commonly used to identify genetic variation and classify the relatedness among varieties, accessions, and species. Consequently, it provides important input in determining resourceful management strategies for ginger improvement programs. Alternatively, a molecular marker could function as a harmonizing tool for documenting species. This review highlights the application of molecular markers (isozyme, RAPD, AFLP, SSR, ISSR and others such as RFLP, SCAR, NBS and SNP) in genetic diversity studies of ginger species. Some insights on the advantages of the markers are discussed. The detection of genetic variation among promising cultivars of ginger has significance for ginger improvement programs. This update of recent literature will help researchers and students select the appropriate molecular markers for ginger-related research.

  3. MOLECULAR EPIDEMIOLOGY: POTENTIAL IMPACTS ON THE ASSESSMENT OF PUBLIC HEALTH

    EPA Science Inventory

    Introduction

    The term "molecular epidemiology" has been used to cover a broad range of scientific activities, often without specific reference to epidemiology. In fact, as noted by Foxman and Riley [1],molecular epidemiology has often been described almost exclusively in...

  4. Molecular approaches to improvement of Jatropha curcas Linn. as a sustainable energy crop.

    PubMed

    Sudhakar Johnson, T; Eswaran, Nalini; Sujatha, M

    2011-09-01

    With the increase in crude oil prices, climate change concerns and limited reserves of fossil fuel, attention has been diverted to alternate renewable energy sources such as biofuel and biomass. Among the potential biofuel crops, Jatropha curcas L, a non-domesticated shrub, has been gaining importance as the most promising oilseed, as it does not compete with the edible oil supplies. Economic relevance of J. curcas for biodiesel production has promoted world-wide prospecting of its germplasm for crop improvement and breeding. However, lack of adequate genetic variation and non-availability of improved varieties limited its prospects of being a successful energy crop. In this review, we present the progress made in molecular breeding approaches with particular reference to tissue culture and genetic transformation, genetic diversity assessment using molecular markers, large-scale transcriptome and proteome studies, identification of candidate genes for trait improvement, whole genome sequencing and the current interest by various public and private sector companies in commercial-scale cultivation, which highlights the revival of Jatropha as a sustainable energy crop. The information generated from molecular markers, transcriptome profiling and whole genome sequencing could accelerate the genetic upgradation of J. curcas through molecular breeding.

  5. A classical reactive potential for molecular clusters of sulphuric acid and water

    SciTech Connect

    Stinson, Jake L.; Kathmann, Shawn M.; Ford, Ian J.

    2015-10-12

    We present a two state empirical valence bond (EVB) potential describing interactions between sulphuric acid and water molecules and designed to model proton transfer between them within a classical dynamical framework. The potential has been developed in order to study the properties of molecular clusters of these species, which are thought to be relevant to atmospheric aerosol nucleation. The particle swarm optimisation method has been used to fit the parameters of the EVB model to density functional theory (DFT) calculations. Features of the parametrised model and DFT data are compared and found to be in satisfactory agreement. In particular, it is found that a single sulphuric acid molecule will donate a proton when clustered with four water molecules at 300 K and that this threshold is temperature dependent. SMK was supported in part by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences; JLS and IJF were supported by the IMPACT scheme at University College London (UCL). We acknowledge the UCL Legion High Performance Computing Facility, and associated support services together with the resources of the National Energy Research Scientific Computing Center (NERSC), which is supported by the U.S. Department of Energy under Contract No. DE-AC02- 05CH11231. JLS thanks Dr. Gregory Schenter, Dr. Theo Kurtén and Prof. Hanna Vehkamäki for important guidance and discussions.

  6. Teaching Field Concept and Potential Energy at A-Level.

    ERIC Educational Resources Information Center

    Poon, C. H.

    1986-01-01

    Argues for a greater emphasis on the reality of fields in electronics and gravitation instruction. Advocates that the potential energy in a system be regarded as stored in the field rather than in the material bodies of the system. Provides a rationale and examples for this position. (ML)

  7. Unified Technical Concepts. Module 7: Potential and Kinetic Energy.

    ERIC Educational Resources Information Center

    Technical Education Research Center, Waco, TX.

    This concept module on potential and kinetic energy is one of thirteen modules that provide a flexible, laboratory-based physics instructional package designed to meet the specialized needs of students in two-year, postsecondary technical schools. Each of the thirteen concept modules discusses a single physics concept and how it is applied to each…

  8. Spectroscopic constants and potential energy curves of PF

    NASA Astrophysics Data System (ADS)

    Latifzadeh, Lida; Balasubramanian, K.

    1995-09-01

    Spectroscopic constants of low-lying bound electronic states and potential energy curves of 19 electronic states of PF arising from the valence dissociation limits are computed using the complete active space self-consistent field (CASSCF) followed by first- and second-order configuration interaction (FOCI, SOCI) methods, which included up to 0.9 million configurations.

  9. Spectroscopic constants and potential energy curves of AsF

    NASA Astrophysics Data System (ADS)

    Latifzadeh, Lida; Balasubramanian, K.

    1996-02-01

    Spectroscopic constants and potential energy curves of 21 electronic states of AsF are computed using the complete active space self-consistent field (CASSCF) followed by first- and second-order configuration interaction (FOCI, SOCI) and multireference singles and doubles configuration interaction (MRSDCI) methods. The computed spectroscopic constants agree with the experimental values for the observed states.

  10. Energy harvesting potential of tuned inertial mass electromagnetic transducers

    NASA Astrophysics Data System (ADS)

    Asai, Takehiko; Araki, Yoshikazu; Ikago, Kohju

    2017-02-01

    The demand for developing renewable energy technologies has been growing in today's society. As one of promising renewable energy sources, large-scale energy harvesting from structural vibrations employing electromagnetic transducers has recently been proposed and considerable effort has been devoted to increase the power generation capability. In this paper, we introduce the mechanism of a tuned inertial mass electromagnetic transducer (TIMET), which can absorb vibratory energy more efficiently by tuning the parameters to adjust the system. Then we propose a new vibratory energy harvester with the TIMET and determine the parameter values for the device with a simple static admittance (SA) control law to maximize the energy harvested from a stationary stochastic disturbance. To investigate the energy harvesting potential of the TIMET further, the performance-guaranteed (PG) control and the LQG control proposed in the literature are applied as well. Then the numerical simulation studies are carried out and the effectiveness of the proposed energy harvester is examined by comparing the traditional electromagnetic transducers.

  11. Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method

    SciTech Connect

    Zeng Xiancheng; Hu Hao; Hu Xiangqian; Yang Weitao

    2009-04-28

    A quantum mechanical/molecular mechanical minimum free energy path (QM/MM-MFEP) method was developed to calculate the redox free energies of large systems in solution with greatly enhanced efficiency for conformation sampling. The QM/MM-MFEP method describes the thermodynamics of a system on the potential of mean force surface of the solute degrees of freedom. The molecular dynamics (MD) sampling is only carried out with the QM subsystem fixed. It thus avoids 'on-the-fly' QM calculations and thus overcomes the high computational cost in the direct QM/MM MD sampling. In the applications to two metal complexes in aqueous solution, the new QM/MM-MFEP method yielded redox free energies in good agreement with those calculated from the direct QM/MM MD method. Two larger biologically important redox molecules, lumichrome and riboflavin, were further investigated to demonstrate the efficiency of the method. The enhanced efficiency and uncompromised accuracy are especially significant for biochemical systems. The QM/MM-MFEP method thus provides an efficient approach to free energy simulation of complex electron transfer reactions.

  12. Dispersion potential between three-bodies with arbitrary electric multipole polarizabilities: Molecular QED theory

    SciTech Connect

    Salam, A.

    2014-01-28

    Molecular quantum electrodynamics is used to obtain an expression for the retarded dispersion energy shift between three arbitrarily electrically polarizable atoms or molecules. A generalized Craig-Power Hamiltonian that depends quadratically on the electric displacement field is employed together with third-order diagrammatic perturbation theory. This approach simplifies the calculation relative to the use of the usual multipolar coupling Hamiltonian that is linear in the displacement field. Specific higher multipole non-additive contributions are then extracted. These include dipole-dipole-quadrupole, dipole-quadrupole-quadrupole, and dipole-dipole-octupole potentials valid for oriented and isotropic species with arbitrary separation distances between particles, extending recent work in which these energy shifts were given for equilateral triangle and collinear geometries. Near-zone limiting forms are found to agree with earlier works in which static inter-particle couplings were used.

  13. Identification and properties of molecular systems of potential use in solar-pumped lasers

    NASA Technical Reports Server (NTRS)

    Micha, D. A.; Oehrn, N. Y.

    1985-01-01

    The concepts and computational tools of theortical chemistry are used to investigate molecular properties needed in direct solar-pumped lasers. Compounds of the type RR'CXY, with R and R' organic groups, and X and Y halide atoms were identified as likely candidates because of their highly enhanced absorption coefficients over compounds with a single halide atom. The use of a combination of vibrational excitation followed by electronic excitation to enhance quantum yields at certain wavelengths is indicated. A self-consistent eikonal approximation to state-to-state transitions was tested for CH3I and is useful for other problems involving electronic energy and charge transfer. An approach to calculate potential energy surfaces and transition dipoles was developed which is based on the generation of eigenstates of the nonrelativisitc Hamiltonian followed by incorporation of the spin-orbit coupling by configuration interaction.

  14. Dispersion potential between three-bodies with arbitrary electric multipole polarizabilities: molecular QED theory.

    PubMed

    Salam, A

    2014-01-28

    Molecular quantum electrodynamics is used to obtain an expression for the retarded dispersion energy shift between three arbitrarily electrically polarizable atoms or molecules. A generalized Craig-Power Hamiltonian that depends quadratically on the electric displacement field is employed together with third-order diagrammatic perturbation theory. This approach simplifies the calculation relative to the use of the usual multipolar coupling Hamiltonian that is linear in the displacement field. Specific higher multipole non-additive contributions are then extracted. These include dipole-dipole-quadrupole, dipole-quadrupole-quadrupole, and dipole-dipole-octupole potentials valid for oriented and isotropic species with arbitrary separation distances between particles, extending recent work in which these energy shifts were given for equilateral triangle and collinear geometries. Near-zone limiting forms are found to agree with earlier works in which static inter-particle couplings were used.

  15. N2(+) bound quartet and sextet state potential energy curves

    NASA Technical Reports Server (NTRS)

    Partridge, H.; Bauschlicher, C. W., Jr.; Stallcop, J. R.

    1985-01-01

    The N2(+) potential energies have been determined from a complete active space self-consistent field calculation with active 2s and 2p electrons. A (6s 4p 3d 1f) Gaussian basis set was used together with additional higher angular momentum and diffuse functions. The calculated potential energy curves for the states 4Sigma(mu)(+), 4Pi(g), and 6Sigma(g)(+), for which there are no spectroscopic observations, are presented. The corresponding spectroscopic constants have been determined from a polynomial curve fit to the computed energies near the well minima and are shown. The 6Sigma(g)(+) state is found to be significantly bound, with a minimum at 1.72 A.

  16. Understanding Potential Climate Variability Impacts on the Offshore Energy Industry

    NASA Astrophysics Data System (ADS)

    Stear, J.

    2014-12-01

    Climate variability may have important implications for the offshore energy industry. Scenarios of increased storm activity and changes in sea level could require the retrofit of existing offshore platforms and coastal infrastructure, the decommissioning of facilities for which upgrade or relocation is not economically viable, and the development of new methods and equipment which are removed from or less sensitive to environmental loads. Over the past years the energy industry has been actively involved in collaborative research efforts with government and academia to identify the potential changes in the offshore operating environment, and corresponding risk implications. This presentation will review several of these efforts, and for several of the hypothetical climate variation scenarios, review the potential impacts on and possible mitigations for offshore and coastal energy infrastructure and operations.

  17. Three-dimensional potential energy surface of Ar–CO

    SciTech Connect

    Sumiyoshi, Yoshihiro; Endo, Yasuki

    2015-01-14

    A three-dimensional intermolecular potential energy surface of the Ar–CO complex has been determined by fitting most of the previously reported spectroscopic data, where observed transition frequencies by microwave, millimeter-wave, submillimeter-wave, and infrared spectroscopy were reproduced simultaneously within their experimental accuracies. A free rotor model Hamiltonian considering all the freedom of motions for an atom-diatom system was applied to calculate vibration-rotation energies. A three-dimensional potential energy surface obtained by ab initio calculations at the CCSD(T)-F12b/aug-cc-pV5Z level of theory was parameterized by a model function consisting of 46 parameters. They were used as initial values for the least-squares analysis of the experimental data. A total of 20 parameters were optimized to reproduce all the spectroscopic data.

  18. Turkey's High Temperature Geothermal Energy Resources and Electricity Production Potential

    NASA Astrophysics Data System (ADS)

    Bilgin, Ö.

    2012-04-01

    Turkey is in the first 7 countries in the world in terms of potential and applications. Geothermal energy which is an alternative energy resource has advantages such as low-cost, clean, safe and natural resource. Geothermal energy is defined as hot water and steam which is formed by heat that accumulated in various depths of the Earth's crust; with more than 20oC temperature and which contain more than fused minerals, various salts and gases than normal underground and ground water. It is divided into three groups as low, medium and high temperature. High-temperature fluid is used in electricity generation, low and medium temperature fluids are used in greenhouses, houses, airport runways, animal farms and places such as swimming pools heating. In this study high temperature geothermal fields in Turkey which is suitable for electricity production, properties and electricity production potential was investigated.

  19. Three-dimensional potential energy surface of Ar-CO.

    PubMed

    Sumiyoshi, Yoshihiro; Endo, Yasuki

    2015-01-14

    A three-dimensional intermolecular potential energy surface of the Ar-CO complex has been determined by fitting most of the previously reported spectroscopic data, where observed transition frequencies by microwave, millimeter-wave, submillimeter-wave, and infrared spectroscopy were reproduced simultaneously within their experimental accuracies. A free rotor model Hamiltonian considering all the freedom of motions for an atom-diatom system was applied to calculate vibration-rotation energies. A three-dimensional potential energy surface obtained by ab initio calculations at the CCSD(T)-F12b/aug-cc-pV5Z level of theory was parameterized by a model function consisting of 46 parameters. They were used as initial values for the least-squares analysis of the experimental data. A total of 20 parameters were optimized to reproduce all the spectroscopic data.

  20. 3D Printing of Molecular Potential Energy Surface Models

    ERIC Educational Resources Information Center

    Lolur, Phalgun; Dawes, Richard

    2014-01-01

    Additive manufacturing, commonly known as 3D printing, is gaining popularity in a variety of applications and has recently become routinely available. Today, 3D printing services are not only found in engineering design labs and through online companies, but also in university libraries offering student access. In addition, affordable options for…

  1. Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach.

    PubMed

    Burusco, Kepa K; Bruce, Neil J; Alibay, Irfan; Bryce, Richard A

    2015-10-26

    Free energy simulations are an established computational tool in modelling chemical change in the condensed phase. However, sampling of kinetically distinct substates remains a challenge to these approaches. As a route to addressing this, we link the methods of thermodynamic integration (TI) and swarm-enhanced sampling molecular dynamics (sesMD), where simulation replicas interact cooperatively to aid transitions over energy barriers. We illustrate the approach by using alchemical alkane transformations in solution, comparing them with the multiple independent trajectory TI (IT-TI) method. Free energy changes for transitions computed by using IT-TI grew increasingly inaccurate as the intramolecular barrier was heightened. By contrast, swarm-enhanced sampling TI (sesTI) calculations showed clear improvements in sampling efficiency, leading to more accurate computed free energy differences, even in the case of the highest barrier height. The sesTI approach, therefore, has potential in addressing chemical change in systems where conformations exist in slow exchange.

  2. U.S. Building-Sector Energy Efficiency Potential

    SciTech Connect

    Brown, Rich; Borgeson, Sam; Koomey, Jon; Biermayer, Peter

    2008-09-30

    This paper presents an estimate of the potential for energy efficiency improvements in the U.S. building sector by 2030. The analysis uses the Energy Information Administration's AEO 2007 Reference Case as a business-as-usual (BAU) scenario, and applies percentage savings estimates by end use drawn from several prior efficiency potential studies. These prior studies include the U.S. Department of Energy's Scenarios for a Clean Energy Future (CEF) study and a recent study of natural gas savings potential in New York state. For a few end uses for which savings estimates are not readily available, the LBNL study team compiled technical data to estimate savings percentages and costs of conserved energy. The analysis shows that for electricity use in buildings, approximately one-third of the BAU consumption can be saved at a cost of conserved energy of 2.7 cents/kWh (all values in 2007 dollars), while for natural gas approximately the same percentage savings is possible at a cost of between 2.5 and 6.9 $/million Btu. This cost-effective level of savings results in national annual energy bill savings in 2030 of nearly $170 billion. To achieve these savings, the cumulative capital investment needed between 2010 and 2030 is about $440 billion, which translates to a 2-1/2 year simple payback period, or savings over the life of the measures that are nearly 3.5 times larger than the investment required (i.e., a benefit-cost ratio of 3.5).

  3. Novel mixture model for the representation of potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Pham, Tien Lam; Kino, Hiori; Terakura, Kiyoyuki; Miyake, Takashi; Dam, Hieu Chi

    2016-10-01

    We demonstrate that knowledge of chemical physics on a materials system can be automatically extracted from first-principles calculations using a data mining technique; this information can then be utilized to construct a simple empirical atomic potential model. By using unsupervised learning of the generative Gaussian mixture model, physically meaningful patterns of atomic local chemical environments can be detected automatically. Based on the obtained information regarding these atomic patterns, we propose a chemical-structure-dependent linear mixture model for estimating the atomic potential energy. Our experiments show that the proposed mixture model significantly improves the accuracy of the prediction of the potential energy surface for complex systems that possess a large diversity in their local structures.

  4. Intra-molecular Triplet Energy Transfer is a General Approach to Improve Organic Fluorophore Photostability

    PubMed Central

    Zheng, Qinsi; Jockusch, Steffen; Rodríguez-Calero, Gabriel G.; Zhou, Zhou; Zhao, Hong; Altman, Roger B.; Abruña, Héctor D.; Blanchard, Scott C.

    2015-01-01

    Bright, long-lasting and non-phototoxic organic fluorophores are essential to the continued advancement of biological imaging. Traditional approaches towards achieving photostability, such as the removal of molecular oxygen and the use of small-molecule additives in solution, suffer from potentially toxic side effects, particularly in the context of living cells. The direct conjugation of small-molecule triplet state quenchers, such as cyclooctatetraene (COT), to organic fluorophores has the potential to bypass these issues by restoring reactive fluorophore triplet states to the ground state through intra-molecular triplet energy transfer. Such methods have enabled marked improvement in cyanine fluorophore photostability spanning the visible spectrum. However, the generality of this strategy to chemically and structurally diverse fluorophore species has yet to be examined. Here, we show that the proximal linkage of COT increases the photon yield of a diverse range of organic fluorophores widely used in biological imaging applications, demonstrating that the intra-molecular triplet energy transfer mechanism is a potentially general approach for improving organic fluorophore performance and photostability. PMID:26700693

  5. Parallel AFMPB solver with automatic surface meshing for calculation of molecular solvation free energy

    NASA Astrophysics Data System (ADS)

    Zhang, Bo; Peng, Bo; Huang, Jingfang; Pitsianis, Nikos P.; Sun, Xiaobai; Lu, Benzhuo

    2015-05-01

    We present PAFMPB, an updated and parallel version of the AFMPB software package for fast calculation of molecular solvation-free energy. The new version has the following new features: (1) The adaptive fast multipole method and the boundary element methods are parallelized; (2) A tool is embedded for automatic molecular VDW/SAS surface mesh generation, leaving the requirement for a mesh file at input optional; (3) The package provides fast calculation of the total solvation-free energy, including the PB electrostatic and nonpolar interaction contributions. PAFMPB is implemented in C and Fortran programming languages, with the Cilk Plus extension to harness the computing power of both multicore and vector processing. Computational experiments demonstrate the successful application of PAFMPB to the calculation of the PB potential on a dengue virus system with more than one million atoms and a mesh with approximately 20 million triangles.

  6. Level-Set Minimization of Potential Controlled Hadwiger Valuations for Molecular Solvation

    PubMed Central

    Cheng, Li-Tien; Li, Bo; Wang, Zhongming

    2012-01-01

    A level-set method is developed for the numerical minimization of a class of Had-wiger valuations with a potential on a set of three-dimensional bodies. Such valuations are linear combinations of the volume, surface area, and surface integral of mean curvature. The potential increases rapidly as the body shrinks beyond a critical size. The combination of the Hadwiger valuation and the potential is the mean-field free-energy functional of the solvation of non-polar molecules in the recently developed variational implicit-solvent model. This functional of surfaces is minimized by the level-set evolution in the steepest decent of the free energy. The normal velocity of this surface evolution consists of both the mean and Gaussian curvatures, and a lower-order, “forcing” term arising from the potential. The forward Euler method is used to discretize the time derivative with a dynamic time stepping that satisfies a CFL condition. The normal velocity is decomposed into two parts. The first part consists of both the mean and Gaussian curvature terms. It is of parabolic type with parameter correction, and is discretized by central differencing. The second part has all the lower-order terms. It is of hyperbolic type, and is discretized by an upwinding scheme. New techniques of local level-set method and numerical integration are developed. Numerical tests demonstrate a second-order convergence of the method. Examples of application to the modeling of molecular solvation are presented. PMID:22323839

  7. An exploration of the ozone dimer potential energy surface

    SciTech Connect

    Azofra, Luis Miguel; Alkorta, Ibon; Scheiner, Steve

    2014-06-28

    The (O{sub 3}){sub 2} dimer potential energy surface is thoroughly explored at the ab initio CCSD(T) computational level. Five minima are characterized with binding energies between 0.35 and 2.24 kcal/mol. The most stable may be characterized as slipped parallel, with the two O{sub 3} monomers situated in parallel planes. Partitioning of the interaction energy points to dispersion and exchange as the prime contributors to the stability, with varying contributions from electrostatic energy, which is repulsive in one case. Atoms in Molecules analysis of the wavefunction presents specific O⋯O bonding interactions, whose number is related to the overall stability of each dimer. All internal vibrational frequencies are shifted to the red by dimerization, particularly the antisymmetric stretching mode whose shift is as high as 111 cm{sup −1}. In addition to the five minima, 11 higher-order stationary points are identified.

  8. Potential energy curves and dissociation energy of group IIA diatomic fluorides

    NASA Astrophysics Data System (ADS)

    Varma, M. P.; Ishwar, N. B.; Jha, B. L.

    1982-04-01

    Reliable (RKRV) potential energy curves have been constructed for different experimentally observed electronic states of BeF, MgF, CaF, SrF and BaF molecules from the latest spectroscopic data using the method of Rao and Venkateswarlu. Using a three-parameters Lippincott potential function the precise values of ground state dissociation energies of these molecules have been obtained. Values so obtained are found to be in close agreement with the experimental results.

  9. Fourfold Clusters of Rovibrational Energies in H2Te Studied With an Ab Initio Potential Energy Function

    NASA Technical Reports Server (NTRS)

    Jensen, Per; Li, Yan; Hirsch, Gerhard; Buenker, Robert J.; Lee, Timothy J.; Arnold, James O. (Technical Monitor)

    1994-01-01

    We report an ab initio investigation of the cluster effect (i.e., the formation of nearly degenerate, four member groups of rotation-vibration energy levels at higher J and K(sub a). values) in the H2Te molecule. The potential energy function has been calculated ab initio at a total of 334 molecular geometries by means of the CCSD(T) method where the (1s-4f) core electrons of Te were described by an effective core potential. The values of the potential energy function obtained cover the region up to around 10,000/cm above the equilibrium energy. On the basis of the ab initio potential, the rotation-vibration energy spectra of H2Te-130 and its deuterated isotopomers have been calculated with the MORBID (Morse Oscillator Rigid Bender Internal Dynamics) Hamiltonian and computer program. In particular, we have calculated the rotational energy manifolds for J less than or = 40 in the vibrational ground state, the upsilon(sub 2) state, the "first triad" (the upsilon(sub l)/upsilon(sub 3)/2upsilon(sub 2) interacting vibrational states), and the "second triad" (the upsilon(sub 1) + upsilon(sub 2/upsilon(sub 2) + upsilon(sub 3)/3upsilon(sub 2) states) of H2Te-130. We find that the cluster formation in H2Te is very similar to those of of H2Se and H2S, which we have studied previously. However, contrary to semiclassical predictions, we do not determine any significant displacement of the clusters towards lower J values relative to H2Se. Hence the experimental observation of the cluster states in H2Te will be at least as difficult as in H2Se.

  10. Potential for luminosity improvement for low-energy RHIC operation

    SciTech Connect

    Fedotov A. V.

    2012-05-20

    At the Brookhaven National Laboratory, a physics program, motivated by the search of the QCD phase transition critical point, requires operation of the Relativistic Heavy Ion Collider (RHIC) with heavy ions at very low beam energies corresponding to 2.5-20 GeV/n. Several physics runs were already successfully performed at these low energies. However, the luminosity is very low at lowest energies of interest (< 10 GeV/n) limited by the intra-beam scattering and space-charge, as well as by machine nonlinearities. At these low energies, electron cooling could be very effective in counteracting luminosity degradation due to the IBS, while it is less effective against other limitations. Overall potential luminosity improvement for low-energy RHIC operation from cooling is summarized for various energies, taking into account all these limitations as well as beam lifetime measured during the low-energy RHIC runs. We also explore a possibility of further luminosity improvement under the space-charge limitation.

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

    NASA Technical Reports Server (NTRS)

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

    1995-01-01

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

  12. Rotational Energy Transfer of N2 Gas Determined Using a New Ab Initio Potential Energy Surface

    NASA Technical Reports Server (NTRS)

    Huo, Winifred M.; Stallcop, James R.; Partridge, Harry; Langhoff, Stephen R. (Technical Monitor)

    1997-01-01

    Rotational energy transfer between two N2 molecules is a fundamental process of some importance. Exchange is expected to play a role, but its importance is somewhat uncertain. Rotational energy transfer cross sections of N2 also have applications in many other fields including modeling of aerodynamic flows, laser operations, and linewidth analysis in nonintrusive laser diagnostics. A number of N2-N2 rigid rotor potential energy surface (PES) has been reported in the literature.

  13. Study of chirally motivated low-energy K - optical potentials

    NASA Astrophysics Data System (ADS)

    Cieplý, A.; Friedman, E.; Gal, A.; Mareš, J.

    2001-12-01

    The K - optical potential in the nuclear medium is evaluated self consistently from a free-space K -N t matrix constructed within a coupled-channel chiral approach to the low-energy K¯N data. The chiral-model parameters are fitted to a select subset of the low-energy data plus the K - atomic data throughout the periodic table. The resulting attractive K - optical potentials are relatively 'shallow', with central depth of the real part about 55 MeV, for a fairly reasonable reproduction of the atomic data with χ2/ N≈2.2. Relatively 'deep' attractive potentials of depth about 180 MeV, which result in other phenomenological approaches with χ2/ N≈1.5, are ruled out within chirally motivated models. Different physical data input is required to distinguish between shallow and deep K - optical potentials. The (K -stop, π) reaction could provide such a test, with exclusive rates differing by over a factor of three for the two classes of potentials. Finally, forward (K -,p) differential cross sections for the production of relatively narrow deeply bound K -nuclear states are evaluated for deep K - optical potentials, yielding values considerably lower than those estimated before.

  14. Residential energy efficiency: Progress since 1973 and future potential

    NASA Astrophysics Data System (ADS)

    Rosenfeld, Arthur H.

    1985-11-01

    Today's 85 million U.S. homes use 100 billion of fuel and electricity (1150/home). If their energy intensity (resource energy/ft2) were still frozen at 1973 levels, they would use 18% more. With well-insulated houses, need for space heat is vanishing. Superinsulated Saskatchewan homes spend annually only 270 for space heat, 150 for water heat, and 400 for appliances, yet they cost only 2000±1000 more than conventional new homes. The concept of Cost of Conserved Energy (CCE) is used to rank conservation technologies for existing and new homes and appliances, and to develop supply curves of conserved energy and a least cost scenario. Calculations are calibrated with the BECA and other data bases. By limiting investments in efficiency to those whose CCE is less than current fuel and electricity prices, the potential residential plus commercial energy use in 2000 AD drops to half of that estimated by DOE, and the number of power plants needed drops by 200. For the whole buildings sector, potential savings by 2000 are 8 Mbod (worth 50B/year), at an average CCE of 10/barrel.

  15. Identifying low variance pathways for free energy calculations of molecular transformations in solution phase.

    PubMed

    Pham, Tri T; Shirts, Michael R

    2011-07-21

    Improving the efficiency of free energy calculations is important for many biological and materials design applications, such as protein-ligand binding affinities in drug design, partitioning between immiscible liquids, and determining molecular association in soft materials. We show that for any pair potential, moderately accurate estimation of the radial distribution function for a solute molecule is sufficient to accurately estimate the statistical variance of a sampling along a free energy pathway. This allows inexpensive analytical identification of low statistical error free energy pathways. We employ a variety of methods to estimate the radial distribution function (RDF) and find that the computationally cheap two-body "dilute gas" limit performs as well or better than 3D-RISM theory and other approximations for identifying low variance free energy pathways. With a RDF estimate in hand, we can search for pairwise interaction potentials that produce low variance. We give an example of a search minimizing statistical variance of solvation free energy over the entire parameter space of a generalized "soft core" potential. The free energy pathway arising from this optimization procedure has lower curvature in the variance and reduces the total variance by at least 50% compared to the traditional soft core solvation pathway. We also demonstrate that this optimized pathway allows free energies to be estimated with fewer intermediate states due to its low curvature. This free energy variance optimization technique is generalizable to solvation in any homogeneous fluid and for any type of pairwise potential and can be performed in minutes to hours, depending on the method used to estimate g(r).

  16. Polarization energy gradients in combined quantum mechanics, effective fragment potential, and polarizable continuum model calculations

    NASA Astrophysics Data System (ADS)

    Li, Hui; Gordon, Mark S.

    2007-03-01

    A method that combines quantum mechanics (QM), typically a solute, the effective fragment potential (EFP) discrete solvent model, and the polarizable continuum model is described. The EFP induced dipoles and polarizable continuum model (PCM) induced surface charges are determined in a self-consistent fashion. The gradients of these two energies with respect to molecular coordinate changes are derived and implemented. In general, the gradients can be formulated as simple electrostatic forces and torques among the QM nuclei, electrons, EFP static multipoles, induced dipoles, and PCM induced charges. Molecular geometry optimizations can be performed efficiently with these gradients. The formulas derived for EFP/PCM can be generally applied to other combined molecular mechanics and continuum methods that employ induced dipoles and charges.

  17. Intramolecular vibrational energy redistribution in bridged azulene-anthracene compounds: Ballistic energy transport through molecular chains

    NASA Astrophysics Data System (ADS)

    Schwarzer, D.; Kutne, P.; Schröder, C.; Troe, J.

    2004-07-01

    Intramolecular vibrational energy flow in excited bridged azulene-anthracene compounds is investigated by time-resolved pump-probe laser spectroscopy. The bridges consist of molecular chains and are of the type (CH2)m with m up to 6 as well as (CH2OCH2)n (n=1,2) and CH2SCH2. After light absorption into the azulene S1 band and subsequent fast internal conversion, excited molecules are formed where the vibrational energy is localized at the azulene side. The vibrational energy transfer through the molecular bridge to the anthracene side and, finally, to the surrounding medium is followed by probing the red edge of the azulene S3 absorption band at 300 nm and/or the anthracene S1 absorption band at 400 nm. In order to separate the time scales for intramolecular and intermolecular energy transfer, most of the experiments were performed in supercritical xenon where vibrational energy transfer to the bath is comparably slow. The intramolecular equilibration proceeds in two steps. About 15%-20% of the excitation energy leaves the azulene side within a short period of 300 fs. This component accompanies the intramolecular vibrational energy redistribution (IVR) within the azulene chromophore and it is caused by dephasing of normal modes contributing to the initial local excitation of the azulene side and extending over large parts of the molecule. Later, IVR in the whole molecule takes place transferring vibrational energy from the azulene through the bridge to the anthracene side and thereby leading to microcanonical equilibrium. The corresponding time constants τIVR for short bridges increase with the chain length. For longer bridges consisting of more than three elements, however, τIVR is constant at around 4-5 ps. Comparison with molecular dynamics simulations suggests that the coupling of these chains to the two chromophores limits the rate of intramolecular vibrational energy transfer. Inside the bridges the energy transport is essentially ballistic and, therefore

  18. Using peat for energy: Potential environmental restraints. Overview

    NASA Astrophysics Data System (ADS)

    Reed, R. M.; Voorhees, L. D.; Mulholland, P. J.

    Serious consideration is being given to using peat as an energy resource in Minnesota, North Carolina, Florida, and some New England States. Potential environmental constraints for using peat as an energy resource are associated with disruption of important regional wetland ecosystems. Mining peatlands may significantly modify ground and surface water hydrology, degrade water quality in downstream receiving systems, contribute to the deterioration of local air quality, disrupt or eliminate plant and animal populations having specialized requirements and limited distributions, and destroy unique wetland ecosystems representing important scientific and educational resources. Careful selection of peatlands to be developed and application of appropriate mitigation and monitoring programs will be necessary to offset these impacts.

  19. [Biomass energy utilization in microbial fuel cells: potentials and challenges].

    PubMed

    Huang, Liping; Cheng, Shaoan

    2010-07-01

    Microbial fuel cells (MFCs) that can harvest biomass energy from organic wastes through microbial catalysis have garnered more and more attention within the past decade due to its potential benefits to ecological environment. In this article, the updated progress in MFCs is reviewed, with a focus on frontier technologies such as chamber configurations, feedstock varieties and the integration of MFCs with microbial electrolysis cells for hydrogen production. And on the other hand, the challenges like development of cost-effective electrode materials, improvement of biomass energy recovery and power output, design and optimization of commercial MFC devices are presented.

  20. The H 2O ++ Ground State Potential Energy Surface

    NASA Astrophysics Data System (ADS)

    Bunker, P. R.; Bludsky, Ota; Jensen, Per; Wesolowski, S. S.; Van Huis, T. J.; Yamaguchi, Y.; Schaefer, H. F.

    1999-12-01

    At the correlation-consistent polarized-valence quadruple-zeta complete active space self-consistent field second-order configuration interaction level of ab initio theory (cc-pVQZ CASSCF-SOCI), we calculated 129 points on the ground electronic state potential energy surface of the water dication H2O++; this calculation includes the energy of X3Σ- OH+ at equilibrium and the energy of the triplet oxygen atom. We determined the parameters in an analytical function that represents this surface out to the (OH+ + H+) and (O + 2H+) dissociation limits, for bending angles from 70 to 180°. There is a metastable minimum in this surface, at an energy of 43 600 cm-1 above the H+ + OH+ dissociation energy, and the geometry at this minimum is linear (D∞h), with an OH bond length of 1.195 Å. On the path to dissociation to H+ + OH+, there is a saddle point at an energy of 530 cm-1 above the minimum, and the geometry at the saddle point is linear (C∞ Kv) with OH bond lengths of 1.121 and 1.489 Å. Using the stabilization method, we calculated the lowest resonance on this surface. Relative to the metastable local minimum on the potential energy surface, the position of the lowest resonance for H2O++, D2O++, and T2O++ is 1977(85), 1473(25), and 1249(10) cm-1, respectively, where the width of each resonance (in cm-1) is given in parentheses.

  1. Assessment of Tidal Stream Energy Potential for the United States

    NASA Astrophysics Data System (ADS)

    Haas, K. A.; Defne, Z.; Jiang, L.; Fritz, H. M.

    2010-12-01

    Tidal streams are high velocity sea currents created by periodic horizontal movement of the tides, often magnified by local topographical features such as headlands, inlets to inland lagoons, and straits. Tidal stream energy extraction is derived from the kinetic energy of the moving flow; analogous to the way a wind turbine operates in air, and as such differs from tidal barrages, which relies on providing a head of water for energy extraction. With the constantly increasing effort in promoting alternative energy, tidal streams have become promising energy sources due to their continuous, predictable and concentrated characteristics. However, the present lack of a full spatial-temporal assessment of tidal currents for the U.S. coastline down to the scale of individual devices is a barrier to the comprehensive development of tidal current energy technology. A methodology for creating a national database of tidal stream energy potential, as well as a GIS tool usable by industry in order to accelerate the market for tidal energy conversion technology has been developed. The tidal flows are simulated using the Regional Ocean Modeling System (ROMS). The model is calibrated and validated using observations and tidal predictions. The calibration includes adjustments to model parameters such as bottom friction coefficient, changed land/water masks, or increased grid resolutions. A systematic validation process has been developed after defining various parameters to quantify the validation results. In order to determine the total tidal stream power resource, a common method frequently proposed is to estimate it as a fraction of the total kinetic energy flux passing through a vertical section; however, this now has been shown to generally underestimate the total available resource. The total tidal energy flux includes not just the kinetic energy but also the energy flux due to the work done by the pressure force associated with the tidal motion on the water column as well

  2. Influence of the membrane potential on the free energy of an intrinsic protein.

    PubMed Central

    Roux, B

    1997-01-01

    A modified Poisson-Boltzmann equation is developed from statistical mechanical considerations to describe the influence of the transmembrane potential on macromolecular systems. Using a Green's function formalism, the electrostatic free energy of a protein associated with the membrane is expressed as the sum of three terms: a contribution from the energy required to charge the system's capacitance, a contribution corresponding to the interaction of the protein charges with the membrane potential, and a contribution corresponding to a voltage-independent reaction field free energy. The membrane potential, which is due to the polarization interface, is calculated in the absence of the protein charges, whereas the reaction field is calculated in the absence of transmembrane potential. Variations in the capacitive energy associated with typical molecular processes are negligible under physiological conditions. The formulation of the theory is closely related to standard algorithms used to solve the Poisson-Boltzmann equation and only small modifications to current source codes are required for its implementation. The theory is illustrated by examining the voltage-dependent membrane insertion of a simple polyalanine alpha-helix and by computing the electrostatic potential across a 60-A-diameter sphere meant to represent a large intrinsic protein. Images FIGURE 2 PMID:9414213

  3. Recent advances in electronic structure theory and their influence on the accuracy of ab initio potential energy surfaces

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

    1988-01-01

    Recent advances in electronic structure theory and the availability of high speed vector processors have substantially increased the accuracy of ab initio potential energy surfaces. The recently developed atomic natural orbital approach for basis set contraction has reduced both the basis set incompleteness and superposition errors in molecular calculations. Furthermore, full CI calculations can often be used to calibrate a CASSCF/MRCI approach that quantitatively accounts for the valence correlation energy. These computational advances also provide a vehicle for systematically improving the calculations and for estimating the residual error in the calculations. Calculations on selected diatomic and triatomic systems will be used to illustrate the accuracy that currently can be achieved for molecular systems. In particular, the F+H2 yields HF+H potential energy hypersurface is used to illustrate the impact of these computational advances on the calculation of potential energy surfaces.

  4. Recent advances in electronic structure theory and their influence on the accuracy of ab initio potential energy surfaces

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

    1989-01-01

    Recent advances in electronic structure theory and the availability of high speed vector processors have substantially increased the accuracy of ab initio potential energy surfaces. The recently developed atomic natural orbital approach for basis set contraction has reduced both the basis set incompleteness and superposition errors in molecular calculations. Furthermore, full CI calculations can often be used to calibrate a CASSCF/MRCI approach that quantitatively accounts for the valence correlation energy. These computational advances also provide a vehicle for systematically improving the calculations and for estimating the residual error in the calculations. Calculations on selected diatomic and triatomic systems will be used to illustrate the accuracy that currently can be achieved for molecular systems. In particular, the F + H2 yields HF + H potential energy hypersurface is used to illustrate the impact of these computational advances on the calculation of potential energy surfaces.

  5. Evaluation of global onshore wind energy potential and generation costs.

    PubMed

    Zhou, Yuyu; Luckow, Patrick; Smith, Steven J; Clarke, Leon

    2012-07-17

    In this study, we develop an updated global estimate of onshore wind energy potential using reanalysis wind speed data, along with updated wind turbine technology performance, land suitability factors, cost assumptions, and explicit consideration of transmission distance in the calculation of transmission costs. We find that wind has the potential to supply a significant portion of the world energy needs, although this potential varies substantially by region and with assumptions such as on what types of land can be used to site wind farms. Total global economic wind potential under central assumptions, that is, intermediate between optimistic and pessimistic, is estimated to be approximately 119.5 petawatt hours per year (13.6 TW) at less than 9 cents/kWh. A sensitivity analysis of eight key parameters is presented. Wind potential is sensitive to a number of input parameters, particularly wind speed (varying by -70% to +450% at less than 9 cents/kWh), land suitability (by -55% to +25%), turbine density (by -60% to +80%), and cost and financing options (by -20% to +200%), many of which have important policy implications. As a result of sensitivities studied here we suggest that further research intended to inform wind supply curve development focus not purely on physical science, such as better resolved wind maps, but also on these less well-defined factors, such as land-suitability, that will also have an impact on the long-term role of wind power.

  6. Mashreq Arab interconnected power system potential for economic energy trading

    SciTech Connect

    Al-Shehri, A.M.; El-Amin, I.M.; Opoku, G.; Al-Baiyat, S.A.; Zedan, F.M.

    1994-12-01

    The Mashreq Arab countries covered in this study are Bahrain, Egypt, Jordan, Lebanon, Oman, Qatar, Saudi Arabia, Syria, the United Arab Emirates, and Yemen. A feasibility study for the interconnection of the electrical networks of the Mashreq Arab countries, sponsored by the Arab Fund, was completed in June 1992. Each country is served by one utility except Saudi Arabia, which is served by four major utilities and some smaller utilities serving remote towns and small load centers. The major utilities are the Saudi consolidated electric Company in the Eastern Province (SCECO East), SCECO Center, SCECO West, and SCECO South. These are the ones considered in this study. The Mashreq Arab region has a considerable mix of energy resources. Egypt and Syria have some limited amounts of hydropower resources, and the Arabian Gulf region is abundant in fossil fuel reserves. Owing to the differences in energy production costs, a potential exists for substantial energy trading between electric utilities in the region. The major objective of this project is to study the feasibility of electric energy trading between the Mashreq Arab countries. The basis, assumptions, and methodologies on which this energy trading study is based relate to the results and conclusions arising out of the previous study, power plant characteristics and costs, assumptions on economic parameters, rules for economy energy exchange, etc. This paper presents the basis, methodology, and major findings of the study.

  7. Data Network Equipment Energy Use and Savings Potential in Buildings

    SciTech Connect

    Lanzisera, Steven; Nordman, Bruce; Brown, Richard E.

    2010-06-09

    Network connectivity has become nearly ubiquitous, and the energy use of the equipment required for this connectivity is growing. Network equipment consists of devices that primarily switch and route Internet Protocol (IP) packets from a source to a destination, and this category specifically excludes edge devices like PCs, servers and other sources and sinks of IP traffic. This paper presents the results of a study of network equipment energy use and includes case studies of networks in a campus, a medium commercial building, and a typical home. The total energy use of network equipment is the product of the stock of equipment in use, the power of each device, and their usage patterns. This information was gathered from market research reports, broadband market penetration studies, field metering, and interviews with network administrators and service providers. We estimate that network equipment in the USA used 18 TWh, or about 1percent of building electricity, in 2008 and that consumption is expected to grow at roughly 6percent per year to 23 TWh in 2012; world usage in 2008 was 51 TWh. This study shows that office building network switches and residential equipment are the two largest categories of energy use consuming 40percent and 30percent of the total respectively. We estimate potential energy savings for different scenarios using forecasts of equipment stock and energy use, and savings estimates range from 20percent to 50percent based on full market penetration of efficient technologies.

  8. Exploring the free energy surface using ab initio molecular dynamics

    SciTech Connect

    Samanta, Amit; Morales, Miguel A.; Schwegler, Eric

    2016-04-22

    Efficient exploration of the configuration space and identification of metastable structures are challenging from both computational as well as algorithmic perspectives. Here, we extend the recently proposed orderparameter aided temperature accelerated sampling schemes to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways within the framework of density functional theory based molecular dynamics. The sampling method is applied to explore the relevant parts of the configuration space in prototypical materials SiO2 and Ti to identify the different metastable structures corresponding to different phases in these materials. In addition, we use the string method in collective variables to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hcp to fcc phase transition in Ti.

  9. Exploring the free energy surface using ab initio molecular dynamics

    DOE PAGES

    Samanta, Amit; Morales, Miguel A.; Schwegler, Eric

    2016-04-22

    Efficient exploration of the configuration space and identification of metastable structures are challenging from both computational as well as algorithmic perspectives. Here, we extend the recently proposed orderparameter aided temperature accelerated sampling schemes to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways within the framework of density functional theory based molecular dynamics. The sampling method is applied to explore the relevant parts of the configuration space in prototypical materials SiO2 and Ti to identify the different metastable structures corresponding to different phases in these materials. In addition, we use the string method inmore » collective variables to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hcp to fcc phase transition in Ti.« less

  10. A global potential energy surface for ArH2

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.; Walch, Stephen P.; Taylor, Peter R.

    1992-01-01

    We describe a simple analytic representation of the ArH2 potential energy surface which well reproduces the results of extensive ab initio electronic structure calculations. The analytic representation smoothly interpolates between the dissociated H2 and strong bonding limits. In the fitting process, emphasis is made on accurately reproducing regions of the potential expected to be important for high temperature (ca. 3000 K) collision processes. Overall, the anisotropy and H2 bond length dependence of the analytic representation well reproduce the input data.

  11. A global potential energy surface for ArH2

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.; Walch, Stephen P.; Taylor, Peter R.

    1993-01-01

    We describe a simple analytic representation of the ArH2 potential energy surface which well reproduces the results of extensive ab initio electronic structure calculations. The analytic representation smoothly interpolates between the dissociated H2 and strong bonding limits. In the fitting process, emphasis is made on accurately reproducing regions of the potential expected to be important for high temperature (ca. 3000 K) collision processes. Overall, the anisotropy and H2 bond length dependence of the analytic representation well reproduce the input data.

  12. Major Energy Plants and Their Potential for Bioenergy Development in China

    NASA Astrophysics Data System (ADS)

    Li, Xiaofeng; Hou, Shenglin; Su, Man; Yang, Mingfeng; Shen, Shihua; Jiang, Gaoming; Qi, Dongmei; Chen, Shuangyan; Liu, Gongshe

    2010-10-01

    China is rich in energy plant resources. In this article, 64 plant species are identified as potential energy plants in China. The energy plant species include 38 oilseed crops, 5 starch-producing crops, 3 sugar-producing crops and 18 species for lignocellulosic biomass. The species were evaluated on the basis of their production capacity and their resistance to salt, drought, and/or low temperature stress. Ten plant species have high production and/or stress resistance and can be potentially developed as the candidate energy plants. Of these, four species could be the primary energy plants in China: Barbados nut ( Jatropha curcas L.), Jerusalem artichoke ( Helianthus tuberosus L.), sweet sorghum ( Sorghum bicolor L.) and Chinese silvergrass ( Miscanthus sinensis Anderss.). We discuss the use of biotechnological techniques such as genome sequencing, molecular markers, and genetic transformation to improve energy plants. These techniques are being used to develop new cultivars and to analyze and manipulate genetic variation to improve attributes of energy plants in China.

  13. Major energy plants and their potential for bioenergy development in China.

    PubMed

    Li, Xiaofeng; Hou, Shenglin; Su, Man; Yang, Mingfeng; Shen, Shihua; Jiang, Gaoming; Qi, Dongmei; Chen, Shuangyan; Liu, Gongshe

    2010-10-01

    China is rich in energy plant resources. In this article, 64 plant species are identified as potential energy plants in China. The energy plant species include 38 oilseed crops, 5 starch-producing crops, 3 sugar-producing crops and 18 species for lignocellulosic biomass. The species were evaluated on the basis of their production capacity and their resistance to salt, drought, and/or low temperature stress. Ten plant species have high production and/or stress resistance and can be potentially developed as the candidate energy plants. Of these, four species could be the primary energy plants in China: Barbados nut (Jatropha curcas L.), Jerusalem artichoke (Helianthus tuberosus L.), sweet sorghum (Sorghum bicolor L.) and Chinese silvergrass (Miscanthus sinensis Anderss.). We discuss the use of biotechnological techniques such as genome sequencing, molecular markers, and genetic transformation to improve energy plants. These techniques are being used to develop new cultivars and to analyze and manipulate genetic variation to improve attributes of energy plants in China.

  14. Free energy generalization of the Peierls potential in iron.

    PubMed

    Gilbert, M R; Schuck, P; Sadigh, B; Marian, J

    2013-08-30

    In body-centered-cubic (bcc) crystals, 1/2<111> screw dislocations exhibit high intrinsic lattice friction as a consequence of their nonplanar core structure, which results in a periodic energy landscape known as the Peierls potential U(P). The main features determining plastic flow, including its stress and temperature dependences, can be derived directly from this potential, hence its importance. In this Letter, we use thermodynamic integration to provide a full thermodynamic extension of U(P) for bcc Fe. We compute the Peierls free energy path as a function of stress and temperature and show that the critical stress vanishes at 700 K, supplying the qualitative elements that explain plastic behavior in the athermal limit.

  15. Nanoparticle Functionalization and Its Potentials for Molecular Imaging

    PubMed Central

    Thiruppathi, Rukmani; Mishra, Sachin; Ganapathy, Mathangi

    2016-01-01

    Functionalization enhances the properties and characteristics of nanoparticles through surface modification, and enables them to play a major role in the field of medicine. In molecular imaging, quality functional images are required with proper differentiation which can be seen with high contrast to obtain viable information. This review article discusses how functionalization enhances molecular imaging and enables multimodal imaging by which images with combination of functions particular to each modality can be obtained. This also explains how nanoparticles interacting at molecular level, when functionalized with molecules can target the cells of interest or substances with high specificity, reducing background signal and allowing simultaneous therapies to be carried out while imaging. Functionalization allows imaging for a prolonged period and enables to track the cells over a period of time. Recent researches and progress in functionalizing the nanoparticles to specifically enhance bioimaging with different modalities and their applications are reviewed in this article. PMID:28331783

  16. The Potential for Energy Efficiency and Renewable Energy in North Carolina

    SciTech Connect

    Hadley, SW

    2003-08-06

    As many states have restructured their electric power industry, they have established a ''systems benefit charge'' to help fund those activities that will no longer be funded by utilities in the new structure. Examples include weatherization of low-income housing, efficiency programs, and renewable energy development. Varying amounts have been collected and allocated depending on state needs and abilities. One question that arises is what are the potential results of funding the different types of programs. What is the potential for energy efficiency or for renewable power, and what would be accomplished given the amount of funding that the system benefit charge may provide? The purpose of this project is to provide an initial estimate of the potential for energy efficiency and renewable energy in North Carolina. This potential could be funded by a public benefits fund resulting from a green power program being considered in the state. It concentrates on electric energy savings and production. Savings in buildings can include improvements to space conditioning as well as improvements to lighting or other appliances. Distributed power potential, through use of combined heat and power and renewables such as photovoltaic, wind, and biomass were examined. The goal is to provide information to decision makers who are developing a green power program in North Carolina. It will not be a complete and detailed study of all efficiency potentials but is more of a scoping exercise to determine the relative impacts and begin the process for a more definitive study at a later date. Statewide energy savings potential cannot be directly measured but must be calculated. First, the word ''potential'' means that the savings have not occurred yet. Second, the savings are often only indirectly measured by estimating what energy use there would have been without the changes in technology or behavior. Calculations through sampling and statistical analysis or by simulation are a necessary

  17. Geothermal Energy Potential of Turkey: Inferred from the Aeromagnetic data

    NASA Astrophysics Data System (ADS)

    Ates, Abdullah; Bilim, Funda; Buyuksarac, Aydin; Bektas, Ozcan

    2010-05-01

    Geothermal energy potential of Turkey is well known. There are lots of hot springs with over 30° C water temperatures. However, the significance of these geothermal energy potential of Turkey is not adequately understood. We believe that the main reason for this; is the lack of exploration methods and tools in a wide area as large as Turkey. We exploited a well known physical property of rocks to estimate the geothermal energy potential. Physically, substances lose their magnetization above a temperature known as the Curie that is the 580° C for magnetite. Properties of the Curie temperature have been exploited to observe the bottom depth of the magnetization. That is the depth where the heat reaches to 580° C. In another word, there is no magnetization below this depth. In normal crust this depth is about 22-24 km. Thus, investigation of the bottom depth of magnetization by using aeromagnetic anomalies can lead to information that if there are any anomalous regions well above the normal crust. The aeromagnetic anomalies of whole of Turkey were surveyed by the Mineral Research and Exploration (MTA) of Turkey. The survey was completed during late 1980's. Five kilometers grid data were available and used for regional exploration purposes. Exploration of the geothermal energy potential of Turkey was done from west to east in the similar way to search for shallow high temperature regions. These are from west to east; i.) Western Turkey: Two major shallow depth regions were determined at the west of Kutahya and the north-east of Denizli. The Curie Point Depths (CPDs) were calculated as about 7 km and about 9 km in Kutahya and Denizli, respectively. Also, high heat flow values and crustal thinning (about 32 km from gravity anomalies of western Turkey) were calculated for western Turkey. ii.) Central Turkey: A CPD depth of 8 km was calculated. This gives us a temperature gradient of 0.073° C/m. Geothermal energy potential was studied using water chemistry and isotopic

  18. Molecular and chemical engineering of bacteriophages for potential medical applications.

    PubMed

    Hodyra, Katarzyna; Dąbrowska, Krystyna

    2015-04-01

    Recent progress in molecular engineering has contributed to the great progress of medicine. However, there are still difficult problems constituting a challenge for molecular biology and biotechnology, e.g. new generation of anticancer agents, alternative biosensors or vaccines. As a biotechnological tool, bacteriophages (phages) offer a promising alternative to traditional approaches. They can be applied as anticancer agents, novel platforms in vaccine design, or as target carriers in drug discovery. Phages also offer solutions for modern cell imaging, biosensor construction or food pathogen detection. Here we present a review of bacteriophage research as a dynamically developing field with promising prospects for further development of medicine and biotechnology.

  19. Theoretical characterization of the potential energy surface for NH + NO

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.

    1993-01-01

    The potential energy surface for NH + NO was characterized using complete active space self-consistent field (CASSCF) gradient calculation to determine the stationary point geometries and frequencies followed by CASSCF/internally contracted configuration interaction calculations to refine the energetics. The present results are in qualitative accord with the BAC-MP4 calculations, but there are differences as large as 8 kcal/mol in the detailed energetics.

  20. MCSCF potential energy surface for photodissociation of formaldehyde

    NASA Technical Reports Server (NTRS)

    Jaffe, R. L.; Morokuma, K.

    1976-01-01

    The ground state potential energy surface for the dissociation of formaldehyde (H2CO to H2 and CO) is calculated with the ab initio MCSCF method with an extended (4-31G) basis set. The location, barrier height, and force constants of the transition state are determined, and the normal coordinate analysis is carried out. The calculated barrier height is 4.5 eV. Based on the calculated quantities, the detailed mechanism of the photochemical dissociation is discussed.

  1. Spectroscopic constants and potential energy curves of GeF +

    NASA Astrophysics Data System (ADS)

    Xu, Hua; Balasubramanian, K.

    1995-05-01

    Spectroscopic constants and potential energy curves of 27 electronic states of GeF + are computed using the complete active space self-consistent field (CASSCF) followed by first- and second-order configuration interaction (FOCI, SOCI) methods that included up to 1.6 million configurations. Our computed spectroscopic constants of the 1Σ+ electronic state fit well with the experimentally observed X ground state. Other yet to be observed properties of several excited electronic states are reported.

  2. Spectroscopic constants and potential energy curves of SnF

    NASA Astrophysics Data System (ADS)

    Dai, Dingguo; Balasubramanian, K.

    1994-07-01

    Spectroscopic constants and potential energy curves of 20 electronic states of SnF arising from valence dissociation limits are computed using the complete active space MCSCF (CASSCF) followed by first- and second-order configuration interaction (FOCI, SOCI) methods, which included up to one million configurations. Our computed spectroscopic constants of five electronic states fit well with the experimentally observed X, A, a, and C states. The dipole moments and other yet to be observed properties of several electronic states are reported.

  3. Spectroscopic Properties and Potential Energy Curves of SnF +

    NASA Astrophysics Data System (ADS)

    Balasubramanian, K.; Xu, H.

    1995-06-01

    Spectroscopic properties and potential energy curves of several electronic states of SnF+ are computed using the complete active space self-consistent field (CASSCF) followed by first- and second-order configuration interaction (FOCI, SOCI) methods that include up to 1.6 million configurations. Spin-orbit effects were incorporated using the relativistic configuration interaction (RCI) method. Spectroscopic properties of several excited electronic states of SnF+ are reported, none of which is observed at present.

  4. The Potential of Renewable Energy Sources in Latvia

    NASA Astrophysics Data System (ADS)

    Sakipova, S.; Jakovics, A.; Gendelis, S.

    2016-02-01

    The article discusses some aspects of the use of renewable energy sources in the climatic conditions prevailing in most of the territory of Latvia, with relatively low wind speeds and a small number of sunny days a year. The paper gives a brief description of the measurement equipment and technology to determine the parameters of the outer air; the results of the measurements are also analysed. On the basis of the data obtained during the last two years at the meteorological station at the Botanical Garden of the University of Latvia, the energy potential of solar radiation and wind was estimated. The values of the possible and the actual amount of produced energy were determined.

  5. CO dimer: new potential energy surface and rovibrational calculations.

    PubMed

    Dawes, Richard; Wang, Xiao-Gang; Carrington, Tucker

    2013-08-15

    The spectrum of CO dimer was investigated by solving the rovibrational Schrödinger equation on a new potential energy surface constructed from coupled-cluster ab initio points. The Schrödinger equation was solved with a Lanczos algorithm. Several 4D (rigid monomer) global ab initio potential energy surfaces (PESs) were made using a previously reported interpolating moving least-squares (IMLS) fitting procedure specialized to describe the interaction of two linear fragments. The potential has two nonpolar minima giving rise to a complicated set of energy level stacks, which are very sensitive to the shapes and relative depths of the two wells. Although the CO dimer has defied previous attempts at an accurate purely ab initio description our best surface yields results in good agreement with experiment. Root-mean-square (rms) fitting errors of less than 0.1 cm(-1) were obtained for each of the fits using 2226 ab initio data at different levels. This allowed direct assessment of the quality of various levels of ab initio theory for prediction of spectra. Our tests indicate that standard CCSD(T) is slow to converge the interaction energy even when sextuple zeta bases as large as ACV6Z are used. The explicitly correlated CCSD(T)-F12b method was found to recover significantly more correlation energy (from singles and doubles) at the CBS limit. Correlation of the core-electrons was found to be important for this system. The best PES was obtained by extrapolation of calculations at the CCSD(T)(AE)-F12b/CVnZ-F12 (n = 3,4) levels. The calculated energy levels were compared to 105 J ≤ 10 levels from experiment. The rms error for 68 levels with J ≤ 6 is only 0.29 cm(-1). The calculated energy levels were assigned stack labels using several tools. New stacks were found. One of them, stack y1, has an energy lower than many previously known stacks and may be observable.

  6. Electromagnetic potentials basis for energy density and power flux

    NASA Astrophysics Data System (ADS)

    Puthoff, H. E.

    2016-09-01

    In rounding out the education of students in advanced courses in applied electromagnetics it is incumbent on us as mentors to raise issues that encourage appreciation of certain subtle aspects that are often overlooked during first exposure to the field. One of these has to do with the interplay between fields and potentials, with the latter often seen as just a convenient mathematical artifice useful in solving Maxwell’s equations. Nonetheless, to those practiced in application it is well understood that various alternatives in the use of fields and potentials are available within electromagnetic (EM) theory for the definitions of energy density, momentum transfer, EM stress-energy tensor, and so forth. Although the various options are all compatible with the basic equations of electrodynamics (e.g., Maxwell’s equations, Lorentz force law, gauge invariance), nonetheless certain alternative formulations lend themselves to being seen as preferable to others with regard to the transparency of their application to physical problems of interest. Here we argue for the transparency of an energy density/power flux option based on the EM potentials alone.

  7. Relation between molecular electrostatic potential, several electronic properties and antibacterial activity of some synthetic furane derivatives

    NASA Astrophysics Data System (ADS)

    Monasterios, Melina; Avendaño, Milagros; Amaro, María Isabel; Infante, Wilson; Charris, Jaime

    2006-10-01

    The present work reports the preliminary evaluation of the antibacterial activity, molecular electrostatic potential (MEP) determination and relevant electronic properties for their behavior as one electron acceptor, of a serial of compounds, active and inactive analogues, derived form furan, that were previously synthesized within our investigation group, with the purpose of establishing the existence of a valid correlation between their antibacterial activity and those electrostatic and electronic properties. According to the balance between the positive and negative areas in combination with the size of the MEP's area it was determined that these derivatives exhibit activity against Gram-positive and Gram-negative bacteria or only against Gram-positive ones. We found no valid correlation between the single point energy, the energy associated to the lowest unoccupied molecular orbital (LUMO); LUMO's density, nucleophilic susceptibility, Log P and the dipole moment, with the experimental activity determined for them. This could be because this is an homologous serial where the properties derived from the electronic distribution just change between those molecules that have a nitro group (active) in contrast with those wherein this group is absent (inactive).

  8. Potential therapeutic targets in energy metabolism pathways of breast cancer.

    PubMed

    Islam, Rowshan Ara; Hossain, Sazzad; Chowdhury, Ezharul Hoque

    2017-03-30

    Mutations in proto-oncogenes and tumor suppressor genes make cancer cells proliferate indefinitely. As they possess almost all mechanisms for cell proliferation and survival like healthy cells, it is difficult to specifically target cancer cells in the body. Current treatments in most of the cases are harmful to healthy cells as well. Thus, it would be of great prudence to target specific characters of cancer cells. Since cancer cells avidly use glucose and glutamine to survive and proliferate by upregulating the relevant enzymes and their specific isoforms having important regulatory roles, it has been of great interest recently to target the energy-related metabolic pathways as part of the therapeutic interventions. This paper summarizes the roles of energy metabolism and their cross-talks with other important signaling pathways in regulating proliferation, invasion and metastasis in breast cancer. As breast cancer is a highly heterogeneous disease, a clear understanding of the variations of energy metabolism in different molecular subtypes would help in treating each type with a very customized, safer and efficient treatment regimen, by targeting specific glucose metabolism and related pathways with gene silencing nucleic acid sequences or small molecule drugs, or the combination of both.

  9. A satellite investigation of energy flux and inferred potential drop in auroral electron energy spectra

    NASA Technical Reports Server (NTRS)

    Menietti, J. D.; Burch, J. L.

    1981-01-01

    The relationship between auroral electron energy flux and the inferred accelerating potential drop for accelerated Maxwellian distributions is investigated on the basis of Atmospheric Explorer D spectral measurements. An analytical approximation for the total downward energy flux carried by an isotropic Maxwellian electron population accelerated by a field-aligned electrostatic potential drop is derived which is valid for values of the electron energy/characteristic accelerated Maxwellian distribution energy which are less than the difference between the ratio of the magnetic field strengths at the altitude of observation and the altitude of potential drop, and unity. Data from the Low Energy Electron Experiment on board AE D obtained on both the dayside and the nightside during periods of significant inverted-V type electron precipitation shows that the 455 energy spectra considered, 160 of them, obtained between 60 and 85 deg invariant latitude, could be fit to accelerated Maxwellian distributions. The 160 Maxwellian spectra are then shown to be in agreement with the predictions of the accelerated Maxwellian model. Finally, analysis of individual spectra suggests that the altitude of the inferred potential drop is at a maximum near the center of the inverted-V structures.

  10. Energy conservation potential of the US Department of Energy interim commercial building standards

    SciTech Connect

    Hadley, D.L.; Halverson, M.A.

    1993-12-01

    This report describes a project conducted to demonstrate the whole-building energy conservation potential achievable from full implementation of the US Department of Energy (DOE) Interim Energy Conservation Performance Standards for New Commercial and Multi-Family High Rise Residential Buildings. DOE`s development and implementation of energy performance standards for commercial buildings were established by the Energy Conservation Standards for New Buildings Act of 1976, as amended, Public Law (PL) 94-385, 42 USC 6831 et seq., hereinafter referred to as the Act. In accordance with the Act, DOE was to establish performance standards for both federal and private sector buildings ``to achieve the maximum practicable improvements in energy efficiency and use of non-depletable resources for all new buildings``.

  11. Metabolic Energy of Action Potentials Modulated by Spike Frequency Adaptation

    PubMed Central

    Yi, Guo-Sheng; Wang, Jiang; Li, Hui-Yan; Wei, Xi-Le; Deng, Bin

    2016-01-01

    Spike frequency adaptation (SFA) exists in many types of neurons, which has been demonstrated to improve their abilities to process incoming information by synapses. The major carrier used by a neuron to convey synaptic signals is the sequences of action potentials (APs), which have to consume substantial metabolic energies to initiate and propagate. Here we use conductance-based models to investigate how SFA modulates the AP-related energy of neurons. The SFA is attributed to either calcium-activated K+ (IAHP) or voltage-activated K+ (IM) current. We observe that the activation of IAHP or IM increases the Na+ load used for depolarizing membrane, while produces few effects on the falling phase of AP. Then, the metabolic energy involved in Na+ current significantly increases from one AP to the next, while for K+ current it is less affected. As a consequence, the total energy cost by each AP gets larger as firing rate decays down. It is also shown that the minimum Na+ charge needed for the depolarization of each AP is unaffected during the course of SFA. This indicates that the activation of either adaptation current makes APs become less efficient to use Na+ influx for their depolarization. Further, our simulations demonstrate that the different biophysical properties of IM and IAHP result in distinct modulations of metabolic energy usage for APs. These investigations provide a fundamental link between adaptation currents and neuronal energetics, which could facilitate to interpret how SFA participates in neuronal information processing. PMID:27909394

  12. Gravitational potential energy of the earth - A spherical harmonic approach

    NASA Technical Reports Server (NTRS)

    Rubincam, D. P.

    1979-01-01

    A spherical harmonic equation for the gravitational potential energy of the earth is derived for an arbitrary density distribution by conceptually bringing in mass-elements from infinity and building up the earth shell upon spherical shell. The zeroth degree term in the spherical harmonic expansion agrees with the usual expression for the energy of a radial density distribution. The second degree terms give a maximum nonhydrostatic energy in the crust and mantle of -2.77 x 10 to the 29th ergs, an order of magnitude below McKenzie's (1966) estimate. McKenzie's result stems from mathematical error. Our figure is almost identical with Kaula's (1963) estimate of the minimum shear strain energy in the mantle, a not unexpected result on the basis of the virial theorem. If the earth is assumed to be a homogeneous viscous oblate spheroid relaxing to an equilibrium shape, then a lower limit to the mantle viscosity of 1.3 x 10 to the 20th P is found by assuming that the total geothermal flux is due to viscous dissipation of energy. This number is almost six orders of magnitude below MacDonald's (1966) estimate of the viscosity and removes his objection to convection. If the nonequilibrium figure is dynamically maintained by the earth acting as a heat engine at 1% efficiency, then the viscosity is 10 to the 22nd P, a number preferred by Cathles (1975) and Peltier and Andrew (1976) as the viscosity of the mantle.

  13. GIS Assessment of Wind Energy Potential in California and Florida

    NASA Astrophysics Data System (ADS)

    Snow, R. K.; Snow, M. M.

    2008-05-01

    Energy efficiency coupled with renewable energy technologies can provide most of the U.S. carbon emissions reductions needed to contain atmospheric carbon concentrations at 450-500 parts per million, considered by many to be a tipping point in mitigating climate change. Among the leaders in the alternative energy sector is wind power, which is now one of the largest sources of new power generation in the U.S. creating jobs and revenue for rural communities while powering our economy with an emissions-free source of energy. In 2006, wind turbines capable of generating more than 2,400 megawatts of electricity were installed in the U.S. and by 2007 this number had risen to 3,000 megawatts. The U.S. generated 31 billion kilowatt-hours of wind power in 2007, which is enough electricity to power the equivalent of nearly 3 million average homes. It is estimated that generating the same amount of electricity would require burning 16 million tons of coal or 50 million barrels of oil. This study examines the wind power potential of sites near populated areas in Florida and California to determine the practicability of installing wind turbines at these locations. A GIS was developed in order to conduct a spatial analysis of these sites based on mean annual wind speed measured in meters per second and wind power density ratings measured in watts per square meter. The analysis indicates that coastal areas of Cocoa Beach, Key West, Hollywood, and West Palm Beach, respectively, possess the greatest potential for wind energy in Florida with mean annual wind speeds of 4.9 m/s and average wind power density ratings of 171 w/m2 peaking at Cocoa Beach followed by wind speeds of 4.64 m/s and wind power ratings of 115 w/m2 at Key West. California wind energy potential is even greater than that of Florida with Fairfield exhibiting mean annual wind speeds of 5.9 m/s and average wind power density ratings of 327 w/m2 followed by the Mojave and Palmdale areas with mean annual wind speeds of

  14. Origin of non-Gaussian site energy disorder in molecular aggregates

    NASA Astrophysics Data System (ADS)

    Rancova, Olga; Jakučionis, Mantas; Valkunas, Leonas; Abramavicius, Darius

    2017-04-01

    Gaussian site energy disorder is an ad hoc concept usually implemented in simulations of excitation dynamics in molecular systems. In this letter we suggest a mechanism which may cause correlated static energy disorder in a broad range of molecular systems. Our approach leads to non-Gaussian site energy distribution, which strongly affects statistical properties of exciton wavefunctions and consequently changes material functional characteristics.

  15. New parameter-free polarization potentials in low-energy positron collisions

    NASA Technical Reports Server (NTRS)

    Jain, Ashok

    1990-01-01

    The polarization potential plays a decisive role in shaping up the cross sections in low energy positron collisions with atoms and molecules. However, its inclusion without involving any adjustable parameter, is still a challenge. Various other techniques employed so far for positron collisions are summarized, and a new, nonadjustable and very simple form of the polarization potential for positron-atom (molecule) collisions below the threshold of positronium formation is discussed. This new recently proposed potential is based on the correlation energy of a single positron in a homogeneous electron gas. The correlation energy was calculated by solving the Schrodinger equation of the positron-electron system and fitted to an analytical form in various ranges of the density parameter. In the outside region, the correlation energy is joined smoothly with the correct asymptotic form. This new positron correlation polarization (PCOP) potential was tested on several atomic and molecular targets such as the Ar, CO, and CH4. The results on the total and differential cross sections on these targets are shown along with the experimental data where available.

  16. Molecular mimicry of photosynthetic energy and electron transfer

    SciTech Connect

    Gust, D.; Moore, T.A.; Moore, A.L. )

    1993-04-01

    Proper application of reaction design considerations can yield artificial photosynthetic devices which credibility mimic the three natural photochemical processes. One approach is to use pigments and electron donors and acceptors related to those found in natural photosynthesis (and thus presumably optimal for that system), but to replace the protein with covalent bonds as an organizing precept. Molecular pentads described herein exemplify the success of this approach. At the heart of these molecules, are two covalently linked synthetic porphyrin moieties (P-P). One of these models for chlorophyll is attached to a carotenoid polyene (C), whereas the other is linked to a rigid diquinone (Q-Q). As discussed later in this paper, excitation of such a pentad is followed by photoinitiated electron transfer steps which ultimately give a C[sup [center dot]+]-P-P-Q-Q[sup [center dot]-] charge-separated state. Depending upon the structure of the pentad and the conditions, these states are formed with quantum yields of up to 0.83, have lifetimes approaching 0.5 ms, and store about one-half of the energy of the exciting singlet state. Related photosynthesis mimics display singlet-singlet energy transfer from carotenoid polyenes to porphyrins and among porphyrin chromophores, and rapid quenching of porphyrin triplet states by attached carotenoids. How have the structures of these and other successful artificial reaction centers evolved, and what will be the next steps in their development The authors will address these questions from the point of view of photoinitiated electron transfer, and then singlet and triplet energy transfer will briefly be considered. 37 refs., 4 figs.

  17. Onshore wind energy potential over Iberia: present and future projections

    NASA Astrophysics Data System (ADS)

    Rochinha, Carlos A.; Santos, João A.; Liberato, Margarida L. R.; Pinto, Joaquim G.

    2014-05-01

    Onshore grid-connected wind power generation has been explored for more than three decades in the Iberian Peninsula. Further, increasing attention has been devoted to renewable energy sources in a climate change context. While advantages of wind energy are widely recognized, its distribution is not spatially homogeneous and not uniform throughout the year. Hence, understanding these spatial-temporal distributions is critical in power system planning. The present study aims at assessing the potential power output estimated from 10 m wind components simulated by a regional climate model (CCLM), driven by ERA40 reanalysis. Datasets are available on a grid with a high spatial resolution (approximately 20 km) and over a 40-yr period (1961-2000). Furthermore, several target sites, located in areas with high installed wind generation capacity, are selected for local-to-regional scale assessments. The results show that potential wind power is higher over northern Iberia, mostly in Cantabria and Galicia, while Andalucía and Cataluña record the lowest values. With respect to the intra-annual variability, summer is by far the season with the lowest potential energy outputs. Furthermore, the inter-annual variability reveals an overall downward long-term trend over the 40-yr period, particularly in the winter time series. A CCLM transient experiment, forced by the SRES A1B emission scenario, is also discussed for a future period (2041-2070), after a model validation/calibration process (bias corrections). Significant changes in the wind power potential are projected for the future throughout Iberia, but their magnitude largely depends on the locations. This work was partially supported by FEDER (Fundo Europeu de Desenvolvimento Regional) funds through the COMPETE (Programa Operacional Factores de Competitividade) and by national funds through FCT (Fundação para a Ciência e a Tecnologia, Portugal) under project STORMEx FCOMP-01-0124-FEDER- 019524 (PTDC/AAC-CLI/121339/2010).

  18. Energy relaxation of intermolecular motions in supercooled water and ice: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Yagasaki, Takuma; Saito, Shinji

    2011-12-01

    We investigate the energy relaxation of intermolecular motions in liquid water at temperatures ranging from 220 K to 300 K and in ice at 220 K using molecular dynamics simulations. We employ the recently developed frequency resolved transient kinetic energy analysis, which provides detailed information on energy relaxation in condensed phases like two-color pump-probe spectroscopy. It is shown that the energy cascading in liquid water is characterized by four processes. The temperature dependences of the earlier three processes, the rotational-rotational, rotational-translational, and translational-translational energy transfers, are explained in terms of the density of states of the intermolecular motions. The last process is the slow energy transfer arising from the transitions between potential energy basins caused by the excitation of the low frequency translational motion. This process is absent in ice because the hydrogen bond network rearrangement, which accompanies the interbasin transitions in liquid water, cannot take place in the solid phase. We find that the last process in supercooled water is well approximated by a stretched exponential function. The stretching parameter, β, decreases from 1 to 0.72 with decreasing temperature. This result indicates that the dynamics of liquid water becomes heterogeneous at lower temperatures.

  19. The energy cost of action potential propagation in dopamine neurons: clues to susceptibility in Parkinson's disease

    PubMed Central

    Pissadaki, Eleftheria K.; Bolam, J. Paul

    2013-01-01

    Dopamine neurons of the substantia nigra pars compacta (SNc) are uniquely sensitive to degeneration in Parkinson's disease (PD) and its models. Although a variety of molecular characteristics have been proposed to underlie this sensitivity, one possible contributory factor is their massive, unmyelinated axonal arbor that is orders of magnitude larger than other neuronal types. We suggest that this puts them under such a high energy demand that any stressor that perturbs energy production leads to energy demand exceeding supply and subsequent cell death. One prediction of this hypothesis is that those dopamine neurons that are selectively vulnerable in PD will have a higher energy cost than those that are less vulnerable. We show here, through the use of a biology-based computational model of the axons of individual dopamine neurons, that the energy cost of axon potential propagation and recovery of the membrane potential increases with the size and complexity of the axonal arbor according to a power law. Thus SNc dopamine neurons, particularly in humans, whose axons we estimate to give rise to more than 1 million synapses and have a total length exceeding 4 m, are at a distinct disadvantage with respect to energy balance which may be a factor in their selective vulnerability in PD. PMID:23515615

  20. The energy cost of action potential propagation in dopamine neurons: clues to susceptibility in Parkinson's disease.

    PubMed

    Pissadaki, Eleftheria K; Bolam, J Paul

    2013-01-01

    Dopamine neurons of the substantia nigra pars compacta (SNc) are uniquely sensitive to degeneration in Parkinson's disease (PD) and its models. Although a variety of molecular characteristics have been proposed to underlie this sensitivity, one possible contributory factor is their massive, unmyelinated axonal arbor that is orders of magnitude larger than other neuronal types. We suggest that this puts them under such a high energy demand that any stressor that perturbs energy production leads to energy demand exceeding supply and subsequent cell death. One prediction of this hypothesis is that those dopamine neurons that are selectively vulnerable in PD will have a higher energy cost than those that are less vulnerable. We show here, through the use of a biology-based computational model of the axons of individual dopamine neurons, that the energy cost of axon potential propagation and recovery of the membrane potential increases with the size and complexity of the axonal arbor according to a power law. Thus SNc dopamine neurons, particularly in humans, whose axons we estimate to give rise to more than 1 million synapses and have a total length exceeding 4 m, are at a distinct disadvantage with respect to energy balance which may be a factor in their selective vulnerability in PD.

  1. Graph theoretical similarity approach to compare molecular electrostatic potentials.

    PubMed

    Marín, Ray M; Aguirre, Nestor F; Daza, Edgar E

    2008-01-01

    In this work we introduce a graph theoretical method to compare MEPs, which is independent of molecular alignment. It is based on the edit distance of weighted rooted trees, which encode the geometrical and topological information of Negative Molecular Isopotential Surfaces. A meaningful chemical classification of a set of 46 molecules with different functional groups was achieved. Structure--activity relationships for the corticosteroid binding affinity (CBG) of 31 steroids by means of hierarchical clustering resulted in a clear partitioning in high, intermediate, and low activity groups, whereas the results from quantitative structure--activity relationships, obtained from a partial least-squares analysis, showed comparable or better cross-validated correlation coefficients than the ones reported for previous methods based solely in the MEP.

  2. Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations.

    PubMed

    Bell, David R; Cheng, Sara Y; Salazar, Heber; Ren, Pengyu

    2017-04-10

    We introduce a coarse-grained RNA model for molecular dynamics simulations, RACER (RnA CoarsE-gRained). RACER achieves accurate native structure prediction for a number of RNAs (average RMSD of 2.93 Å) and the sequence-specific variation of free energy is in excellent agreement with experimentally measured stabilities (R(2) = 0.93). Using RACER, we identified hydrogen-bonding (or base pairing), base stacking, and electrostatic interactions as essential driving forces for RNA folding. Also, we found that separating pairing vs. stacking interactions allowed RACER to distinguish folded vs. unfolded states. In RACER, base pairing and stacking interactions each provide an approximate stability of 3-4 kcal/mol for an A-form helix. RACER was developed based on PDB structural statistics and experimental thermodynamic data. In contrast with previous work, RACER implements a novel effective vdW potential energy function, which led us to re-parameterize hydrogen bond and electrostatic potential energy functions. Further, RACER is validated and optimized using a simulated annealing protocol to generate potential energy vs. RMSD landscapes. Finally, RACER is tested using extensive equilibrium pulling simulations (0.86 ms total) on eleven RNA sequences (hairpins and duplexes).

  3. Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations

    PubMed Central

    Bell, David R.; Cheng, Sara Y.; Salazar, Heber; Ren, Pengyu

    2017-01-01

    We introduce a coarse-grained RNA model for molecular dynamics simulations, RACER (RnA CoarsE-gRained). RACER achieves accurate native structure prediction for a number of RNAs (average RMSD of 2.93 Å) and the sequence-specific variation of free energy is in excellent agreement with experimentally measured stabilities (R2 = 0.93). Using RACER, we identified hydrogen-bonding (or base pairing), base stacking, and electrostatic interactions as essential driving forces for RNA folding. Also, we found that separating pairing vs. stacking interactions allowed RACER to distinguish folded vs. unfolded states. In RACER, base pairing and stacking interactions each provide an approximate stability of 3–4 kcal/mol for an A-form helix. RACER was developed based on PDB structural statistics and experimental thermodynamic data. In contrast with previous work, RACER implements a novel effective vdW potential energy function, which led us to re-parameterize hydrogen bond and electrostatic potential energy functions. Further, RACER is validated and optimized using a simulated annealing protocol to generate potential energy vs. RMSD landscapes. Finally, RACER is tested using extensive equilibrium pulling simulations (0.86 ms total) on eleven RNA sequences (hairpins and duplexes). PMID:28393861

  4. 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.

  5. Intermolecular potential energy surface and thermophysical properties of ethylene oxide

    NASA Astrophysics Data System (ADS)

    Crusius, Johann-Philipp; Hellmann, Robert; Hassel, Egon; Bich, Eckard

    2014-10-01

    A six-dimensional potential energy hypersurface (PES) for two interacting rigid ethylene oxide (C2H4O) molecules was determined from high-level quantum-chemical ab initio calculations. The counterpoise-corrected supermolecular approach at the MP2 and CCSD(T) levels of theory was utilized to determine interaction energies for 10178 configurations of two molecules. An analytical site-site potential function with 19 sites per ethylene oxide molecule was fitted to the interaction energies and fine tuned to agree with data for the second acoustic virial coefficient from accurate speed of sound measurements. The PES was validated by computing the second virial coefficient, shear viscosity, and thermal conductivity. The values of these properties are substantiated by the best experimental data as they tend to fall within the uncertainty intervals and also obey the experimental temperature functions, except for viscosity, where experimental data are insufficient. Due to the lack of reliable data, especially for the transport properties, our calculated values are currently the most accurate estimates for these properties of ethylene oxide.

  6. Potential for energy conservation in the cement industry

    SciTech Connect

    Garrett-Price, B.A.

    1985-02-01

    This report assesses the potential for energy conservation in the cement industry. Energy consumption per ton of cement decreased 20% between 1972 and 1982. During this same period, the cement industry became heavily dependent on coal and coke as its primary fuel source. Although the energy consumed per ton of cement has declined markedly in the past ten years, the industry still uses more than three and a half times the fuel that is theoretically required to produce a ton of clinker. Improving kiln thermal efficiency offers the greatest opportunity for saving fuel. Improving the efficiency of finish grinding offers the greatest potential for reducing electricity use. Technologies are currently available to the cement industry to reduce its average fuel consumption per ton by product by as much as 40% and its electricity consumption per ton by about 10%. The major impediment to adopting these technologies is the cement industry's lack of capital as a result of low or no profits in recent years.

  7. Intermolecular potential energy surface and thermophysical properties of ethylene oxide

    SciTech Connect

    Crusius, Johann-Philipp Hassel, Egon; Hellmann, Robert; Bich, Eckard

    2014-10-28

    A six-dimensional potential energy hypersurface (PES) for two interacting rigid ethylene oxide (C{sub 2}H{sub 4}O) molecules was determined from high-level quantum-chemical ab initio calculations. The counterpoise-corrected supermolecular approach at the MP2 and CCSD(T) levels of theory was utilized to determine interaction energies for 10178 configurations of two molecules. An analytical site-site potential function with 19 sites per ethylene oxide molecule was fitted to the interaction energies and fine tuned to agree with data for the second acoustic virial coefficient from accurate speed of sound measurements. The PES was validated by computing the second virial coefficient, shear viscosity, and thermal conductivity. The values of these properties are substantiated by the best experimental data as they tend to fall within the uncertainty intervals and also obey the experimental temperature functions, except for viscosity, where experimental data are insufficient. Due to the lack of reliable data, especially for the transport properties, our calculated values are currently the most accurate estimates for these properties of ethylene oxide.

  8. ForceFit: a code to fit classical force fields to quantum mechanical potential energy surfaces.

    PubMed

    Waldher, Benjamin; Kuta, Jadwiga; Chen, Samuel; Henson, Neil; Clark, Aurora E

    2010-09-01

    The ForceFit program package has been developed for fitting classical force field parameters based upon a force matching algorithm to quantum mechanical gradients of configurations that span the potential energy surface of the system. The program, which runs under UNIX and is written in C++, is an easy-to-use, nonproprietary platform that enables gradient fitting of a wide variety of functional force field forms to quantum mechanical information obtained from an array of common electronic structure codes. All aspects of the fitting process are run from a graphical user interface, from the parsing of quantum mechanical data, assembling of a potential energy surface database, setting the force field, and variables to be optimized, choosing a molecular mechanics code for comparison to the reference data, and finally, the initiation of a least squares minimization algorithm. Furthermore, the code is based on a modular templated code design that enables the facile addition of new functionality to the program.

  9. Diffusion energy profiles in silica mesoporous molecular sieves modelled with the fragment molecular orbital method

    NASA Astrophysics Data System (ADS)

    Roskop, Luke; Fedorov, Dmitri G.; Gordon, Mark S.

    2013-07-01

    The fragment molecular orbital (FMO) method is used to model truncated portions of mesoporous silica nanoparticle (MSN) pores. The application of the FMO/RHF (restricted Hartree-Fock) method to MCM-41 type MSNs is discussed and an error analysis is given. The FMO/RHF method is shown to reliably approximate the RHF energy (error ∼0.2 kcal/mol), dipole moment (error ∼0.2 debye) and energy gradient (root mean square [RMS] error ∼0.2 × 10-3 a.u./bohr). Several FMO fragmentation schemes are employed to provide guidance for future applications to MSN models. An MSN pore model is functionalised with (phenyl)propyl substituents and the diffusion barrier for benzene passing through the pore is computed by the FMO/RHF-D method with the Grimme dispersion correction (RHF-D). For the reaction coordinates examined here, the maximum FMO/RHF-D interaction energies range from -0.3 to -5.8 kcal/mol.

  10. Correlation energy and dispersion interaction in the ab initio potential energy curve of the neon dimer.

    PubMed

    Bytautas, Laimutis; Ruedenberg, Klaus

    2008-06-07

    A close approximation to the empirical potential energy curve of the neon dimer is obtained by coupled-cluster singles plus doubles plus noniterative triples calculations by using nonaugmented correlation-consistent basis sets without counterpoise corrections and complementing them by three-term extrapolations to the complete basis set limit. The potential energy is resolved into a self-consistent-field Hartree-Fock contribution and a correlation contribution. The latter is shown to decay in the long-range region in accordance with the empirical dispersion expansion.

  11. Potential impacts of nanotechnology on energy transmission applications and needs.

    SciTech Connect

    Elcock, D.; Environmental Science Division

    2007-11-30

    The application of nanotechnologies to energy transmission has the potential to significantly impact both the deployed transmission technologies and the need for additional development. This could be a factor in assessing environmental impacts of right-of-way (ROW) development and use. For example, some nanotechnology applications may produce materials (e.g., cables) that are much stronger per unit volume than existing materials, enabling reduced footprints for construction and maintenance of electricity transmission lines. Other applications, such as more efficient lighting, lighter-weight materials for vehicle construction, and smaller batteries having greater storage capacities may reduce the need for long-distance transport of energy, and possibly reduce the need for extensive future ROW development and many attendant environmental impacts. This report introduces the field of nanotechnology, describes some of the ways in which processes and products developed with or incorporating nanomaterials differ from traditional processes and products, and identifies some examples of how nanotechnology may be used to reduce potential ROW impacts. Potential environmental, safety, and health impacts are also discussed.

  12. Potential environmental effects of energy conservation measures in northwest industries

    SciTech Connect

    Baechler, M C; Gygi, K F; Hendrickson, P L

    1992-01-01

    The Bonneville Power Administration (Bonneville) has identified 101 plants in the Pacific Northwest that account for 80% of the region's industrial electricity consumption. These plants offer a precise target for a conservation program. PNL determined that most of these 101 plants were represented by 11 major industries. We then reviewed 36 major conservation technologies used in these 11 industrial settings to determine their potential environmental impacts. Energy efficiency technologies designed for industrial use may result in direct or indirect environmental impacts. Effects may result from the production of the conservation measure technology, changes in the working environment due to different energy and material requirements, or changes to waste streams. Industry type, work-place conditions, worker training, and environmental conditions inside and outside the plant are all key variables that may affect environmental outcomes. To address these issues this report has three objectives: Describe potential conservation measures that Bonneville may employ in industrial programs and discuss potential primary impacts. Characterize industrial systems and processes where the measure may be employed and describe general environmental issues associated with each industry type. Review environmental permitting, licensing, and other regulatory actions required for industries and summarize the type of information available from these sources for further analysis.

  13. Quantum dot-based energy transfer: perspectives and potential for applications in photodynamic therapy.

    PubMed

    Samia, Anna C S; Dayal, Smita; Burda, Clemens

    2006-01-01

    Quantum dots have emerged as an important class of material that offers great promise to a diverse range of applications ranging from energy conversion to biomedicine. Here, we review the potential of using quantum dots and quantum dot conjugates as sensitizers for photodynamic therapy (PDT). The photophysics of singlet oxygen generation in relation to quantum dot-based energy transfer is discussed and the possibility of using quantum dots as photosensitizer in PDT is assessed, including their current limitations to applications in biological systems. The biggest advantage of quantum dots over molecular photosensitizers that comes into perspective is their tunable optical properties and surface chemistries. Recent developments in the preparation and photophysical characterization of quantum dot energy transfer processes are also presented in this review, to provide insights on the future direction of quantum dot-based photosensitization studies from the viewpoint of our ongoing research.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  15. Expressions of Energy and Potential due to Orbital Polarization

    NASA Astrophysics Data System (ADS)

    Narita, Akira; Higuchi, Masahiko

    2006-02-01

    The simple and tractable representation for the LS-multiplet energy in l1l2-configuration in an atom is derived in the form of the polynomials being a function of l1\\cdotl2 which obey the recurrence formulae, and is suitable for the vector model. Moreover, it is extended to ln configurations. On a basis of the model, the definition of the orbital polarization energy is given. The more precise expressions of the energies compared to those so far proposed by Eriksson et al. are derived for the maximal spin multiplets in pn, dn, and fn. They are composed of two terms depending on -3L2/2 and n(n-2l-1). They are the exact for pn and dn, but it for fn is correct only for a ground multiplet. Other expressions are also derived as a function of L2 for fn, though more complicated. For the actual atomic and band structure calculations based on local-spin-density-approximation (LSDA), the modified expression for the energy is proposed. The potential is derived from its expression in terms of the density functional theory, and can be applied to their structure calculations.

  16. Emissive Molecular Aggregates and Energy Migration in Luminescent Solar Concentrators.

    PubMed

    Banal, James L; Zhang, Bolong; Jones, David J; Ghiggino, Kenneth P; Wong, Wallace W H

    2017-01-17

    of chromophores exhibiting aggregation-induced emission (AIE) behavior are attractive candidates for LSC applications. Strategic application of AIE chromophores has led to the development of the first organic-based transparent solar concentrator that harvests UV light as well as the demonstration of reabsorption reduction by taking advantage of energy migration processes between chromophores. Further developments led us to the application of perylene diimides using an energy migration/energy transfer approach. To prevent concentration quenching, a molecularly insulated perylene diimide with bulky substituents attached to the imide positions was designed and synthesized. By combining the insulated perylene diimide with a commercial perylene dye as an energy donor-acceptor emitter pair, detrimental luminescence reabsorption was reduced while achieving a high chromophore concentration for efficient light absorption. This Account reviews and reinspects some of our recent work and the improvements in the field of LSCs.

  17. Stabilized quasi-Newton optimization of noisy potential energy surfaces

    SciTech Connect

    Schaefer, Bastian; Goedecker, Stefan; Alireza Ghasemi, S.; Roy, Shantanu

    2015-01-21

    Optimizations of atomic positions belong to the most commonly performed tasks in electronic structure calculations. Many simulations like global minimum searches or characterizations of chemical reactions require performing hundreds or thousands of minimizations or saddle computations. To automatize these tasks, optimization algorithms must not only be efficient but also very reliable. Unfortunately, computational noise in forces and energies is inherent to electronic structure codes. This computational noise poses a severe problem to the stability of efficient optimization methods like the limited-memory Broyden–Fletcher–Goldfarb–Shanno algorithm. We here present a technique that allows obtaining significant curvature information of noisy potential energy surfaces. We use this technique to construct both, a stabilized quasi-Newton minimization method and a stabilized quasi-Newton saddle finding approach. We demonstrate with the help of benchmarks that both the minimizer and the saddle finding approach are superior to comparable existing methods.

  18. Stabilized quasi-Newton optimization of noisy potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Schaefer, Bastian; Ghasemi, S. Alireza; Roy, Shantanu; Goedecker, Stefan; Goedecker Group Team

    Optimizations of atomic positions belong to the most frequently performed tasks in electronic structure calculations. Many simulations like global minimum searches or the identification of chemical reaction pathways can require the computation of hundreds or thousands of minimizations or saddle points. To automatize these tasks, optimization algorithms must not only be efficient but also very reliable. Unfortunately, computational noise in forces and energies is inherent to electronic structure codes. This computational noise poses a severe problem to the stability of efficient optimization methods like the limited-memory Broyden-Fletcher-Goldfarb-Shanno algorithm. In this talk a recently published technique that allows to obtain significant curvature information of noisy potential energy surfaces is presented. This technique was used to construct both, a stabilized quasi-Newton minimization method and a stabilized quasi-Newton saddle finding approach. With the help of benchmarks both the minimizer and the saddle finding approach were demonstrated to be superior to comparable existing methods.

  19. Stabilized quasi-Newton optimization of noisy potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Schaefer, Bastian; Alireza Ghasemi, S.; Roy, Shantanu; Goedecker, Stefan

    2015-01-01

    Optimizations of atomic positions belong to the most commonly performed tasks in electronic structure calculations. Many simulations like global minimum searches or characterizations of chemical reactions require performing hundreds or thousands of minimizations or saddle computations. To automatize these tasks, optimization algorithms must not only be efficient but also very reliable. Unfortunately, computational noise in forces and energies is inherent to electronic structure codes. This computational noise poses a severe problem to the stability of efficient optimization methods like the limited-memory Broyden-Fletcher-Goldfarb-Shanno algorithm. We here present a technique that allows obtaining significant curvature information of noisy potential energy surfaces. We use this technique to construct both, a stabilized quasi-Newton minimization method and a stabilized quasi-Newton saddle finding approach. We demonstrate with the help of benchmarks that both the minimizer and the saddle finding approach are superior to comparable existing methods.

  20. Domestic refrigeration appliances in Poland: Potential for improving energy efficiency

    SciTech Connect

    Meyers, S.; Schipper, L.; Lebot, B.

    1993-08-01

    This report is based on information collected from the main Polish manufacturer of refrigeration appliances. We describe their production facilities, and show that the energy consumption of their models for domestic sale is substantially higher than the average for similar models made in W. Europe. Lack of data and uncertainty about future production costs in Poland limits our evaluation of the cost-effective potential to increase energy efficiency, but it appears likely that considerable improvement would be economic from a societal perspective. Many design options are likely to have a simple payback of less than five years. We found that the production facilities are in need of substantial modernization in order to produce higher quality and more efficient appliances. We discuss policy options that could help to build a market for more efficient appliances in Poland and thereby encourage investment to produce such equipment.

  1. Calorific evaluation and energy potential of grape pomace

    NASA Astrophysics Data System (ADS)

    Burg, Patrik; Ludín, David; Rutkowski, Kazimierz; Krakowiak-Bal, Anna; Trávníček, Petr; Zemánek, Pavel; Turan, Jan; Višacki, Vladimir

    2016-04-01

    This article deals with energetic evaluation and potential of pomace - a waste product originating during production of grape wine. Calorimetric analysis of 19 grapevine varieties was performed in 2013 and 2014. The aim was to specify their combustible limit and the gross calorific value. The evaluations were performed on pristine pomace, pomace without seeds, and only on seeds themselves. The results obtained imply that pomace is an interesting energetic resource with a gross calorific value of 16.07-18.97 MJ kg-1. Lower calorific values were detected in pomace after seed separation ie 14.60-17.75 MJ kg-1; on the contrary, seeds alone had the highest calorific values of 19.78-21.13 MJ kg-1. It can be assumed from the results of energetic evaluation of pomace in Czech Republic conditions that, by purposeful and efficient usage of pomace, 6.4 GWh of electric energy and 28 GWh of thermal energy can be generated.

  2. Energy strategy and mitigation potential in energy sector of the Russian federation

    SciTech Connect

    Yakovlev, A.F.; Petrov, V.N.; Chupyatov, V.P.

    1996-12-31

    This paper describes the mitigation potential in the Russian energy sector and presents CO{sub 2} - emission scenarios. Based on the Russian energy strategy, energy conservation potential has been estimated and three groups of energy conservation measures have been pointed out. Taking into account the economic development scenarios and the scenarios of energy consumption and energy conservation, future CO{sub 2} emission scenarios for 2000 and 2010 have been prepared. Some important characteristics of these scenarios have been presented and discussed. For the period 2000-2010 annual growth rates for CO{sub 2} emission in the Russian energy sector will not exceed 0.9-1.3 %, and emission levels in 2000 make up - 75-78 %, and in 2010 - 81-88 % of the 1990 level. For the probable scenario the CO{sub 2} emission reducing will make up about 6% and 25% (for the optimistic scenario about 16% and 31%) of CO{sub 2} emission for reference scenario in 2000 and 2010 respectively. Additional CO{sub 2} emission reducing (3-5% of domestic CO{sub 2} emission) will result from increasing share of natural gas consumption.

  3. Molecular Modeling of Environmentally Important Processes: Reduction Potentials

    ERIC Educational Resources Information Center

    Lewis, Anne; Bumpus, John A.; Truhlar, Donald G.; Cramer, Christopher J.

    2004-01-01

    The increasing use of computational quantum chemistry in the modeling of environmentally important processes is described. The employment of computational quantum mechanics for the prediction of oxidation-reduction potential for solutes in an aqueous medium is discussed.

  4. Energy expenditure estimates during school physical education: Potential vs. reality?

    PubMed

    Kahan, David; McKenzie, Thomas L

    2017-02-01

    Schools are salient locations for addressing the high prevalence of overweight and obesity. Most US states require some physical education (PE) and the energy expended during PE has potential to positively affect energy balance. We previously used 2012 data to examine state policies for PE to calculate estimated student energy expenditure (EEE) under potential (i.e., recommendations followed) and existing conditions. Since then, data have been updated on both state policies and the conduct of PE. Based on updated data, we used PE frequency, duration, and intensity, student mass, and class size to calculate EEE for the delivery of PE under (a) national professional recommendations, (b) 2016 state policies, and (c) school-reported conditions. Although increased from four years ago, only 22 states currently have policies mandating specific PE minutes. EEE over 10years shows the enormous impact PE could have on energy balance. For the average recommended-size PE class, resultant annual EEE based on professional recommendations for min/week far exceeded those based on average state (n=22) policy for min/week by 44.5% for elementary, 62.7% for middle, and 59.5% for high schools. Since 2012 more states adopted policies for PE minutes than dropped them, however, EEE over 10years showed a net loss of 1200kcal/student. With no overall recent improvements in state PE policy and professional recommendations currently not being met, PE remains an underutilized public health resource for EEE. Strong policies, coupled with enhanced accountability of PE teachers and administrators, are needed to ensure PE exists in schools.

  5. Freezing of Energy of a Soliton in an External Potential

    NASA Astrophysics Data System (ADS)

    Bambusi, D.; Maspero, A.

    2016-05-01

    In this paper we study the dynamics of a soliton in the generalized NLS with a small external potential ɛV of Schwartz class. We prove that there exists an effective mechanical system describing the dynamics of the soliton and that, for any positive integer r, the energy of such a mechanical system is almost conserved up to times of order ɛ - r . In the rotational invariant case we deduce that the true orbit of the soliton remains close to the mechanical one up to times of order ɛ - r .

  6. Terahertz absorption spectra and potential energy distribution of liquid crystals.

    PubMed

    Chen, Zezhang; Jiang, Yurong; Jiang, Lulu; Ma, Heng

    2016-01-15

    In this work, the terahertz (THz) absorption spectra of a set of nematic liquid crystals were studied using the density functional theories (DFT). An accurate assignment of the vibrational modes corresponding to absorption frequencies were performed using potential energy distribution (PED) in a frequency range of 0-3 THz. The impacts of different core structures on THz absorption spectra were discussed. The results indicate that scope of application must be considered in the LC-based THz device designing. This proposed work may give a useful suggestion on the design of novel liquid crystal material in THz wave.

  7. Terahertz absorption spectra and potential energy distribution of liquid crystals

    NASA Astrophysics Data System (ADS)

    Chen, Zezhang; Jiang, Yurong; Jiang, Lulu; Ma, Heng

    2016-01-01

    In this work, the terahertz (THz) absorption spectra of a set of nematic liquid crystals were studied using the density functional theories (DFT). An accurate assignment of the vibrational modes corresponding to absorption frequencies were performed using potential energy distribution (PED) in a frequency range of 0-3 THz. The impacts of different core structures on THz absorption spectra were discussed. The results indicate that scope of application must be considered in the LC-based THz device designing. This proposed work may give a useful suggestion on the design of novel liquid crystal material in THz wave.

  8. Spectroscopic Constants and Potential Energy Curves for GeF

    NASA Astrophysics Data System (ADS)

    Liao, D. W.; Balasubramanian, K.

    1994-01-01

    The spectroscopic constants of the electronic states of GeF lying below the 60000 cm -1 region are obtained using the complete active space multiconfiguration self-consistent field followed by first- and second-order configuration interaction (FOCI. SOCI) methods which included up to a million configurations. The potential energy curves of the low-lying electronic states are also computed. The computed spectroscopic constants confirm the assignments of the X, A, a, C, C', and D' states of GeF. In addition the spectroscopic constants of several electronic states of GeF are predicted which are yet to be observed.

  9. Spectroscopic constants and potential energy curves for TaH

    NASA Astrophysics Data System (ADS)

    Cheng, W.; Balasubramanian, K.

    1991-09-01

    Spectroscopic constants and potential energy curves of 21 electronic states of the diatomic TaH are computed using complete active space multiconfiguration self-consistent field (CASSCF) followed by second-order configuration interaction (SOCI) calculations. In addition spin-orbit effects were included using the relativistic configuration interaction method (RCI). The ground state of TaH was found to be a 0 + state, which is a mixture of 5Δ(0 +), 5Π(0 +), 3Σ -(0 +), and 3Π(0 +). The spin-orbit effects were found to be significant for TaH. Several spectroscopic transitions are predicted for TaH none of which is observed.

  10. Spectroscopic Constants and Potential Energy Curves for GeBr

    NASA Astrophysics Data System (ADS)

    Liao, D. W.; Balasubramanian, K.

    1993-12-01

    Spectroscopic constants and potential energy curves of several low-lying electronic states of the GeBr radical are computed using the complete active space multiconfiguration self-consistent filed (CASSCF) followed by first- and second-order configuration interaction (FOCI, SOCI) methods which included up to a million configurations. Our computed spectroscopic constants confirm the assignments of X, A, A‧, B, and C states. Spectroscopic properties of several other electronic states below 30 000 cm-1 are predicted, which are yet to be observed.

  11. Pairwise contact energy statistical potentials can help to find probability of point mutations.

    PubMed

    Saravanan, K M; Suvaithenamudhan, S; Parthasarathy, S; Selvaraj, S

    2017-01-01

    To adopt a particular fold, a protein requires several interactions between its amino acid residues. The energetic contribution of these residue-residue interactions can be approximated by extracting statistical potentials from known high resolution structures. Several methods based on statistical potentials extracted from unrelated proteins are found to make a better prediction of probability of point mutations. We postulate that the statistical potentials extracted from known structures of similar folds with varying sequence identity can be a powerful tool to examine probability of point mutation. By keeping this in mind, we have derived pairwise residue and atomic contact energy potentials for the different functional families that adopt the (α/β)8 TIM-Barrel fold. We carried out computational point mutations at various conserved residue positions in yeast Triose phosphate isomerase enzyme for which experimental results are already reported. We have also performed molecular dynamics simulations on a subset of point mutants to make a comparative study. The difference in pairwise residue and atomic contact energy of wildtype and various point mutations reveals probability of mutations at a particular position. Interestingly, we found that our computational prediction agrees with the experimental studies of Silverman et al. (Proc Natl Acad Sci 2001;98:3092-3097) and perform better prediction than iMutant and Cologne University Protein Stability Analysis Tool. The present work thus suggests deriving pairwise contact energy potentials and molecular dynamics simulations of functionally important folds could help us to predict probability of point mutations which may ultimately reduce the time and cost of mutation experiments. Proteins 2016; 85:54-64. © 2016 Wiley Periodicals, Inc.

  12. Energy landscape of LeuT from molecular simulations

    NASA Astrophysics Data System (ADS)

    Gur, Mert; Zomot, Elia; Cheng, Mary Hongying; Bahar, Ivet

    2015-12-01

    The bacterial sodium-coupled leucine transporter (LeuT) has been broadly used as a structural model for understanding the structure-dynamics-function of mammalian neurotransmitter transporters as well as other solute carriers that share the same fold (LeuT fold), as the first member of the family crystallographically resolved in multiple states: outward-facing open, outward-facing occluded, and inward-facing open. Yet, a complete picture of the energy landscape of (sub)states visited along the LeuT transport cycle has been elusive. In an attempt to visualize the conformational spectrum of LeuT, we performed extensive simulations of LeuT dimer dynamics in the presence of substrate (Ala or Leu) and co-transported Na+ ions, in explicit membrane and water. We used both conventional molecular dynamics (MD) simulations (with Anton supercomputing machine) and a recently introduced method, collective MD, that takes advantage of collective modes of motions predicted by the anisotropic network model. Free energy landscapes constructed based on ˜40 μs trajectories reveal multiple substates occluded to the extracellular (EC) and/or intracellular (IC) media, varying in the levels of exposure of LeuT to EC or IC vestibules. The IC-facing transmembrane (TM) helical segment TM1a shows an opening, albeit to a smaller extent and in a slightly different direction than that observed in the inward-facing open crystal structure. The study provides insights into the spectrum of conformational substates and paths accessible to LeuT and highlights the differences between Ala- and Leu-bound substates.

  13. Energy landscape of LeuT from molecular simulations.

    PubMed

    Gur, Mert; Zomot, Elia; Cheng, Mary Hongying; Bahar, Ivet

    2015-12-28

    The bacterial sodium-coupled leucine transporter (LeuT) has been broadly used as a structural model for understanding the structure-dynamics-function of mammalian neurotransmitter transporters as well as other solute carriers that share the same fold (LeuT fold), as the first member of the family crystallographically resolved in multiple states: outward-facing open, outward-facing occluded, and inward-facing open. Yet, a complete picture of the energy landscape of (sub)states visited along the LeuT transport cycle has been elusive. In an attempt to visualize the conformational spectrum of LeuT, we performed extensive simulations of LeuT dimer dynamics in the presence of substrate (Ala or Leu) and co-transported Na(+) ions, in explicit membrane and water. We used both conventional molecular dynamics (MD) simulations (with Anton supercomputing machine) and a recently introduced method, collective MD, that takes advantage of collective modes of motions predicted by the anisotropic network model. Free energy landscapes constructed based on ∼40 μs trajectories reveal multiple substates occluded to the extracellular (EC) and/or intracellular (IC) media, varying in the levels of exposure of LeuT to EC or IC vestibules. The IC-facing transmembrane (TM) helical segment TM1a shows an opening, albeit to a smaller extent and in a slightly different direction than that observed in the inward-facing open crystal structure. The study provides insights into the spectrum of conformational substates and paths accessible to LeuT and highlights the differences between Ala- and Leu-bound substates.

  14. Energy landscape of LeuT from molecular simulations

    PubMed Central

    Gur, Mert; Zomot, Elia; Cheng, Mary Hongying; Bahar, Ivet

    2015-01-01

    The bacterial sodium-coupled leucine transporter (LeuT) has been broadly used as a structural model for understanding the structure-dynamics-function of mammalian neurotransmitter transporters as well as other solute carriers that share the same fold (LeuT fold), as the first member of the family crystallographically resolved in multiple states: outward-facing open, outward-facing occluded, and inward-facing open. Yet, a complete picture of the energy landscape of (sub)states visited along the LeuT transport cycle has been elusive. In an attempt to visualize the conformational spectrum of LeuT, we performed extensive simulations of LeuT dimer dynamics in the presence of substrate (Ala or Leu) and co-transported Na+ ions, in explicit membrane and water. We used both conventional molecular dynamics (MD) simulations (with Anton supercomputing machine) and a recently introduced method, collective MD, that takes advantage of collective modes of motions predicted by the anisotropic network model. Free energy landscapes constructed based on ∼40 μs trajectories reveal multiple substates occluded to the extracellular (EC) and/or intracellular (IC) media, varying in the levels of exposure of LeuT to EC or IC vestibules. The IC-facing transmembrane (TM) helical segment TM1a shows an opening, albeit to a smaller extent and in a slightly different direction than that observed in the inward-facing open crystal structure. The study provides insights into the spectrum of conformational substates and paths accessible to LeuT and highlights the differences between Ala- and Leu-bound substates. PMID:26723619

  15. Assessing geothermal energy potential in upstate New York. Final report

    SciTech Connect

    Hodge, D.S.

    1996-08-01

    The potential of geothermal energy for future electric power generation in New York State is evaluated using estimates of temperatures of geothermal reservoir rocks. Bottom hole temperatures from over 2000 oil and gas wells in the region were integrated into subsurface maps of the temperatures for specific geothermal reservoirs. The Theresa/Potsdam formation provides the best potential for extraction of high volumes of geothermal fluids. The evaluation of the Theresa/Potsdam geothermal reservoir in upstate New York suggests that an area 30 miles east of Elmira, New York has the highest temperatures in the reservoir rock. The Theresa/Potsdam reservoir rock should have temperatures about 136 {degrees}C and may have as much as 450 feet of porosity in excess of 8%. Estimates of the volumes of geothermal fluids that can be extracted are provided and environmental considerations for production from a geothermal well is discussed.

  16. Global Expression for Representing Diatomic Potential-Energy Curves

    NASA Technical Reports Server (NTRS)

    Ferrante, John; Schlosser, Herbert; Smith, John R.

    1991-01-01

    A three-parameter expression that gives an accurate fit to diatomic potential curves over the entire range of separation for charge transfers between 0 and 1. It is based on a generalization of the universal binding-energy relation of Smith et al. (1989) with a modification that describes the crossover from a partially ionic state to the neutral state at large separations. The expression is tested by comparison with first-principles calculations of the potential curves ranging from covalently bonded to ionically bonded. The expression is also used to calculate spectroscopic constants form a curve fit to the first-principles curves. A comparison is made with experimental values of the spectroscopic constants.

  17. Nutraceuticals: Potential for Chondroprotection and Molecular Targeting of Osteoarthritis

    PubMed Central

    Leong, Daniel J.; Choudhury, Marwa; Hirsh, David M.; Hardin, John A.; Cobelli, Neil J.; Sun, Hui B.

    2013-01-01

    Osteoarthritis (OA) is a degenerative joint disease and a leading cause of adult disability. There is no cure for OA, and no effective treatments which arrest or slow its progression. Current pharmacologic treatments such as analgesics may improve pain relief but do not alter OA disease progression. Prolonged consumption of these drugs can result in severe adverse effects. Given the nature of OA, life-long treatment will likely be required to arrest or slow its progression. Consequently, there is an urgent need for OA disease-modifying therapies which also improve symptoms and are safe for clinical use over long periods of time. Nutraceuticals—food or food products that provide medical or health benefits, including the prevention and/or treatment of a disease—offer not only favorable safety profiles, but may exert disease- and symptom-modification effects in OA. Forty-seven percent of OA patients use alternative medications, including nutraceuticals. This review will overview the efficacy and mechanism of action of commonly used nutraceuticals, discuss recent experimental and clinical data on the effects of select nutraceuticals, such as phytoflavonoids, polyphenols, and bioflavonoids on OA, and highlight their known molecular actions and limitations of their current use. We will conclude with a proposed novel nutraceutical-based molecular targeting strategy for chondroprotection and OA treatment. PMID:24284399

  18. Exploring the free energy surface using ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Samanta, Amit; Morales, Miguel A.; Schwegler, Eric

    2016-04-01

    Efficient exploration of configuration space and identification of metastable structures in condensed phase systems are challenging from both computational and algorithmic perspectives. In this regard, schemes that utilize a set of pre-defined order parameters to sample the relevant parts of the configuration space [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006); J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B 112, 15742 (2008)] have proved useful. Here, we demonstrate how these order-parameter aided temperature accelerated sampling schemes can be used within the Born-Oppenheimer and the Car-Parrinello frameworks of ab initio molecular dynamics to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways. We have used these methods to identify the metastable structures and reaction pathways in SiO2 and Ti. In addition, we have used the string method [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002); L. Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] within the density functional theory to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hexagonal closed packed to face centered cubic phase transition in Ti.

  19. Bandwidth Study on Energy Use and Potential Energy Saving Opportunities in U.S. Pulp and Paper Manufacturing

    SciTech Connect

    Sabine Brueske, Caroline Kramer, Aaron Fisher

    2015-06-01

    Energy bandwidth studies of U.S. manufacturing sectors can serve as foundational references in framing the range (or bandwidth) of potential energy savings opportunities. This bandwidth study examines energy consumption and potential energy savings opportunities in U.S. pulp and paper manufacturing. The study relies on multiple sources to estimate the energy used in six individual process areas, representing 52% of sector-wide energy consumption. Energy savings opportunities for individual processes are based on technologies currently in use or under development; the potential savings are then extrapolated to estimate sector-wide energy savings opportunity

  20. Bandwidth Study on Energy Use and Potential Energy Saving Opportunities in U.S. Iron and Steel Manufacturing

    SciTech Connect

    Keith Jamison, Caroline Kramer, Sabine Brueske, Aaron Fisher

    2015-06-01

    Energy bandwidth studies of U.S. manufacturing sectors can serve as foundational references in framing the range (or bandwidth) of potential energy savings opportunities. This bandwidth study examines energy consumption and potential energy savings opportunities in U.S. iron and steel manufacturing. The study relies on multiple sources to estimate the energy used in six individual process areas and select subareas, representing 82% of sector-wide energy consumption. Energy savings opportunities for individual processes and subareas are based on technologies currently in use or under development; the potential savings are then extrapolated to estimate sector-wide energy savings opportunity.

  1. Febrifugine analogues as Leishmania donovani trypanothione reductase inhibitors: binding energy analysis assisted by molecular docking, ADMET and molecular dynamics simulation.

    PubMed

    Pandey, Rajan Kumar; Kumbhar, Bajarang Vasant; Srivastava, Shubham; Malik, Ruchi; Sundar, Shyam; Kunwar, Ambarish; Prajapati, Vijay Kumar

    2017-01-01

    Visceral leishmaniasis affects people from 70 countries worldwide, mostly from Indian, African and south American continent. The increasing resistance to antimonial, miltefosine and frequent toxicity of amphotericin B drives an urgent need to develop an antileishmanial drug with excellent efficacy and safety profile. In this study we have docked series of febrifugine analogues (n = 8813) against trypanothione reductase in three sequential docking modes. Extra precision docking resulted into 108 ligands showing better docking score as compared to two reference ligand. Furthermore, 108 febrifugine analogues and reference inhibitor clomipramine were subjected to ADMET, QikProp and molecular mechanics, the generalized born model and solvent accessibility study to ensure the toxicity caused by compounds and binding-free energy, respectively. Two best ligands (FFG7 and FFG2) qualifying above screening parameters were further subjected to molecular dynamics simulation. Conducting these studies, here we confirmed that 6-chloro-3-[3-(3-hydroxy-2-piperidyl)-2-oxo-propyl]-7-(4-pyridyl) quinazolin-4-one can be potential drug candidate to fight against Leishmania donovani parasites.

  2. Material and energy recovery in integrated waste management systems: the potential for energy recovery.

    PubMed

    Consonni, Stefano; Viganò, Federico

    2011-01-01

    This article is part of a set of six coordinated papers reporting the main findings of a research project carried out by five Italian universities on "Material and energy recovery in Integrated Waste Management Systems (IWMS)". An overview of the project and a summary of the most relevant results can be found in the introductory article of the series. This paper describes the work related to the evaluation of mass and energy balances, which has consisted of three major efforts (i) development of a model for quantifying the energy content and the elemental compositions of the waste streams appearing in a IWMS; (ii) upgrade of an earlier model to predict the performances of Waste-to-Energy (WtE) plants; (iii) evaluation of mass and energy balances of all the scenarios and the recovery paths considered in the project. Results show that not only the amount of material available for energy recovery is significantly higher than the Unsorted Residual Waste (URW) left after Separate Collection (SC), because selection and recycling generate significant amounts of residues, but its heating value is higher than that of the original, gross waste. Therefore, the energy potential of what is left after recycling is always higher than the complement to 100% of the Source Separation Level (SSL). Also, increasing SSL has marginal effects on the potential for energy recovery: nearly doubling SSL (from 35% to 65%) reduces the energy potential only by one fourth. Consequently, even at high SSL energy recovery is a fundamental step of a sustainable waste management system. Variations of SSL do bring about variations of the composition, heating value and moisture content of the material fed to WtE plants, but these variations (i) are smaller than one can expect; (ii) have marginal effects on the performances of the WtE plant. These considerations suggest that the mere value of SSL is not a good indicator of the quality of the waste management system, nor of its energy and environmental

  3. Wind and Solar Energy Potential Assessment for Development of Renewables Energies Applications in Bucaramanga, Colombia

    NASA Astrophysics Data System (ADS)

    Ordóñez, G.; Osma, G.; Vergara, P.; Rey, J.

    2014-06-01

    Currently, the trend of micro-grids and small-scale renewable generation systems implementation in urban environments requires to have historical and detailed information about the energy potential resource in site. In Colombia, this information is limited and do not favor the design of these applications; for this reason, must be made detailed studies of the energy potential in their cities. In this paper is presented the wind and solar energy resource assessment for the city of Bucaramanga, based on the monitoring on four strategic points during the years 2010, 2011 and 2012. According to the analysis, is evidenced a significant solar resource throughout the year ascending on average to 1 734 kWh/m2, equivalent to 4.8 kWh/m2/day. Also, from a wind statistical study based on the Weibull probability distribution and Wind Power Density (WPD) was established the wind potential as Class 1 according to the scale of the Department of Energy of the United States (DOE), since the average speed is near 1.4 m/s. Due this, it is technically unfeasible the using of micro-turbines in the city, even so their potential for natural ventilation of building was analyzed. Finally, is presented a methodology to analyze solar harvesting by sectors in the city, according to the solar motion and shadowing caused by existing structures.

  4. Global potential energy hypersurface for dynamical studies of energy transfer in HF--HF collisions

    SciTech Connect

    Redmon, M.J.; Binkley, J.S.

    1987-07-15

    The interaction energy of two HF molecules at 1332 individual points has been calculated with Moeller--Plesset (many--body) perturbation theory at the MP4-SDTQ level using a 6-311G** basis set. 293 of the points correspond to stretching of one HF molecule from its equilibrium geometry. No attempt was made to use a sufficiently fine grid to accurately describe the well region corresponding to hydrogen bonding. However, the location and minimum energy are consistent with experiment and other accurate theoretical results. An extensive global fit (rms error of 1 kcal/mol) is reported of 1319 points (below 10 eV of potential energy) using a modified London potential with corrections obtained using polynomials through four-body interactions. A model electrostatic potential represents the long-range interaction. In addition, the use of an expansion in products of three Legendre functions is discussed. It is shown that the latter approach, although accurately fitting the ab initio data, has difficulties interpolating in regions of the surface exhibiting diverse magnitudes of potential energy, and therefore must be used with caution. This surface should be useful for studies of T--V--R processes in this system.

  5. A "First Principles" Potential Energy Surface for Liquid Water from VRT Spectroscopy of Water Clusters

    SciTech Connect

    Goldman, N; Leforestier, C; Saykally, R J

    2004-05-25

    We present results of gas phase cluster and liquid water simulations from the recently determined VRT(ASP-W)III water dimer potential energy surface. VRT(ASP-W)III is shown to not only be a model of high ''spectroscopic'' accuracy for the water dimer, but also makes accurate predictions of vibrational ground-state properties for clusters up through the hexamer. Results of ambient liquid water simulations from VRT(ASP-W)III are compared to those from ab initio Molecular Dynamics, other potentials of ''spectroscopic'' accuracy, and to experiment. The results herein represent the first time that a ''spectroscopic'' potential surface is able to correctly model condensed phase properties of water.

  6. The natural flavonoid pinocembrin: molecular targets and potential therapeutic applications

    PubMed Central

    Lan, Xi; Wang, Wenzhu; Li, Qiang; Wang, Jian

    2015-01-01

    Pinocembrin is a natural flavonoid compound extracted from honey, propolis, ginger roots, wild marjoram, and other plants. In preclinical studies, it has shown anti-inflammatory and neuroprotective effects as well as the ability to reduce reactive oxygen species, protect the blood-brain barrier, modulate mitochondrial function, and regulate apoptosis. Considering these pharmaceutical characteristics, pinocembrin has potential as a drug to treat ischemic stroke and other clinical conditions. In this review, we summarize its pharmacologic characteristics and discuss its mechanisms of action and potential therapeutic applications. PMID:25744566

  7. Theoretical investigation of energy storage in atomic and molecular systems: Metastable molecular fuels

    NASA Astrophysics Data System (ADS)

    Saxon, Roberta P.

    1990-12-01

    Ion-pair species bound by the coulomb attraction between a stable positive and stable negative ion have been investigated theoretically as candidate high-energy fuels that could form the basis of new propulsion schemes. Theoretical results for H3O, Li3H, and H3F are presented along with specific impulse, I(sub sp), predictions based on calculated energies. The ion-pair local minimum on the first excited potential surface of H3O is found to be unstable with respect to dissociation to H2 + H + O. The ion-pair state of H3F has a double degenerate imaginary frequency. These results support the general conclusion that ion-pair states based on the H3 cation will not be stable because back-charge transfer to H3(+) leads to neutral H3, which is unstable with respect to H2 + H. However, the ion-pair state of Li3H is found to be a local minimum with a very small barrier to conversion to the lower energy planar form. Even the lowest energy form of Li3H as an additive to hydrogen is predicted to provide a 16 percent improvement in I(sub sp).

  8. Molecular and Therapeutic Potential and Toxicity of Valproic Acid

    PubMed Central

    Chateauvieux, Sébastien; Morceau, Franck; Dicato, Mario; Diederich, Marc

    2010-01-01

    Valproic acid (VPA), a branched short-chain fatty acid, is widely used as an antiepileptic drug and a mood stabilizer. Antiepileptic properties have been attributed to inhibition of Gamma Amino Butyrate (GABA) transaminobutyrate and of ion channels. VPA was recently classified among the Histone Deacetylase Inhibitors, acting directly at the level of gene transcription by inhibiting histone deacetylation and making transcription sites more accessible. VPA is a widely used drug, particularly for children suffering from epilepsy. Due to the increasing number of clinical trials involving VPA, and interesting results obtained, this molecule will be implicated in an increasing number of therapies. However side effects of VPA are substantially described in the literature whereas they are poorly discussed in articles focusing on its therapeutic use. This paper aims to give an overview of the different clinical-trials involving VPA and its side effects encountered during treatment as well as its molecular properties. PMID:20798865

  9. Tea polyphenols, their biological effects and potential molecular targets.

    PubMed

    Chen, D; Milacic, V; Chen, M S; Wan, S B; Lam, W H; Huo, C; Landis-Piwowar, K R; Cui, Q C; Wali, A; Chan, T H; Dou, Q P

    2008-04-01

    Tea is the most popular beverage in the world, second only to water. Tea contains an infusion of the leaves from the Camellia sinensis plant rich in polyphenolic compounds known as catechins, the most abundant of which is (-)-EGCG. Although tea has been consumed for centuries, it has only recently been studied extensively as a health-promoting beverage that may act to prevent a number of chronic diseases and cancers. The results of several investigations indicate that green tea consumption may be of modest benefit in reducing the plasma concentration of cholesterol and preventing atherosclerosis. Additionally, the cancer-preventive effects of green tea are widely supported by results from epidemiological, cell culture, animal and clinical studies. In vitro cell culture studies show that tea polyphenols potently induce apoptotic cell death and cell cycle arrest in tumor cells but not in their normal cell counterparts. Green tea polyphenols were shown to affect several biological pathways, including growth factor-mediated pathway, the mitogen-activated protein (MAP) kinase-dependent pathway, and ubiquitin/proteasome degradation pathways. Various animal studies have revealed that treatment with green tea inhibits tumor incidence and multiplicity in different organ sites such as skin, lung, liver, stomach, mammary gland and colon. Recently, phase I and II clinical trials have been conducted to explore the anticancer effects of green tea in humans. A major challenge of cancer prevention is to integrate new molecular findings into clinical practice. Therefore, identification of more molecular targets and biomarkers for tea polyphenols is essential for improving the design of green tea trials and will greatly assist in a better understanding of the mechanisms underlying its anti-cancer activity.

  10. Microscopically derived potential energy surfaces from mostly structural considerations

    SciTech Connect

    Ermamatov, M.J.; Hess, Peter O.

    2016-08-15

    A simple procedure to estimate the quadrupole Potential-Energy-Surface (PES) is presented, using mainly structural information, namely the content of the shell model space and the Pauli exclusion principle. Further microscopic properties are implicitly contained through the use of results from the Möller and Nix tables or experimental information. A mapping to the geometric potential is performed yielding the PES. The General Collective Model is used in order to obtain an estimate on the spectrum and quadrupole transitions, adjusting only the mass parameter. First, we test the conjecture on known nuclei, deriving the PES and compare them to known data. We will see that the PES approximates very well the structure expected. Having acquired a certain confidence, we predict the PES of several chain of isotopes of heavy and super-heavy nuclei and at the end we investigate the structure of nuclei in the supposed island of stability. One of the main points to show is that simple assumptions can provide already important information on the structure of nuclei outside known regions and that spectra and electromagnetic transitions can be estimated without using involved calculations and assumptions. The procedure does not allow to calculate binding energies. The method presented can be viewed as a starting point for further improvements.

  11. An Ab Initio Based Potential Energy Surface for Water

    NASA Technical Reports Server (NTRS)

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

    1996-01-01

    We report a new determination of the water potential energy surface. A high quality ab initio potential energy surface (PES) and dipole moment function of water have been computed. This PES is empirically adjusted to improve the agreement between the computed line positions and those from the HITRAN 92 data base. The adjustment is small, nonetheless including an estimate of core (oxygen 1s) electron correlation greatly improves the agreement with experiment. Of the 27,245 assigned transitions in the HITRAN 92 data base for H2(O-16), the overall root mean square (rms) deviation between the computed and observed line positions is 0.125/cm. However the deviations do not correspond to a normal distribution: 69% of the lines have errors less than 0.05/cm. Overall, the agreement between the line intensities computed in the present work and those contained in the data base is quite good, however there are a significant number of line strengths which differ greatly.

  12. POTLIB 2001: A potential energy surface library for chemical systems

    NASA Astrophysics Data System (ADS)

    Duchovic, Ronald J.; Volobuev, Yuri L.; Lynch, Gillian C.; Truhlar, Donald G.; Allison, Thomas C.; Wagner, Albert F.; Garrett, Bruce C.; Corchado, Jose C.

    2002-04-01

    POTLIB 2001 is a computer program library of global chemical potential energy surface (PES) functions (91 functions in version 1.0) along with test data, a suite of utility programs, and a convenient user interface. The PES programs are written in ANSI standard FORTRAN77 and can be used to determine the Born-Oppenheimer potential energy of chemical systems as a function of the internal coordinates. The accompanying test data allow users to verify local implementations of this library. Finally, the utility programs permit use of this library in conjunction with a variety of chemical dynamics and chemical kinetics computer codes. Interface routines are provided for the POLYRATE and ABCRATE program packages of Truhlar and co-workers, the VENUS96 program package of Hase and co-workers, and the VARIFLEX program package of Klippenstein and co-workers; the routines in this library can also be used in conjunction with the DYNASOL program package of Zhang and co-workers. This article describes the library and the utility programs and outlines the systematic conventions used for interfaces in the computer programs contained in the library. Adherence to these conventions will allow future PESs to be compatible with this library.

  13. Free molecular collision cross section calculation methods for nanoparticles and complex ions with energy accommodation

    SciTech Connect

    Larriba, Carlos Hogan, Christopher J.

    2013-10-15

    The structures of nanoparticles, macromolecules, and molecular clusters in gas phase environments are often studied via measurement of collision cross sections. To directly compare structure models to measurements, it is hence necessary to have computational techniques available to calculate the collision cross sections of structural models under conditions matching measurements. However, presently available collision cross section methods contain the underlying assumption that collision between gas molecules and structures are completely elastic (gas molecule translational energy conserving) and specular, while experimental evidence suggests that in the most commonly used background gases for measurements, air and molecular nitrogen, gas molecule reemission is largely inelastic (with exchange of energy between vibrational, rotational, and translational modes) and should be treated as diffuse in computations with fixed structural models. In this work, we describe computational techniques to predict the free molecular collision cross sections for fixed structural models of gas phase entities where inelastic and non-specular gas molecule reemission rules can be invoked, and the long range ion-induced dipole (polarization) potential between gas molecules and a charged entity can be considered. Specifically, two calculation procedures are described detail: a diffuse hard sphere scattering (DHSS) method, in which structures are modeled as hard spheres and collision cross sections are calculated for rectilinear trajectories of gas molecules, and a diffuse trajectory method (DTM), in which the assumption of rectilinear trajectories is relaxed and the ion-induced dipole potential is considered. Collision cross section calculations using the DHSS and DTM methods are performed on spheres, models of quasifractal aggregates of varying fractal dimension, and fullerene like structures. Techniques to accelerate DTM calculations by assessing the contribution of grazing gas

  14. Gravitational potential energy of the earth: A spherical harmonic approach

    NASA Technical Reports Server (NTRS)

    Rubincam, D. P.

    1977-01-01

    A spherical harmonic equation for the gravitational potential energy of the earth is derived for an arbitrary density distribution by conceptually bringing in mass-elements from infinity and building up the earth shell upon spherical shell. The zeroth degree term in the spherical harmonic equation agrees with the usual expression for the energy of a radial density distribution. The second degree terms give a maximum nonhydrostatic energy in the mantle and crust of -2.77 x 10 to the twenty-ninth power ergs, an order of magnitude. If the earth is assumed to be a homogeneous viscous oblate spheroid relaxing to an equilibrium shape, then a lower limit to the mantle viscosity of 1.3 x 10 to the twentieth power poises is found by assuming the total geothermal flux is due to viscous dissipation. If the nonequilibrium figure is dynamically maintained by the earth acting as a heat engine at one per cent efficiency, then the viscosity is ten to the twenty second power poises, a number preferred by some as the viscosity of the mantle.

  15. Material and energy recovery in integrated waste management systems: The potential for energy recovery

    SciTech Connect

    Consonni, Stefano; Vigano, Federico

    2011-09-15

    Highlights: > The amount of waste available for energy recovery is significantly higher than the Unsorted Residual Waste (URW). > Its energy potential is always higher than the complement to 100% of the Source Separation Level (SSL). > Increasing SSL has marginal effects on the potential for energy recovery. > Variations in the composition of the waste fed to WtE plants affect only marginally their performances. > A large WtE plant with a treatment capacity some times higher than a small plant achieves electric efficiency appreciably higher. - Abstract: This article is part of a set of six coordinated papers reporting the main findings of a research project carried out by five Italian universities on 'Material and energy recovery in Integrated Waste Management Systems (IWMS)'. An overview of the project and a summary of the most relevant results can be found in the introductory article of the series. This paper describes the work related to the evaluation of mass and energy balances, which has consisted of three major efforts (i) development of a model for quantifying the energy content and the elemental compositions of the waste streams appearing in a IWMS; (ii) upgrade of an earlier model to predict the performances of Waste-to-Energy (WtE) plants; (iii) evaluation of mass and energy balances of all the scenarios and the recovery paths considered in the project. Results show that not only the amount of material available for energy recovery is significantly higher than the Unsorted Residual Waste (URW) left after Separate Collection (SC), because selection and recycling generate significant amounts of residues, but its heating value is higher than that of the original, gross waste. Therefore, the energy potential of what is left after recycling is always higher than the complement to 100% of the Source Separation Level (SSL). Also, increasing SSL has marginal effects on the potential for energy recovery: nearly doubling SSL (from 35% to 65%) reduces the energy

  16. Confining interparticle potential makes both heat transport and energy diffusion anomalous in one-dimensional phononic systems

    NASA Astrophysics Data System (ADS)

    Kosevich, Yuriy A.; Savin, Alexander V.

    2016-10-01

    We provide molecular dynamics simulation of heat transport and energy diffusion in one-dimensional molecular chains with different interparticle pair potentials at zero and non-zero temperature. We model the thermal conductivity (TC) and energy diffusion (ED) in the chain of coupled rotators and in the Lennard-Jones chain either without or with the confining parabolic interparticle potential. The considered chains without the confining potential have normal TC and ED at non-zero temperature, while the corresponding chains with the confining potential are characterized by anomalous (diverging with the system length) TC and superdiffusion of energy. Similar effect is produced by the anharmonic quartic confining pair potential. We confirm in such a way that, surprisingly, the confining pair potential makes both heat transport and energy diffusion anomalous in one-dimensional phononic systems. We show that the normal TC is always accompanied by the normal ED in the thermalized anharmonic chains, while the superdiffusion of energy occurs in the thermalized chains with only anomalous heat transport.

  17. Numerical approximations for the molecular beam epitaxial growth model based on the invariant energy quadratization method

    NASA Astrophysics Data System (ADS)

    Yang, Xiaofeng; Zhao, Jia; Wang, Qi

    2017-03-01

    The Molecular Beam Epitaxial model is derived from the variation of a free energy, that consists of either a fourth order Ginzburg-Landau double well potential or a nonlinear logarithmic potential in terms of the gradient of a height function. One challenge in solving the MBE model numerically is how to develop proper temporal discretization for the nonlinear terms in order to preserve energy stability at the time-discrete level. In this paper, we resolve this issue by developing a first and second order time-stepping scheme based on the "Invariant Energy Quadratization" (IEQ) method. The novelty is that all nonlinear terms are treated semi-explicitly, and the resulted semi-discrete equations form a linear system at each time step. Moreover, the linear operator is symmetric positive definite and thus can be solved efficiently. We then prove that all proposed schemes are unconditionally energy stable. The semi-discrete schemes are further discretized in space using finite difference methods and implemented on GPUs for high-performance computing. Various 2D and 3D numerical examples are presented to demonstrate stability and accuracy of the proposed schemes.

  18. Characterization of the dynamics of glass-forming liquids from the properties of the potential energy landscape.

    PubMed

    Banerjee, Sumilan; Dasgupta, Chandan

    2012-02-01

    We develop a framework for understanding the difference between strong and fragile behavior in the dynamics of glass-forming liquids from the properties of the potential energy landscape. Our approach is based on a master equation description of the activated jump dynamics among the local minima of the potential energy (the so-called inherent structures) that characterize the potential energy landscape of the system. We study the dynamics of a small atomic cluster using this description as well as molecular dynamics simulations and demonstrate the usefulness of our approach for this system. Many of the remarkable features of the complex dynamics of glassy systems emerge from the activated dynamics in the potential energy landscape of the atomic cluster. The dynamics of the system exhibits typical characteristics of a strong supercooled liquid when the system is allowed to explore the full configuration space. This behavior arises because the dynamics is dominated by a few lowest-lying minima of the potential energy and the potential energy barriers between these minima. When the system is constrained to explore only a limited region of the potential energy landscape that excludes the basins of attraction of a few lowest-lying minima, the dynamics is found to exhibit the characteristics of a fragile liquid.

  19. Transportation Energy Futures Series. Potential for Energy Efficiency Improvement Beyond the Light-Duty-Vehicle Sector

    SciTech Connect

    Vyas, A. D.; Patel, D. M.; Bertram, K. M.

    2013-02-01

    Considerable research has focused on energy efficiency and fuel substitution options for light-duty vehicles, while much less attention has been given to medium- and heavy-duty trucks, buses, aircraft, marine vessels, trains, pipeline, and off-road equipment. This report brings together the salient findings from an extensive review of literature on future energy efficiency options for these non-light-duty modes. Projected activity increases to 2050 are combined with forecasts of overall fuel efficiency improvement potential to estimate the future total petroleum and greenhouse gas (GHG) emissions relative to current levels. This is one of a series of reports produced as a result of the Transportation Energy Futures (TEF) project, a Department of Energy-sponsored multi-agency project initiated to pinpoint underexplored strategies for abating GHGs and reducing petroleum dependence related to transportation.

  20. Transportation Energy Futures Series: Potential for Energy Efficiency Improvement Beyond the Light-Duty-Vehicle Sector

    SciTech Connect

    Vyas, A. D.; Patel, D. M.; Bertram, K. M.

    2013-03-01

    Considerable research has focused on energy efficiency and fuel substitution options for light-duty vehicles, while much less attention has been given to medium- and heavy-duty trucks, buses, aircraft, marine vessels, trains, pipeline, and off-road equipment. This report brings together the salient findings from an extensive review of literature on future energy efficiency options for these non-light-duty modes. Projected activity increases to 2050 are combined with forecasts of overall fuel efficiency improvement potential to estimate the future total petroleum and greenhouse gas (GHG) emissions relative to current levels. This is one of a series of reports produced as a result of the Transportation Energy Futures (TEF) project, a Department of Energy-sponsored multi-agency project initiated to pinpoint underexplored strategies for abating GHGs and reducing petroleum dependence related to transportation.

  1. Molecular Dynamics Simulation Study on Energy Exchange Between Vibration Modes of a Square Graphene Nanoflake Oscillator.

    PubMed

    Lee, Eunae; Kang, Jeong Won; Kim, Ki-Sub; Kwon, Oh-Kuen

    2016-02-01

    Superlubricity in nanoscale graphene structures has been of interest for developing graphene-based nanoelectromechanical systems, as well as for the study of basic mechanical properties. Here, we investigated the translational and rotational motions of a square graphene nanoflake with retracting motions by performing classical molecular dynamics simulations. Our results show that the kinetic energy of the translational motion was exchanged into the kinetic energy of the rotational motion. Thus, square graphene nanoflake oscillators have very low quality factors in translational motions. We discuss that square graphene nanoflakes have great potential to be a core component in nanoelectromechanical systems by detecting their motions with ultrahigh sensitivity to facilitate the development of sensor, memory, and quantum computing.

  2. ERRATUM: A `magnetic' interatomic potential for molecular dynamics simulations.

    NASA Astrophysics Data System (ADS)

    L, Dudarev S.; M, Derlet P.

    2007-06-01

    Our colleagues pointed out that the format of numerical values given in table 3 of our paper may cause confusion and lead to an error in the numerical implementation of the potential. Below we list the values given in table 3 of our original paper, this time using conventional decimal notations. These values correspond to the same choice of parameter ρc=1. Please see the pdf for table 3

  3. Molecular and cellular regulation of hypothalamic melanocortin neurons controlling food intake and energy metabolism.

    PubMed

    Koch, M; Horvath, T L

    2014-07-01

    The brain receives and integrates environmental and metabolic information, transforms these signals into adequate neuronal circuit activities, and generates physiological behaviors to promote energy homeostasis. The responsible neuronal circuitries show lifetime plasticity and guaranty metabolic health and survival. However, this highly evolved organization has become challenged nowadays by chronic overload with nutrients and reduced physical activity, which results in an ever-increasing number of obese individuals worldwide. Research within the last two decades has aimed to decipher the responsible molecular and cellular mechanisms for regulation of the hypothalamic melanocortin neurons, which have a key role in the control of food intake and energy metabolism. This review maps the central connections of the melanocortin system and highlights its global position and divergent character in physiological and pathological metabolic events. Moreover, recently uncovered molecular and cellular processes in hypothalamic neurons and glial cells that drive plastic morphological and physiological changes in these cells, and account for regulation of food intake and energy metabolism, are brought into focus. Finally, potential functional interactions between metabolic disorders and psychiatric diseases are discussed.

  4. Molecular simulation of fluids with non-identical intermolecular potentials: Thermodynamic properties of 10-5 + 12-6 Mie potential binary mixtures

    SciTech Connect

    Stiegler, Thomas; Sadus, Richard J.

    2015-02-28

    General methods for combining interactions between particles characterised by non-identical intermolecular potentials are investigated. The combination methods are tested by performing molecular dynamics simulations to determine the pressure, energy, isochoric and isobaric heat capacities, thermal expansion coefficient, isothermal compressibility, Joule-Thomson coefficient, and speed of sound of 10-5 + 12-6 Mie potential binary mixtures. In addition to the two non-identical Mie potentials, mixtures are also studied with non-identical intermolecular parameters. The combination methods are compared with results obtained by simply averaging the Mie exponents. When either the energy or size parameters are non-identical, very significant differences emerge in the thermodynamic properties predicted by the alternative combination methods. The isobaric heat capacity is the thermodynamic property that is most affected by the relative magnitude of the intermolecular potential parameters and the method for combining non-identical potentials. Either the arithmetic or geometric combination of potentials provides a simple and effective way of performing simulations involving mixtures of components characterised by non-identical intermolecular potentials, which is independent of their functional form.

  5. Molecular simulation of fluids with non-identical intermolecular potentials: Thermodynamic properties of 10-5 + 12-6 Mie potential binary mixtures

    NASA Astrophysics Data System (ADS)

    Stiegler, Thomas; Sadus, Richard J.

    2015-02-01

    General methods for combining interactions between particles characterised by non-identical intermolecular potentials are investigated. The combination methods are tested by performing molecular dynamics simulations to determine the pressure, energy, isochoric and isobaric heat capacities, thermal expansion coefficient, isothermal compressibility, Joule-Thomson coefficient, and speed of sound of 10-5 + 12-6 Mie potential binary mixtures. In addition to the two non-identical Mie potentials, mixtures are also studied with non-identical intermolecular parameters. The combination methods are compared with results obtained by simply averaging the Mie exponents. When either the energy or size parameters are non-identical, very significant differences emerge in the thermodynamic properties predicted by the alternative combination methods. The isobaric heat capacity is the thermodynamic property that is most affected by the relative magnitude of the intermolecular potential parameters and the method for combining non-identical potentials. Either the arithmetic or geometric combination of potentials provides a simple and effective way of performing simulations involving mixtures of components characterised by non-identical intermolecular potentials, which is independent of their functional form.

  6. Molecular simulation of fluids with non-identical intermolecular potentials: thermodynamic properties of 10-5 + 12-6 Mie potential binary mixtures.

    PubMed

    Stiegler, Thomas; Sadus, Richard J

    2015-02-28

    General methods for combining interactions between particles characterised by non-identical intermolecular potentials are investigated. The combination methods are tested by performing molecular dynamics simulations to determine the pressure, energy, isochoric and isobaric heat capacities, thermal expansion coefficient, isothermal compressibility, Joule-Thomson coefficient, and speed of sound of 10-5 + 12-6 Mie potential binary mixtures. In addition to the two non-identical Mie potentials, mixtures are also studied with non-identical intermolecular parameters. The combination methods are compared with results obtained by simply averaging the Mie exponents. When either the energy or size parameters are non-identical, very significant differences emerge in the thermodynamic properties predicted by the alternative combination methods. The isobaric heat capacity is the thermodynamic property that is most affected by the relative magnitude of the intermolecular potential parameters and the method for combining non-identical potentials. Either the arithmetic or geometric combination of potentials provides a simple and effective way of performing simulations involving mixtures of components characterised by non-identical intermolecular potentials, which is independent of their functional form.

  7. Networks of triboelectric nanogenerators for harvesting water wave energy: a potential approach toward blue energy.

    PubMed

    Chen, Jun; Yang, Jin; Li, Zhaoling; Fan, Xing; Zi, Yunlong; Jing, Qingshen; Guo, Hengyu; Wen, Zhen; Pradel, Ken C; Niu, Simiao; Wang, Zhong Lin

    2015-03-24

    With 70% of the earth's surface covered with water, wave energy is abundant and has the potential to be one of the most environmentally benign forms of electric energy. However, owing to lack of effective technology, water wave energy harvesting is almost unexplored as an energy source. Here, we report a network design made of triboelectric nanogenerators (TENGs) for large-scale harvesting of kinetic water energy. Relying on surface charging effect between the conventional polymers and very thin layer of metal as electrodes for each TENG, the TENG networks (TENG-NW) that naturally float on the water surface convert the slow, random, and high-force oscillatory wave energy into electricity. On the basis of the measured output of a single TENG, the TENG-NW is expected to give an average power output of 1.15 MW from 1 km(2) surface area. Given the compelling features, such as being lightweight, extremely cost-effective, environmentally friendly, easily implemented, and capable of floating on the water surface, the TENG-NW renders an innovative and effective approach toward large-scale blue energy harvesting from the ocean.

  8. 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.

  9. Plant adaptation to low atmospheric pressures: potential molecular responses.

    PubMed

    Ferl, Robert J; Schuerger, Andrew C; Paul, Anna-Lisa; Gurley, William B; Corey, Kenneth; Bucklin, Ray

    2002-01-01

    There is an increasing realization that it may be impossible to attain Earth normal atmospheric pressures in orbital, lunar, or Martian greenhouses, simply because the construction materials do not exist to meet the extraordinary constraints imposed by balancing high engineering requirements against high lift costs. This equation essentially dictates that NASA have in place the capability to grow plants at reduced atmospheric pressure. Yet current understanding of plant growth at low pressures is limited to just a few experiments and relatively rudimentary assessments of plant vigor and growth. The tools now exist, however, to make rapid progress toward understanding the fundamental nature of plant responses and adaptations to low pressures, and to develop strategies for mitigating detrimental effects by engineering the growth conditions or by engineering the plants themselves. The genomes of rice and the model plant Arabidopsis thaliana have recently been sequenced in their entirety, and public sector and commercial DNA chips are becoming available such that thousands of genes can be assayed at once. A fundamental understanding of plant responses and adaptation to low pressures can now be approached and translated into procedures and engineering considerations to enhance plant growth at low atmospheric pressures. In anticipation of such studies, we present here the background arguments supporting these contentions, as well as informed speculation about the kinds of molecular physiological responses that might be expected of plants in low-pressure environments.

  10. Emerging Anticancer Potentials of Goniothalamin and Its Molecular Mechanisms

    PubMed Central

    Bukhari, Syed Nasir Abbas

    2014-01-01

    The treatment of most cancers is still inadequate, despite tremendous steady progress in drug discovery and effective prevention. Nature is an attractive source of new therapeutics. Several medicinal plants and their biomarkers have been widely used for the treatment of cancer with less known scientific basis of their functioning. Although a wide array of plant derived active metabolites play a role in the prevention and treatment of cancer, more extensive scientific evaluation of their mechanisms is still required. Styryl-lactones are a group of secondary metabolites ubiquitous in the genus Goniothalamus that have demonstrated to possess antiproliferative activity against cancer cells. A large body of evidence suggests that this activity is associated with the induction of apoptosis in target cells. In an effort to promote further research on the genus Goniothalamus, this review offers a broad analysis of the current knowledge on Goniothalamin (GTN) or 5, 6, dihydro-6-styryl-2-pyronone (C13H12O2), a natural occurring styryl-lactone. Therefore, it includes (i) the source of GTN and other metabolites; (ii) isolation, purification, and (iii) the molecular mechanisms of actions of GTN, especially the anticancer properties, and summarizes the role of GTN which is crucial for drug design, development, and application in future for well-being of humans. PMID:25247178

  11. Plant adaptation to low atmospheric pressures: potential molecular responses

    NASA Technical Reports Server (NTRS)

    Ferl, Robert J.; Schuerger, Andrew C.; Paul, Anna-Lisa; Gurley, William B.; Corey, Kenneth; Bucklin, Ray

    2002-01-01

    There is an increasing realization that it may be impossible to attain Earth normal atmospheric pressures in orbital, lunar, or Martian greenhouses, simply because the construction materials do not exist to meet the extraordinary constraints imposed by balancing high engineering requirements against high lift costs. This equation essentially dictates that NASA have in place the capability to grow plants at reduced atmospheric pressure. Yet current understanding of plant growth at low pressures is limited to just a few experiments and relatively rudimentary assessments of plant vigor and growth. The tools now exist, however, to make rapid progress toward understanding the fundamental nature of plant responses and adaptations to low pressures, and to develop strategies for mitigating detrimental effects by engineering the growth conditions or by engineering the plants themselves. The genomes of rice and the model plant Arabidopsis thaliana have recently been sequenced in their entirety, and public sector and commercial DNA chips are becoming available such that thousands of genes can be assayed at once. A fundamental understanding of plant responses and adaptation to low pressures can now be approached and translated into procedures and engineering considerations to enhance plant growth at low atmospheric pressures. In anticipation of such studies, we present here the background arguments supporting these contentions, as well as informed speculation about the kinds of molecular physiological responses that might be expected of plants in low-pressure environments.

  12. Molecular Approaches to Understand Nutritional Potential of Coarse Cereals

    PubMed Central

    Singh, Amit Kumar; Singh, Rakesh; Subramani, Rajkumar; Kumar, Rajesh; Wankhede, Dhammaprakash P.

    2016-01-01

    Coarse grains are important group of crops that constitutes staple food for large population residing primarily in the arid and semi-arid regions of the world. Coarse grains are designated as nutri-cereals as they are rich in essential amino acids, minerals and vitamins. In spite of having several nutritional virtues in coarse grain as mentioned above, there is still scope for improvement in quality parameters such as cooking qualities, modulation of nutritional constituents and reduction or elimination of anti-nutritional factors. Besides its use in traditional cooking, coarse grains have been used mainly in the weaning food preparation and other malted food production. Improvement in quality parameters will certainly increase consumer’s preference for coarse grains and increase their demand. The overall genetic gain in quality traits of economic importance in the cultivated varieties will enhance their industrial value and simultaneously increase income of farmers growing these varieties. The urgent step for improvement of quality traits in coarse grains requires a detailed understanding of molecular mechanisms responsible for varied level of different nutritional contents in different genotypes of these crops. In this review we have discussed the progresses made in understanding of coarse grain biology with various omics tool coupled with modern breeding approaches and the current status with regard to our effort towards dissecting traits related to improvement of quality and nutritional constituents of grains. PMID:27252585

  13. Molecular biology of breast cancer stem cells: potential clinical applications.

    PubMed

    Nguyen, Nam P; Almeida, Fabio S; Chi, Alex; Nguyen, Ly M; Cohen, Deirdre; Karlsson, Ulf; Vinh-Hung, Vincent

    2010-10-01

    Breast cancer stem cells (CSC) have been postulated recently as responsible for failure of breast cancer treatment. The purpose of this study is to review breast CSCs molecular biology with respect to their mechanism of resistance to conventional therapy, and to develop treatment strategies that may improve survival of breast cancer patients. A literature search has identified in vitro and in vivo studies of breast CSCs. Breast CSCs overexpress breast cancer resistance protein (BCRP) which allows cancer cells to transport actively chemotherapy agents out of the cells. Radioresistance is modulated through activation of Wnt signaling pathway and overexpression of genes coding for glutathione. Lapatinib can selectively target HER-2 positive breast CSCs and improves disease-free survival in these patients. Metformin may target basal type breast CSCs. Parthenolide and oncolytic viruses are promising targeting agents for breast CSCs. Future clinical trials for breast cancer should include anti-cancer stem cells targeting agents in addition to conventional chemotherapy. Hypofractionation radiotherapy may be indicated for residual disease post chemotherapy.

  14. Molecular Approaches to Understand Nutritional Potential of Coarse Cereals.

    PubMed

    Singh, Amit Kumar; Singh, Rakesh; Subramani, Rajkumar; Kumar, Rajesh; Wankhede, Dhammaprakash P

    2016-06-01

    Coarse grains are important group of crops that constitutes staple food for large population residing primarily in the arid and semi-arid regions of the world. Coarse grains are designated as nutri-cereals as they are rich in essential amino acids, minerals and vitamins. In spite of having several nutritional virtues in coarse grain as mentioned above, there is still scope for improvement in quality parameters such as cooking qualities, modulation of nutritional constituents and reduction or elimination of anti-nutritional factors. Besides its use in traditional cooking, coarse grains have been used mainly in the weaning food preparation and other malted food production. Improvement in quality parameters will certainly increase consumer's preference for coarse grains and increase their demand. The overall genetic gain in quality traits of economic importance in the cultivated varieties will enhance their industrial value and simultaneously increase income of farmers growing these varieties. The urgent step for improvement of quality traits in coarse grains requires a detailed understanding of molecular mechanisms responsible for varied level of different nutritional contents in different genotypes of these crops. In this review we have discussed the progresses made in understanding of coarse grain biology with various omics tool coupled with modern breeding approaches and the current status with regard to our effort towards dissecting traits related to improvement of quality and nutritional constituents of grains.

  15. Computed Potential Energy Surfaces and Minimum Energy Pathways for Chemical Reactions

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.; Langhoff, S. R. (Technical Monitor)

    1994-01-01

    Computed potential energy surfaces are often required for computation of such parameters as rate constants as a function of temperature, product branching ratios, and other detailed properties. For some dynamics methods, global potential energy surfaces are required. In this case, it is necessary to obtain the energy at a complete sampling of all the possible arrangements of the nuclei, which are energetically accessible, and then a fitting function must be obtained to interpolate between the computed points. In other cases, characterization of the stationary points and the reaction pathway connecting them is sufficient. These properties may be readily obtained using analytical derivative methods. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method to obtain accurate energetics, gives usefull results for a number of chemically important systems. The talk will focus on a number of applications including global potential energy surfaces, H + O2, H + N2, O(3p) + H2, and reaction pathways for complex reactions, including reactions leading to NO and soot formation in hydrocarbon combustion.

  16. Energy of Cohesion, Compressibility, and the Potential Energy Functions of the Graphite System

    NASA Technical Reports Server (NTRS)

    Girifalco, L. A.; Lad, R. A.

    1956-01-01

    The lattice summations of the potential energy of importance in the graphite system have been computed by direct summation assuming a Lennard-Jones 6-12 potential between carbon atoms. From these summations, potential energy curves were constructed for interactions between a carbon atom and a graphite monolayer, between a carbon atom and a graphite surface, between a graphite monolayer and a semi-infinite graphite crystal and between two graphite semi-infinite crystals. Using these curves, the equilibrium distance between two isolated physically interacting carbon atoms was found to be 2.70 a, where a is the carbon-carbon distance in a graphite sheet. The distance between a surface plane and the rest of the crystal was found to be 1.7% greater than the interlayer spacing. Theoretical values of the energy of cohesion and the compressibility were calculated from the potential curve for the interaction between two semi-infinite crystals. They were (delta)E(sub c) = -330 ergs/sq cm and beta =3.18x10(exp -12)sq cm/dyne, respectively. These compared favorably with the experimental values of (delta)E(sub c) = -260 ergs/sq cm and beta = 2.97 X 10(exp -2) sq cm/dyne.

  17. An interatomic potential model for molecular dynamics simulation of silicon etching by Br{sup +}-containing plasmas

    SciTech Connect

    Ohta, H.; Iwakawa, A.; Eriguchi, K.; Ono, K.

    2008-10-01

    An interatomic potential model for Si-Br systems has been developed for performing classical molecular dynamics (MD) simulations. This model enables us to simulate atomic-scale reaction dynamics during Si etching processes by Br{sup +}-containing plasmas such as HBr and Br{sub 2} plasmas, which are frequently utilized in state-of-the-art techniques for the fabrication of semiconductor devices. Our potential form is based on the well-known Stillinger-Weber potential function, and the model parameters were systematically determined from a database of potential energies obtained from ab initio quantum-chemical calculations using GAUSSIAN03. For parameter fitting, we propose an improved linear scheme that does not require any complicated nonlinear fitting as that in previous studies [H. Ohta and S. Hamaguchi, J. Chem. Phys. 115, 6679 (2001)]. In this paper, we present the potential derivation and simulation results of bombardment of a Si(100) surface using a monoenergetic Br{sup +} beam.

  18. Molecular Dynamic Studies of Particle Wake Potentials in Plasmas

    NASA Astrophysics Data System (ADS)

    Ellis, Ian; Graziani, Frank; Glosli, James; Strozzi, David; Surh, Michael; Richards, David; Decyk, Viktor; Mori, Warren

    2010-11-01

    Fast Ignition studies require a detailed understanding of electron scattering, stopping, and energy deposition in plasmas with variable values for the number of particles within a Debye sphere. Presently there is disagreement in the literature concerning the proper description of these processes. Developing and validating proper descriptions requires studying the processes using first-principle electrostatic simulations and possibly including magnetic fields. We are using the particle-particle particle-mesh (P^3M) code ddcMD to perform these simulations. As a starting point in our study, we examined the wake of a particle passing through a plasma. In this poster, we compare the wake observed in 3D ddcMD simulations with that predicted by Vlasov theory and those observed in the electrostatic PIC code BEPS where the cell size was reduced to .03λD.

  19. Lennard-Jones systems near solid walls: computing interfacial free energies from molecular simulation methods.

    PubMed

    Benjamin, Ronald; Horbach, Jürgen

    2013-08-28

    Different computational techniques in combination with molecular dynamics computer simulation are used to determine the wall-liquid and the wall-crystal interfacial free energies of a modified Lennard-Jones (LJ) system in contact with a solid wall. Two different kinds of solid walls are considered: a flat structureless wall and a structured wall consisting of an ideal crystal with the particles rigidly attached to fcc lattice sites. Interfacial free energies are determined by a thermodynamic integration scheme, the anisotropy of the pressure tensor, the non-equilibrium work method based on Bennett acceptance criteria, and a method using Cahn's adsorption equations based on the interfacial thermodynamics of Gibbs. For the flat wall, interfacial free energies as a function of different densities of the LJ liquid and as a function of temperature along the coexistence curve are calculated. In the case of a structured wall, the interaction strength between the wall and the LJ system and the lattice constant of the structured wall are varied. Using the values of the wall-liquid and wall-crystal interfacial energies along with the value for the crystal-liquid interfacial free energy determined previously for the same system by the "cleaving potential method," we obtain the contact angle as a function of various parameters; in particular, the conditions are found under which partial wetting occurs.

  20. Molecular detection of a potentially toxic diatom species.

    PubMed

    Dhar, Bidhan Chandra; Cimarelli, Lucia; Singh, Kumar Saurabh; Brandi, Letizia; Brandi, Anna; Puccinelli, Camilla; Marcheggiani, Stefania; Spurio, Roberto

    2015-05-06

    A few diatom species produce toxins that affect human and animal health. Among these, members of the Pseudo-nitzschia genus were the first diatoms unambiguously identified as producer of domoic acid, a neurotoxin affecting molluscan shell-fish, birds, marine mammals, and humans. Evidence exists indicating the involvement of another diatom genus, Amphora, as a potential producer of domoic acid. We present a strategy for the detection of the diatom species Amphora coffeaeformis based on the development of species-specific oligonucleotide probes and their application in microarray hybridization experiments. This approach is based on the use of two marker genes highly conserved in all diatoms, but endowed with sufficient genetic divergence to discriminate diatoms at the species level. A region of approximately 450 bp of these previously unexplored marker genes, coding for elongation factor 1-a (eEF1-a) and silicic acid transporter (SIT), was used to design oligonucleotide probes that were tested for specificity in combination with the corresponding fluorescently labeled DNA targets. The results presented in this work suggest a possible use of this DNA chip technology for the selective detection of A. coffeaeformis in environmental settings where the presence of this potential toxin producer may represent a threat to human and animal health. In addition, the same basic approach can be adapted to a wider range of diatoms for the simultaneous detection of microorganisms used as biomarkers of different water quality levels.

  1. In silico analysis and molecular docking studies of potential angiotensin-converting enzyme inhibitor using quercetin glycosides

    PubMed Central

    Muhammad, Syed Aun; Fatima, Nighat

    2015-01-01

    The purpose of this study was to analyze the inhibitory action of quercetin glycosides by computational docking studies. For this, natural metabolite quercetin glycosides isolated from buckwheat and onions were used as ligand for molecular interaction. The crystallographic structure of molecular target angiotensin-converting enzyme (ACE) (peptidyl-dipeptidase A) was obtained from PDB database (PDB ID: 1O86). Enalapril, a well-known brand of ACE inhibitor was taken as the standard for comparative analysis. Computational docking analysis was performed using PyRx, AutoDock Vina option based on scoring functions. The quercetin showed optimum binding affinity with a molecular target (angiotensin-converting-enzyme) with the binding energy of −8.5 kcal/mol as compared to the standard (−7.0 kcal/mol). These results indicated that quercetin glycosides could be one of the potential ligands to treat hypertension, myocardial infarction, and congestive heart failure. PMID:26109757

  2. Theoretical calculations and vibrational potential energy surface of 4-silaspiro(3,3)heptane

    SciTech Connect

    Ocola, Esther J.; Medders, Cross; Laane, Jaan; Meinander, Niklas

    2014-04-28

    Theoretical computations have been carried out on 4-silaspiro(3,3)heptane (SSH) in order to calculate its molecular structure and conformational energies. The molecule has two puckered four-membered rings with dihedral angles of 34.2° and a tilt angle of 9.4° between the two rings. Energy calculations were carried out for different conformations of SSH. These results allowed the generation of a two-dimensional ring-puckering potential energy surface (PES) of the form V = a(x{sub 1}{sup 4} + x{sub 2}{sup 4}) – b(x{sub 1}{sup 2} + x{sub 2}{sup 2}) + cx{sub 1}{sup 2}x{sub 2}{sup 2}, where x{sub 1} and x{sub 2} are the ring-puckering coordinates for the two rings. The presence of sufficiently high potential energy barriers prevents the molecule from undergoing pseudorotation. The quantum states, wave functions, and predicted spectra resulting from the PESs were calculated.

  3. Improved DFT Potential Energy Surfaces via Improved Densities.

    PubMed

    Kim, Min-Cheol; Park, Hansol; Son, Suyeon; Sim, Eunji; Burke, Kieron

    2015-10-01

    Density-corrected DFT is a method that cures several failures of self-consistent semilocal DFT calculations by using a more accurate density instead. A novel procedure employs the Hartree-Fock density to bonds that are more severely stretched than ever before. This substantially increases the range of accurate potential energy surfaces obtainable from semilocal DFT for many heteronuclear molecules. We show that this works for both neutral and charged molecules. We explain why and explore more difficult cases, for example, CH(+), where density-corrected DFT results are even better than sophisticated methods like CCSD. We give a simple criterion for when DC-DFT should be more accurate than self-consistent DFT that can be applied for most cases.

  4. Potential alternative energy technologies on the Outer Continental Shelf.

    SciTech Connect

    Elcock, D.; Environmental Assessment

    2007-04-20

    This technical memorandum (TM) describes the technology requirements for three alternative energy technologies for which pilot and/or commercial projects on the U.S. Outer Continental Shelf (OCS) are likely to be proposed within the next five to seven years. For each of the alternative technologies--wind, wave, and ocean current--the TM first presents an overview. After each technology-specific overview, it describes the technology requirements for four development phases: site monitoring and testing, construction, operation, and decommissioning. For each phase, the report covers the following topics (where data are available): facility description, electricity generated, ocean area (surface and bottom) occupied, resource requirements, emissions and noise sources, hazardous materials stored or used, transportation requirements, and accident potential. Where appropriate, the TM distinguishes between pilot-scale (or demonstration-scale) facilities and commercial-scale facilities.

  5. Spectroscopic constants and potential energy curves of HfH

    NASA Astrophysics Data System (ADS)

    Balasubramanian, K.; Das, Kalyan K.

    1991-01-01

    Complete active space multiconfiguration self-consistent field (CAS-MCSFC) followed by full second-roder CI (SOCI) and relativistic configuration interaction (RCI) including spin-orbit coupling calculations are carried out on 14 λ- s and 10 ω-ω states of HfH. The spectroscopic constants ( re, Te, ωe, μe, De) of these states are computed. The potential energy curves of these states are also reported. We find several electronic transitions in the IR-UV regions for HfH which are yet to be observed. The ground state of HfH is found to be a {3}/{2} state (82% 2Δ, 8% 2Π) with r e = 1.854 Å, ωe = 1704 cm -1 and μe = 0.66 D. The spin-orbit effects are found to be very significant for HfH.

  6. Spectroscopic Constants and Potential Energy Curves of PbI

    NASA Astrophysics Data System (ADS)

    Benavidesgarcia, M.; Balasubramanian, K.

    1993-10-01

    The spectroscopic constants and potential energy curves of the PbI diatomic were computed using complete active space SCF (CASSCF) followed by first-order CI (FOCI) and second-order CI (SOCI) calculations which included 607 000 configurations. Spin-orbit coupling was studied using the relativistic CI (RCI) method. The spectroscopic properties of the 2Π1/2 state are Re = 2.885 Å, ωe, = 153 cm-1, and De = 2.54(eV), while for the 2Π3/2 state the corresponding values are Re = 2.859 Å, ωe = 162 cm-1, and Te = 8255 cm-1. Our computed constants are in good agreement with experiment for the observed states. We also computed the properties and curves for several excited states which are yet to be observed.

  7. Generalization of classical mechanics for nuclear motions on nonadiabatically coupled potential energy surfaces in chemical reactions.

    PubMed

    Takatsuka, Kazuo

    2007-10-18

    Classical trajectory study of nuclear motion on the Born-Oppenheimer potential energy surfaces is now one of the standard methods of chemical dynamics. In particular, this approach is inevitable in the studies of large molecular systems. However, as soon as more than a single potential energy surface is involved due to nonadiabatic coupling, such a naive application of classical mechanics loses its theoretical foundation. This is a classic and fundamental issue in the foundation of chemistry. To cope with this problem, we propose a generalization of classical mechanics that provides a path even in cases where multiple potential energy surfaces are involved in a single event and the Born-Oppenheimer approximation breaks down. This generalization is made by diagonalization of the matrix representation of nuclear forces in nonadiabatic dynamics, which is derived from a mixed quantum-classical representation of the electron-nucleus entangled Hamiltonian [Takatsuka, K. J. Chem. Phys. 2006, 124, 064111]. A manifestation of quantum fluctuation on a classical subsystem that directly contacts with a quantum subsystem is discussed. We also show that the Hamiltonian thus represented gives a theoretical foundation to examine the validity of the so-called semiclassical Ehrenfest theory (or mean-field theory) for electron quantum wavepacket dynamics, and indeed, it is pointed out that the electronic Hamiltonian to be used in this theory should be slightly modified.

  8. Quorum sensing inhibitory potential and molecular docking studies of sesquiterpene lactones from Vernonia blumeoides.

    PubMed

    Aliyu, Abubakar Babando; Koorbanally, Neil Anthony; Moodley, Brenda; Singh, Parvesh; Chenia, Hafizah Yousuf

    2016-06-01

    The increasing incidence of multidrug-resistant Gram-negative bacterial pathogens has focused research on the suppression of bacterial virulence via quorum sensing inhibition strategies, rather than the conventional antimicrobial approach. The anti-virulence potential of eudesmanolide sesquiterpene lactones previously isolated from Vernonia blumeoides was assessed by inhibition of quorum sensing and in silico molecular docking. Inhibition of quorum sensing-controlled violacein production in Chromobacterium violaceum was quantified using violacein inhibition assays. Qualitative modulation of quorum sensing activity and signal synthesis was investigated using agar diffusion double ring assays and C. violaceum and Agrobacterium tumefaciens biosensor systems. Inhibition of violacein production was concentration-dependent, with ⩾90% inhibition being obtained with ⩾2.4 mg ml(-1) of crude extracts. Violacein inhibition was significant for the ethyl acetate extract with decreasing inhibition being observed with dichloromethane, hexane and methanol extracts. Violacein inhibition ⩾80% was obtained with 0.071 mg ml(-1) of blumeoidolide B in comparison with ⩾3.6 mg ml(-1) of blumeoidolide A. Agar diffusion double ring assays indicated that only the activity of the LuxI synthase homologue, CviI, was modulated by blumeoidolides A and B, and V. blumeoides crude extracts, suggesting that quorum sensing signal synthesis was down-regulated or competitively inhibited. Finally, molecular docking was conducted to explore the binding conformations of sesquiterpene lactones into the binding sites of quorum sensing regulator proteins, CviR and CviR'. The computed binding energy data suggested that the blumeoidolides have a tendency to inhibit both CviR and CviR' with varying binding affinities. Vernonia eudesmanolide sesquiterpene lactones have the potential to be novel therapeutic agents, which might be important in reducing virulence and pathogenicity of drug-resistant bacteria

  9. Spectroscopic constants and potential energy curves of tungsten carbide

    SciTech Connect

    Balasubramanian, K.

    2000-05-01

    Spectroscopic constants (R{sub e},{omega}{sub e},T{sub e},{mu}{sub e}) and potential energy curves for 40 low-lying electronic states of the diatomic tungsten carbide (WC) were obtained using the complete active space multiconfiguration self-consistent field followed by the multireference singles+doubles configuration interaction and full first- and second-order configuration interaction calculations that included up to 6.4 mil configurations. Spin-orbit effects were included through the enhanced relativistic configuration interaction method described here for 28 electronic states of WC lying below {approx}20 000 cm-1. The spin-orbit splitting of the ground state of WC was found to be very large (4394 cm-1). The ground and excited electronic states of the W atom were also computed and were found to be in good agreement with the experimental data. The nature of bonding was analyzed through the composition of orbitals, leading configurations, Mulliken populations, and dipole moments. The dissociation energy of WC was computed including spin-orbit and electron correlation effects. The recent photoelectron spectra of WC{sup -} were assigned on the basis of our computed results. (c) 2000 American Institute of Physics.

  10. 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

  11. Spectroscopic properties and potential energy surfaces of GeH

    NASA Astrophysics Data System (ADS)

    Balasubramanian, K.; Li, Junqing

    1988-04-01

    MCSCF (complete active space SCF) followed by configuration interaction calculations are carried out on 12 electronic states of GeH. Relativistic configuration interaction calculations are carried out with the objective of computing the spin-orbit corrections for the low-lying states. These calculations reveal the existence of 10 bound electronic states of GeH for which spectroscopic properties are computed. The three experimentally observed bands ( a- X, A- X, B- X) are assigned and the uncertainties in the experimental Te and ωe values of these states are corrected. In addition, the spectroscopic properties of 8 states are calculated which are yet to be observed. The spin-orbit coupling constant for the ground state X( 2Π) is calculated to be 869 cm -1. An accurate dissociation energy of 2.81 eV was obtained using {MCSCF}/{SOCI} calculation which employed a large Gaussian basis set questioning the experimental De of ˜3.3 eV obtained from the predissociation in the A2Δ state. It is shown that the intersection of the repulsive 4Π curve which dissociates into the ground state atoms causes predissociation in the A( 2Δ) , B( 2Σ +) , 2Σ +(III), and 2Π(II) states. The potential energy surfaces of a few excited states contain barriers. The calculated ground state dipole moment of 0.098 D is in disagreement with an experimental value of 1.24 D, questioning the experimental dipole moment.

  12. Molecular and cellular MR imaging: potentials and challenges for neurological applications.

    PubMed

    Hoehn, Mathias; Himmelreich, Uwe; Kruttwig, Klaus; Wiedermann, Dirk

    2008-05-01

    This review presents the state of the art of molecular MRI and its application to experimental neurology and neuroscience. We do not repeat a broad, comprehensive overview over the rapidly growing literature in the field of "molecular MRI," which is achieved by several recent reviews. Instead, we focus here on the potential of this imaging technique and its challenges to achieve useful new information in various fields of application with the aim of visualizing cellular processes in the brain, in both the physiological and pathophysiological context. Particular attention will be given to the visualization of cells grafted into the brain. For this goal, the recent most exciting studies are selected as the best examples to elucidate the method's fast expanding potentials. Attention is also given to the aspects of producing synergies by combining molecular MRI with other molecular imaging modalities, thus generating the most complex pictures of cellular and molecular events in the brain under in vivo conditions.

  13. Molecular mechanisms underlying the potential antiobesity-related diseases effect of cocoa polyphenols.

    PubMed

    Ali, Faisal; Ismail, Amin; Kersten, Sander

    2014-01-01

    Obesity and related metabolic diseases (e.g., type 2 diabetes, cardiovascular diseases, and hypertension) are the most prevailing nutrition-related issues in the world. An emerging feature of obesity is their relationship with chronic inflammation that begins in white adipose tissue and eventually becomes systemic. One potential dietary strategy to reduce glucose intolerance and inflammation is consumption of polyphenol-rich cocoa-like cocoa or their by-products. In vitro as well as in vivo data indicate that cocoa polyphenols (CPs) may exhibit antioxidant and anti-inflammatory properties. Polyphenols commonly found in cocoa have been reported to regulate lipid metabolism via inducing metabolic gene expression or activating transcription factors that regulate the expression of numerous genes, many of which play an important role in energy metabolism. Currently, several molecular targets (e.g., nuclear factor Kappa B, activated protein-1, peroxisome proliferator-activated receptors, liver X receptors, and adiponectin gene) have been identified, which may explain potential beneficial obesity-associated diseases effects of CPs. Further studies have been performed regarding the protective effects of CPs against metabolic diseases by suppressing transcription factors that antagonize lipid accumulation. Thus, polyphenols-rich cocoa products may diminish obesity-mediated metabolic diseases by multiple mechanisms, thereby attenuating chronic inflammation.

  14. Molecular dynamics study on β -phase vanadium monohydride with machine learning potential

    NASA Astrophysics Data System (ADS)

    Miwa, Kazutoshi; Ohno, Hiroshi

    2016-11-01

    The formalism to construct the machine learning potentials (MLPs) is presented. We introduce the spilling factor for the simultaneous error estimation and the recursive bisection method for the reduction of the computational cost. The formalism is applied for the β -phase vanadium monohydride. The first-principles calculations based on density functional theory (DFT) are used to prepare the sample data set from which the MLP for the vanadium monohydride (VH) system is constructed. In the molecular dynamics simulation with the MLP, the time-averaged structure of β -VH is predicted correctly to be the body-centered tetragonal structure with the octahedral (O ) site occupation of H. The average lattice constants are in good agreement with the experimental data which are not able to be reproduced by the static DFT calculation. The O -site occupation of H observed in the average structure is, however, a saddle point on the potential-energy surface, and the actual hydrogen occupation is found to be the 4 T configuration.

  15. Molecular Breeding to Create Optimized Crops: From Genetic Manipulation to Potential Applications in Plant Factories

    PubMed Central

    Hiwasa-Tanase, Kyoko; Ezura, Hiroshi

    2016-01-01

    Crop cultivation in controlled environment plant factories offers great potential to stabilize the yield and quality of agricultural products. However, many crops are currently unsuited to these environments, particularly closed cultivation systems, due to space limitations, low light intensity, high implementation costs, and high energy requirements. A major barrier to closed system cultivation is the high running cost, which necessitates the use of high-margin crops for economic viability. High-value crops include those with enhanced nutritional value or containing additional functional components for pharmaceutical production or with the aim of providing health benefits. In addition, it is important to develop cultivars equipped with growth parameters that are suitable for closed cultivation. Small plant size is of particular importance due to the limited cultivation space. Other advantageous traits are short production cycle, the ability to grow under low light, and high nutriculture availability. Cost-effectiveness is improved from the use of cultivars that are specifically optimized for closed system cultivation. This review describes the features of closed cultivation systems and the potential application of molecular breeding to create crops that are optimized for cost-effectiveness and productivity in closed cultivation systems. PMID:27200016

  16. Molecular hydrogen as a preventive and therapeutic medical gas: initiation, development and potential of hydrogen medicine.

    PubMed

    Ohta, Shigeo

    2014-10-01

    Molecular hydrogen (H2) has been accepted to be an inert and nonfunctional molecule in our body. We have turned this concept by demonstrating that H2 reacts with strong oxidants such as hydroxyl radical in cells, and proposed its potential for preventive and therapeutic applications. H2 has a number of advantages exhibiting extensive effects: H2 rapidly diffuses into tissues and cells, and it is mild enough neither to disturb metabolic redox reactions nor to affect signaling reactive oxygen species; therefore, there should be no or little adverse effects of H2. There are several methods to ingest or consume H2; inhaling H2 gas, drinking H2-dissolved water (H2-water), injecting H2-dissolved saline (H2-saline), taking an H2 bath, or dropping H2-saline into the eyes. The numerous publications on its biological and medical benefits revealed that H2 reduces oxidative stress not only by direct reactions with strong oxidants, but also indirectly by regulating various gene expressions. Moreover, by regulating the gene expressions, H2 functions as an anti-inflammatory and anti-apoptotic, and stimulates energy metabolism. In addition to growing evidence obtained by model animal experiments, extensive clinical examinations were performed or are under investigation. Since most drugs specifically act to their targets, H2 seems to differ from conventional pharmaceutical drugs. Owing to its great efficacy and lack of adverse effects, H2 has promising potential for clinical use against many diseases.

  17. Molecular Breeding to Create Optimized Crops: From Genetic Manipulation to Potential Applications in Plant Factories.

    PubMed

    Hiwasa-Tanase, Kyoko; Ezura, Hiroshi

    2016-01-01

    Crop cultivation in controlled environment plant factories offers great potential to stabilize the yield and quality of agricultural products. However, many crops are currently unsuited to these environments, particularly closed cultivation systems, due to space limitations, low light intensity, high implementation costs, and high energy requirements. A major barrier to closed system cultivation is the high running cost, which necessitates the use of high-margin crops for economic viability. High-value crops include those with enhanced nutritional value or containing additional functional components for pharmaceutical production or with the aim of providing health benefits. In addition, it is important to develop cultivars equipped with growth parameters that are suitable for closed cultivation. Small plant size is of particular importance due to the limited cultivation space. Other advantageous traits are short production cycle, the ability to grow under low light, and high nutriculture availability. Cost-effectiveness is improved from the use of cultivars that are specifically optimized for closed system cultivation. This review describes the features of closed cultivation systems and the potential application of molecular breeding to create crops that are optimized for cost-effectiveness and productivity in closed cultivation systems.

  18. Sculpting Molecular Potentials to Design Optimized Materials: The Inverse Design of New Molecular Structures

    DTIC Science & Technology

    2010-05-10

    Miloradovic, A. Persoons, T . Verbiest, M. J . Therien, and K. Clays, "Molecular Symmetry and Solution Phase Structure Interrogated by Hyper-Raleigh...34 Nano Lett., 8, 2814-2818 (2008).  T . V. Duncan, K. Song, S.- T . Hung, I. Miloradovic, A. Persoons, T . Verbiest, M. J . Therien, and K. Clays...Beratan, Weitao Yang, Michael J . Therien, Koen Clays Duke University Office of Research Support Duke University Durham, NC 27705 - REPORT

  19. Sphingolipids: A Potential Molecular Approach to Treat Allergic Inflammation

    PubMed Central

    Sun, Wai Y.; Bonder, Claudine S.

    2012-01-01

    Allergic inflammation is an immune response to foreign antigens, which begins within minutes of exposure to the allergen followed by a late phase leading to chronic inflammation. Prolonged allergic inflammation manifests in diseases such as urticaria and rhino-conjunctivitis, as well as chronic asthma and life-threatening anaphylaxis. The prevalence of allergic diseases is profound with 25% of the worldwide population affected and a rising trend across all ages, gender, and racial groups. The identification and avoidance of allergens can manage this disease, but this is not always possible with triggers being common foods, prevalent air-borne particles and only extremely low levels of allergen exposure required for sensitization. Patients who are sensitive to multiple allergens require prophylactic and symptomatic treatments. Current treatments are often suboptimal and associated with adverse effects, such as the interruption of cognition, sleep cycles, and endocrine homeostasis, all of which affect quality of life and are a financial burden to society. Clearly, a better therapeutic approach for allergic diseases is required. Herein, we review the current knowledge of allergic inflammation and discuss the role of sphingolipids as potential targets to regulate inflammatory development in vivo and in humans. We also discuss the benefits and risks of using sphingolipid inhibitors. PMID:23316248

  20. Evaluating molecular mechanical potentials for helical peptides and proteins.

    PubMed

    Thompson, Erik J; DePaul, Allison J; Patel, Sarav S; Sorin, Eric J

    2010-04-07

    Multiple variants of the AMBER all-atom force field were quantitatively evaluated with respect to their ability to accurately characterize helix-coil equilibria in explicit solvent simulations. Using a global distributed computing network, absolute conformational convergence was achieved for large ensembles of the capped A(21) and F(s) helical peptides. Further assessment of these AMBER variants was conducted via simulations of a flexible 164-residue five-helix-bundle protein, apolipophorin-III, on the 100 ns timescale. Of the contemporary potentials that had not been assessed previously, the AMBER-99SB force field showed significant helix-destabilizing tendencies, with beta bridge formation occurring in helical peptides, and unfolding of apolipophorin-III occurring on the tens of nanoseconds timescale. The AMBER-03 force field, while showing adequate helical propensities for both peptides and stabilizing apolipophorin-III, (i) predicts an unexpected decrease in helicity with ALA-->ARG(+) substitution, (ii) lacks experimentally observed 3(10) helical content, and (iii) deviates strongly from average apolipophorin-III NMR structural properties. As is observed for AMBER-99SB, AMBER-03 significantly overweighs the contribution of extended and polyproline backbone configurations to the conformational equilibrium. In contrast, the AMBER-99phi force field, which was previously shown to best reproduce experimental measurements of the helix-coil transition in model helical peptides, adequately stabilizes apolipophorin-III and yields both an average gyration radius and polar solvent exposed surface area that are in excellent agreement with the NMR ensemble.