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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. Molecular Multipole Potential Energy Functions for Water.

    PubMed

    Tan, Ming-Liang; Tran, Kelly N; Pickard, Frank C; Simmonett, Andrew C; Brooks, Bernard R; Ichiye, Toshiko

    2016-03-01

    Water is the most common liquid on this planet, with many unique properties that make it essential for life as we know it. These properties must arise from features in the charge distribution of a water molecule, so it is essential to capture these features in potential energy functions for water to reproduce its liquid state properties in computer simulations. Recently, models that utilize a multipole expansion located on a single site in the water molecule, or "molecular multipole models", have been shown to rival and even surpass site models with up to five sites in reproducing both the electrostatic potential around a molecule and a variety of liquid state properties in simulations. However, despite decades of work using multipoles, confusion still remains about how to truncate the multipole expansions efficiently and accurately. This is particularly important when using molecular multipole expansions to describe water molecules in the liquid state, where the short-range interactions must be accurate, because the higher order multipoles of a water molecule are large. Here, truncation schemes designed for a recent efficient algorithm for multipoles in molecular dynamics simulations are assessed for how well they reproduce results for a simple three-site model of water when the multipole moments and Lennard-Jones parameters of that model are used. In addition, the multipole analysis indicates that site models that do not account for out-of-plane electron density overestimate the stability of a non-hydrogen-bonded conformation, leading to serious consequences for the simulated liquid. PMID:26562223

  3. 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.

  4. Molecular potential energy surfaces for interstellar chemistry and fusion applications

    NASA Astrophysics Data System (ADS)

    Braams, Bastiaan J.; Huang, Xinchuan; Jin, Zhong; Xie, Zhen; Zhang, Xiubin; Bowman, Joel M.; Sharma, Amit Raj; Scheider, Ralf

    2006-04-01

    In the Born-Oppenheimer approximation the electronic Schr"odinger equation is solved given the nuclear positions as parameters, and this defines the potential energy surface. We have used computational invariant theory and the MAGMA computer algebra system as an aid to develop representations for the potential energy and dipole moment surfaces that are fully invariant under permutations of like nuclei, extending an approach that for 3-body and 4-body systems has a long history, e.g. [J. N. Murrell et al. Molecular Potential Energy Functions, Wiley, 1984]. A many-body (cluster) expansion is used to describe reaction complexes. The methods have been applied in an almost routine way for systems of up to 7 nuclei, including several molecules that are of interest for interstellar chemistry and for the issue of hydrocarbon breakdown in fusion edge plasma: H5^+, CH5, CH5^+, C2H3^+, and their fragments, with C2H5^+ on the way. The mathematical and computional methods and the hydrocarbon applications will be presented.

  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. (Molecular understanding of mutagenicity using potential energy methods)

    SciTech Connect

    Broyde, S.

    1990-01-01

    The objective of our work has been, for many year, to elucidate on a molecular level at atomic resolution the structures of DNAs modified by highly mutagenic polycyclic aromatic amines and hydrocarbons, and their less mutagenic chemically related analogs and unmodified DNAs, as controls. The ultimate purpose of this undertaking is to obtain an understanding of the relationship DNA structures and mutagenicity. Our methods for elucidating structures are computational, but we keep in close contact with experimental developments, and have, very recently, been able to incorporate the first experimental information from NMR studies by other workers in our calculations. The specific computational methods we employ are minimized potential energy calculations using the torsion angle space program DUPLEX, developed and written by Dr. Brain Hingerty to yield static views. Molecular dynamics simulations of the important static structures with full solvation and salt are carried out with the program AMBER; this yields mobile views in a milieu that best mimics the natural environment of the cell. In addition, we have been developing new strategies for searching conformation space and building DNA duplexes from favored subunit structures. 30 refs., 12 figs.

  7. An adaptive interpolation scheme for molecular potential energy surfaces.

    PubMed

    Kowalewski, Markus; Larsson, Elisabeth; Heryudono, Alfa

    2016-08-28

    The calculation of potential energy surfaces for quantum dynamics can be a time consuming task-especially when a high level of theory for the electronic structure calculation is required. We propose an adaptive interpolation algorithm based on polyharmonic splines combined with a partition of unity approach. The adaptive node refinement allows to greatly reduce the number of sample points by employing a local error estimate. The algorithm and its scaling behavior are evaluated for a model function in 2, 3, and 4 dimensions. The developed algorithm allows for a more rapid and reliable interpolation of a potential energy surface within a given accuracy compared to the non-adaptive version. PMID:27586901

  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.

    PubMed

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

    2012-11-21

    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. PMID:23181297

  10. 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.

  11. 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

    2016-09-01

    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. PMID:27500886

  12. A general method for constructing multidimensional molecular potential energy surfaces from {ital ab} {ital initio} calculations

    SciTech Connect

    Ho, T.; Rabitz, H.

    1996-02-01

    A general interpolation method for constructing smooth molecular potential energy surfaces (PES{close_quote}s) from {ital ab} {ital initio} data are proposed within the framework of the reproducing kernel Hilbert space and the inverse problem theory. The general expression for an {ital a} {ital posteriori} error bound of the constructed PES is derived. It is shown that the method yields globally smooth potential energy surfaces that are continuous and possess derivatives up to second order or higher. Moreover, the method is amenable to correct symmetry properties and asymptotic behavior of the molecular system. Finally, the method is generic and can be easily extended from low dimensional problems involving two and three atoms to high dimensional problems involving four or more atoms. Basic properties of the method are illustrated by the construction of a one-dimensional potential energy curve of the He{endash}He van der Waals dimer using the exact quantum Monte Carlo calculations of Anderson {ital et} {ital al}. [J. Chem. Phys. {bold 99}, 345 (1993)], a two-dimensional potential energy surface of the HeCO van der Waals molecule using recent {ital ab} {ital initio} calculations by Tao {ital et} {ital al}. [J. Chem. Phys. {bold 101}, 8680 (1994)], and a three-dimensional potential energy surface of the H{sup +}{sub 3} molecular ion using highly accurate {ital ab} {ital initio} calculations of R{umlt o}hse {ital et} {ital al}. [J. Chem. Phys. {bold 101}, 2231 (1994)]. In the first two cases the constructed potentials clearly exhibit the correct asymptotic forms, while in the last case the constructed potential energy surface is in excellent agreement with that constructed by R{umlt o}hse {ital et} {ital al}. using a low order polynomial fitting procedure. {copyright} {ital 1996 American Institute of Physics.}

  13. 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

  14. 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

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

    PubMed

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

    2013-11-01

    A systematic vibrational spectroscopic assignment and analysis of pramipexole [(S)-N(6)-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. PMID:23831980

  16. Molecular electrostatic potentials by systematic molecular fragmentation

    SciTech Connect

    Reid, David M.; Collins, Michael A.

    2013-11-14

    A simple method is presented for estimating the molecular electrostatic potential in and around molecules using systematic molecular fragmentation. This approach estimates the potential directly from the electron density. The accuracy of the method is established for a set of organic molecules and ions. The utility of the approach is demonstrated by estimating the binding energy of a water molecule in an internal cavity in the protein ubiquitin.

  17. 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.

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

    PubMed

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

    2016-07-13

    Almost 50 years have passed from the first computer simulations of water, and a large number of molecular models have been proposed since then to elucidate the unique behavior of water across different phases. In this article, we review the recent progress in the development of analytical potential energy functions that aim at correctly representing many-body effects. Starting from the many-body expansion of the interaction energy, specific focus is on different classes of potential energy functions built upon a hierarchy of approximations and on their ability to accurately reproduce reference data obtained from state-of-the-art electronic structure calculations and experimental measurements. We show that most recent potential energy functions, which include explicit short-range representations of two-body and three-body effects along with a physically correct description of many-body effects at all distances, predict the properties of water from the gas to the condensed phase with unprecedented accuracy, thus opening the door to the long-sought "universal model" capable of describing the behavior of water under different conditions and in different environments. PMID:27186804

  19. Absolute Binding Free Energy Calculations Using Molecular Dynamics Simulations with Restraining Potentials

    PubMed Central

    Wang, Jiyao; Deng, Yuqing; Roux, Benoît

    2006-01-01

    The absolute (standard) binding free energy of eight FK506-related ligands to FKBP12 is calculated using free energy perturbation molecular dynamics (FEP/MD) simulations with explicit solvent. A number of features are implemented to improve the accuracy and enhance the convergence of the calculations. First, the absolute binding free energy is decomposed into sequential steps during which the ligand-surrounding interactions as well as various biasing potentials restraining the translation, orientation, and conformation of the ligand are turned “on” and “off.” Second, sampling of the ligand conformation is enforced by a restraining potential based on the root mean-square deviation relative to the bound state conformation. The effect of all the restraining potentials is rigorously unbiased, and it is shown explicitly that the final results are independent of all artificial restraints. Third, the repulsive and dispersive free energy contribution arising from the Lennard-Jones interactions of the ligand with its surrounding (protein and solvent) is calculated using the Weeks-Chandler-Andersen separation. This separation also improves convergence of the FEP/MD calculations. Fourth, to decrease the computational cost, only a small number of atoms in the vicinity of the binding site are simulated explicitly, while all the influence of the remaining atoms is incorporated implicitly using the generalized solvent boundary potential (GSBP) method. With GSBP, the size of the simulated FKBP12/ligand systems is significantly reduced, from ∼25,000 to 2500. The computations are very efficient and the statistical error is small (∼1 kcal/mol). The calculated binding free energies are generally in good agreement with available experimental data and previous calculations (within ∼2 kcal/mol). The present results indicate that a strategy based on FEP/MD simulations of a reduced GSBP atomic model sampled with conformational, translational, and orientational restraining

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

    ScienceCinema

    Sayre, Richard [LANL

    2013-01-22

    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.

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

    SciTech Connect

    Sayre, Richard

    2012-03-22

    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.

  2. The inherent dynamics of a molecular liquid: Geodesic pathways through the potential energy landscape of a liquid of linear molecules

    NASA Astrophysics Data System (ADS)

    Jacobson, Daniel; Stratt, Richard M.

    2014-05-01

    Because the geodesic pathways that a liquid follows through its potential energy landscape govern its slow, diffusive motion, we suggest that these pathways are logical candidates for the title of a liquid's "inherent dynamics." Like their namesake "inherent structures," these objects are simply features of the system's potential energy surface and thus provide views of the system's structural evolution unobstructed by thermal kinetic energy. This paper shows how these geodesic pathways can be computed for a liquid of linear molecules, allowing us to see precisely how such molecular liquids mix rotational and translational degrees of freedom into their dynamics. The ratio of translational to rotational components of the geodesic path lengths, for example, is significantly larger than would be expected on equipartition grounds, with a value that scales with the molecular aspect ratio. These and other features of the geodesics are consistent with a picture in which molecular reorientation adiabatically follows translation—molecules largely thread their way through narrow channels available in the potential energy landscape.

  3. Water models based on a single potential energy surface and different molecular degrees of freedom

    NASA Astrophysics Data System (ADS)

    Saint-Martin, Humberto; Hernández-Cobos, Jorge; Ortega-Blake, Iván

    2005-06-01

    Up to now it has not been possible to neatly assess whether a deficient performance of a model is due to poor parametrization of the force field or the lack of inclusion of enough molecular properties. This work compares several molecular models in the framework of the same force field, which was designed to include many-body nonadditive effects: (a) a polarizable and flexible molecule with constraints that account for the quantal nature of the vibration [B. Hess, H. Saint-Martin, and H. J. C. Berendsen, J. Chem. Phys. 116, 9602 (2002), H. Saint-Martin, B. Hess, and H. J. C. Berendsen, J. Chem. Phys. 120, 11133 (2004)], (b) a polarizable and classically flexible molecule [H. Saint-Martin, J. Hernández-Cobos, M. I. Bernal-Uruchurtu, I. Ortega-Blake, and H. J. C. Berendsen, J. Chem. Phys. 113, 10899 (2000)], (c) a polarizable and rigid molecule, and finally (d) a nonpolarizable and rigid molecule. The goal is to determine how significant the different molecular properties are. The results indicate that all factors—nonadditivity, polarizability, and intramolecular flexibility—are important. Still, approximations can be made in order to diminish the computational cost of the simulations with a small decrease in the accuracy of the predictions, provided that those approximations are counterbalanced by the proper inclusion of an effective molecular property, that is, an average molecular geometry or an average dipole. Hence instead of building an effective force field by parametrizing it in order to reproduce the properties of a specific phase, a building approach is proposed that is based on adequately restricting the molecular flexibility and/or polarizability of a model potential fitted to unimolecular properties, pair interactions, and many-body nonadditive contributions. In this manner, the same parental model can be used to simulate the same substance under a wide range of thermodynamic conditions. An additional advantage of this approach is that, as the force

  4. Confinement effects on excitation energies and regioselectivity as probed by the Fukui function and the molecular electrostatic potential

    NASA Astrophysics Data System (ADS)

    Borgoo, Alex; Tozer, David; Geerlings, Paul; de Proft, Frank

    2009-03-01

    When a molecule is placed as a guest inside a zeolite pore, its electronic structure will be altered, among others by the effect of the so-called ``confinement". It has been established that the compression of the molecular orbitals influences a system's reactivity. In this work we use a simple potential barrier method to quantify the importance of confinement effects on chemical reactivity. In the first part, excitation energies and molecular orbital energy gaps are evaluated for molecules placed in cavities of different sizes. Our results for ethylene and formaldehyde reveal an increase in excitation energy and the gap between the occupied and the unoccupied levels. In the case of the larger molecules naphthalene and anthracene, the HOMO-LUMO gap shows very little sensitivity to the confinement. To investigate the role of confinement effects on local aspects of chemical reactivity and on regioselectivity, we evaluated its effect on the Fukui function and the molecular electrostatic potential, reactivity indices that are central in the description of orbital and charge controlled reactions. The results indicate that confinement can influence the regioselectivity and that the reactivity of anions is expected to change, due to the artificial binding of the exess electron.

  5. Potential energy curves for the 48 lowest-lying molecular states of LiH +

    NASA Astrophysics Data System (ADS)

    Alikacem, A.; Aubert-Frécon, M.

    1985-05-01

    The electronic energies of the 20 lowest lying 2Σ + states, the 14 lowest lying 2Π states, and the 14 lowest lying 2Δ states of LiH + have been calculated in the range 2 ≤ R ≤ 20 a.u. from a model potential approach and using truncated diatomic orbitals (TDO) as basis set. Results in very good agreement with the more recent literature were obtained for the spectroscopic constants, Re and De, for the ground state X2Σ +.

  6. 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. PMID:24083374

  7. 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.

  8. 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…

  9. Numerical investigation of molecular nano-array in potential-energy profile for a single dsDNA.

    PubMed

    Alishahi, Marzieh; Kamali, Reza; Abouali, Omid

    2016-04-01

    A Rigorous numerical investigation on dsDNA translocation in quasi-2-dimensional nano-array filter is performed using Molecular Dynamics (MD) method. Various dsDNA molecules with different sizes are chosen in order to model Ogston sieving in a nano-array filter. The radius of gyration of dsDNA molecule is less than the characteristic length of the shallow region in nano-array. The dsDNA molecule is assumed to be in the 0.05M NaCl electrolyte. MD shows acceptable results for potential-energy profile for nano-array filter. According to the MD outcomes, the dsDNA electrophoretic mobility decreases almost linearly with dsDNA size and show the same trend as Ogston sieving for gel electrophoresis. In addition, different shapes for nano-array filter are studied for a unique dsDNA molecule. It is concluded that steeping the nano-array wall can cause the retardation of dsDNA translocation and decreases dsDNA electrophoretic mobility. PMID:27125679

  10. 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 ...

  11. 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...

  12. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  14. 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.

  15. 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. PMID:26661376

  16. The origins of intra- and inter-molecular vibrational couplings: A case study of H2O-Ar on full and reduced-dimensional potential energy surface

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

    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 H2O-Ar, which explicitly incorporates interdependence on the intramolecular (Q1, Q2, Q3) normal-mode coordinates of the H2O 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 (v1, v2, v3) = (0, 0, 0), (0, 0, 1), (1, 0, 0), (0, 1, 0) states of H2O 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-1, and required only 58 parameters. With the 3D PESs of H2O-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-1 for all three rotational branches of the asymmetric stretch fundamental transitions. The infrared band origin shifts associated with three fundamental bands of H2O in H2O-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.

  17. Assessing the accuracy of SAPT(DFT) interaction energies by comparison with experimentally derived noble gas potentials and molecular crystal lattice energies.

    PubMed

    Bordner, Andrew J

    2012-12-01

    The density functional version of symmetry-adapted perturbation theory, SAPT(DFT), is a computationally efficient method for calculating intermolecular interaction energies. We evaluate its accuracy by comparison with experimentally determined noble gas interaction potentials and sublimation enthalpies, most of which have not been previously calculated using this method. In order to compare the results with wavefunction methods, we also calculate these quantities using MP2 and, for noble gas dimers, using CCSD(T). For the crystal lattice energy calculations, we include corrections to the dispersion, electrostatic, and induction energies that account for the finite interaction distance cutoff and higher-order induction contributions. Overall, the energy values extrapolated to the complete basis set limit show that SAPT(DFT) achieves significantly better agreement with experiment than MP2. PMID:23060262

  18. Molecular potentials and relaxation dynamics

    NASA Astrophysics Data System (ADS)

    Karo, A. M.

    1981-03-01

    The use of empirical pseudopotentials, in evaluating interatomic potentials, provides and inexpensive and convenient method for obtaining highly accurate potential curves and permits the modeling of core-valence correlation, and the inclusion of relativistic effects when these are significant. As an example, recent calculations of the chi and the a 3 Sigma + states of LiH, NaH, KH, RbH, and CsH and the chi 2 Sigma + states of their anions are discussed. Pseudopotentials, including core polarization terms, have been used to replace the core electrons, and this has been coupled with the development of compact, highly-optimized basis sets for the corresponding one- and two-electron atoms. Comparisons of the neutral potential curves with experiment and other ab initio calculations show good agreement (within 1000/cm over most of the potential curves) with the difference curves being considerably more accurate.

  19. 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

  20. Molecular potentials and relaxation dynamics

    SciTech Connect

    Karo, A.M.

    1981-03-27

    The use of empirical pseudopotentials, in evaluating interatomic potentials, provides an inexpensive and convenient method for obtaining highly accurate potential curves and permits the modeling of core-valence correlation, and the inclusion of relativistic effects when these are significant. As an example, recent calculations of the chi/sup 1/..sigma../sup +/ and a/sup 3/..sigma../sup +/ states of LiH, NaH, KH, RbH, and CsH and the chi/sup 2/..sigma../sup +/ states of their anions are discussed. Pseudopotentials, including core polarization terms, have been used to replace the core electrons, and this has been coupled with the development of compact, highly-optimized basis sets for the corresponding one- and two-electron atoms. Comparisons of the neutral potential curves with experiment and other ab initio calculations show good agreement (within 1000 cm/sup -1/ over most of the potential curves) with the difference curves being considerably more accurate.

  1. 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.

  2. Quantum tunneling in testosterone 6beta-hydroxylation by cytochrome P450: reaction dynamics calculations employing multiconfiguration molecular-mechanical potential energy surfaces.

    PubMed

    Zhang, Yan; Lin, Hai

    2009-10-29

    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 6beta-hydrogen abstraction and the 6beta-d(1)-testosterone 6beta-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. PMID:19480428

  3. The origins of intra- and inter-molecular vibrational couplings: A case study of H2O-Ar on full and reduced-dimensional potential energy surface.

    PubMed

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

    2016-01-01

    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 H2O-Ar, which explicitly incorporates interdependence on the intramolecular (Q1,  Q2,  Q3) normal-mode coordinates of the H2O 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 (v1,  v2,  v3) =  (0,  0,  0), (0,  0,  1), (1,  0,  0), (0,  1,  0) states of H2O 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(-1), and required only 58 parameters. With the 3D PESs of H2O-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(-1) for all three rotational branches of the asymmetric stretch fundamental transitions. The infrared band origin shifts associated with three fundamental bands of H2O in H2O-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. PMID:26747800

  4. 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.

  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. 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.

  7. Molecular energies from an incremental fragmentation method

    NASA Astrophysics Data System (ADS)

    Meitei, Oinam Romesh; Heßelmann, Andreas

    2016-02-01

    The systematic molecular fragmentation method by Collins and Deev [J. Chem. Phys. 125, 104104 (2006)] has been used to calculate total energies and relative conformational energies for a number of small and extended molecular systems. In contrast to the original approach by Collins, we have tested the accuracy of the fragmentation method by utilising an incremental scheme in which the energies at the lowest level of the fragmentation are calculated on an accurate quantum chemistry level while lower-cost methods are used to correct the low-level energies through a high-level fragmentation. In this work, the fragment energies at the lowest level of fragmentation were calculated using the random-phase approximation (RPA) and two recently developed extensions to the RPA while the incremental corrections at higher levels of the fragmentation were calculated using standard density functional theory (DFT) methods. The complete incremental fragmentation method has been shown to reproduce the supermolecule results with a very good accuracy, almost independent on the molecular type, size, or type of decomposition. The fragmentation method has also been used in conjunction with the DFT-SAPT (symmetry-adapted perturbation theory) method which enables a breakdown of the total nonbonding energy contributions into individual interaction energy terms. Finally, the potential problems of the method connected with the use of capping hydrogen atoms are analysed and two possible solutions are supplied.

  8. 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

  9. Molecular Electrostatic Potentials from Invariom Point Charges.

    PubMed

    Wandtke, Claudia M; Lübben, Jens; Dittrich, Birger

    2016-07-18

    A set of look-up point charges for generating molecular electrostatic potentials is provided. The set relies on atom classification of the invariom database, which has already been applied to assign aspherical scattering factors in single-crystal X-ray diffraction. The focus of the investigation is on improving the accuracy of electrostatic potentials calculated by using tabulated point charges. In this respect, the performance of invariom point charges is compared with 1) those from a restrained fit to the electrostatic potential directly following quantum-chemical DFT computations, 2) semi-empirical AM1-bcc charges, and 3) conceptually similar TPACM4 look-up charges. Invariom classification gives charges that perform better than those from TPACM4, although tabulated charges remain inferior to those from molecule-specific computations. Point-charge electrostatic potentials also agree favorably with those from charge-density studies on the basis of X-ray experiments, without requiring the considerable effort of the latter. PMID:26999276

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. 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)].

  15. Molecular digital pathology: progress and potential of exchanging molecular data.

    PubMed

    Roy, Somak; Pfeifer, John D; LaFramboise, William A; Pantanowitz, Liron

    2016-09-01

    Many of the demands to perform next generation sequencing (NGS) in the clinical laboratory can be resolved using the principles of telepathology. Molecular telepathology can allow facilities to outsource all or a portion of their NGS operation such as cloud computing, bioinformatics pipelines, variant data management, and knowledge curation. Clinical pathology laboratories can electronically share diverse types of molecular data with reference laboratories, technology service providers, and/or regulatory agencies. Exchange of electronic molecular data allows laboratories to perform validation of rare diseases using foreign data, check the accuracy of their test results against benchmarks, and leverage in silico proficiency testing. This review covers the emerging subject of molecular telepathology, describes clinical use cases for the appropriate exchange of molecular data, and highlights key issues such as data integrity, interoperable formats for massive genomic datasets, security, malpractice and emerging regulations involved with this novel practice. PMID:27471996

  16. Potential molecular targets for Ewing's sarcoma therapy.

    PubMed

    Jully, Babu; Rajkumar, Thangarajan

    2012-10-01

    Ewing's sarcoma (ES) is a highly malignant tumor of children and young adults. Modern therapy for Ewing's sarcoma combines high-dose chemotherapy for systemic control of disease, with advanced surgical and/or radiation therapeutic approaches for local control. Despite optimal management, the cure rate for localized disease is only approximately 70%, whereas the cure rate for metastatic disease at presentation is less than 30%. Patients who experience long-term disease-free survival are at risk for significant side-effects of therapy, including infertility, limb dysfunction and an increased risk for second malignancies. The identification of new targets for innovative therapeutic approaches is, therefore, strongly needed for its treatment. Many new pharmaceutical agents have been tested in early phases of clinical trials in ES patients who have recurrent disease. While some agents led to partial response or stable disease, the percentages of drugs eliciting responses or causing an overall effect have been minimal. Furthermore, of the new pharmaceuticals being introduced to clinical practice, the most effective agents also have dose-limiting toxicities. Novel approaches are needed to minimize non-specific toxicity, both for patients with recurrence and at diagnosis. This report presents an overview of the potential molecular targets in ES and highlights the possibility that they may serve as therapeutic targets for the disease. Although additional investigations are required before most of these approaches can be assessed in the clinic, they provide a great deal of hope for patients with Ewing's sarcoma. PMID:23580819

  17. Renewable energy potential in Colombia

    NASA Astrophysics Data System (ADS)

    Correa Guzman, Jose Luis

    2008-12-01

    Renewable energy flows are very large in comparison with humankind's use of energy. In principle, all our energy needs, both now and into the future, can be met by energy from renewable sources. After many years trying to develop the alternative energy potential of Colombia, a major effort is principally being made since 2000 to explore and assess the renewable resources of the entire country. Until 2000, the availability of conventional energy sources in Colombia prevented renewable energy exploration from reaching a higher level. However, the extreme energy crisis of 1992 - 1993 alerted the authorities and the community to the necessity for exploring alternative energy sources. This energy study is a general approach to the current and future renewable energy scenario of Colombia. It was prepared in response to the increased interest around the world and in particular in Colombia to develop its non-fossil energy prospective. It, therefore, represents a working document giving an initial impression of the possible scale of the main renewables sources as a response to the concern about energy security and fossil fuel dependence problems. The assumptions made and calculations reported may therefore be subject to revision as more information becomes available. The aim of this dissertation is not only to improve the public understanding and discussion of renewable energy matters in Colombia but also to stimulate the development and application of renewable energy, wherever they have prospects of economic viability and environmental acceptability. To achieve such goal this paper reviews several renewable technologies, their availability, contribution and feasibility in Colombia.

  18. A Molecular Full-Potential LMTO Calculation for Copper Clusters

    NASA Astrophysics Data System (ADS)

    Datta, Radhika Prosad; Banerjea, Amitava; Mookerjee, Abhijit; Bhattacharyya, A. K.

    We study the electronic properties of small (10-20 atoms) copper clusters using the newly-developed molecular full-potential linearized muffin-tin orbital two-centre-fit (TCF) method of Methfessel and van Schilfgaarde. The geometric structures of the clusters had earlier been determined by us through simulated annealing using the Equivalent Crystal Theory to compute total energies. We report the variation of the binding energy, as obtained from the TCF calculations, with cluster size and compare these to the binding energies determined, for the same structures, from the ECT. We also show the variation of the HOMO-LUMO gap with cluster size, and the pseudo-density of states for select cluster sizes.

  19. 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.

  20. 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.

  1. 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.

  2. Ridge-based bias potentials to accelerate molecular dynamics.

    PubMed

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

    2015-12-28

    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. PMID:26723648

  3. On the ionization potential of molecular oxygen

    NASA Technical Reports Server (NTRS)

    Samson, J. A. R.; Gardner, J. L.

    1974-01-01

    The ionization potential of O2 was measured by the technique of high resolution photoelectron spectroscopy taking into account the influence of rotational structure on the shape of the vibrational bands. A value of 12.071 + or - .001 eV (1027.1 + or - 0.1 A) was found for the ionization potential. A lowering of the ionization potential caused by a branch-head when delta N = -2 gave an appearance potential for ionization of 12.068 + or - .001 eV (1027.4 + or - 0.1 A).

  4. 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.

  5. Extracting molecular potentials from incomplete spectroscopic information

    NASA Astrophysics Data System (ADS)

    Li, Xuan; Dutta, Sourav

    2015-12-01

    We extend our recently developed inversion method to extract excited-state potentials from fluorescence line positions and line strengths. We consider a previous limitation of the method arising due to insufficient input data in cases where the relatively weaker emission data are not experimentally available. We develop a solution to this problem by 'regenerating' these weak transition lines via applying a model potential, e.g. a Morse potential. The result of this procedure, illustrated for the Q-branch emission from the lowest three vibrational levels of the B(1Π) state of LiRb, is shown to have an error of 0.29 cm-1 in the classically allowed region and a global error of 5.67 cm-1 for V ≤ E(ν‧ = 10). The robustness of this procedure is also demonstrated by considering the statistical error in the measured line intensities.

  6. 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.

  7. Molecular electrostatic potential at the atomic sites in the effective core potential approximation.

    PubMed

    Lesiuk, Michał; Zachara, Janusz

    2013-02-21

    Considering calculations of the molecular electrostatic potential at the atomic sites (MEP@AS) in the presence of effective core potentials (ECP), we found that the consequent use of the definition of MEP@AS based on the energy derivative with respect to nuclear charge leads to a formula that differs by one term from the result of simple application of Coulomb's law. We have developed a general method to analytically treat derivatives of ECP with respect to nuclear charge. Benchmarking calculations performed on a set of simple molecules show that our formula leads to a systematic decrease in the error connected with the introduction of ECP when compared to all-electron results. Because of a straightforward implementation and relatively low costs of the developed procedure we suggest to use it by default. PMID:23444997

  8. Molecular electrostatic potential at the atomic sites in the effective core potential approximation

    NASA Astrophysics Data System (ADS)

    Lesiuk, Michał; Zachara, Janusz

    2013-02-01

    Considering calculations of the molecular electrostatic potential at the atomic sites (MEP@AS) in the presence of effective core potentials (ECP), we found that the consequent use of the definition of MEP@AS based on the energy derivative with respect to nuclear charge leads to a formula that differs by one term from the result of simple application of Coulomb's law. We have developed a general method to analytically treat derivatives of ECP with respect to nuclear charge. Benchmarking calculations performed on a set of simple molecules show that our formula leads to a systematic decrease in the error connected with the introduction of ECP when compared to all-electron results. Because of a straightforward implementation and relatively low costs of the developed procedure we suggest to use it by default.

  9. 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

  10. Energy transfer in a molecular motor in the Kramers regime.

    PubMed

    Challis, K J; Jack, Michael W

    2013-10-01

    We present a theoretical treatment of energy transfer in a molecular motor described in terms of overdamped Brownian motion on a multidimensional tilted periodic potential. The tilt represents a thermodynamic force driving the system out of equilibrium and, for nonseparable potentials, energy transfer occurs between degrees of freedom. For deep potential wells, the continuous theory transforms to a discrete master equation that is tractable analytically. We use this master equation to derive formal expressions for the hopping rates, drift and diffusion, and the efficiency and rate of energy transfer in terms of the thermodynamic force. These results span both strong and weak coupling between degrees of freedom, describe the near and far from equilibrium regimes, and are consistent with generalized detailed balance and the Onsager relations. We thereby derive a number of diverse results for molecular motors within a single theoretical framework. PMID:24229123

  11. 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…

  12. Molecular chaperones: multiple functions, pathologies, and potential applications.

    PubMed

    Macario, Alberto J L; Conway de Macario, Everly

    2007-01-01

    Cell stressors are ubiquitous and frequent, challenging cells often, which leads to the stress response with activation of anti-stress mechanisms. These mechanisms involve a variety of molecules, including molecular chaperones also known as heat-shock proteins (Hsp). The chaperones treated in this article are proteins that assist other proteins to fold, refold, travel to their place of residence (cytosol, organelle, membrane, extracellular space), and translocate across membranes. Molecular chaperones participate in a variety of physiological processes and are widespread in organisms, tissues, and cells. It follows that chaperone failure will have an impact, possibly serious, on one or more cellular function, which may lead to disease. Chaperones must recognize and interact with proteins in need of assistance or client polypeptides (e.g., nascent at the ribosome, or partially denatured by stressors), and have to interact with other chaperones because the chaperoning mechanism involves teams of chaperone molecules, i.e., multimolecular assemblies or chaperone machines. Consequently, chaperone molecules have structural domains with distinctive functions: bind the client polypeptide, interact with other chaperone molecules to build a machine, and interact with other complexes that integrate the chaperoning network. Also, various chaperones have ATP-binding and ATPase sites because the chaperoning process requires as, a rule, energy from ATP hydrolysis. Alterations in any one of these domains due to a mutation or an aberrant post-translational modification can disrupt the chaperoning process and cause diseases termed chaperonopathies. This article presents the pathologic concept of chaperonopathy with examples, and discusses the potential of using chaperones (genes or proteins) in treatment (chaperonotherapy). In addition, emerging topics within the field of study of chaperones (chaperonology) are highlighted, e.g., genomics (chaperonomics), systems biology

  13. 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.

  14. Potential energy of a dinuclear system

    SciTech Connect

    Adamyan, G.G.; Antonenko, N.V.; Jolos, R.V.; Ivanova, S.P.; Mel`nikova, O.I.

    1994-11-01

    An effective method for calculating the potential energy of a dinuclear system is proposed. Analytic expressions for calculating the nuclear part of the nucleus-nucleus potential in the double-folding form are obtained. A relationship between this potential and the proximity potential is found. Effects of deformation and mutual orientation of nuclei on the interaction potential are studied. It follows from a comparison of calculated potential energies with nuclear binding energies that excited states of some nuclei can be treated as dinuclear or trinuclear systems. 27 refs., 7 figs.

  15. Arbitrary l-state solutions of the Feynman propagator with the Deng-Fan molecular potential

    NASA Astrophysics Data System (ADS)

    Diaf, Ahmed

    2015-01-01

    The bound state solutions of the Feynman propagator with the rotating Deng- Fan molecular potential are presented approximately. An approximation of the centrifugal potential is used and nonlinear space-time transformations are applied. A relation between the original path integral and the Green function of a new quantum soluble system is derived. The energy spectrum and the normalized eigenfunctions are both obtained for the application of this technique to the Deng-Fan molecular potential. Our results are in very good agreement with those found by using numerical and other methods.

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

    PubMed

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

    2016-08-21

    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. PMID:27544080

  17. Exam Question Exchange: Potential Energy Surfaces.

    ERIC Educational Resources Information Center

    Alexander, John J., Ed.

    1988-01-01

    Presents three examination questions, graded in difficulty, that explore the topic of potential energy surfaces using a diagrammatic approach. Provides and discusses acceptable solutions including diagrams. (CW)

  18. 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 ...

  19. Energy pooling upconversion in organic molecular systems.

    PubMed

    LaCount, Michael D; Weingarten, Daniel; Hu, Nan; Shaheen, Sean E; van de Lagemaat, Jao; Rumbles, Garry; Walba, David M; Lusk, Mark T

    2015-04-30

    A combination of molecular quantum electrodynamics, perturbation theory, and ab initio calculations was used to create a computational methodology capable of estimating the rate of three-body singlet upconversion in organic molecular assemblies. The approach was applied to quantify the conditions under which such relaxation rates, known as energy pooling, become meaningful for two test systems, stilbene-fluorescein and hexabenzocoronene-oligothiophene. Both exhibit low intramolecular conversion, but intermolecular configurations exist in which pooling efficiency is at least 90% when placed in competition with more conventional relaxation pathways. For stilbene-fluorescein, the results are consistent with data generated in an earlier experimental investigation. Exercising these model systems facilitated the development of a set of design rules for the optimization of energy pooling. PMID:25793313

  20. Contrastive studies of potential energy functions of some diatomic molecules

    NASA Astrophysics Data System (ADS)

    Abdallah, Hassan H.; Abdullah, Hewa Y.

    2016-03-01

    It was proposed that iron hydride, FeH, would be formed only on grains at the clouds through the reaction of the adsorbed H atoms or H2 molecules with the adsorbed Fe atoms on the grains. The importance of FeH in Astrophysics presents an additional motivation to study its energetic, spectroscopic constants and Potential Energy Curves. The structural optimization for ground state of FeH was calculated by different theoretical methods, namely, Hartree-Fock (HF), the density functional theory (DFT), B3LYP, MP2 method and QCISD(T) methods and compared with available data from the literature. The single ionized forms, cation and anion, were also obtained at the same level of calculations. Charges, dipole moment, geometrical parameters, molecular orbital energies and spectroscopic parameters were calculated and reported. In addition, the molecular ionization potential, electron affinity and dissociation energy were investigated.

  1. 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.

  2. 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)

  3. The Interaction Potential of an Open Nanotube and its Permeability: Molecular Dynamics Simulation

    NASA Astrophysics Data System (ADS)

    Bubenchikov, Mikhail A.; Potekaev, Alexander I.; Bubenchikov, Alexey M.; Usenko, Olesya V.; Malozemov, Alexander V.; Tarasov, Egor A.

    2016-02-01

    The integration of the modified LJ-potential allowed revealing the universal effect of the open carbon tube on the molecular objects moving within or proximate to the tube. There has been established that there are modes of the molecule motion without the energy exchange with the atoms of the carbon framing, under which the moving molecules are subjected to the considerable activation in the tube. The potential holes being the sorption zones in fact are localized.

  4. Zoonotic Potential and Molecular Epidemiology of Giardia Species and Giardiasis†

    PubMed Central

    Feng, Yaoyu; Xiao, Lihua

    2011-01-01

    Summary: 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. PMID:21233509

  5. A molecularly based theory for electron transfer reorganization energy

    NASA Astrophysics Data System (ADS)

    Zhuang, Bilin; Wang, Zhen-Gang

    2015-12-01

    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.

  6. 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.

  7. On the potential for molecular imaging with Cerenkov luminescence

    PubMed Central

    Lewis, Matthew A.; Kodibagkar, Vikram D.; Öz, Orhan K.; Mason, Ralph P.

    2011-01-01

    Recent observation of optical luminescence due to beta decay from suitable radiotracers has led to the possible development of new preclinical optical imaging methods. The generation of photons that can be detected using instrumentation optimized for bioluminescence imaging has been putatively associated with the Cerenkov effect. We describe the simultaneous utilization of fluorescence reporters to convert the Cerenkov luminescence to longer wavelengths for better tissue penetration and also for modulating the luminescence spectrum for potential molecular imaging strategies. PMID:21124555

  8. Near homogeneous variation of potentials in large systems and the electronic structure of molecular quantum dots.

    PubMed

    Luo, Ji; Yang, Zhong Qin; Xue, Zeng Quan; Liu, Wei Min; Wu, Jin Lei

    2006-09-01

    It is shown from Kohn-Sham (KS) density-functional theory that in a large molecular system, the Coulomb potential, molecular electrostatic potential, and KS effective potential may exhibit an approximately homogeneous variation in space, in response to a small change of the electron number. The homogeneous variation of potentials underlies the constant interaction (CI) model of quantum dots (QDs) and is related to the delocalization and invariance of KS orbitals, the identical shift of KS levels, and a natural definition of the QD capacitance. Calculation results of a fullerene C60 and a single-walled carbon nanotube are presented. Although the homogeneity of the potential variation is not perfect, it seems to lead to fairly good approximation of the CI model to the addition energy spectra of these systems. PMID:16965100

  9. Near homogeneous variation of potentials in large systems and the electronic structure of molecular quantum dots

    NASA Astrophysics Data System (ADS)

    Luo, Ji; Yang, Zhong Qin; Xue, Zeng Quan; Liu, Wei Min; Wu, Jin Lei

    2006-09-01

    It is shown from Kohn-Sham (KS) density-functional theory that in a large molecular system, the Coulomb potential, molecular electrostatic potential, and KS effective potential may exhibit an approximately homogeneous variation in space, in response to a small change of the electron number. The homogeneous variation of potentials underlies the constant interaction (CI) model of quantum dots (QDs) and is related to the delocalization and invariance of KS orbitals, the identical shift of KS levels, and a natural definition of the QD capacitance. Calculation results of a fullerene C60 and a single-walled carbon nanotube are presented. Although the homogeneity of the potential variation is not perfect, it seems to lead to fairly good approximation of the CI model to the addition energy spectra of these systems.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. Potential of energy production from conserved forages

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Forages have a potential role in meeting the demand for energy. Perennial forages are attractive for various reasons. One, both the monetary and energy cost of planting is spread over many years. Two, we already have the equipment for harvesting, storing and transporting this source of biomass. Thre...

  16. Theoretical studies of potential energy surfaces

    SciTech Connect

    Harding, L.B.

    1995-07-01

    MRCI (configuration interaction) calculations were used to examine possible pathways for the O{sub 2} + CCH reaction. The H{sub 2} + CN potential surface was examined. An initial survey was made of the HCl + CN potential energy surface at a low level of theory.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. Theoretical studies of potential energy surfaces and computational methods.

    SciTech Connect

    Shepard, R.

    2006-01-01

    This project involves the development, implementation, and application of theoretical methods for the calculation and characterization of potential energy surfaces (PES) involving molecular species that occur in hydrocarbon combustion. These potential energy surfaces require an accurate and balanced treatment of reactants, intermediates, and products. Most of our work focuses on 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 molecular 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.

  4. The Role of Molecular Dynamics Potential of Mean Force Calculations in the Investigation of Enzyme Catalysis.

    PubMed

    Yang, Y; Pan, L; Lightstone, F C; Merz, K M

    2016-01-01

    The potential of mean force simulations, widely applied in Monte Carlo or molecular dynamics simulations, are useful tools to examine the free energy variation as a function of one or more specific reaction coordinate(s) for a given system. Implementation of the potential of mean force in the simulations of biological processes, such as enzyme catalysis, can help overcome the difficulties of sampling specific regions on the energy landscape and provide useful insights to understand the catalytic mechanism. The potential of mean force simulations usually require many, possibly parallelizable, short simulations instead of a few extremely long simulations and, therefore, are fairly manageable for most research facilities. In this chapter, we provide detailed protocols for applying the potential of mean force simulations to investigate enzymatic mechanisms for several different enzyme systems. PMID:27498632

  5. 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.

  6. Geothermal energy and its potential. [Utah

    SciTech Connect

    Berge, C.W.

    1980-06-01

    A brief review of geothermal energy and its potential as a future energy source is presented. The type of geothermal systems and their geologic occurrence is discussed, and the Phillips Petroleum Company's exploration and drilling programs in the Roosevelt Hot Springs area in parts of Iron, Beaver, and Millard Counties, Utah are detailed. A section on the rock behavior and mechanical properties of rocks in the Roosevelt Hot Springs area is included. (JMT)

  7. Potential energy surfaces and reaction dynamics of polyatomic molecules

    SciTech Connect

    Chang, Yan-Tyng.

    1991-11-01

    A simple empirical valence bond (EVB) model approach is suggested for constructing global potential energy surfaces for reactions of polyatomic molecular systems. This approach produces smooth and continuous potential surfaces which can be directly utilized in a dynamical study. Two types of reactions are of special interest, the unimolecular dissociation and the unimolecular isomerization. For the first type, the molecular dissociation dynamics of formaldehyde on the ground electronic surface is investigated through classical trajectory calculations on EVB surfaces. The product state distributions and vector correlations obtained from this study suggest very similar behaviors seen in the experiments. The intramolecular hydrogen atom transfer in the formic acid dimer is an example of the isomerization reaction. High level ab initio quantum chemistry calculations are performed to obtain optimized equilibrium and transition state dimer geometries and also the harmonic frequencies.

  8. 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.

  9. Potential reduction of DSN uplink energy cost

    NASA Technical Reports Server (NTRS)

    Dolinsky, S.; Degroot, N. F.

    1982-01-01

    DSN Earth stations typically transmit more power than that required to meet minimum specifications for uplink performance. Energy and cost savings that could result from matching the uplink power to the amount required for specified performance are studied. The Galileo mission was selected as a case study. Although substantial reduction in transmitted energy is possible, potential savings in source energy (oil or electricity) savings are much less. This is because of the rising inefficiency in power conversion and radio frequency power generation that accompanies reduced power output.

  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 studies on silane dimers

    NASA Astrophysics Data System (ADS)

    Mahlanen, Riina; Pakkanen, Tapani A.

    2011-04-01

    Intermolecular interactions and parameters for use in MD studies of large molecule systems have earlier been determined for hydrocarbons, carbon tetrahalides and sulfur. The paper reports a model representing nonbonding interactions between silane molecules, which were examined in the same way as hydrocarbons in an earlier (neopentane, isopropane, propane, and ethane) study. Intermolecular potentials were determined for 11 combinations of silane compound pairs (silane SiH 4, disilane Si 2H 6, trisilane Si 3H 8, isotetrasilane Si 4H 10 and neopentasilane Si 5H 12) with MP2/aug(df)-6-311G ∗ab initio calculations. The most stable dimer configurations were identified. With use of the modified Morse potential model to represent the interactions, 276 new potential energy surfaces were generated for silane dimers. Separate and generic pair potentials were calculated for the silanes. The pair potentials can be used in MD studies of silanes.

  12. Molecular docking using the molecular lipophilicity potential as hydrophobic descriptor: impact on GOLD docking performance.

    PubMed

    Nurisso, Alessandra; Bravo, Juan; Carrupt, Pierre-Alain; Daina, Antoine

    2012-05-25

    GOLD is a molecular docking software widely used in drug design. In the initial steps of docking, it creates a list of hydrophobic fitting points inside protein cavities that steer the positioning of ligand hydrophobic moieties. These points are generated based on the Lennard-Jones potential between a carbon probe and each atom of the residues delimitating the binding site. To thoroughly describe hydrophobic regions in protein pockets and properly guide ligand hydrophobic moieties toward favorable areas, an in-house tool, the MLP filter, was developed and herein applied. This strategy only retains GOLD hydrophobic fitting points that match the rigorous definition of hydrophobicity given by the molecular lipophilicity potential (MLP), a molecular interaction field that relies on an atomic fragmental system based on 1-octanol/water experimental partition coefficients (log P(oct)). MLP computations in the binding sites of crystallographic protein structures revealed that a significant number of points considered hydrophobic by GOLD were actually polar according to the MLP definition of hydrophobicity. To examine the impact of this new tool, ligand-protein complexes from the Astex Diverse Set and the PDB bind core database were redocked with and without the use of the MLP filter. Reliable docking results were obtained by using the MLP filter that increased the quality of docking in nonpolar cavities and outperformed the standard GOLD docking approach. PMID:22462609

  13. Molecular thermometers for potential applications in thermal ablation procedures

    NASA Astrophysics Data System (ADS)

    Zhegalova, Natalia G.; Aydt, Alex; Wang, Steven T.; Berezin, Mikhail Y.

    2013-02-01

    Thermal ablation is a promising minimally invasive method for treating tumors without surgical intervention. Thermal ablation uses thermal sources such as lasers, radiowaves or focused ultrasound to increase the temperature of the tumor to levels lethal to cancer cells. This treatment based on heat therapy may be problematic as the temperature of the operation site is unknown. To address this problem, we developed optical molecular thermometers that can potentially measure the temperature on a molecular scale and be compatible with in vivo measurements. The thermometers are centered on a combination of two fluorophores emitting in two distinct spectral ranges and having different temperature-dependent emission properties. In this design, a fluorophore with relatively insensitive temperature-dependent fluorescence serves as a reference while another sensitive fluorophore serves as a sensor. We have demonstrated the feasibility of this approach using a coumarin-rhodamine conjugate. The sensitivity of the construct to the clinically relevant ablation temperatures (20-85 °C) was demonstrated in vitro.

  14. 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.

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

    NASA Astrophysics Data System (ADS)

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

    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 <1 0 0> symmetrical tilt Σ5 and the <1 1 0> symmetrical tilt Σ3 ({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 Σ3 boundary was found to be more prone to fracture than the Σ5 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.

  16. MOLECULAR ALTERATIONS IN GLIOBLASTOMA: POTENTIAL TARGETS FOR IMMUNOTHERAPY

    PubMed Central

    Haque, Azizul; Banik, Naren L.; Ray, Swapan K.

    2015-01-01

    Glioblastoma is the most common and deadly brain tumor, possibly arising from genetic and epigenetic alterations in normal astroglial cells. Multiple cytogenetic, chromosomal, and genetic alterations have been identified in glioblastoma, with distinct expression of antigens (Ags) and biomarkers that may alter therapeutic potential of this aggressive cancer. Current therapy consists of surgical resection, followed by radiation therapy and chemotherapy. In spite of these treatments, the prognosis for glioblastoma patients is poor. Although recent studies have focused on the development of novel immunotherapeutics against glioblastoma, little is known about glioblastoma specific immune responses. A better understanding of the molecular interactions among glioblastoma tumors, host immune cells, and the tumor microenvironment may give rise to novel integrated approaches for the simultaneous control of tumor escape pathways and the activation of antitumor immune responses. This review provides a detailed overview concerning genetic alterations in glioblastoma, their effects on Ag and biomarker expression and the future design of chemoimmunotherapeutics against glioblastoma. PMID:21199773

  17. Potential energy savings from aquifer thermal energy storage

    SciTech Connect

    Anderson, M.R.; Weijo, R.O.

    1988-07-01

    Pacific Northwest Laboratory researchers developed an aggregate-level model to estimate the short- and long-term potential energy savings from using aquifer thermal storage (ATES) in the United States. The objectives of this effort were to (1) develop a basis from which to recommend whether heat or chill ATES should receive future research focus and (2) determine which market sector (residential, commercial, or industrial) offers the largest potential energy savings from ATES. Information was collected on the proportion of US land area suitable for ATES applications. The economic feasibility of ATES applications was then evaluated. The potential energy savings from ATES applications was calculated. Characteristic energy use in the residential, commercial, and industrial sectors was examined, as was the relationship between waste heat production and consumption by industrial end-users. These analyses provided the basis for two main conclusions: heat ATES applications offer higher potential for energy savings than do chill ATES applications; and the industrial sector can achieve the highest potential energy savings for the large consumption markets. Based on these findings, it is recommended that future ATES research and development efforts be directed toward heat ATES applications in the industrial sector. 11 refs., 6 figs., 9 tabs.

  18. 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

  19. 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)

  20. Combining a reactive potential with a harmonic approximation for molecular dynamics simulation of failure: construction of a reduced potential

    NASA Astrophysics Data System (ADS)

    Tejada, I. G.; Brochard, L.; Stoltz, G.; Legoll, F.; Lelièvre, T.; Cancès, E.

    2015-01-01

    Molecular dynamics is a simulation technique that can be used to study failure in solids, provided the inter-atomic potential energy is able to account for the complex mechanisms at failure. Reactive potentials fitted on ab initio results or on experimental values have the ability to adapt to any complex atomic arrangement and, therefore, are suited to simulate failure. But the complexity of these potentials, together with the size of the systems considered, make simulations computationally expensive. In order to improve the efficiency of numerical simulations, simpler harmonic potentials can be used instead of complex reactive potentials in the regions where the system is close to its ground state and a harmonic approximation reasonably fits the actual reactive potential. However the validity and precision of such an approach has not been investigated in detail yet. We present here a methodology for constructing a reduced potential and combining it with the reactive one. We also report some important features of crack propagation that may be affected by the coupling of reactive and reduced potentials. As an illustrative case, we model a crystalline two-dimensional material (graphene) with a reactive empirical bond-order potential (REBO) or with harmonic potentials made of bond and angle springs that are designed to reproduce the second order approximation of REBO in the ground state. We analyze the consistency of this approximation by comparing the mechanical behavior and the phonon spectra of systems modeled with these potentials. These tests reveal when the anharmonicity effects appear. As anharmonic effects originate from strain, stress or temperature, the latter quantities are the basis for establishing coupling criteria for on the fly substitution in large simulations.

  1. Engineering Molecular Transformations for Sustainable Energy Conversion

    SciTech Connect

    Neurock, Matthew

    2010-12-03

    Future strategies for sustainable energy production will undoubtedly require processes and materials that can efficiently convert renewable resources into fuels. Nature’s enzymes can exquisitely integrate highly active catalytic centers within flexible environments that can adaptively guide reactants to products with very high activities and selectivities. They are limited, however, by their stability and ability to integrate into large scale production processes. The design of more robust heterogeneous catalytic materials that mimic the performance of enzymes, however, has been hindered by our limited understanding of how such transformations proceed. The tremendous advances in ab initio quantum mechanical methods, atomistic simulations, and high performance computing that have occurred over the past two decades, however, provide unprecedented ability to track molecular transformations and how they proceed at specific sites and within particular environments. This information together with the advances in in situ spectroscopic methods that follow such transformations can begin to enable the design of atomic surface ensembles and nanoscale reaction environments. This paper provides the author’s perspective on how theory and simulation can be used to move from current onedimensional design efforts based on catalytic descriptors to the design of two-dimensional surfaces, threedimensional reaction environments, and proton-coupled electron transfer systems that mimic enzymes in the transformation of molecules.

  2. Flat-Band Potentials of Molecularly Thin Metal Oxide Nanosheets.

    PubMed

    Xu, Pengtao; Milstein, Tyler J; Mallouk, Thomas E

    2016-05-11

    Exfoliated nanosheets derived from Dion-Jacobson phase layer perovskites (TBAxH1-xA2B3O10, A = Sr, Ca, B = Nb, Ta) were grown layer-by-layer on fluorine-doped tin oxide and gold electrode surfaces. Electrochemical impedance spectra (EIS) of the five-layer nanosheet films in contact with aqueous electrolyte solutions were analyzed by the Mott-Schottky method to obtain flat-band potentials (VFB) of the oxide semiconductors as a function of pH. Despite capacitive contributions from the electrode-solution interface, reliable values could be obtained from capacitance measurements over a limited potential range near VFB. The measured values of VFB shifted -59 mV/pH over the pH range of 4-8 and were in close agreement with the empirical correlation between conduction band-edge potentials and optical band gaps proposed by Matsumoto ( J. Solid State Chem. 1996, 126 (2), 227-234 ). Density functional theory calculations showed that A-site substitution influenced band energies by modulating the strength of A-O bonding, and that subsitution of Ta for Nb on B-sites resulted in a negative shift of the conduction band-edge potential. PMID:27102083

  3. 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).

  4. 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.

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

    NASA Astrophysics Data System (ADS)

    Heaps, Charles W.; Mazziotti, David A.

    2016-04-01

    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.

  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. PMID:27131532

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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

  12. 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.

  13. 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. PMID:26562413

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

    PubMed

    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

  15. 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

  16. 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

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

    SciTech Connect

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

    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{sup +}, Cl{sup -}, and Ag{sup +} 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 ({Delta}G{sub 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{sup +}/Cl{sup -} and Ag{sup +}/Cl{sup -} AIMD {Delta}G{sub 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{sup +}+Ni{sup +}{yields}Ag+Ni{sup 2+} in water. The predictions for this reaction suggest that existing estimates of {Delta}G{sub hyd} for unstable radiolysis intermediates such as Ni{sup +} may need to be extensively revised.

  18. Electronic structure, molecular electrostatic potential and hydrogen bonding in DMSO-X complexes (X = ethanol, methanol and water)

    NASA Astrophysics Data System (ADS)

    Dhumal, Nilesh R.

    2011-08-01

    In the present work, we have studied the electronic structure, molecular electrostatic potential (MEP) and hydrogen bonding in DMSO-ethanol, DMSO-methanol and DMSO-water complexes by employing the MP2 method. Different conformers were simulated on the basis of possible binding sites guided by molecular electrostatic potential topology. The stronger hydrogen bonded interaction lowers the energy of the conformer. Molecular electron density topology and natural bond orbital analysis were used to explain the strength of interactions. Experimental vibrations are also compared with the calculated normal vibrations. Blue shift is predicted for SC vibration in experimental and theoretical spectra as well. Molecular electrostatic potential and topology are used to understand the interaction strength of the conformer.

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. The wind energy potential of western Greece

    SciTech Connect

    Katsoulis, B.D.; Metaxas, D.A. )

    1992-12-01

    In this study wind data were used to determine the monthly and annual variations of the wind at 13 meterological stations in western Greece. An analysis of the available wind data for the Ionian Sea islands and the western coasts of Greece is carried out to ascertain its potential for wind energy development. The effect of the limited number of daily observations available on the accuracy of the mean wind speed and annual wind energy estimates is ascertained. The wind speed and direction distributions are represented with Weibull functions. Besides, a mass-consistent numerical mesoscale model was used to give an overview of the wind prospecting and siting problem, and an example of its use for Corfu (Kerkira), an island in the Ionian Sea, is given. The comparison of the accuracy of the stimulation results versus measured wind at an available site is quite encouraging even though it cannot be conclusive since only one station is available.

  4. 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.

  5. Theoretical studies of potential energy surfaces.

    SciTech Connect

    Harding, L. B.

    2006-01-01

    The goal of this program is to calculate accurate potential energy surfaces for both reactive and nonreactive systems. To do this the electronic Schroedinger equation must be solved. Our approach starts with multiconfiguration self-consistent field (MCSCF) reference wave functions. These reference wavefunctions are designed to be sufficiently flexible to accurately describe changes in electronic structure over a broad range of geometries. Dynamical electron correlation effects are included via multireference, singles and doubles configuration interaction (MRCI) calculations. With this approach, we are able to provide chemically useful predictions of the energetics for many systems. A second aspect of this program is the development of techniques to fit multi-dimensional potential surfaces to convenient, global, analytic functions that can then be used in dynamics calculations.

  6. 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.

  7. Control of ultrafast molecular photodissociation by laser-field-induced potentials

    NASA Astrophysics Data System (ADS)

    Corrales, M. E.; González-Vázquez, J.; Balerdi, G.; Solá, I. R.; de Nalda, R.; Bañares, L.

    2014-09-01

    Experiments aimed at understanding ultrafast molecular processes are now routine, and the notion that external laser fields can constitute an additional reagent is also well established. The possibility of externally controlling a reaction with radiation increases immensely when its intensity is sufficiently high to distort the potential energy surfaces at which chemists conceptualize reactions take place. Here we explore the transition from the weak- to the strong-field regimes of laser control for the dissociation of a polyatomic molecule, methyl iodide. The control over the yield of the photodissociation reaction proceeds through the creation of a light-induced conical intersection. The control of the velocity of the product fragments requires external fields with both high intensities and short durations. This is because the mechanism by which control is exerted involves modulating the potentials around the light-induced conical intersection, that is, creating light-induced potentials.

  8. 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...

  9. Potentials and limitations of molecular diagnostic methods in food safety

    PubMed Central

    Mariani, Paola O.

    2008-01-01

    Molecular methods allow the detection of pathogen nucleic acids (DNA and RNA) and, therefore, the detection of contamination in food is carried out with high selectivity and rapidity. In the last 2 decades molecular methods have accompanied traditional diagnostic methods in routine pathogen detection, and might replace them in the upcoming future. In this review the implementation in diagnostics of four of the most used molecular techniques (PCR, NASBA, microarray, LDR) are described and compared, highlighting advantages and limitations of each of them. Drawbacks of molecular methods with regard to traditional ones and the difficulties encountered in pathogen detection from food or clinical specimen are also discussed. Moreover, criteria for the choice of the target sequence for a secure detection and classification of pathogens and possible developments in molecular diagnostics are also proposed. PMID:19067016

  10. Myostatin/activin pathway antagonism: molecular basis and therapeutic potential.

    PubMed

    Han, H Q; Zhou, Xiaolan; Mitch, William E; Goldberg, Alfred L

    2013-10-01

    Muscle wasting is associated with a wide range of catabolic diseases. This debilitating loss of muscle mass and functional capacity reduces the quality of life and increases the risks of morbidity and mortality. Major progress has been made in understanding the biochemical mechanisms and signaling pathways regulating muscle protein balance under normal conditions and the enhanced protein loss in atrophying muscles. It is now clear that activation of myostatin/activin signaling is critical in triggering the accelerated muscle catabolism that causes muscle loss in multiple disease states. Binding of myostatin and activin to the ActRIIB receptor complex on muscle cell membrane leads to activation of Smad2/3-mediated transcription, which in turn stimulates FoxO-dependent transcription and enhanced muscle protein breakdown via ubiquitin-proteasome system and autophagy. In addition, Smad activation inhibits muscle protein synthesis by suppressing Akt signaling. Pharmacological blockade of the myostatin/activin-ActRIIB pathway has been shown to prevent or reverse the loss of muscle mass and strength in various disease models including cancer cachexia and renal failure. Moreover, it can markedly prolong the lifespan of animals with cancer-associated muscle loss. Furthermore, inhibiting myostatin/activin actions also improves insulin sensitivity, reduces excessive adiposity, attenuates systemic inflammation, and accelerates bone fracture healing in disease models. Based on these exciting advances, the potential therapeutic benefits of myostatin/activin antagonism are now being tested in multiple clinical settings. This article is part of a Directed Issue entitled: Molecular basis of muscle wasting. PMID:23721881

  11. 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.

  12. 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.

  13. Energy potential of sugarcane and sweet sorghum

    SciTech Connect

    Elawad, S.H.; Gascho, G.J.; Shih, S.F.

    1980-01-01

    The potential of sugarcane and sweet sorghum as raw materials for the production of ethanol and petrochemical substitutes is discussed. Both crops belong to the grass family and are classified as C/sub 4/ malateformers which have the highest rate of photosynthesis among terrestrial plants. Large amounts of biomass are required to supply a significant fraction of US energy consumption. Biomass production could be substantially increased by including tops and leaves, adopting narrow row spacing and improving cultural practices. This presents challenges for cultivating, harvesting, and hauling the biomass to processing centers. Large plants and heavy capital investment are essential for energy production. Ethanol and ammonia are the most promising candidates of a biomass program. If sugarcane were to be used for biomass production, breeding programs should be directed for more fermentable sugars and fiber. Energy research on sweet sorghum should be done with syrup varieties. Sweet sorghum needs to be incorporated with other crops because of its short growing season. The disposal of stillage from an extensive ethanol industry may pose environmental problems.

  14. Induced Seismicity Potential of Energy Technologies

    NASA Astrophysics Data System (ADS)

    Hitzman, Murray

    2013-03-01

    Earthquakes attributable to human activities-``induced seismic events''-have received heightened public attention in the United States over the past several years. Upon request from the U.S. Congress and the Department of Energy, the National Research Council was asked to assemble a committee of experts to examine the scale, scope, and consequences of seismicity induced during fluid injection and withdrawal associated with geothermal energy development, oil and gas development, and carbon capture and storage (CCS). The committee's report, publicly released in June 2012, indicates that induced seismicity associated with fluid injection or withdrawal is caused in most cases by change in pore fluid pressure and/or change in stress in the subsurface in the presence of faults with specific properties and orientations and a critical state of stress in the rocks. The factor that appears to have the most direct consequence in regard to induced seismicity is the net fluid balance (total balance of fluid introduced into or removed from the subsurface). Energy technology projects that are designed to maintain a balance between the amount of fluid being injected and withdrawn, such as most oil and gas development projects, appear to produce fewer seismic events than projects that do not maintain fluid balance. Major findings from the study include: (1) as presently implemented, the process of hydraulic fracturing for shale gas recovery does not pose a high risk for inducing felt seismic events; (2) injection for disposal of waste water derived from energy technologies does pose some risk for induced seismicity, but very few events have been documented over the past several decades relative to the large number of disposal wells in operation; and (3) CCS, due to the large net volumes of injected fluids suggested for future large-scale carbon storage projects, may have potential for inducing larger seismic events.

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

    NASA Astrophysics Data System (ADS)

    Melnikov, V. V.

    2015-06-01

    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 H2 in Si, and the obtained dispersion law is analyzed.

  16. 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.

  17. Surface free energy of platinum nanoparticles at zero pressure: A molecular dynamic study

    NASA Astrophysics Data System (ADS)

    Akbarzadeh, Hamed; Abroshan, Hadi; Parsafar, Gholam Abbas

    2010-02-01

    Metallic nanoparticles are interesting because of their use in catalysis and sensors. The surface energy of the FCC platinum nanoparticles are investigated via molecular dynamics simulation using Quantum Sutton-Chen (QSC) potential. We have calculated the Gibbs free energy for the FCC platinum bulk and also for its nanoparticle. All calculations have been carried out at zero pressure. We have used the thermodynamic integration method to obtain the Gibbs free energy. The total Gibbs free energy is taken as the sum of its central bulk and its surface free energy. We have calculated the free energy of a platinum nanoparticle as a function of temperature.

  18. Fast and accurate modeling of molecular atomization energies with machine learning.

    PubMed

    Rupp, Matthias; Tkatchenko, Alexandre; Müller, Klaus-Robert; von Lilienfeld, O Anatole

    2012-02-01

    We introduce a machine learning model to predict atomization energies of a diverse set of organic molecules, based on nuclear charges and atomic positions only. The problem of solving the molecular Schrödinger equation is mapped onto a nonlinear statistical regression problem of reduced complexity. Regression models are trained on and compared to atomization energies computed with hybrid density-functional theory. Cross validation over more than seven thousand organic molecules yields a mean absolute error of ∼10  kcal/mol. Applicability is demonstrated for the prediction of molecular atomization potential energy curves. PMID:22400967

  19. Certification and the potential energy landscape

    SciTech Connect

    Mehta, Dhagash; Hauenstein, Jonathan D.; Wales, David J.

    2014-06-14

    Typically, there is no guarantee that a numerical approximation obtained using standard nonlinear equation solvers is indeed an actual solution, meaning that it lies in the quadratic convergence basin. Instead, it may lie only in the linear convergence basin, or even in a chaotic region, and hence not converge to the corresponding stationary point when further optimization is attempted. In some cases, these non-solutions could be misleading. Proving that a numerical approximation will quadratically converge to a stationary point is termed certification. In this report, we provide details of how Smale's α-theory can be used to certify numerically obtained stationary points of a potential energy landscape, providing a mathematical proof that the numerical approximation does indeed correspond to an actual stationary point, independent of the precision employed.

  20. 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

    2016-09-01

    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

  1. 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.

  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. PMID:27355042

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. Calculations of molecular ionization energies using a self-consistent-charge Hartree-Fock-Slater method

    NASA Technical Reports Server (NTRS)

    Rosen, A.; Ellis, D. E.; Adachi, H.; Averill, F. W.

    1976-01-01

    A numerical-variational method for performing self-consistent molecular calculations in the Hartree-Fock-Slater (HFS) model is presented. Molecular wavefunctions are expanded in terms of basis sets constructed from numerical HFS solutions of selected one-center atomlike problems. Binding energies and wavefunctions for the molecules are generated using a discrete variational method for a given molecular potential. In the self-consistent-charge (SCC) approximation to the complete self-consistent-field (SCF) method, results of a Mulliken population analysis of the molecular eigenfunctions are used in each iteration to produce 'atomic' occupation numbers. The simplest SCC potential is then obtained from overlapping spherical atomlike charge distributions. Molecular ionization energies are calculated using the transition-state procedure; results are given for CO, H2O, H2S, AlCl, InCl, and the Ni5O surface complex. Agreement between experimental and theoretical ionization energies for the free-molecule valence levels is generally within 1 eV. The simple SCC procedure gives a reasonably good approximation to the molecular potential, as shown by comparison with experiment, and with complete SCF calculations for CO, H2O, and H2S.

  8. Explicit Polarization (X-Pol) Potential Using ab Initio Molecular Orbital Theory and Density Functional Theory†

    PubMed Central

    Song, Lingchun; Han, Jaebeom; Lin, Yen-lin; Xie, Wangshen; Gao, Jiali

    2010-01-01

    The explicit polarization (X-Pol) method has been examined using ab initio molecular orbital theory and density functional theory. The X-Pol potential was designed to provide a novel theoretical framework for developing next-generation force fields for biomolecular simulations. Importantly, the X-Pol potential is a general method, which can be employed with any level of electronic structure theory. The present study illustrates the implementation of the X-Pol method using ab initio Hartree—Fock theory and hybrid density functional theory. The computational results are illustrated by considering a set of bimolecular complexes of small organic molecules and ions with water. The computed interaction energies and hydrogen bond geometries are in good accord with CCSD(T) calculations and B3LYP/aug-cc-pVDZ optimizations. PMID:19618944

  9. Piperine derivatives as potential inhibitors of Survivin: An in silico molecular docking.

    PubMed

    Sattarinezhad, Elham; Bordbar, Abdol-Khalegh; Fani, Najmeh

    2015-08-01

    Targeting Survivin, as an inhibitor of apoptosis and a regulator of cell division, has become a worldwide controversial issue. Piperine as a pungent alkaloid has been identified as the most potent adjuvant at enhancing the efficacy of tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-based therapies in triple-negative breast cancer (TNBC) cells in vitro and in vivo, which might be mediated through inhibition of Survivin. In this work, the binding energies, inhibition constants and binding modes of a group of previously synthesized Piperine derivatives at the binding site of Survivin have been studied using molecular docking tools and the best compounds with minimum binding energies are proposed as potential drugs for the inhibition of Survivin. A comprehensive SAR analysis has been done on the results that can be used for designing new Piperine analogs with higher efficacy. Molecular docking computations also show that the studied compounds can bind to BIR domain of Survivin in the same binding site as that of Smac/DIABLO with a suitable binding energy. This binding may result in the segregation of Smac/DIABLO in the cytosol and subsequently free Smac/DIABLO molecules could be available for binding with inhibitors of apoptosis to initiate caspase mediated apoptosis. PMID:26093789

  10. Accurate prediction of lattice energies and structures of molecular crystals with molecular quantum chemistry methods.

    PubMed

    Fang, Tao; Li, Wei; Gu, Fangwei; Li, Shuhua

    2015-01-13

    We extend the generalized energy-based fragmentation (GEBF) approach to molecular crystals under periodic boundary conditions (PBC), and we demonstrate the performance of the method for a variety of molecular crystals. With this approach, the lattice energy of a molecular crystal can be obtained from the energies of a series of embedded subsystems, which can be computed with existing advanced molecular quantum chemistry methods. The use of the field compensation method allows the method to take long-range electrostatic interaction of the infinite crystal environment into account and make the method almost translationally invariant. The computational cost of the present method scales linearly with the number of molecules in the unit cell. Illustrative applications demonstrate that the PBC-GEBF method with explicitly correlated quantum chemistry methods is capable of providing accurate descriptions on the lattice energies and structures for various types of molecular crystals. In addition, this approach can be employed to quantify the contributions of various intermolecular interactions to the theoretical lattice energy. Such qualitative understanding is very useful for rational design of molecular crystals. PMID:26574207

  11. 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.

  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

    2016-02-01

    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. PMID:26731197

  13. Free energy calculations for molecular solids using GROMACS

    NASA Astrophysics Data System (ADS)

    Aragones, J. L.; Noya, E. G.; Valeriani, C.; Vega, C.

    2013-07-01

    In this work, we describe a procedure to evaluate the free energy of molecular solids with the GROMACS molecular dynamics package. The free energy is calculated using the Einstein molecule method that can be regarded as a small modification of the Einstein crystal method. Here, the position and orientation of the molecules is fixed by using an Einstein field that binds with harmonic springs at least three non-collinear atoms (or points of the molecule) to their reference positions. The validity of the Einstein field is tested by performing free-energy calculations of methanol, water (ice), and patchy colloids molecular solids. The free energies calculated with GROMACS show a very good agreement with those obtained using Monte Carlo and with previously published results.

  14. Potential Molecular and Cellular Mechanism of Psychotropic Drugs

    PubMed Central

    Seo, Myoung Suk; Scarr, Elizabeth; Lai, Chi-Yu

    2014-01-01

    Psychiatric disorders are among the most debilitating of all medical illnesses. Whilst there are drugs that can be used to treat these disorders, they give sub-optimal recovery in many people and a significant number of individuals do not respond to any treatments and remain treatment resistant. Surprisingly, the mechanism by which psychotropic drugs cause their therapeutic benefits remain unknown but likely involves the underlying molecular pathways affected by the drugs. Hence, in this review, we have focused on recent findings on the molecular mechanism affected by antipsychotic, mood stabilizing and antidepressant drugs at the levels of epigenetics, intracellular signalling cascades and microRNAs. We posit that understanding these important interactions will result in a better understanding of how these drugs act which in turn may aid in considering how to develop drugs with better efficacy or increased therapeutic reach. PMID:25191500

  15. ASSESSMENT OF ENERGY RECOVERY POTENTIAL OF INDUSTRIAL COMBUSTION EQUIPMENT

    EPA Science Inventory

    An assessment was conducted to evaluate the waste heat content and energy recovery potential of flue gases from 30 industrial combustion devices. Pollution controls on nine of the devices were evaluated to estimate energy requirements and particulate reduction; energy requirement...

  16. 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.

  17. 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)

  18. Determination of Multidimensional Intermolecular Potential Energy Surfaces

    NASA Astrophysics Data System (ADS)

    Cohen, Ronald Carl

    High resolution spectroscopy of the low frequency van der Waals vibrations (also referred to as Vibration -Rotation-Tunneling (VRT) spectroscopy) in weakly bound complexes provides the means to probe intermolecular forces with unprecedented detail and precision. We present an overview of the experimental information on intermolecular forces and intermolecular dynamics which has been obtained by far infrared VRT spectroscopy of 18 complexes. We then turn to a detailed examination of the Ar-H_2O complex, a simple prototype for the study of intermolecular forces. The measurement and analysis of 9 VRT bands is described. These data are first used to obtain a qualitative description of the intermolecular potential energy surface (IPS). A new simple and efficient method for calculating the eigenvalues of the multidimensional intermolecular dynamics on the IPS has been developed. This algorithm (an adaptation of the Collocation Method) was then used in a direct fit to obtain an accurate and detailed description of the intermolecular forces acting within the Ar-H_2O complex.

  19. Permutation invariant polynomial neural network approach to fitting potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Jiang, Bin; Guo, Hua

    2013-08-01

    A simple, general, and rigorous scheme for adapting permutation symmetry in molecular systems is proposed and tested for fitting global potential energy surfaces using neural networks (NNs). The symmetry adaptation is realized by using low-order permutation invariant polynomials (PIPs) as inputs for the NNs. This so-called PIP-NN approach is applied to the H + H2 and Cl + H2 systems and the analytical potential energy surfaces for these two systems were accurately reproduced by PIP-NN. The accuracy of the NN potential energy surfaces was confirmed by quantum scattering calculations.

  20. 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.

  1. Free energy calculations from adaptive molecular dynamics simulations with adiabatic reweighting

    NASA Astrophysics Data System (ADS)

    Cao, Lingling; Stoltz, Gabriel; Lelièvre, Tony; Marinica, Mihai-Cosmin; Athènes, Manuel

    2014-03-01

    We propose an adiabatic reweighting algorithm for computing the free energy along an external parameter from adaptive molecular dynamics simulations. The adaptive bias is estimated using Bayes identity and information from all the sampled configurations. We apply the algorithm to a structural transition in a cluster and to the migration of a crystalline defect along a reaction coordinate. Compared to standard adaptive molecular dynamics, we observe an acceleration of convergence. With the aid of the algorithm, it is also possible to iteratively construct the free energy along the reaction coordinate without having to differentiate the gradient of the reaction coordinate or any biasing potential.

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

    NASA Astrophysics Data System (ADS)

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

    2008-12-01

    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.

  3. 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.

  4. 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.

  5. Modulation of Energy Conversion Processes in Carbonaceous Molecular Bearings.

    PubMed

    Hitosugi, Shunpei; Ohkubo, Kei; Kawashima, Yuki; Matsuno, Taisuke; Kamata, Sho; Nakamura, Kosuke; Kono, Hirohiko; Sato, Sota; Fukuzumi, Shunichi; Isobe, Hiroyuki

    2015-11-01

    The energetics and photodynamics of carbonaceous molecular bearings with discrete molecular structures were investigated. A series of supramolecular bearings comprising belt-persistent tubular cycloarylene and fullerene molecules accepted photonic stimuli to afford charge-separated species via a photoinduced electron transfer process. The energy conversion processes associated with the photoexcitation, however, differed depending on the molecular structure. A π-lengthened tubular molecule allowed for the emergence of an intermediary triplet excited state at the bearing, which should lead to an energy conversion to thermal energy. On the other hand, low-lying charge-separated species induced by an endohedral lithium ion in fullerene enabled back electron transfer processes to occur without involving triplet excited species. The structure-photodynamics relationship was analyzed in terms of the Marcus theory to reveal a large electronic coupling in this dynamic supramolecular system. PMID:26195132

  6. 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

  7. Review on Molecular and Chemopreventive Potential of Nimbolide in Cancer

    PubMed Central

    Arunakaran, Jagadeesan

    2014-01-01

    Cancer is the most dreaded disease in human and also major health problem worldwide. Despite its high occurrence, the exact molecular mechanisms of the development and progression are not fully understood. The existing cancer therapy based on allopathic medicine is expensive, exhibits side effects; and may also alter the normal functioning of genes. Thus, a non-toxic and effective mode of treatment is needed to control cancer development and progression. Some medicinal plants offer a safe, effective and affordable remedy to control the cancer progression. Nimbolide, a limnoid derived from the neem (Azadirachta indica) leaves and flowers of neem, is widely used in traditional medical practices for treating various human diseases. Nimbolide exhibits several pharmacological effects among which its anticancer activity is the most promising. The previous studies carried out over the decades have shown that nimbolide inhibits cell proliferation and metastasis of cancer cells. This review highlights the current knowledge on the molecular targets that contribute to the observed anticancer activity of nimbolide related to induction of apoptosis and cell cycle arrest; and inhibition of signaling pathways related to cancer progression. PMID:25705153

  8. Comparison of Methods To Reweight from Classical Molecular Simulations to QM/MM Potentials.

    PubMed

    Dybeck, Eric C; König, Gerhard; Brooks, Bernard R; Shirts, Michael R

    2016-04-12

    We examine methods to reweight classical molecular mechanics solvation calculations to more expensive QM/MM energy functions. We first consider the solvation free energy difference between ethane and methanol in a QM/MM Hamiltonian from configurations generated in a cheaper MM potential. The solute molecules in the QM/MM Hamiltonian are treated with B3LYP/6-31G*, and the solvent water molecules are treated classically. The free energy difference in the QM/MM Hamiltonian is estimated using Boltzmann reweighting with both the non-Boltzmann Bennett method (NBB) and the multistate Bennett acceptance ratio (MBAR), and the variance of each method is directly compared for an identical data set. For this system, MBAR-derived methods are found to produce smaller overall uncertainties than NBB-based methods. Additionally, we show that to reduce the variance in the overall free energy difference estimate in this system for a fixed amount of QM/MM calculations, the energy re-evaluations in the Boltzmann reweighting step should be concentrated on the physical MM states with the highest overlap to the QM/MM states, rather than allocated equally over all sampled MM states. We also show that reallocating the QM/MM re-evaluations can be used to diagnose poor overlap between the sampled and target state. The solvation free energies for molecules in the SAMPL4 solvation data set are also calculated in the QM/MM Hamiltonian with NBB and MBAR, and the variances are marginally smaller for MBAR. Overall, NBB and MBAR produce similar variances for systems with poor sampling efficiency, and MBAR provides smaller variances than NBB in systems with high sampling efficiency. Both NBB and MBAR converge to identical solvation free energy estimates in the QM/MM Hamiltonian, and the RMSD to experimental values for molecules in the SAMPL4 solvation data set decreases by approximately 28% when switching from the MM Hamiltonian to the QM/MM Hamiltonian. PMID:26928941

  9. Use of Nonequilibrium Work Methods to Compute Free Energy Differences Between Molecular Mechanical and Quantum Mechanical Representations of Molecular Systems.

    PubMed

    Hudson, Phillip S; Woodcock, H Lee; Boresch, Stefan

    2015-12-01

    Carrying out free energy simulations (FES) using quantum mechanical (QM) Hamiltonians remains an attractive, albeit elusive goal. Renewed efforts in this area have focused on using "indirect" thermodynamic cycles to connect "low level" simulation results to "high level" free energies. The main obstacle to computing converged free energy results between molecular mechanical (MM) and QM (ΔA(MM→QM)), as recently demonstrated by us and others, is differences in the so-called "stiff" degrees of freedom (e.g., bond stretching) between the respective energy surfaces. Herein, we demonstrate that this problem can be efficiently circumvented using nonequilibrium work (NEW) techniques, i.e., Jarzynski's and Crooks' equations. Initial applications of computing ΔA(NEW)(MM→QM), for blocked amino acids alanine and serine as well as to generate butane's potentials of mean force via the indirect QM/MM FES method, showed marked improvement over traditional FES approaches. PMID:26539729

  10. 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.

  11. Potential contribution of the wastewater sector to energy supply.

    PubMed

    Heubeck, S; de Vos, R M; Craggs, R

    2011-01-01

    The biological treatment of wastewater could yield high energy fuels such as methane and alcohols, however most conventional treatment systems do not recover this energy potential. with a simple model of the energy yields of various wastewater treatment technologies it is possible to demonstrate how minor shifts in technology selection can lead the industry from being identified as predominantly energy intensive, to being recognised as a source of energy resources. The future potential energy yield is estimated by applying energy yield factors to alternative use scenarios of the same wastewater loads. The method for identifying the energy potential of wastewater was demonstrated for the New Zealand wastewater sector, but can equally be applied to other countries or regions. The model suggests that by using technologies that maximise the recovery of energy from wastewater, the potential energy yield from this sector would be substantially increased (six fold for New Zealand). PMID:21866779

  12. The Natural Flavonoid Pinocembrin: Molecular Targets and Potential Therapeutic Applications.

    PubMed

    Lan, Xi; Wang, Wenzhu; Li, Qiang; Wang, Jian

    2016-04-01

    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

  13. 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

  14. Tea polyphenols, their biological effects and potential molecular targets

    PubMed Central

    Chen, Di; Milacic, Vesna; Chen, Marina Si; Wan, Sheng Biao; Lam, Wai Har; Huo, Congde; Landis-Piwowar, Kristin R.; Cui, Qiuzhi Cindy; Wali, Anil; Chan, Tak Hang; Dou, Q. Ping

    2013-01-01

    Summary 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. PMID:18228206

  15. Free energy calculations using dual-level Born-Oppenheimer molecular dynamics

    NASA Astrophysics Data System (ADS)

    Retegan, Marius; Martins-Costa, Marilia; Ruiz-López, Manuel F.

    2010-08-01

    We describe an efficient and accurate method to compute free energy changes in complex chemical systems that cannot be described through classical molecular dynamics simulations, examples of which are chemical and photochemical reactions in solution, enzymes, interfaces, etc. It is based on the use of dual-level Born-Oppenheimer molecular dynamics simulations. A low-level quantum mechanical method is employed to calculate the potential of mean force through the umbrella sampling technique. Then, a high-level quantum mechanical method is used to estimate a free energy correction on selected points of the reaction coordinate using perturbation theory. The precision of the results is comparable to that of ab initio molecular dynamics methods such as the Car-Parrinello approach but the computational cost is much lower, roughly by two to three orders of magnitude. The method is illustrated by discussing the association free energy of simple organometallic compounds, although the field of application is very broad.

  16. The use of model potentials in molecular calculations. II

    NASA Astrophysics Data System (ADS)

    Sakai, Y.; Huzinaga, S.

    1982-03-01

    The model potential method is applied to CO, HCl, P2, Cl2, SH2, Cu2, Br2, Ni(CO)4, and Pd(CO)4. The results are generally very satisfactory. Reduction of computing cost is substantial for molecules containing heavy atoms.

  17. 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..

  18. 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.

  19. Molecular Recognition of Gangliosides and Their Potential for Cancer Immunotherapies

    PubMed Central

    Krengel, Ute; Bousquet, Paula A.

    2014-01-01

    Gangliosides are sialic-acid-containing glycosphingolipids expressed on all vertebrate cells. They are primarily positioned in the plasma membrane with the ceramide part anchored in the membrane and the glycan part exposed on the surface of the cell. These lipids have highly diverse structures, not the least with respect to their carbohydrate chains, with N-acetylneuraminic acid (NeuAc) and N-glycolylneuraminic acid (NeuGc) being the two most common sialic-acid residues in mammalian cells. Generally, human healthy tissue is deficient in NeuGc, but this molecule is expressed in tumors and in human fetal tissues, and was hence classified as an onco-fetal antigen. Gangliosides perform important functions through carbohydrate-specific interactions with proteins, for example, as receptors in cell–cell recognition, which can be exploited by viruses and other pathogens, and also by regulating signaling proteins, such as the epidermal growth factor receptor (EGFR) and the vascular endothelial growth factor receptor (VEGFR), through lateral interaction in the membrane. Through both mechanisms, tumor-associated gangliosides may affect malignant progression, which makes them attractive targets for cancer immunotherapies. In this review, we describe how proteins recognize gangliosides, focusing on the molecular recognition of gangliosides associated with cancer immunotherapy, and discuss the importance of these molecules in cancer research. PMID:25101077

  20. 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.

  1. 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. PMID:27252585

  2. Advances in Carcinogenic Metal Toxicity and Potential Molecular Markers

    PubMed Central

    Koedrith, Preeyaporn; Seo, Young Rok

    2011-01-01

    Metal compounds such as arsenic, cadmium, chromium, cobalt, lead, mercury, and nickel are classified as carcinogens affecting human health through occupational and environmental exposure. However, the underlying mechanisms involved in tumor formation are not well clarified. Interference of metal homeostasis may result in oxidative stress which represents an imbalance between production of free radicals and the system’s ability to readily detoxify reactive intermediates. This event consequently causes DNA damage, lipid peroxidation, protein modification, and possibly symptomatic effects for various diseases including cancer. This review discusses predominant modes of action and numerous molecular markers. Attention is paid to metal-induced generation of free radicals, the phenomenon of oxidative stress, damage to DNA, lipid, and proteins, responsive signal transduction pathways with major roles in cell growth and development, and roles of antioxidant enzymatic and DNA repair systems. Interaction of non-enzymatic antioxidants (carotenoids, flavonoids, glutathione, selenium, vitamin C, vitamin E, and others) with cellular oxidative stress markers (catalase, glutathione peroxidase, and superoxide dismutase) as well as certain regulatory factors, including AP-1, NF-κB, Ref-1, and p53 is also reviewed. Dysregulation of protective pathways, including cellular antioxidant network against free radicals as well as DNA repair deficiency is related to oncogenic stimulation. These observations provide evidence that emerging oxidative stress-responsive regulatory factors and DNA repair proteins are putative predictive factors for tumor initiation and progression. PMID:22272150

  3. 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. PMID:26932065

  4. 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.

  5. 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.

  6. Pterostilbene as a potential novel telomerase inhibitor: molecular docking studies and its in vitro evaluation.

    PubMed

    Tippani, Radhika; Prakhya, Laxmi Jaya Shankar; Porika, Mahendar; Sirisha, Kalam; Abbagani, Sadanandam; Thammidala, Christopher

    2014-01-01

    Pterostilbene is a naturally occurring dimethyl ether analog of resveratrol identified in several plant species. Telomerase is important in tumor initiation and cellular immortalization. Given the striking correlations between telomerase activity and proliferation capacity in tumor cells, telomerase had been considered as a potentially important molecular target in cancer therapeutics. Molecular docking studies were performed on pterostilbene with the crystal structure of telomerase (3DU6). Pterostilbene was evaluated for its in vitro cytotoxicity in breast (MCF7) and lung cancer (NCI H-460) cell lines, antimitotic activity in green grams and telomerase activity. Curcumin was used as a standard. Docking results indicated good interaction between pterostilbene and the active site of telomerase and the docked energy of pterostilbene was -7.10 kcal/mol. Pterostilbene showed strong inhibitory effect on in vitro telomerase activity and cell growth in both the cell lines tested in a dose dependent manner. Cancer cells treated with 80 µM pterostilbene exhibited significant telomerase inhibition, after 72 hours (MCF-7 and NCI H-460; 81.52% and 74.69% reduction, respectively, compared to control). The IC50 of pterostilbene for anti-proliferative activity in MCF7 and NCI H-460 cell lines were found to be 30.0 and 47.2 µM, respectively. The best antimitotic activity was obtained with 80 μM of pterostilbene (100% reduction in water imbibition). All the above results were comparable to that of curcumin. The drug-related properties of pterostilbene were calculated using Molinspiration, Osiris Property Explorer and ACD/Chemsketch softwares. Pterostilbene obeyed Lipinski's Rule of Five indicating its therapeutic potential in humans. It was found that the telomerase inhibitory activity exhibited by pterostilbene was dependent of the cell viability and has the potential to be a new drug candidate against breast and lung cancers. PMID:24433502

  7. HIGH ENERGY PHYSICS POTENTIAL AT MUON COLLIDERS

    SciTech Connect

    PARSA,Z.

    2000-04-07

    In this paper, high energy physics possibilities and future colliders are discussed. The {mu}{sup +} {mu}{sup {minus}} collider and experiments with high intensity muon beams as the stepping phase towards building Higher Energy Muon Colliders (HEMC) are briefly reviewed and encouraged.

  8. 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,…

  9. 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. PMID:26357347

  10. 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.

  11. QUANTITATIVE COMPARISON OF MOLECULAR ELECTROSTATIC POTENTIALS FOR STRUCTURE-ACTIVITY STUDIES

    EPA Science Inventory

    Further development of an approach for representing, efficiently calculating and comparing discreet 3-dimensional molecular electrostatic potentials using a quantitative similarity index (MEP-SI) based on the Carbo formalism is presented. adial-type (MACRA) grid representation is...

  12. New fitting scheme to obtain effective potential from Car-Parrinello molecular-dynamics simulations: Application to silica

    NASA Astrophysics Data System (ADS)

    Carré, A.; Horbach, J.; Ispas, S.; Kob, W.

    2008-04-01

    A fitting scheme is proposed to obtain effective potentials from Car-Parrinello molecular-dynamics (CPMD) simulations. It is used to parameterize a new pair potential for silica. MD simulations with this new potential are done to determine structural and dynamic properties and to compare these properties to those obtained from CPMD and a MD simulation using the so-called BKS potential. The new potential reproduces accurately the liquid structure generated by the CPMD trajectories, the experimental activation energies for the self-diffusion constants and the experimental density of amorphous silica. Also lattice parameters and elastic constants of α-quartz are well reproduced, showing the transferability of the new potential.

  13. Analytical potential curves of some hydride molecules using algebraic and energy-consistent method

    NASA Astrophysics Data System (ADS)

    Fan, Qunchao; Sun, Weiguo; Feng, Hao; Zhang, Yi; Wang, Qi

    2014-01-01

    Based on the algebraic method (AM) and the energy consistent method (ECM), an AM-ECM protocol for analytical potential energy curves of stable diatomic electronic states is proposed as functions of the internuclear distance. Applications of the AM-ECM to the 6 hydride electronic states of HF-X1Σ+, DF-X1Σ+, D35Cl-X1Σ+, 6LiH-X1Σ+, 7LiH-X1Σ+, and 7LiD-X1Σ+ show that the AM-ECM potentials are in excellent agreement with the experimental RKR data and the full AM-RKR data, and that the AM-ECM can obtain reliable analytical potential energies in the molecular asymptotic and dissociation region for these molecular electronic states.

  14. Photoinduced charge and energy transfer in molecular wires.

    PubMed

    Gilbert, Mélina; Albinsson, Bo

    2015-02-21

    Exploring charge and energy transport in donor-bridge-acceptor systems is an important research field which is essential for the fundamental knowledge necessary to develop future applications. These studies help creating valuable knowledge to respond to today's challenges to develop functionalized molecular systems for artificial photosynthesis, photovoltaics or molecular scale electronics. This tutorial review focuses on photo-induced charge/energy transfer in covalently linked donor-bridge-acceptor (D-B-A) systems. Of utmost importance in such systems is to understand how to control signal transmission, i.e. how fast electrons or excitation energy could be transferred between the donor and acceptor and the role played by the bridge (the "molecular wire"). After a brief description of the electron and energy transfer theory, we aim to give a simple yet accurate picture of the complex role played by the bridge to sustain donor-acceptor electronic communication. Special emphasis is put on understanding bridge energetics and conformational dynamics effects on the distance dependence of the donor-acceptor electronic coupling and transfer rates. Several examples of donor-bridge-acceptor systems from the literature are described as a support to the discussion. Finally, porphyrin-based molecular wires are introduced, and the relationship between their electronic structure and photophysical properties is outlined. In strongly conjugated porphyrin systems, limitations of the existing electron transfer theory to interpret the distance dependence of the transfer rates are also discussed. PMID:25212903

  15. Molecular approach to identify antidiabetic potential of Azadirachta indica

    PubMed Central

    Satyanarayana, K.; Sravanthi, K.; Shaker, I. Anand; Ponnulakshmi, R.

    2015-01-01

    Background: Azadirachta indica (Neem) is a medicinal plant, used in Ayurveda for treating various diseases, one of which is diabetes mellitus. It is known to possess antiinflammatory, antipyretic, antimicrobial, antidiabetic and diverse pharmacological properties. However, the molecular mechanism underlying the effect of A. indica on insulin signal transduction and glucose homeostasis is obscure. Objective: The aim was to study the effects of A. indica aqueous leaf extract on the expression of insulin signaling molecules and glucose oxidation in target tissue of high-fat and fructose-induced type-2 diabetic male rat. Materials and Methods: The oral effective dose of A. indica leaf extract (400 mg/kg body weight [b.wt]) was given once daily for 30 days to high-fat diet-induced diabetic rats. At the end of the experimental period, fasting blood glucose, oral glucose tolerance, serum lipid profile, and the levels of insulin signaling molecules, glycogen, glucose oxidation in gastrocnemius muscle were assessed. Results: Diabetic rats showed impaired glucose tolerance and impairment in insulin signaling molecules (insulin receptor, insulin receptor substrate-1, phospho-IRS-1Tyr632, phospho-IRS-1Ser636, phospho-AktSer473, and glucose transporter 4 [GLUT4] proteins), glycogen concentration and glucose oxidation. The treatment with A. indica leaf extract normalized the altered levels of blood glucose, serum insulin, lipid profile and insulin signaling molecules as well as GLUT4 proteins at 400 mg/kg b.wt dose. Conclusion: It is concluded from the present study that A. indica may play a significant role in the management of type-2 diabetes mellitus, by improving the insulin signaling molecules and glucose utilization in the skeletal muscle. PMID:26604551

  16. Molecular Detection of a Potentially Toxic Diatom Species

    PubMed Central

    Dhar, Bidhan Chandra; Cimarelli, Lucia; Singh, Kumar Saurabh; Brandi, Letizia; Brandi, Anna; Puccinelli, Camilla; Marcheggiani, Stefania; Spurio, Roberto

    2015-01-01

    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. PMID:25955528

  17. Stretching the inflaton potential with kinetic energy

    SciTech Connect

    Lidsey, James E.

    2007-08-15

    Inflation near a maximum of the potential is studied when nonlocal derivative operators are included in the inflaton Lagrangian. Such terms can impose additional sources of friction on the field. For an arbitrary spacetime geometry, these effects can be quantified in terms of a local field theory with a potential whose curvature around the turning point is strongly suppressed. This implies that a prolonged phase of slow-roll inflation can be achieved with potentials that are otherwise too steep to drive quasiexponential expansion. We illustrate this mechanism within the context of p-adic string theory.

  18. Energy functions for rubber from microscopic potentials

    NASA Astrophysics Data System (ADS)

    Johal, A. S.; Dunstan, D. J.

    2007-04-01

    The finite deformation theory of rubber and related materials is based on energy functions that describe the macroscopic response of these materials under deformation. Energy functions and elastic constants are here derived from a simple microscopic (ball-and-spring) model. Exact uniaxial force-extension relationships are given for Hooke's Law and for the thermodynamic entropy-based microscopic model using the Gaussian and the inverse Langevin statistical approximations. Methods are given for finding the energy functions as expansions of tensor invariants of deformation, with exact solutions for functions that can be expressed as expansions in even powers of the extension. Comparison with experiment shows good agreement with the neo-Hookean energy function and we show how this derives directly from the simple Gaussian statistical model with a small modification.

  19. Acinetobacter lipases: molecular biology, biochemical properties and biotechnological potential.

    PubMed

    Snellman, Erick A; Colwell, Rita R

    2004-10-01

    Lipases (EC 3.1.1.3) have received increased attention recently, evidenced by the increasing amount of information about lipases in the current literature. The renewed interest in this enzyme class is due primarily to investigations of their role in pathogenesis and their increasing use in biotechnological applications. Also, many microbial lipases are available as commercial products, the majority of which are used in detergents, cosmetic production, food flavoring, and organic synthesis. Lipases are valued biocatalysts because they act under mild conditions, are highly stable in organic solvents, show broad substrate specificity, and usually show high regio- and/or stereo-selectivity in catalysis. A number of lipolytic strains of Acinetobacter have been isolated from a variety of sources and their lipases possess many biochemical properties similar to those that have been developed for biotechnological applications. This review discusses the biology of lipase expression in Acinetobacter, with emphasis on those aspects relevant to potential biotechnology applications. PMID:15378387

  20. Photoswitchable Molecular Rings for Solar-Thermal Energy Storage

    SciTech Connect

    Durgun, E; Grossman, JC

    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.

  1. Energy offsets within a molecular monolayer: the influence of the molecular environment

    NASA Astrophysics Data System (ADS)

    Willenbockel, M.; Stadtmüller, B.; Schönauer, K.; Bocquet, F. C.; Lüftner, D.; Reinisch, E. M.; Ules, T.; Koller, G.; Kumpf, C.; Soubatch, S.; Puschnig, P.; Ramsey, M. G.; Tautz, F. S.

    2013-03-01

    The compressed 3,4,9,10-perylene tetracarboxylic dianhydride (PTCDA) herringbone monolayer structure on Ag(110) is used as a model system to investigate the role of molecule-molecule interactions at metal-organic interfaces. By means of the orbital tomography technique, we can not only distinguish the two inequivalent molecules in the unit cell but also resolve their different energy positions for the highest occupied and the lowest unoccupied molecular orbitals. Density functional theory calculations of a freestanding PTCDA layer identify the electrostatic interaction between neighboring molecules, rather than the adsorption site, as the main reason for the molecular level splitting observed experimentally.

  2. Evaluating Molecular Mechanical Potentials for Helical Peptides and Proteins

    PubMed Central

    Thompson, Erik J.; DePaul, Allison J.; Patel, Sarav S.; Sorin, Eric J.

    2010-01-01

    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 A21 and Fs 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 310 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-99φ 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. PMID:20418937

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

    PubMed

    Cawkwell, M J; Niklasson, Anders M N

    2012-10-01

    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. PMID:23039583

  4. Molecular partitioning based on the kinetic energy density

    NASA Astrophysics Data System (ADS)

    Noorizadeh, Siamak

    2016-05-01

    Molecular partitioning based on the kinetic energy density is performed to a number of chemical species, which show non-nuclear attractors (NNA) in their gradient maps of the electron density. It is found that NNAs are removed using this molecular partitioning and although the virial theorem is not valid for all of the basins obtained in the being used AIM, all of the atoms obtained using the new approach obey this theorem. A comparison is also made between some atomic topological parameters which are obtained from the new partitioning approach and those calculated based on the electron density partitioning.

  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. 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 ⩾2.4mgml(-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 0.071mgml(-1) of blumeoidolide B in comparison with ⩾3.6mgml(-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 in

  7. 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.

  8. 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.

  9. 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.

  10. 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)

  11. 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

  12. Energy savings potential from energy-conserving irrigation systems

    SciTech Connect

    Wilfert, G.L.; Patton, W.P.; Harrer, B.J.; Clark, M.A.

    1982-11-01

    This report systematically compares, within a consistent framework, the technical and economic characteristics of energy-conserving irrigation systems with those of conventional irrigation systems and to determine total energy savings. Levelized annual costs of owning and operating both energy-conserving and conventional irrigation systems have been developed and compared for all 17 states to account for the differences in energy costs and irrigation conditions in each state. Market penetration of energy-conserving systems is assessed for those systems having lower levelized annual costs than conventional systems performing the same function. Annual energy savings were computed by matching the energy savings per system with an assumed maximum market penetration of 100 percent in those markets where the levelized annual costs of energy-conserving systems are lower than the levelized annual costs of conventional systems.

  13. 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.

  14. Modified embedded-atom method interatomic potential and interfacial thermal conductance of Si-Cu systems: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Abs da Cruz, Carolina; Chantrenne, Patrice; Gomes de Aguiar Veiga, Roberto; Perez, Michel; Kleber, Xavier

    2013-01-01

    Thermal contact conductance of metal-dielectric systems is a key parameter that has to be taken into account for the design and reliability of nanostructured microelectronic systems. This paper aims to predict this value for Si-Cu interfaces using molecular dynamics simulations. To achieve this goal, a modified embedded atom method interatomic potential for Si-Cu system has been set based upon previous MEAM potentials for pure Cu and pure Si. The Si-Cu cross potential is determined by fitting key properties of the alloy to results obtained by ab initio calculations. It has been further evaluated by comparing the structure and energies of Cu dimmers in bulk Si and CumSin clusters to ab initio calculations. The comparison between MD and ab initio calculation also concerns the energy barrier of Cu migration along the (110) channel in bulk Si. Using this interatomic potential, non equilibrium molecular dynamics has been performed to calculate the thermal contact conductance of a Si-Cu interface at different temperature level. The results obtained are in line with previous experimental results for different kind of interfaces. This confirms that the temperature variation of the thermal conductance might not find its origin in the electron-phonon interactions at the interface nor in the quantification of the energy of the vibration modes. The diffuse mismatch model is also used in order to discuss these results.

  15. 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. PMID:22779438

  16. FINITE EXPANSION METHOD FOR THE CALCULATION AND INTERPRETATION OF MOLECULAR ELECTROSTATIC POTENTIALS

    EPA Science Inventory

    Because it is useful to have the molecular electrostatic potential as an element in a complex scheme to assess the toxicity of large molecules, efficient and reliable methods are needed for the calculation and characterization of these potentials. A multicenter multipole expansio...

  17. 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.

  18. Molecular effective coverage surface area of optical clearing agents for predicting optical clearing potential

    NASA Astrophysics Data System (ADS)

    Feng, Wei; Ma, Ning; Zhu, Dan

    2015-03-01

    The improvement of methods for optical clearing agent prediction exerts an important impact on tissue optical clearing technique. The molecular dynamic simulation is one of the most convincing and simplest approaches to predict the optical clearing potential of agents by analyzing the hydrogen bonds, hydrogen bridges and hydrogen bridges type forming between agents and collagen. However, the above analysis methods still suffer from some problem such as analysis of cyclic molecule by reason of molecular conformation. In this study, a molecular effective coverage surface area based on the molecular dynamic simulation was proposed to predict the potential of optical clearing agents. Several typical cyclic molecules, fructose, glucose and chain molecules, sorbitol, xylitol were analyzed by calculating their molecular effective coverage surface area, hydrogen bonds, hydrogen bridges and hydrogen bridges type, respectively. In order to verify this analysis methods, in vitro skin samples optical clearing efficacy were measured after 25 min immersing in the solutions, fructose, glucose, sorbitol and xylitol at concentration of 3.5 M using 1951 USAF resolution test target. The experimental results show accordance with prediction of molecular effective coverage surface area. Further to compare molecular effective coverage surface area with other parameters, it can show that molecular effective coverage surface area has a better performance in predicting OCP of agents.

  19. Energy-weighted sum rules and the analysis of vibrational structure in molecular spectra

    NASA Astrophysics Data System (ADS)

    Smith, W. L.

    2015-10-01

    The energy-weighted sum SV = Σn (E‧n - E″m)|<ψ″m|ψ‧n>|2 = <ψ″m|ΔV|ψ″m> for the vibrational potential functions V‧, V″ associated with transitions between two electronic states of diatomic molecular species is investigated and specific formulae are given using Morse functions for V‧ and V″. It is found that these formulae are useful approximations which provide a convenient way to analyse the vibrational structure of real spectra to give estimates of molecular parameters such as the change in internuclear distance accompanying a transition.

  20. Molecular Dynamics Studies of Dislocations in CdTe Crystals from a New Bond Order Potential.

    PubMed

    Zhou, Xiaowang; Ward, Donald K; Wong, Bryan M; Doty, F Patrick; Zimmerman, Jonathan A

    2012-08-23

    Cd(1-x)Zn(x)Te (CZT) crystals are the leading semiconductors for radiation detection, but their application is limited by the high cost of detector-grade materials. High crystal costs primarily result from property nonuniformity that causes low manufacturing yield. Although tremendous efforts have been made in the past to reduce Te inclusions/precipitates in CZT, this has not resulted in an anticipated improvement in material property uniformity. Moreover, it is recognized that in addition to Te particles, dislocation cells can also cause electric field perturbations and the associated property nonuniformities. Further improvement of the material, therefore, requires that dislocations in CZT crystals be understood and controlled. Here, we use a recently developed CZT bond order potential to perform representative molecular dynamics simulations to study configurations, energies, and mobilities of 29 different types of possible dislocations in CdTe (i.e., x = 1) crystals. An efficient method to derive activation free energies and activation volumes of thermally activated dislocation motion will be explored. Our focus gives insight into understanding important dislocations in the material and gives guidance toward experimental efforts for improving dislocation network structures in CZT crystals. PMID:22962626

  1. 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

  2. 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. PMID:24259381

  3. 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. PMID:27200016

  4. 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. PMID:24769081

  5. Implementing molecular dynamics on hybrid high performance computers—Three-body potentials

    NASA Astrophysics Data System (ADS)

    Brown, W. Michael; Yamada, Masako

    2013-12-01

    The use of coprocessors or accelerators such as graphics processing units (GPUs) has become popular in scientific computing applications due to their low cost, impressive floating-point capabilities, high memory bandwidth, and low electrical power requirements. Hybrid high-performance computers, defined as machines with nodes containing more than one type of floating-point processor (e.g. CPU and GPU), are now becoming more prevalent due to these advantages. Although there has been extensive research into methods to use accelerators efficiently to improve the performance of molecular dynamics (MD) codes employing pairwise potential energy models, little is reported in the literature for models that include many-body effects. 3-body terms are required for many popular potentials such as MEAM, Tersoff, REBO, AIREBO, Stillinger-Weber, Bond-Order Potentials, and others. Because the per-atom simulation times are much higher for models incorporating 3-body terms, there is a clear need for efficient algorithms usable on hybrid high performance computers. Here, we report a shared-memory force-decomposition for 3-body potentials that avoids memory conflicts to allow for a deterministic code with substantial performance improvements on hybrid machines. We describe modifications necessary for use in distributed memory MD codes and show results for the simulation of water with Stillinger-Weber on the hybrid Titan supercomputer. We compare performance of the 3-body model to the SPC/E water model when using accelerators. Finally, we demonstrate that our approach can attain a speedup of 5.1 with acceleration on Titan for production simulations to study water droplet freezing on a surface.

  6. Implementing Molecular Dynamics on Hybrid High Performance Computers - Three-Body Potentials

    SciTech Connect

    Brown, W Michael; Yamada, Masako

    2013-01-01

    The use of coprocessors or accelerators such as graphics processing units (GPUs) has become popular in scientific computing applications due to their low cost, impressive floating-point capabilities, high memory bandwidth, and low electrical power re- quirements. Hybrid high-performance computers, defined as machines with nodes containing more than one type of floating-point processor (e.g. CPU and GPU), are now becoming more prevalent due to these advantages. Although there has been extensive research into methods to efficiently use accelerators to improve the performance of molecular dynamics (MD) employing pairwise potential energy models, little is reported in the literature for models that include many-body effects. 3-body terms are required for many popular potentials such as MEAM, Tersoff, REBO, AIREBO, Stillinger-Weber, Bond-Order Potentials, and others. Because the per-atom simulation times are much higher for models incorporating 3-body terms, there is a clear need for efficient algo- rithms usable on hybrid high performance computers. Here, we report a shared-memory force-decomposition for 3-body potentials that avoids memory conflicts to allow for a deterministic code with substantial performance improvements on hybrid machines. We describe modifications necessary for use in distributed memory MD codes and show results for the simulation of water with Stillinger-Weber on the hybrid Titan supercomputer. We compare performance of the 3-body model to the SPC/E water model when using accelerators. Finally, we demonstrate that our approach can attain a speedup of 5.1 with acceleration on Titan for production simulations to study water droplet freezing on a surface.

  7. 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.

  8. 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

    2016-01-01

    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

  9. 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

  10. Molecular structure, spectroscopy (FT-IR, FT-Raman), thermodynamic parameters, molecular electrostatic potential and HOMO-LUMO analysis of 2, 6-dichlorobenzamide

    NASA Astrophysics Data System (ADS)

    Tao, Yaping; Han, Ligang; Li, Xiaofeng; Han, Yunxia; Liu, Zhaojun

    2016-03-01

    2, 6-dichlorobenzamide is the degradation product of 2, 6-dichlorobenzonitrile, which is often used as herbicide and can cause groundwater pollution. The FT-IR and FT-Raman spectra of 2, 6-dichlorobenzamide at room temperature were recorded and analyzed in the range 4000-400 and 3700-100 cm-1, respectively. In order to obtain the most stable structure, a potential energy surface (PES) scan for internal rotations was carried out at the B3LYP/6-31G(d) level. The optimized geometry, structural parameters energies, theoretical IR and Raman spectra for the title compound have been obtained by employing B3LYP exchange-correlation functional with high-quality aug-cc-pVTZ basis-set. Detailed vibrational assignments of vibrational spectra have been made on the basis of the potential energy distributions (PED) analysis. In addition, the HOMO-LUMO gap and molecular electrostatic potential (MEP) were studied theoretically. Finally, the thermodynamic functions (heat capacity, entropy, enthalpy, and Gibbs free energy) of 2, 6-dichlorobenzamide were obtained in the range of 100-1000 K.

  11. 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.

  12. 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. PMID:27366935

  13. 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.

  14. Effects of electronic coupling and electrostatic potential on charge transport in carbon-based molecular electronic junctions.

    PubMed

    McCreery, Richard L

    2016-01-01

    Molecular junctions consisting of 2-20 nm thick layers of organic oligomers oriented between a conducting carbon substrate and a carbon/gold top contact have proven to be reproducible and reliable, and will soon enter commercial production in audio processing circuits. The covalent, conjugated bond between one or both sp(2)-hybridized carbon contacts and an aromatic molecular layer is distinct from the more common metal/molecule or silicon/molecule structures in many reported molecular junctions. Theoretical observations based on density functional theory are presented here, which model carbon-based molecular junctions as single molecules and oligomers between fragments of graphene. Electronic coupling between the molecules and the contacts is demonstrated by the formation of hybrid orbitals in the model structure, which have significant electron density on both the graphene and the molecule. The energies of such hybrid orbitals correlate with tunneling barriers determined experimentally, and electronic coupling between the two graphene fragments in the model correlates with experimentally observed attenuation of transport with molecular layer thickness. Electronic coupling is affected significantly by the dihedral angle between the planes of the graphene and the molecular π-systems, but is absent only when the two planes are orthogonal. Coupling also results in partial charge transfer between the graphene contacts and the molecular layer, which results in a shift in electrostatic potential which affects the observed tunneling barrier. Although the degree of partial charge transfer is difficult to calculate accurately, it does provide a basis for the "vacuum level shift" observed in many experiments, including transport and ultraviolet photoelectron spectroscopy of molecular layers on conductors. PMID:26925350

  15. Effects of electronic coupling and electrostatic potential on charge transport in carbon-based molecular electronic junctions

    PubMed Central

    2016-01-01

    Summary Molecular junctions consisting of 2–20 nm thick layers of organic oligomers oriented between a conducting carbon substrate and a carbon/gold top contact have proven to be reproducible and reliable, and will soon enter commercial production in audio processing circuits. The covalent, conjugated bond between one or both sp2-hybridized carbon contacts and an aromatic molecular layer is distinct from the more common metal/molecule or silicon/molecule structures in many reported molecular junctions. Theoretical observations based on density functional theory are presented here, which model carbon-based molecular junctions as single molecules and oligomers between fragments of graphene. Electronic coupling between the molecules and the contacts is demonstrated by the formation of hybrid orbitals in the model structure, which have significant electron density on both the graphene and the molecule. The energies of such hybrid orbitals correlate with tunneling barriers determined experimentally, and electronic coupling between the two graphene fragments in the model correlates with experimentally observed attenuation of transport with molecular layer thickness. Electronic coupling is affected significantly by the dihedral angle between the planes of the graphene and the molecular π-systems, but is absent only when the two planes are orthogonal. Coupling also results in partial charge transfer between the graphene contacts and the molecular layer, which results in a shift in electrostatic potential which affects the observed tunneling barrier. Although the degree of partial charge transfer is difficult to calculate accurately, it does provide a basis for the “vacuum level shift” observed in many experiments, including transport and ultraviolet photoelectron spectroscopy of molecular layers on conductors. PMID:26925350

  16. Turbine under Gulf Stream: Potential energy source

    SciTech Connect

    Venezia, W.A.; Holt, J.

    1995-09-01

    Turbine under the Gulf Stream (TUGS) is a project to design, build, and deploy the prototypes necessary to demonstrate the economic and technical feasibility of generating electric power from the Gulf Stream. The project is based in part on new generator designs and emerging materials technologies. Its successful completion would demonstrate the technology and produce prototype turbines that can be mass produced and sold with service support. Past research and experimentation indicates that energy can be generated from the Gulf Stream. Problems exist such as fluctuations in the current`s axis and inconsistency. Above all, the ocean is a difficult environment in which to work. Therefore, the question is not whether or not a generator can be put in the ocean to generate electricity, but rather can it be done in an economically and environmentally sound way and still be practical?

  17. Topographies and dynamics on multidimensional potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Ball, Keith Douglas

    The stochastic master equation is a valuable tool for elucidating potential energy surface (PES) details that govern structural relaxation in clusters, bulk systems, and protein folding. This work develops a comprehensive framework for studying non-equilibrium relaxation dynamics using the master equation. Since our master equations depend upon accurate partition function models for use in Rice-Ramsperger-Kassel-Marcus (RRK(M) transition state theory, this work introduces several such models employing various harmonic and anharmonic approximations and compares their predicted equilibrium population distributions with those determined from molecular dynamics. This comparison is performed for the fully-delineated surfaces (KCl)5 and Ar9 to evaluate model performance for potential surfaces with long- and short-range interactions, respectively. For each system, several models perform better than a simple harmonic approximation. While no model gives acceptable results for all minima, and optimal modeling strategies differ for (KCl)5 and Ar9, a particular one-parameter model gives the best agreement with simulation for both systems. We then construct master equations from these models and compare their isothermal relaxation predictions for (KCl)5 and Ar9 with molecular dynamics simulations. This is the first comprehensive test of the kinetic performance of partition function models of its kind. Our results show that accurate modeling of transition-state partition functions is more important for (KCl)5 than for Ar9 in reproducing simulation results, due to a marked stiffening anharmonicity in the transition-state normal modes of (KCl)5. For both systems, several models yield qualitative agreement with simulation over a large temperature range. To examine the robustness of the master equation when applied to larger systems, for which full topographical descriptions would be either impossible or infeasible, we compute relaxation predictions for Ar11 using a master equation

  18. 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…

  19. Periodic discrete energy for long-range potentials

    NASA Astrophysics Data System (ADS)

    Hardin, D. P.; Saff, E. B.; Simanek, B.

    2014-12-01

    We consider periodic energy problems in Euclidean space with a special emphasis on long-range potentials that cannot be defined through the usual infinite sum. One of our main results builds on more recent developments of Ewald summation to define the periodic energy corresponding to a large class of long-range potentials. Two particularly interesting examples are the logarithmic potential and the Riesz potential when the Riesz parameter is smaller than the dimension of the space. For these examples, we use analytic continuation methods to provide concise formulas for the periodic kernel in terms of the Epstein Hurwitz Zeta function. We apply our energy definition to deduce several properties of the minimal energy including the asymptotic order of growth and the distribution of points in energy minimizing configurations as the number of points becomes large. We conclude with some detailed calculations in the case of one dimension, which shows the utility of this approach.

  20. 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.

  1. 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.

  2. Scattering with absorptive interaction: Energy-dependent potentials

    NASA Astrophysics Data System (ADS)

    Cassing, W.; Stingl, M.; Weiguny, A.

    1983-05-01

    The energy dependence and analytic structure of the effective interaction for elastic scattering of composite particles are investigated using Feshbach's projection technique. A generalized Levinson theorem is established for complex, nonlocal, and energy-dependent interactions. The analytical results are illustrated by means of Argand diagrams for a solvable model and the effect of energy averaging is discussed. NUCLEAR REACTIONS Scattering theory, S matrix for absorptive, energy-dependent potentials, Levinson theorem.

  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. Exploring wind energy potential off the California coast

    NASA Astrophysics Data System (ADS)

    Jiang, Qingfang; Doyle, James D.; Haack, Tracy; Dvorak, Michael J.; Archer, Cristina L.; Jacobson, Mark Z.

    2008-10-01

    Wind energy represents the nearest term cost-effective renewable energy source. While efforts have been made to assess wind energy potential over land around the world, offshore wind energy resources are largely unexplored, in part because these regions have relatively sparse wind observations. In this study, the wind energy potential offshore of the California coast is evaluated using a well-tested high-resolution numerical model dataset. We found that along the coastline, the low-level winds exhibit strong spatial variation and are characterized by alternating windspeed maxima and minima near coastal promontories associated with the interaction between the marine boundary layer and coastal topography. Further analysis highlights the enormous and reliable wind energy development potential in these persistent offshore windspeed maxima.

  5. Assessing the Potential for Renewable Energy on Public Lands

    SciTech Connect

    Not Available

    2003-02-01

    This report represents an initial activity of the Bureau of Land Managements (BLM) proposed National Energy Policy Implementation Plan: identify and evaluate renewable energy resources on federal lands and any limitations on accessing them. Ultimately, BLM will prioritize land-use planning activities to increase industrys development of renewable energy resources. These resources include solar, biomass, geothermal, water, and wind energy. To accomplish this, BLM and the Department of Energys National Renewable Energy Laboratory (NREL) established a partnership to conduct an assessment of renewable energy resources on BLM lands in the western United States. The objective of this collaboration was to identify BLM planning units in the western states with the highest potential for private-sector development of renewable resources. The assessment resulted in the following findings: (1) 63 BLM planning units in nine western states have high potential for one or more renewable energy technologies; and (2) 20 BLM planning units in seven western states have high potential for power production from three or more renewable energy sources. This assessment report provides BLM with information needed to prioritize land-use planning activities on the basis of potential for the development of energy from renewable resources.

  6. Solutions of the Dirac equation with the Morse potential energy model in higher spatial dimensions

    NASA Astrophysics Data System (ADS)

    Zhang, Peng; Long, Hui-Cheng; Jia, Chun-Sheng

    2016-04-01

    Analytical solutions of the Dirac equation with the Morse potential energy model in higher spatial dimensions have been explored. We present the bound-state energy equation and the corresponding upper and lower radial wave functions. We find that the behavior of the higher-dimensional relativistic vibrational energies remains similar to that of the three-dimensional molecular system for the X^2sum^+ state of the CP molecule. This symmetry phenomenon will break at the critical point through which the system undergoes a phase transition from a stable to an unstable state.

  7. New approach to calculating the potential energy of colliding nuclei

    SciTech Connect

    Kurmanov, R. S.; Kosenko, G. I.

    2014-12-15

    The differential method proposed by the present authors earlier for the reduction of volume integrals in calculating the potential energy of a compound nucleus is generalized to the case of two interacting nuclei. The Coulomb interaction energy is obtained for the cases of a sharp and a diffuse boundary of nuclei, while the nuclear interaction energy is found only for nuclei with a sharp boundary, the finiteness of the nuclear-force range being taken into account. The present method of calculations permits reducing the time it takes to compute the potential energy at least by two orders of magnitude.

  8. Non-Hermitian quantum mechanics: wave packet propagation on autoionizing potential energy surfaces.

    PubMed

    Moiseyev, N; Scheit, S; Cederbaum, L S

    2004-07-01

    The correspondence between the time-dependent and time-independent molecular dynamic formalisms is shown for autoionizing processes. We demonstrate that the definition of the inner product in non-Hermitian quantum mechanics plays a key role in the proof. When the final state of the process is dissociative, it is technically favorable to introduce a complex absorbing potential into the calculations. The conditions which this potential should fulfill are briefly discussed. An illustrative numerical example is presented involving three potential energy surfaces. PMID:15260598

  9. A Frontier orbital energy approach to redox potentials

    NASA Astrophysics Data System (ADS)

    Conradie, Jeanet

    2015-09-01

    The prediction of the oxidation and reduction potentials of molecules is important in many research areas. A review of relationships obtained between frontier orbital energies (eV), the calculated ionization potentials (IP in eV), or adiabatic electron affinities (EA in eV) with the experimental oxidation and reduction potentials is presented, for selected series of β- diketones, rhodium-β-diketonato complexes, as well as metal-tris-β-diketonato complexes, with the metal Fe or Mn. The good linear relationships obtained for related series of complexes show that the oxidation and reduction potentials of these complexes can be predicted by their DFT-calculated energies.

  10. 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.

  11. 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.

  12. Re-examining Potential for Geothermal Energy in United States

    NASA Astrophysics Data System (ADS)

    Showstack, Randy

    New technological initiatives, along with potential policy and economic incentives, could help to bring about a resurgence in geothermal energy development in the United States, said several experts at a 22 May forum in Washington, D.C. The forum was sponsored by the House and Senate Renewable Energy and Energy Efficiency Caucuses, the Sustainable Energy Coalition, and the Environmental and Energy Study Institute. Among these initiatives is an ambitious program of the U.S. Department of Energy to expand existing geothermal energy fields and potentially create new fields through ``enhanced geothermal systems.'' In addition, a program of the Bush administration encourages geothermal development on some public lands, and current legislation would provide tax credits and other incentives for geothermal development.

  13. 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. PMID:18215439

  14. 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.

  15. A molecular electrostatic potential analysis of hydrogen, halogen, and dihydrogen bonds.

    PubMed

    Mohan, Neetha; Suresh, Cherumuttathu H

    2014-03-01

    Hydrogen, halogen, and dihydrogen bonds in weak, medium and strong regimes (<1 to ∼ 60 kcal/mol) have been investigated for several intermolecular donor-acceptor (D-A) complexes at ab initio MP4//MP2 method coupled with atoms-in-molecules and molecular electrostatic potential (MESP) approaches. Electron density ρ at bond critical point correlates well with interaction energy (Enb) for each homogeneous sample of complexes, but its applicability to the entire set of complexes is not satisfactory. Analysis of MESP minimum (V(min)) and MESP at the nuclei (Vn) shows that in all D-A complexes, MESP of A becomes more negative and that of D becomes less negative suggesting donation of electrons from D to A leading to electron donor-acceptor (eDA) interaction between A and D. MESP based parameter ΔΔVn measures donor-acceptor strength of the eDA interactions as it shows a good linear correlation with Enb for all D-A complexes (R(2) = 0.976) except the strongly bound bridged structures. The bridged structures are classified as donor-acceptor-donor complexes. MESP provides a clear evidence for hydrogen, halogen, and dihydrogen bond formation and defines them as eDA interactions in which hydrogen acts as electron acceptor in hydrogen and dihydrogen bonds while halogen acts as electron acceptor in halogen bonds. PMID:24506527

  16. Chemical Potential of Triethylene Glycol Adsorbed on Surfaces Relevant to Gas Transport and Processing - Studies Using Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Kvamme, B.; Olsen, R.; Sjöblom, S.; Leirvik, K. N.; Kuznetsova, T.

    2014-12-01

    Natural gas will inevitably contain trace amounts of water and other impurities during different stages of processing and transport. Glycols, such as triethylene glycol (TEG), will in many cases follow the water. The glycol contents of the gas can originate from preceding glycol-drying units or it can be a residue from the direct injection of glycols used to prevent hydrate formation. Thus, it is important to know how glycol contents will affect the different paths leading to hydrate formation. Glycols may in some cases dominate the condensed water phase. If this occurs, it will lead to the well-documented shift in the hydrate stability curve, due to the altered activity of the water. A great deal of information on the molecular path of a glycol through the system can be obtained from calculating the chemical potential. Due to difficulties in measuring interfacial chemical potentials, these often need to be estimated using theoretical tools. We used molecular dynamics (MD) to study how TEG behaves in the vicinity of mineral surfaces such as calcite and hematite. Many methods exist for estimating chemical potentials based on MD trajectories. These include techniques such as free energy perturbation theory (FEP) and thermodynamic integration (TI). Such methods require sufficient sampling of configurations where free energy is to be estimated. Thus, it can be difficult to estimate chemical potentials on surfaces. There are several methods to circumvent this problem, such as blue moon sampling and umbrella sampling. These have been considered and the most important have been used to estimate chemical potentials of TEG adsorbed on the mineral surfaces. The resulting chemical potentials were compared to the chemical potential of TEG in bulk water, which was estimated using temperature thermodynamic integration.

  17. 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.

  18. 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. PMID:21584678

  19. Potential energy landscapes of elemental and heterogeneous chalcogen clusters

    SciTech Connect

    Mauro, John C.; Loucks, Roger J.; Balakrishnan, Jitendra; Varshneya, Arun K.

    2006-02-15

    We describe the potential energy landscapes of elemental S{sub 8}, Se{sub 8}, and Te{sub 8} clusters using disconnectivity graphs. Inherent structures include both ring and chain configurations, with rings especially dominant in Se{sub 8}. We also map the potential energy landscapes of heterogeneous Se{sub n}(S,Te){sub 8-n} clusters, which offer insights into the structure of heterogeneous chalcogen glasses.

  20. Teaching Potential Energy Functions and Stability with Slap Bracelets

    NASA Astrophysics Data System (ADS)

    Van Hook, Stephen J.

    2005-10-01

    The slap bracelet, an inexpensive child's toy, makes it easy to engage students in hands-on exploration of potential energy curves as well as of stable, unstable, and meta-stable states. Rather than just observing the teacher performing a demonstration, the students can manipulate the equipment themselves and make their own observations, which are then pooled to focus a class discussion on potential energy functions and stability.

  1. Enhanced Interatomic Potential for Skutterudite CoSb3 in Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Yang, Xuqiu; Zhou, An; Liu, Lisheng; Zhang, Qingjie; Zhai, Pengcheng

    2010-09-01

    To find a suitable potential for the interatomic interactions in molecular dynamics (MD) simulations for the study of the mechanical properties of the nanostructured thermoelectric material CoSb3, the advantages and disadvantages of existing potentials for the material are first reviewed and discussed, and then an enhanced potential is proposed in which both bond-stretching and bond-angle distortions are considered. The structural stability and elastic properties of the crystalline CoSb3 model within the developed potential are validated at finite temperature using classic MD tests. Comparison of the mechanical behavior of bulk single-crystal CoSb3, including the stress-strain curve and configuration evolution under tension, shows that the enhanced potential exhibits better reliability than the other potentials. Finally, the significance of the potential and its possible further improvement for broader application are briefly discussed.

  2. 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

  3. Molecular insights into the terminal energy acceptor in cyanobacterial phycobilisome.

    PubMed

    Gao, Xiang; Wei, Tian-Di; Zhang, Nan; Xie, Bin-Bin; Su, Hai-Nan; Zhang, Xi-Ying; Chen, Xiu-Lan; Zhou, Bai-Cheng; Wang, Zhi-Xin; Wu, Jia-Wei; Zhang, Yu-Zhong

    2012-09-01

    The linker protein L(CM) (ApcE) is postulated as the major component of the phycobilisome terminal energy acceptor (TEA) transferring excitation energy from the phycobilisome to photosystem II. L(CM) is the only phycobilin-attached linker protein in the cyanobacterial phycobilisome through auto-chromophorylation. However, the underlying mechanism for the auto-chromophorylation of L(CM) and the detailed molecular architecture of TEA is still unclear. Here, we demonstrate that the N-terminal phycobiliprotein-like domain of L(CM) (Pfam00502, LP502) can specifically recognize phycocyanobilin (PCB) by itself. Biochemical assays indicated that PCB binds into the same pocket in LP502 as that in the allophycocyanin α-subunit and that Ser152 and Asp155 play a vital role in LP502 auto-chromophorylation. By carefully conducting computational simulations, we arrived at a rational model of the PCB-LP502 complex structure that was supported by extensive mutational studies. In the PCB-LP502 complex, PCB binds into a deep pocket of LP502 with a distorted conformation, and Ser152 and Asp155 form several hydrogen bonds to PCB fixing the PCB Ring A and Ring D. Finally, based on our results, the dipoles and dipole-dipole interactions in TEA are analysed and a molecular structure for TEA is proposed, which gives new insights into the energy transformation mechanism of cyanobacterial phycobilisome. PMID:22758351

  4. Folding of Trp-cage Mini Protein Using Temperature and Biasing Potential Replica—Exchange Molecular Dynamics Simulations

    PubMed Central

    Kannan, Srinivasaraghavan; Zacharias, Martin

    2009-01-01

    The folding process of the 20 residue Trp-cage mini-protein was investigated using standard temperature replica exchange molecular dynamics (T-RexMD) simulation and a biasing potential RexMD (BP-RexMD) method. In contrast to several conventional molecular dynamics simulations, both RexMD methods sampled conformations close to the native structure after 10–20 ns simulation time as the dominant conformational states. In contrast, to T-RexMD involving 16 replicas the BP-RexMD method achieved very similar sampling results with only five replicas. The result indicates that the BP-RexMD method is well suited to study folding processes of proteins at a significantly smaller computational cost, compared to T-RexMD. Both RexMD methods sampled not only similar final states but also agreed on the sampling of intermediate conformations during Trp-cage folding. The analysis of the sampled potential energy contributions indicated that Trp-cage folding is favored by both van der Waals and to a lesser degree electrostatic contributions. Folding does not introduce any significant sterical strain as reflected by similar energy distributions of bonded energy terms (bond length, bond angle and dihedral angle) of folded and unfolded Trp-cage structures. PMID:19399241

  5. MOLECULAR ANALYSIS OF HUMAN SPERMATOZOA: POTENTIAL FOR INFERTILITY RESEARCH AND SCREENING

    EPA Science Inventory

    Molecular Analysis of Human Spermatozoa: Potential for Infertility Research and Screening
    David Miller1, David Dix2, Robert Reid3, Susan Wykes3 and Stephen Krawetz3
    1Reproductive Biology Group, University of Leeds, UK
    2Reproductive Toxicology Division, U.S. Environmenta...

  6. Molecular dynamics simulation of alkali borate glass using coordination dependent potential

    SciTech Connect

    Park, B.; Cormack, A.N.

    1997-12-31

    The structure of sodium borate glass was investigated by molecular dynamics simulation using coordination dependent potential model. The simulated alkali borate glass consists of basic units, BO{sub 3} triangle, BO{sub 4} tetrahedra and structural groups such as boroxol ring and triborate units. The coordination of boron is converted from 3 to 4 by adding alkali oxide.

  7. 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.

  8. The Department of Defense energy vulnerabilities: Potential problems and observations

    NASA Astrophysics Data System (ADS)

    Freiwald, D. A.; Berger, M. E.; Roach, J. F.

    1982-08-01

    The Department of Defense is almost entirely dependent on civilian energy supplies to meet its needs in both peacetime and periods of heightened conflict. There are a number of potential vulnerabilities to the continual and timely supply of energy to both the civilian and military sectors. These include denial of the energy resources themselves, disruption of critical transportation networks, destruction of storage facilities, and interruption of electrical power. This report briefly reviews the present situation for provision of energy from the civilian sector to the military. General vulnerabilities of the existing energy supply system are identified, along with the potential for armed aggression (including terrorist and sabotage activities) against the energy network. Conclusions and some tentative observations are made as to a proper response to the existing vulnerabilities.

  9. DoD energy vulnerabilities: potential problems and observations

    SciTech Connect

    Freiwald, D A; Berger, M E; Roach, J F

    1982-08-01

    The Department of Defense is almost entirely dependent on civilian energy supplies to meet its needs in both peacetime and periods of heightened conflict. There are a number of potential vulnerabilities to the continual and timely supply of energy to both the civilian and military sectors. These include denial of the energy resources themselves, disruption of critical transportation networks, destruction of storage facilities, and interruption of electrical power. This report briefly reviews the present situation for provision of energy from the civilian sector to the military. General vulnerabilities of the existing energy supply system are identified, along with the potential for armed aggression (including terrorist and sabotage activities) against the energy network. Conclusions and some tentative observations are made as to a proper response to the existing vulnerabilities.

  10. 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.

  11. 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.

  12. Potential geothermal energy applications for Idaho Elks Rehabilitation Hospital

    SciTech Connect

    Austin, J.C.

    1981-11-01

    Several potential applications of geothermal energy for the Idaho Elks Rehabilitation Hospital are outlined. A brief background on the resource and distribution system, is provided; which hospital heating systems should be considered for potential geothermal retrofit is discussed; and technical and economic feasibility are addressed.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. Investigating energy-saving potentials in the cloud.

    PubMed

    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. 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.

  19. Data-mining of potential antitubercular activities from molecular ingredients of traditional Chinese medicines

    PubMed Central

    Jamal, Salma

    2014-01-01

    Background. Traditional Chinese medicine encompasses a well established alternate system of medicine based on a broad range of herbal formulations and is practiced extensively in the region for the treatment of a wide variety of diseases. In recent years, several reports describe in depth studies of the molecular ingredients of traditional Chinese medicines on the biological activities including anti-bacterial activities. The availability of a well-curated dataset of molecular ingredients of traditional Chinese medicines and accurate in-silico cheminformatics models for data mining for antitubercular agents and computational filters to prioritize molecules has prompted us to search for potential hits from these datasets. Results. We used a consensus approach to predict molecules with potential antitubercular activities from a large dataset of molecular ingredients of traditional Chinese medicines available in the public domain. We further prioritized 160 molecules based on five computational filters (SMARTSfilter) so as to avoid potentially undesirable molecules. We further examined the molecules for permeability across Mycobacterial cell wall and for potential activities against non-replicating and drug tolerant Mycobacteria. Additional in-depth literature surveys for the reported antitubercular activities of the molecular ingredients and their sources were considered for drawing support to prioritization. Conclusions. Our analysis suggests that datasets of molecular ingredients of traditional Chinese medicines offer a new opportunity to mine for potential biological activities. In this report, we suggest a proof-of-concept methodology to prioritize molecules for further experimental assays using a variety of computational tools. We also additionally suggest that a subset of prioritized molecules could be used for evaluation for tuberculosis due to their additional effect against non-replicating tuberculosis as well as the additional hepato-protection offered by

  20. Interpolating moving least-squares methods for fitting potential energy surfaces : computing high-density potential energy surface data from low-density ab initio data points.

    SciTech Connect

    Dawes, R.; Thompson, D. L.; Guo, Y.; Wagner, A. F.; Minkoff, M.; Chemistry; Univ. of Missouri-Columbia; Oklahoma State Univ.

    2007-05-11

    A highly accurate and efficient method for molecular global potential energy surface (PES) construction and fitting is demonstrated. An interpolating-moving-least-squares (IMLS)-based method is developed using low-density ab initio Hessian values to compute high-density PES parameters suitable for accurate and efficient PES representation. The method is automated and flexible so that a PES can be optimally generated for classical trajectories, spectroscopy, or other applications. Two important bottlenecks for fitting PESs are addressed. First, high accuracy is obtained using a minimal density of ab initio points, thus overcoming the bottleneck of ab initio point generation faced in applications of modified-Shepard-based methods. Second, high efficiency is also possible (suitable when a huge number of potential energy and gradient evaluations are required during a trajectory calculation). This overcomes the bottleneck in high-order IMLS-based methods, i.e., the high cost/accuracy ratio for potential energy evaluations. The result is a set of hybrid IMLS methods in which high-order IMLS is used with low-density ab initio Hessian data to compute a dense grid of points at which the energy, Hessian, or even high-order IMLS fitting parameters are stored. A series of hybrid methods is then possible as these data can be used for neural network fitting, modified-Shepard interpolation, or approximate IMLS. Results that are indicative of the accuracy, efficiency, and scalability are presented for one-dimensional model potentials as well as for three-dimensional (HCN) and six-dimensional (HOOH) molecular PESs

  1. Ambient-Potential Composite Ewald Method for ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation.

    PubMed

    Giese, Timothy J; York, Darrin M

    2016-06-14

    A new approach for performing Particle Mesh Ewald in ab initio quantum mechanical/molecular mechanical (QM/MM) simulations with extended atomic orbital basis sets is presented. The new approach, the Ambient-Potential Composite Ewald (CEw) method, does not perform the QM/MM interaction with Mulliken charges nor electrostatically fit charges. Instead the nuclei and electron density interact directly with the MM environment, but in a manner that avoids the use of dense Fourier transform grids. By performing the electrostatics with the underlying QM density, the CEw method avoids self-consistent field instabilities that have been encountered with simple charge mapping procedures. Potential of mean force (PMF) profiles of the p-nitrophenyl phosphate dissociation reaction in explicit solvent are computed from PBE0/6-31G* QM/MM molecular dynamics simulations with various electrostatic protocols. The CEw profiles are shown to be stable with respect to real-space Ewald cutoff, whereas the PMFs computed from truncated and switched electrostatics produce artifacts. PBE0/6-311G**, AM1/d-PhoT, and DFTB2 QM/MM simulations are performed to generate two-dimensional PMF profiles of the phosphoryl transesterification reactions with ethoxide and phenoxide leaving groups. The semiempirical models incorrectly produce a concerted ethoxide mechanism, whereas PBE0 correctly produces a stepwise mechanism. The ab initio reaction barriers agree more closely to experiment than the semiempirical models. The failure of Mulliken-charge QM/MM-Ewald is analyzed. PMID:27171914

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. Molecular wave function and effective adiabatic potentials calculated by extended multi-configuration time-dependent Hartree-Fock method

    NASA Astrophysics Data System (ADS)

    Kato, Tsuyoshi; Ide, Yoshihiro; Yamanouchi, Kaoru

    2015-12-01

    We first calculate the ground-state molecular wave function of 1D model H2 molecule by solving the coupled equations of motion formulated in the extended multi-configuration time-dependent Hartree-Fock (MCTDHF) method by the imaginary time propagation. From the comparisons with the results obtained by the Born-Huang (BH) expansion method as well as with the exact wave function, we observe that the memory size required in the extended MCTDHF method is about two orders of magnitude smaller than in the BH expansion method to achieve the same accuracy for the total energy. Second, in order to provide a theoretical means to understand dynamical behavior of the wave function, we propose to define effective adiabatic potential functions and compare them with the conventional adiabatic electronic potentials, although the notion of the adiabatic potentials is not used in the extended MCTDHF approach. From the comparison, we conclude that by calculating the effective potentials we may be able to predict the energy differences among electronic states even for a time-dependent system, e.g., time-dependent excitation energies, which would be difficult to be estimated within the BH expansion approach.

  7. Analytic ab initio-based molecular interaction potential for the BrO⋅H2O complex.

    PubMed

    Hoehn, Ross D; Yeole, Sachin D; Kais, Sabre; Francisco, Joseph S

    2016-05-28

    Radical halogen oxide species play important roles within atmospheric processes, specifically those responsible for the removal of O3. To facilitate future investigations on this family of compounds, RCCSD(T)/aug-cc-pVQZ-level electronic structure calculations were employed to generate individual-molecule optimized geometries, as well as to determine the global minimum energy structure for the BrO⋅H2O complex. This information facilitated the generation of several one-dimensional potential energy surface (PES) scans for the BrO⋅H2O complex. Scans were performed for both the ground state and the first excited state; this inclusion is due to a low-lying first electronic excited-state energy. These rigid-geometry PES scans were used both to generate a novel analytic interaction potential by modifying the existing Thole-type model used for water and to the fitted potential function. This interaction potential features anisotropic atomic polarizabilities facilitating appropriate modeling of the physics regarding the unpaired electron residing within the p-orbitals of the oxygen atom of the bromine oxide radical. The intention of this work is to facilitate future molecular dynamics simulations involving the interaction between the BrO radical and water clusters as a first step in devising possible novel chemistries taking place at the water interface of clouds within the atmosphere. PMID:27250293

  8. Molecular wave function and effective adiabatic potentials calculated by extended multi-configuration time-dependent Hartree-Fock method

    SciTech Connect

    Kato, Tsuyoshi; Ide, Yoshihiro; Yamanouchi, Kaoru

    2015-12-31

    We first calculate the ground-state molecular wave function of 1D model H{sub 2} molecule by solving the coupled equations of motion formulated in the extended multi-configuration time-dependent Hartree-Fock (MCTDHF) method by the imaginary time propagation. From the comparisons with the results obtained by the Born-Huang (BH) expansion method as well as with the exact wave function, we observe that the memory size required in the extended MCTDHF method is about two orders of magnitude smaller than in the BH expansion method to achieve the same accuracy for the total energy. Second, in order to provide a theoretical means to understand dynamical behavior of the wave function, we propose to define effective adiabatic potential functions and compare them with the conventional adiabatic electronic potentials, although the notion of the adiabatic potentials is not used in the extended MCTDHF approach. From the comparison, we conclude that by calculating the effective potentials we may be able to predict the energy differences among electronic states even for a time-dependent system, e.g., time-dependent excitation energies, which would be difficult to be estimated within the BH expansion approach.

  9. Analytic ab initio-based molecular interaction potential for the BrOṡH2O complex

    NASA Astrophysics Data System (ADS)

    Hoehn, Ross D.; Yeole, Sachin D.; Kais, Sabre; Francisco, Joseph S.

    2016-05-01

    Radical halogen oxide species play important roles within atmospheric processes, specifically those responsible for the removal of O3. To facilitate future investigations on this family of compounds, RCCSD(T)/aug-cc-pVQZ-level electronic structure calculations were employed to generate individual-molecule optimized geometries, as well as to determine the global minimum energy structure for the BrOṡH2O complex. This information facilitated the generation of several one-dimensional potential energy surface (PES) scans for the BrOṡH2O complex. Scans were performed for both the ground state and the first excited state; this inclusion is due to a low-lying first electronic excited-state energy. These rigid-geometry PES scans were used both to generate a novel analytic interaction potential by modifying the existing Thole-type model used for water and to the fitted potential function. This interaction potential features anisotropic atomic polarizabilities facilitating appropriate modeling of the physics regarding the unpaired electron residing within the p-orbitals of the oxygen atom of the bromine oxide radical. The intention of this work is to facilitate future molecular dynamics simulations involving the interaction between the BrO radical and water clusters as a first step in devising possible novel chemistries taking place at the water interface of clouds within the atmosphere.

  10. Using Electronic Energy Derivative Information in Automated Potential Energy Surface Construction for Vibrational Calculations.

    PubMed

    Sparta, Manuel; Hansen, Mikkel B; Matito, Eduard; Toffoli, Daniele; Christiansen, Ove

    2010-10-12

    The availability of an accurate representation of the potential energy surface (PES) is an essential prerequisite in an anharmonic vibrational calculation. At the same time, the high dimensionality of the fully coupled PES and the adverse scaling properties with respect to the molecular size make the construction of an accurate PES a computationally demanding task. In the past few years, our group tested and developed a series of tools and techniques aimed at defining computationally efficient, black-box protocols for the construction of PESs for use in vibrational calculations. This includes the definition of an adaptive density-guided approach (ADGA) for the construction of PESs from an automatically generated set of evaluation points. Another separate aspect has been the exploration of the use of derivative information through modified Shepard (MS) interpolation/extrapolation procedures. With this article, we present an assembled machinery where these methods are embedded in an efficient way to provide both a general machinery as well as concrete computational protocols. In this framework we introduce and discuss the accuracy and computational efficiency of two methods, called ADGA[2gx3M] and ADGA[2hx3M], where the ADGA recipe is used (with MS interpolation) to automatically define modest sized grids for up to two-mode couplings, while MS extrapolation based on, respectively, gradients only and gradients and Hessians from the ADGA determined points provides access to sufficiently accurate three-mode couplings. The performance of the resulting potentials is investigated in vibrational coupled cluster (VCC) calculations. Three molecular systems serve as benchmarks: a trisubstituted methane (CHFClBr), methanimine (CH2NH), and oxazole (C3H3NO). Furthermore, methanimine and oxazole are addressed in accurate calculations aiming to reproduce experimental results. PMID:26616778

  11. Semi-infinite jellium: Thermodynamic potential, chemical potential, and surface energy

    NASA Astrophysics Data System (ADS)

    Kostrobij, P. P.; Markovych, B. M.

    2015-08-01

    A general expression for the thermodynamic potential of the model of semi-infinite jellium is obtained. By using this expression, the surface energy for the infinite barrier model is calculated. The behavior of the surface energy and of the chemical potential as functions of the Wigner-Seitz radius and the influence of the Coulomb interaction between electrons on the calculated values is studied. It is shown that taking into account the Coulomb interaction between electrons leads to growth of the surface energy. The surface energy is positive in the entire area of the Wigner-Seitz radius. It is shown that taking into account the Coulomb interaction between electrons leads to a decrease of the chemical potential.

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

    PubMed Central

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

    2015-01-01

    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. PMID:26418190

  13. Exploring the Gradient Paths and Zero Flux Surfaces of Molecular Electrostatic Potential.

    PubMed

    Kumar, Anmol; Gadre, Shridhar R

    2016-04-12

    The gradient vector field of molecular electrostatic potential, ∇V(r), has remained relatively unexplored in molecular quantum mechanics. The present article explores the conceptual as well as practical aspects of this vector field. A three-dimensional atomic partition of molecular space has been achieved on the basis of zero flux surfaces (ZFSs) of ∇V(r). Such ZFSs may completely enclose some of the atoms in the molecule, unlike what is observed in density-based atomic partitioning. The demonstration of this phenomenon is elucidated through typical examples, e.g., N2, CO, H2O, H2CO, OF(•), :CH2, and NH3BF3, where the electronegative atoms or group of atoms (group electronegativity) exhibits a closed ZFS of ∇V(r) around them. The present article determines an explicit reason for this phenomenon and also provides a necessary and sufficient condition for such a closed ZFS of ∇V(r) to exist. It also describes how the potential-based picture of atoms in molecules differs from its electron density-based analogue. This work further illustrates the manifestation of anisotropy in the gradient paths of MESP of some molecular systems, with respect to CO, (•)OH, H2O, and H2CO, and points to its potential in understanding the reactivity patterns of the interacting molecules. PMID:26881455

  14. 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.)

  15. Molecular Mechanism and Potential Targets for Blocking HPV-Induced Lesion Development

    PubMed Central

    Guzmán-Olea, E.; Bermúdez-Morales, V. H.; Peralta-Zaragoza, O.; Torres-Poveda, K.; Madrid-Marina, V.

    2012-01-01

    Persistent infection with high-risk HPV is the etiologic agent associated with the development of cervical cancer (CC) development. However, environmental, social, epidemiological, genetic, and host factors may have a joint influence on the risk of disease progression. Cervical lesions caused by HPV infection can be removed naturally by the host immune response and only a small percentage may progress to cancer; thus, the immune response is essential for the control of precursor lesions and CC. We present a review of recent research on the molecular mechanisms that allow HPV-infected cells to evade immune surveillance and potential targets of molecular therapy to inhibit tumor immune escape. PMID:22220169

  16. Molecular Mechanism and Potential Targets for Blocking HPV-Induced Lesion Development.

    PubMed

    Guzmán-Olea, E; Bermúdez-Morales, V H; Peralta-Zaragoza, O; Torres-Poveda, K; Madrid-Marina, V

    2012-01-01

    Persistent infection with high-risk HPV is the etiologic agent associated with the development of cervical cancer (CC) development. However, environmental, social, epidemiological, genetic, and host factors may have a joint influence on the risk of disease progression. Cervical lesions caused by HPV infection can be removed naturally by the host immune response and only a small percentage may progress to cancer; thus, the immune response is essential for the control of precursor lesions and CC. We present a review of recent research on the molecular mechanisms that allow HPV-infected cells to evade immune surveillance and potential targets of molecular therapy to inhibit tumor immune escape. PMID:22220169

  17. 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.

  18. 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}.

  19. Molecular Dynamics and Energy Minimization Based on Embedded Atom Method

    Energy Science and Technology Software Center (ESTSC)

    1995-03-01

    This program performs atomic scale computer simulations of the structure and dynamics of metallic system using energetices based on the Embedded Atom Method. The program performs two types of calculations. First, it performs local energy minimization of all atomic positions to determine ground state and saddle point energies and structures. Second, it performs molecular dynamics simulations to determine thermodynamics or miscroscopic dynamics of the system. In both cases, various constraints can be applied to themore » system. The volume of the system can be varied automatically to achieve any desired external pressure. The temperature in molecular dynamics simulations can be controlled by a variety of methods. Further, the temperature control can be applied either to the entire system or just a subset of the atoms that would act as a thermal source/sink. The motion of one or more of the atoms can be constrained to either simulate the effects of bulk boundary conditions or to facilitate the determination of saddle point configurations. The simulations are performed with periodic boundary conditions.« less

  20. 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.

  1. 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. PMID:25973916

  2. Binding energies of five molecular pincers calculated by explicit and implicit solvent models.

    PubMed

    Kessler, Jiří; Jakubek, Milan; Dolenský, Bohumil; Bouř, Petr

    2012-11-01

    Molecular pincers or tweezers are designed to hold and release the target molecule. Potential applications involve drug distribution in medicine, environment technologies, or microindustrial techniques. Typically, the binding is dominated by van der Waals forces. Modeling of such complexes can significantly enhance their design; yet obtaining accurate complexation energies by theory is difficult. In this study, density functional theory (DFT) computations combined with dielectric continuum solvent model are compared with the potential of mean force approach using umbrella sampling and the weighted histogram analysis method (WHAM) with molecular dynamics (MD) simulations. For DFT, functional and basis set effects are discussed. The computed results are compared to experimental data based on NMR spectroscopic measurements of five synthesized tweezers based on the Tröger's basis. Whereas the DFT computations correctly provided the observed trends in complex stability, they failed to produce realistic magnitudes of complexation energies. Typically, the binding was overestimated by DFT if compared to experiment. The simpler semiempirical PM6-DH2X scheme proposed lately yielded better magnitudes of the binding energies than DFT but not the right order. The MD-WHAM simulations provided the most realistic Gibbs binding energies, although the approximate MD force fields were not able to reproduce completely the ordering of relative stabilities of model complexes found by NMR. Yet the modeling provides interesting insight into the complex geometry and flexibility and appears as a useful tool in the tweezers' design. PMID:22782845

  3. Split kinetic energy method for quantum systems with competing potentials

    SciTech Connect

    Mineo, H.; Chao, Sheng D.

    2012-09-15

    For quantum systems with competing potentials, the conventional perturbation theory often yields an asymptotic series and the subsequent numerical outcome becomes uncertain. To tackle such a kind of problems, we develop a general solution scheme based on a new energy dissection idea. Instead of dividing the potential energy into 'unperturbed' and 'perturbed' terms, a partition of the kinetic energy is performed. By distributing the kinetic energy term in part into each individual potential, the Hamiltonian can be expressed as the sum of the subsystem Hamiltonians with respective competing potentials. The total wavefunction is expanded by using a linear combination of the basis sets of respective subsystem Hamiltonians. We first illustrate the solution procedure using a simple system consisting of a particle under the action of double {delta}-function potentials. Next, this method is applied to the prototype systems of a charged harmonic oscillator in strong magnetic field and the hydrogen molecule ion. Compared with the usual perturbation approach, this new scheme converges much faster to the exact solutions for both eigenvalues and eigenfunctions. When properly extended, this new solution scheme can be very useful for dealing with strongly coupling quantum systems. - Highlights: Black-Right-Pointing-Pointer A new basis set expansion method is proposed. Black-Right-Pointing-Pointer Split kinetic energy method is proposed to solve quantum eigenvalue problems. Black-Right-Pointing-Pointer Significant improvement has been obtained in converging to exact results. Black-Right-Pointing-Pointer Extension of such methods is promising and discussed.

  4. 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.

  5. 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.

  6. Optimizing potential energy functions for maximal intrinsic hyperpolarizability

    SciTech Connect

    Zhou Juefei; Szafruga, Urszula B.; Kuzyk, Mark G.; Watkins, David S.

    2007-11-15

    We use numerical optimization to study the properties of (1) the class of one-dimensional potential energy functions and (2) systems of point nuclei in two dimensions that yield the largest intrinsic hyperpolarizabilities, which we find to be within 30% of the fundamental limit. In all cases, we use a one-electron model. It is found that a broad range of optimized potentials, each of very different character, yield the same intrinsic hyperpolarizability ceiling of 0.709. Furthermore, all optimized potential energy functions share common features such as (1) the value of the normalized transition dipole moment to the dominant state, which forces the hyperpolarizability to be dominated by only two excited states and (2) the energy ratio between the two dominant states. All optimized potentials are found to obey the three-level ansatz to within about 1%. Many of these potential energy functions may be implementable in multiple quantum well structures. The subset of potentials with undulations reaffirm that modulation of conjugation may be an approach for making better organic molecules, though there appear to be many others. Additionally, our results suggest that one-dimensional molecules may have larger diagonal intrinsic hyperpolarizability {beta}{sub xxx}{sup int} than higher-dimensional systems.

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

    DOE PAGESBeta

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

    2015-06-04

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

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

    SciTech Connect

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

    2015-06-04

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

  9. Averaged Solvent Embedding Potential Parameters for Multiscale Modeling of Molecular Properties.

    PubMed

    Beerepoot, Maarten T P; Steindal, Arnfinn Hykkerud; List, Nanna Holmgaard; Kongsted, Jacob; Olsen, Jógvan Magnus Haugaard

    2016-04-12

    We derive and validate averaged solvent parameters for embedding potentials to be used in polarizable embedding quantum mechanics/molecular mechanics (QM/MM) molecular property calculations of solutes in organic solvents. The parameters are solvent-specific atom-centered partial charges and isotropic polarizabilities averaged over a large number of geometries of solvent molecules. The use of averaged parameters reduces the computational cost to obtain the embedding potential, which can otherwise be a rate-limiting step in calculations involving large environments. The parameters are evaluated by analyzing the quality of the resulting molecular electrostatic potentials with respect to full QM potentials. We show that a combination of geometry-specific parameters for solvent molecules close to the QM region and averaged parameters for solvent molecules further away allows for efficient polarizable embedding multiscale modeling without compromising the accuracy. The results are promising for the development of general embedding parameters for biomolecules, where the reduction in computational cost can be considerable. PMID:26938368

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

    NASA Technical Reports Server (NTRS)

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

    1995-01-01

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

  11. Molecular docking studies of (X-methylphenyl)-5-nitro-6-amino-3-pyridinecarboxmide (X=2,3,4,5,6) as potential inhibitors for Alzheimer's disease

    NASA Astrophysics Data System (ADS)

    Premkumar, S.; Asath, R. Mohamed; Rekha, T. N.; Jawahar, A.; Mathavan, T.; Benial, A. Milton Franklin

    2016-05-01

    An insilico and density functional theory (DFT) calculations were carried out for (X-methylphenyl)-5-nitro-6-amino-3-pyridinecarboxmide (X-MPNAPC),{X=2,3,4,5,6} to evaluate the potential inhibitors for Alzheimer's disease. The molecular structure of 2-MPNAPC, 3-MPNAPC, 4-MPNAPC, 5-MPNAPC and 6-MPNAPC molecules was optimized by the DFT/B3LYP method with cc-pVTZ basis set using the Gaussian 09 program. The inhibitory nature of the molecules against enzyme acetylcholinesterase (AChE) catalyzes was evaluated by molecular docking studies. The molecular docking parameters such as binding energy, inhibition constant and intermolecular energy were calculated by the AutoDock 4.0 software. The higher binding energy, intermolecular energy and lower inhibition constant values suggested that the 2-MPNAPC molecule has higher inhibitory nature against the AChE catalyzes, which confirm that the 2-MPNAPC molecule is a potential inhibitor for the Alzheimer's disease. The molecular reactivity was also studied by the frontier molecular orbitals analysis.

  12. Tersoff potential with improved accuracy for simulating graphene in molecular dynamics environment

    NASA Astrophysics Data System (ADS)

    Rajasekaran, G.; Kumar, Rajesh; Parashar, Avinash

    2016-03-01

    Graphene is an elementary unit for various carbon based nanostructures. The recent technological developments have made it possible to manufacture hybrid and sandwich structures with graphene. In order to model these nanostructures in atomistic scale, a compatible interatomic potential is required to successfully model these nanostructures. In this article, an interatomic potential with modified cut-off function for Tersoff potential was proposed to avoid overestimation and also to predict the realistic mechanical behavior of single sheet of graphene. In order to validate the modified form of cut-off function for Tersoff potential, simulations were performed with different set of temperatures and strain rates, and results were made to compare with available experimental data and molecular dynamics simulation results obtained with the help of other empirical interatomic potentials.

  13. Molecular interaction of 2-mercaptobenzimidazole with catalase reveals a potentially toxic mechanism of the inhibitor.

    PubMed

    Teng, Yue; Zou, Luyi; Huang, Ming; Zong, Wansong

    2014-12-01

    2-Mercaptobenzimidazole (MBI) is widely utilized as a corrosion inhibitor, copper-plating brightener and rubber accelerator. The residue of MBI in the environment possesses a potential risk to human health. In this work, the toxic interaction of MBI with the important antioxidant enzyme catalase (CAT) was investigated using spectroscopic and molecular docking methods under physiological conditions. MBI can spontaneously bind with CAT with one binding site through hydrogen bonds and van der Waals forces to form MBI-CAT complex. The molecular docking study revealed that MBI bound into the CAT interface of chains B and C, which led to some conformational and microenvironmental changes of CAT and further resulted in the inhibition of CAT activity. This present study provides direct evidence at a molecular level to show that exposure to MBI could induce changes in the structure and function of the enzyme CAT. PMID:25463673

  14. Molecular Targets Related to Inflammation and Insulin Resistance and Potential Interventions

    PubMed Central

    Hirabara, Sandro M.; Gorjão, Renata; Vinolo, Marco A.; Rodrigues, Alice C.; Nachbar, Renato T.; Curi, Rui

    2012-01-01

    Inflammation and insulin resistance are common in several chronic diseases, such as obesity, type 2 diabetes mellitus, metabolic syndrome, cancer, and cardiovascular diseases. Various studies show a relationship between these two factors, although the mechanisms involved are not completely understood yet. Here, we discuss the molecular basis of insulin resistance and inflammation and the molecular aspects on inflammatory pathways interfering in insulin action. Moreover, we explore interventions based on molecular targets for preventing or treating correlated disorders, advances for a better characterization, and understanding of the mechanisms and mediators involved in the different inflammatory and insulin resistance conditions. Finally, we address biotechnological studies for the development of new potential therapies and interventions. PMID:23049242

  15. Warm Body Temperature Facilitates Energy Efficient Cortical Action Potentials

    PubMed Central

    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. PMID:22511855

  16. 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%.

  17. 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. PMID:23019353

  18. 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

  19. 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.

  20. 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.

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

    NASA Astrophysics Data System (ADS)

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

    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.

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

    NASA Astrophysics Data System (ADS)

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

    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.

  3. Glass Formation of n-Butanol: Coarse-grained Molecular Dynamics Simulations Using Gay-Berne Potential Model

    NASA Astrophysics Data System (ADS)

    Xie, Gui-long; Zhang, Yong-hong; Huang, Shi-ping

    2012-04-01

    Using coarse-grained molecular dynamics simulations based on Gay-Berne potential model, we have simulated the cooling process of liquid n-butanol. A new set of GB parameters are obtained by fitting the results of density functional theory calculations. The simulations are carried out in the range of 290-50 K with temperature decrements of 10 K. The cooling characteristics are determined on the basis of the variations of the density, the potential energy and orientational order parameter with temperature, whose slopes all show discontinuity. Both the radial distribution function curves and the second-rank orientational correlation function curves exhibit splitting in the second peak. Using the discontinuous change of these thermodynamic and structure properties, we obtain the glass transition at an estimate of temperature Tg=120±10 K, which is in good agreement with experimental results 110±1 K.

  4. 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. PMID:18345872

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

    NASA Astrophysics Data System (ADS)

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

    2008-03-01

    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 Carathéodory's relation to derive in a rigorous manner the proposed parametrization of the IRC path. Since this Carathéodory'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.

  6. A molecular H2 potential for heterogeneous simulations including polarization and many-body van der Waals interactions.

    PubMed

    McLaughlin, Keith; Cioce, Christian R; Belof, Jonathan L; Space, Brian; Space, Brian B

    2012-05-21

    A highly accurate aniostropic intermolecular potential for diatomic hydrogen has been developed that is transferable for molecular modeling in heterogeneous systems. The potential surface is designed to be efficacious in modeling mixed sorbates in metal-organic materials that include sorption interactions with charged interfaces and open metal sites. The potential parameters are compatible for mixed simulations but still maintain high accuracy while deriving dispersion parameters from a proven polarizability model. The potential includes essential physical interactions including: short-range repulsions, dispersion, and permanent and induced electrostatics. Many-body polarization is introduced via a point-atomic polarizability model that is also extended to account for many-body van der Waals interactions in a consistent fashion. Permanent electrostatics are incorporated using point partial charges on atomic sites. However, contrary to expectation, the best potentials are obtained by permitting the charges to take on values that do not reproduce the first non-vanishing moment of the electrostatic potential surface, i.e., the quadrupole moment. Potential parameters are fit to match ab initio energies for a representative range of dimer geometries. The resulting potential is shown to be highly effective by comparing to electronic structure calculations for a thermal distribution of trimer geometries, and by reproducing experimental bulk pressure-density isotherms. The surface is shown to be superior to other similarly portable potential choices even in tests on homogeneous systems without strong polarizing fields. The present streamlined approach to developing such potentials allows for a simple adaptation to other molecules amenable to investigation by high-level electronic structure methods. PMID:22612090

  7. Potential structural material problems in a hydrogen energy system

    NASA Technical Reports Server (NTRS)

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

    1976-01-01

    Potential structural material problems that may be encountered in the three components of a hydrogen energy system - production, transmission/storage, and utilization - have been 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. An awareness of probable shortages of strategic materials has been maintained in these suggested programs.

  8. 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.

  9. 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.

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

    NASA Astrophysics Data System (ADS)

    Zeng, Xiancheng; Hu, Hao; Hu, Xiangqian; Yang, Weitao

    2009-04-01

    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.

  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. Investigation of torsional potentials, molecular structure, vibrational properties, molecular characteristics and NBO analysis of some bipyridines using experimental and theoretical tools

    NASA Astrophysics Data System (ADS)

    Prashanth, J.; Reddy, B. Venkatram; Rao, G. Ramana

    2016-08-01

    The Fourier Transform Infrared (FTIR) and Fourier Transform Raman (FT-Raman) spectra of 2,2‧-bipyridine (2BPE); 4,4‧-bipyridine (4BPE); and 2,4‧-bipyridine (24BPE) were measured in the range 4000-450 cm-1 and 4000-50 cm-1, respectively. Torsional potentials were evaluated at various angles of rotation around the C-C inter-ring bond for the three molecules in order to arrive at the molecular conformation of lowest energy. This conformation was further optimized to get ground state geometry. Vibrational frequencies along with infrared and Raman intensities were computed. In the above calculations, DFT employing B3LYP functional with 6311++G(d,p) basis set was used. The rms error between observed and calculated frequencies was 10.0, 10.9 and 10.2 cm-1 for 2BPE, 4BPE and 24BPE, respectively. A 54-parameter modified valence force field was derived by solving inverse vibrational problem using Wilson's GF matrix method. The force constants were refined using 117 experimental frequencies of the three molecules in overlay least-squares technique. The average error between observed and computed frequencies was 12.44 cm-1. PED and eigen vectors calculated in the process were used to make unambiguous vibrational assignments of all the fundamental vibrations. The values of dipole moment, polarizability and hyperpolarizability were computed to determine the NLO behaviour of these molecules. The HOMO and LUMO energies, thermodynamic parameters and molecular electrostatic surface potentials (MESP) were also evaluated. Stability of the molecules arising from hyper conjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis.

  13. Synthesis of Optical Molecular Probes for electric potential across a cell membrane

    NASA Astrophysics Data System (ADS)

    Lamichhane, Roshan

    Optical Imaging of neuronal activities is an attractive method, but the two widely used optical imaging methods based on Fluorescence Resonance Transfer (FRET) and electrochromism have some deficiencies that Photo Induced Electron Transfer (PeT) method has eliminated. In the paper we talk about the synthesis of optical molecular probes that rely on PeT mechanism, and which could possibly be used to measure the transmembrane potential across the neuronal cell membranes.

  14. Marine Low Molecular Weight Natural Products as Potential Cancer Preventive Compounds

    PubMed Central

    Stonik, Valentin A.; Fedorov, Sergey N.

    2014-01-01

    Due to taxonomic positions and special living environments, marine organisms produce secondary metabolites that possess unique structures and biological activities. This review is devoted to recently isolated and/or earlier described marine compounds with potential or established cancer preventive activities, their biological sources, molecular mechanisms of their action, and their associations with human health and nutrition. The review covers literature published in 2003–2013 years and focuses on findings of the last 2 years. PMID:24473167

  15. Temperature dependent effective potential method for accurate free energy calculations of solids

    NASA Astrophysics Data System (ADS)

    Hellman, Olle; Steneteg, Peter; Abrikosov, I. A.; Simak, S. I.

    2013-03-01

    We have developed a thorough and accurate method of determining anharmonic free energies, the temperature dependent effective potential technique (TDEP). It is based on ab initio molecular dynamics followed by a mapping onto a model Hamiltonian that describes the lattice dynamics. The formalism and the numerical aspects of the technique are described in detail. A number of practical examples are given, and results are presented, which confirm the usefulness of TDEP within ab initio and classical molecular dynamics frameworks. In particular, we examine from first principles the behavior of force constants upon the dynamical stabilization of the body centered phase of Zr, and show that they become more localized. We also calculate the phase diagram for 4He modeled with the Aziz potential and obtain results which are in favorable agreement both with respect to experiment and established techniques.

  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. Coarse Point Charge Models For Proteins From Smoothed Molecular Electrostatic Potentials.

    PubMed

    Leherte, Laurence; Vercauteren, Daniel P

    2009-12-01

    To generate coarse electrostatic models of proteins, we developed an original approach to hierarchically locate maxima and minima in smoothed molecular electrostatic potentials. A charge-fitting program was used to assign charges to the so-obtained reduced representations. Templates are defined to easily generate coarse point charge models for protein structures, in the particular cases of the Amber99 and Gromos43A1 force fields. Applications to four small peptides and to the ion channel KcsA are presented. Electrostatic potential values generated by the reduced models are compared with the corresponding values obtained using the original sets of atomic charges. PMID:26602509

  18. Semiclassical vibration-rotation transition probabilities for motion in molecular state averaged potentials.

    NASA Technical Reports Server (NTRS)

    Stallcop, J. R.

    1971-01-01

    Collision-induced vibration-rotation transition probabilities are calculated from a semiclassical three-dimensional model, in which the collision trajectory is determined by the classical motion in the interaction potential that is averaged over the molecular rotational state, and compared with those for which the motion is governed by a spherically averaged potential. For molecules that are in highly excited rotational states, thus dominating the vibrational relaxation rate at high temperature, it is found that the transition probability for rotational state averaging is smaller than that for spherical averaging. For typical collisions, the transition cross section is decreased by a factor of about 1.5 to 2.

  19. Exploring the free energy surface using ab initio molecular dynamics

    DOE PAGESBeta

    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

  20. 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.

  1. 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/.

  2. Energy savings potential in air conditioners and chiller systems

    DOE PAGESBeta

    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

  3. Molecular dynamics simulation of bipartite bimetallic clusters under low-energy argon ion bombardment

    NASA Astrophysics Data System (ADS)

    Shirokorad, D. V.; Kornich, G. V.; Buga, S. G.

    2016-02-01

    The evolution of bipartite bimetallic atomic clusters within 5 ps under bombardment with monoenergetic argon ions at the initial energy ranging from 1 eV to 1.4 keV has been simulated by the classical molecular dynamics method with a target obtained from Ni‒Al and Cu‒Au clusters consisting of 78 and 390 atoms, equally divided between the corresponding monometallic parts, the simulated pairs of which have different heats of intermixing. The changes in the potential energy and temperature, the sputtering yields, and the intensity of the ion-stimulated movement of atoms at the interface of the monometallic parts of clusters of both sizes have been determined as functions of the energy of the bombardment.

  4. Molecular dynamics study of electrostatic potential along lipid bilayer with gramicidin A

    NASA Astrophysics Data System (ADS)

    Saito, Hiroaki; Nishimura, Megumi; Takagi, Hiroyuki; Miyakawa, Takeshi; Kawaguchi, Kazutomo; Nagao, Hidemi

    2013-02-01

    The structure and electrostatic potential profile of the DMPC lipid bilayers with a gramicidin A (GA) were studied by molecular dynamics (MD) simulation. The MD simulation reproduced the effect of GA on the membrane structure; the area per lipid decreases and membrane thickness increases, and the observed membrane structures correspond to the experimental data. The polar headgroup of lipid was found to orient toward the membrane normal as the lipid approaches the GA. The observed electrostatic potential map showed that the electrostatic potential around the region of GA gate was lower than the others at the same level of the membrane normal and the values of electrostatic potential in the pore region of GA were negative. These results indicate that a cation in the aqueous region of membrane can be electrostatically led to the GA entrance and penetrate the GA channel following the gradient of ion concentration.

  5. Counterpoise-corrected interaction energy analysis based on the fragment molecular orbital scheme

    NASA Astrophysics Data System (ADS)

    Okiyama, Yoshio; Fukuzawa, Kaori; Yamada, Haruka; Mochizuki, Yuji; Nakano, Tatsuya; Tanaka, Shigenori

    2011-06-01

    Basis set superposition error (BSSE) correction with counterpoise (CP) procedure under the environmental electrostatic potential is newly introduced to interfragment interaction energy (IFIE), which is important for interaction analysis in the fragment molecular orbital method. The CP correction for IFIE is applied to a stacked dimer of base pair and a protein-ligand complex of estrogen receptor and 17β-estradiol with scaled third-order Møller-Plesset perturbation theory. The BSSEs amount to about quarter of IFIE for hydrogen-bonding and electrostatic interactions and half or even more for dispersion interactions. Estimation of IFIE with the CP correction is therefore preferred for the quantitative discussion.

  6. Photoinduced Charge and Energy Transfer Processes in Molecular Aggregates

    SciTech Connect

    John F. Endicott

    2009-10-20

    This project involved the experimental probing of the electronic excited states generated by photoinduced (center-to-center) electron and energy transfer processes in several classes of transition metal donor/acceptor (D/A) complexes. Some of the general properties inferred from these studies should be useful in the design of new systems for energy conversion applications. Pursuit of the project goals has involved the determination of electron transfer efficiencies and the detailed study of variations in the electronic spectra of D/A complexes. This has resulted in the study of some very fundamental issues of photoinduced charge transfer and the identification of some of the constraints on its efficiency. The experimental studies of the competition between the degradative non-radiative unimolecular relaxation of transition metal excited states and their transfer of charge from these excited states to external acceptors have involved a range of techniques such as transient decay kinetics, photoacoustic calorimetry and transient or stationary state spectroscopy. The substrates synthesized for these studies were selected to provide model systems, or series of model systems to probe the validity of models of electronic excited states and their reactivity. The work during the last few years has focused largely, but not exclusively, on the use of emission spectral band shapes to probe the properties of charge transfer (CT) excited states. Bandshape variations are one of the very few approaches for systematically probing electronic excited states and good band shape resolution is necessary in order to gain information about the structural variations that correlate with excited state reactivity. Differences in molecular structure correlate with differences in chemical reactivity, and the variations in emission bandshapes are well known to relate to variations in the molecular structural differences between the excited and ground electronic states. However, it is has been

  7. 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.

  8. Regularizing the molecular potential in electronic structure calculations. I. SCF methods

    SciTech Connect

    Bischoff, Florian A.

    2014-11-14

    We present a method to remove the singular nuclear potential in a molecule and replace it with a regularized potential that is more amenable to be represented numerically. The singular nuclear potential is canceled by the similarity-transformed kinetic energy operator giving rise to an effective nuclear potential that contains derivative operators acting on the wave function. The method is fully equivalent to the non-similarity-transformed version. We give numerical examples within the framework of multi-resolution analysis for medium-sized molecules.

  9. 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)

  10. High energy scattering of Dirac particles on smooth potentials

    NASA Astrophysics Data System (ADS)

    Han, Nguyen Suan; Dung, Le Anh; Xuan, Nguyen Nhu; Thang, Vu Toan

    2016-08-01

    The derivation of the Glauber type representation for the high energy scattering amplitude of particles of spin 1/2 is given within the framework of the Dirac equation in the Foldy-Wouthuysen (FW) representation and two-component formalism. The differential cross-sections on the Yukawa and Gaussian potentials are also considered and discussed.

  11. 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…

  12. 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

  13. Energy expressions for Kohn-Sham potentials and their relation to the Slater-Janak theorem.

    PubMed

    Elkind, Pavel D; Staroverov, Viktor N

    2012-03-28

    Direct approximation of exchange-correlation potentials is a promising approach to accurate prediction of molecular response properties. However, little is known about ways of obtaining total energies from model potentials other than by using the Levy-Perdew virial relation. We introduce and explore several alternative formulas which arise as line integrals of potentials taken along density scaling and aufbau-filling paths, and which are not limited to the exchange term. The relaxed-orbital variant of the aufbau-path energy expression is shown to be closely related to the Slater-Janak theorem. Although the Levy-Perdew relation generally yields reasonable energies for all model exchange potentials, the relaxed-orbital aufbau path gives better results for those potentials that predict accurate highest-occupied orbital eigenvalues, such as the potential of Räsänen, Pittalis, and Proetto [J. Chem. Phys. 132, 044112 (2010)]. The ideas presented in this work may guide the development of new types of density-functional approximations for exchange and correlation. PMID:22462843

  14. Generalized gradient approximation exchange energy functional with correct asymptotic behavior of the corresponding potential

    SciTech Connect

    Carmona-Espíndola, Javier; Gázquez, José L.; Vela, Alberto; Trickey, S. B.

    2015-02-07

    A new non-empirical exchange energy functional of the generalized gradient approximation (GGA) type, which gives an exchange potential with the correct asymptotic behavior, is developed and explored. In combination with the Perdew-Burke-Ernzerhof (PBE) correlation energy functional, the new CAP-PBE (CAP stands for correct asymptotic potential) exchange-correlation functional gives heats of formation, ionization potentials, electron affinities, proton affinities, binding energies of weakly interacting systems, barrier heights for hydrogen and non-hydrogen transfer reactions, bond distances, and harmonic frequencies on standard test sets that are fully competitive with those obtained from other GGA-type functionals that do not have the correct asymptotic exchange potential behavior. Distinct from them, the new functional provides important improvements in quantities dependent upon response functions, e.g., static and dynamic polarizabilities and hyperpolarizabilities. CAP combined with the Lee-Yang-Parr correlation functional gives roughly equivalent results. Consideration of the computed dynamical polarizabilities in the context of the broad spectrum of other properties considered tips the balance to the non-empirical CAP-PBE combination. Intriguingly, these improvements arise primarily from improvements in the highest occupied and lowest unoccupied molecular orbitals, and not from shifts in the associated eigenvalues. Those eigenvalues do not change dramatically with respect to eigenvalues from other GGA-type functionals that do not provide the correct asymptotic behavior of the potential. Unexpected behavior of the potential at intermediate distances from the nucleus explains this unexpected result and indicates a clear route for improvement.

  15. Calculating the free energy of nearly jammed hard-particle packings using molecular dynamics

    NASA Astrophysics Data System (ADS)

    Donev, Aleksandar; Stillinger, Frank H.; Torquato, Salvatore

    2007-07-01

    We present a new event-driven molecular dynamics (MD) algorithm for measuring the free energy of nearly jammed packings of spherical and non-spherical hard particles. This Bounding Cell Molecular Dynamics (BCMD) algorithm exactly calculates the free-energy of a single-occupancy cell (SOC) model in which each particle is restricted to a neighborhood of its initial position using a hard-wall bounding cell. Our MD algorithm generalizes previous ones in the literature by enabling us to study non-spherical particles as well as to measure the free-energy change during continuous irreversible transformations. Moreover, we make connections to the well-studied problem of computing the volume of convex bodies in high dimensions using random walks. We test and verify the numerical accuracy of the method by comparing against rigorous asymptotic results for the free energy of jammed and isostatic disordered packings of both hard spheres and ellipsoids, for which the free energy can be calculated directly as the volume of a high-dimensional simplex. We also compare our results to previously published Monte Carlo results for hard-sphere crystals near melting and jamming and find excellent agreement. We have successfully used the BCMD algorithm to determine the configurational and free-volume contributions to the free energy of glassy states of binary hard disks [A. Donev, F.H. Stillinger, S. Torquato, Do binary hard disks exhibit an ideal glass transition? Phys. Rev. Lett. 96 (22) (2006) 225502]. The algorithm can also be used to determine phases with locally- or globally-minimal free energy, to calculate the free-energy cost of point and extended crystal defects, or to calculate the elastic moduli of glassy or crystalline solids, among other potential applications.

  16. A new ab initio potential energy surface for the Ne-H 2 interaction

    NASA Astrophysics Data System (ADS)

    Lique, François

    2009-03-01

    A new accurate three-dimensional potential energy surface for the Ne-H 2 system, which explicitly takes into account the r-dependence of the H 2 vibration, was determined from ab initio calculations. It was obtained with the single and double excitation coupled-cluster method with noniterative perturbational treatment of triple excitation [CCSD(T)]. Calculations was been performed using the augmented correlation-consistent polarized quintuple zeta basis set (aug-cc-pV5Z) for the three atoms. We checked the accuracy of the present ab initio calculations. We have determined, using the new Ne-H 2 potential energy surface, differential cross-sections for the rotational excitation of the H 2 and D 2 molecules in collision with Ne and we have compared them with experimental results of Faubel et al. [M. Faubel, F.A. Gianturco, F. Ragnetti, L.Y. Rusin, F. Sondermann, U. Tappe, J.P. Toennies, J. Chem. Phys. 101 (1994) 8800]. The overall agreement confirms that the new potential energy surface can be used for the simulation of molecular collisions and/or molecular spectroscopy of the van der Waals complex Ne-H 2.

  17. Optimised cut-off function for Tersoff-like potentials for a BN nanosheet: a molecular dynamics study.

    PubMed

    Kumar, Rajesh; Rajasekaran, G; Parashar, Avinash

    2016-02-26

    In this article, molecular dynamics based simulations were carried out to study the tensile behaviour of boron nitride nanosheets (BNNSs). Four different sets of Tersoff potential parameters were used in the simulations for estimating the interatomic interactions between boron and nitrogen atoms. Modifications were incorporated in the Tersoff cut-off function to improve the accuracy of results with respect to fracture stress, fracture strain and Young's modulus. In this study, the original cut-off function was optimised in such a way that small and large cut-off distances were made equal, and hence a single cut-off distance was used with all sets of Tersoff potential parameters. The single value of cut-off distance for the Tersoff potential was chosen after analysing the potential energy and bond forces experienced by boron and nitrogen atoms subjected to bond stretching. The simulations performed with the optimised cut-off function help in identifying the Tersoff potential parameters that reproduce the experimentally evaluated mechanical behaviour of BNNSs. PMID:26820110

  18. 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.

  19. 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.

  20. Global interior eddy available potential energy diagnosed from Argo floats

    NASA Astrophysics Data System (ADS)

    Roullet, Guillaume; Capet, Xavier; Maze, Guillaume

    2014-03-01

    By combining all Argo profiles for the period 2002 to present, a cumulative density function is constructed on a 3-D grid of the global ocean. This function quantifies the statistics of isopycnals: time-averaged density, root-mean square of isopycnal displacement, and eddy available potential energy (EAPE). EAPE is the analogue of the eddy kinetic energy, but for the potential energy reservoir. Because it is essentially tied to the spatial structure and magnitude of mesoscale activity, EAPE is an important quantity that should be useful to evaluate eddy resolving/permitting model turbulence and circulation. Among other striking features are the turbulent behavior of Pacific and southern Atlantic Tsuchiya jets and subsurface EAPE maxima in some parts of the ocean, particularly in the Southern Ocean.

  1. Heterobarrier for converting hot-phonon energy to electric potential

    NASA Astrophysics Data System (ADS)

    Shin, Seungha; Melnick, Corey; Kaviany, Massoud

    2013-02-01

    We show that hot phonons emitted in energy conversion or resistive processes can be converted to electric potential in heterobarrier structures. Using phonon and electron interaction kinetics and self-consistent ensemble Monte Carlo, we find the favorable conditions for unassisted absorption of hot phonons and design graded heterobarriers for their direct conversion into electric energy. Tandem barriers with nearly optical-phonon height allow for substantial potential gain without current loss. We find that 19% of hot phonons can be harvested with an optimized GaAs/AlxGa1-xAs barrier structure over a range of current and electron densities, thus enhancing the overall energy conversion efficiency and reducing waste heat.

  2. pH-Dependent Reduction Potentials and Proton-Coupled Electron Transfer Mechanisms in Hydrogen-Producing Nickel Molecular Electrocatalysts

    SciTech Connect

    Horvath, Samantha; Fernandez, Laura; Appel, Aaron M.; Hammes-Schiffer, Sharon

    2013-04-01

    The nickel-based Ph Bz 2 2 P N electrocatalysts, which are comprised of a nickel atom and two 1,5-dibenzyl-3,7-diphenyl-1,5-diaza-3,7-diphosphacyclooctane ligands, have been shown to effectively catalyze H2 production in acetonitrile. Recent electrochemical experiments revealed a linear dependence of the NiII/I reduction potential on pH, suggesting a proton-coupled electron transfer (PCET) reaction. In the proposed mechanism, the catalytic cycle begins with a PCET process involving electrochemical electron transfer to the nickel center and intermolecular proton transfer from an acid to the pendant amine ligand. This paper presents quantum mechanical calculations of this PCET process to examine the thermodynamics of the sequential mechanisms, in which either the electron or the proton transfers first (ET–PT and PT–ET, respectively), and the concerted mechanism (EPT). The favored mechanism depends on a balance among many factors, including the acid strength, association free energy for the acid–catalyst complex, PT free energy barrier, and ET reduction potential. The ET reduction potential is less negative after PT, favoring the PT–ET mechanism, and the association free energy is less positive after reduction, favoring the ET–PT mechanism. The calculations, along with analysis of the experimental data, indicate that the sequential ET–PT mechanism is favored for weak acids because of the substantial decrease in the association free energy after reduction. For strong acids, however, the PT–ET mechanism may be favored because the association free energy is somewhat smaller and PT is more thermodynamically favorable. The concerted mechanism could also occur, particularly for intermediate acid strengths. In the context of the entire catalytic cycle for H2 production, the initial PCET process involving intermolecular PT has a more negative reduction potential than the subsequent PCET process involving intramolecular PT. As a result, the second PCET should

  3. Predicting Low Energy Dopant Implant Profiles in Semiconductors using Molecular Dynamics

    SciTech Connect

    Beardmore, K.M.; Gronbech-Jensen, N.

    1999-05-02

    The authors present a highly efficient molecular dynamics scheme for calculating dopant density profiles in group-IV alloy, and III-V zinc blende structure materials. Their scheme incorporates several necessary methods for reducing computational overhead, plus a rare event algorithm to give statistical accuracy over several orders of magnitude change in the dopant concentration. The code uses a molecular dynamics (MD) model to describe ion-target interactions. Atomic interactions are described by a combination of 'many-body' and pair specific screened Coulomb potentials. Accumulative damage is accounted for using a Kinchin-Pease type model, inelastic energy loss is represented by a Firsov expression, and electronic stopping is described by a modified Brandt-Kitagawa model which contains a single adjustable ion-target dependent parameter. Thus, the program is easily extensible beyond a given validation range, and is therefore truly predictive over a wide range of implant energies and angles. The scheme is especially suited for calculating profiles due to low energy and to situations where a predictive capability is required with the minimum of experimental validation. They give examples of using the code to calculate concentration profiles and 2D 'point response' profiles of dopants in crystalline silicon and gallium-arsenide. Here they can predict the experimental profile over five orders of magnitude for <100> and <110> channeling and for non-channeling implants at energies up to hundreds of keV.

  4. 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).

  5. Intramolecular electronic energy transfer in bichromophoric molecular macrocyclic systems

    NASA Astrophysics Data System (ADS)

    Speiser, Shammai

    1993-01-01

    The structures and spectral properties of several bichromophoric molecules, suitable for optical data processing, are presented. The bichromophoric molecules are composed of an aromatic ring connected by two methylene chains to an (alpha) -diketone moiety. Both the absorption and emission spectra of these compounds can be attributed to a superposition of the individual spectra of the separate chromophores. The critical transfer radia for electronic energy transfer from the aromatic (donor) chromophore to the (alpha) -diketone (acceptor) chromophore was calculated from the spectral overlap between the fluorescence spectrum of the aromatic ring with the absorption spectrum of the (alpha) -diketone chromophore. The results show that this series of molecules is well suited for a mechanistic study of short-range intramolecular electronic energy transfer (intra-EET). The temperature and the molecular structure dependence of the intra-EET efficiency in this series was measured and analyzed for both singlet-singlet and triplet-triplet routes. The results show that the transfer efficiency is strongly temperature and structure dependent, indicating that exchange interaction is responsible for intra-EET between close chromophores in a bichromophoric molecule. The relative contributions of interchromophoric distance and that of the relative orientation of the two chromophores to exchange interaction are discussed.

  6. Molecular Insights into the Potential Toxicological Interaction of 2-Mercaptothiazoline with the Antioxidant Enzyme—Catalase

    PubMed Central

    Huang, Zhenxing; Huang, Ming; Mi, Chenyu; Wang, Tao; Chen, Dong; Teng, Yue

    2016-01-01

    2-mercaptothiazoline (2-MT) is widely used in many industrial fields, but its residue is potentially harmful to the environment. In this study, to evaluate the biological toxicity of 2-MT at protein level, the interaction between 2-MT and the pivotal antioxidant enzyme—catalase (CAT) was investigated using multiple spectroscopic techniques and molecular modeling. The results indicated that the CAT fluorescence quenching caused by 2-MT should be dominated by a static quenching mechanism through formation of a 2-MT/CAT complex. Furthermore, the identifications of the binding constant, binding forces, and the number of binding sites demonstrated that 2-MT could spontaneously interact with CAT at one binding site mainly via Van der Waals’ forces and hydrogen bonding. Based on the molecular docking simulation and conformation dynamic characterization, it was found that 2-MT could bind into the junctional region of CAT subdomains and that the binding site was close to enzyme active sites, which induced secondary structural and micro-environmental changes in CAT. The experiments on 2-MT toxicity verified that 2-MT significantly inhibited CAT activity via its molecular interaction, where 2-MT concentration and exposure time both affected the inhibitory action. Therefore, the present investigation provides useful information for understanding the toxicological mechanism of 2-MT at the molecular level. PMID:27537873

  7. Quantification and classification of substituent effects in organic chemistry: a theoretical molecular electrostatic potential study.

    PubMed

    Remya, Geetha S; Suresh, Cherumuttathu H

    2016-07-27

    Substituent effects in organic chemistry are generally described in terms of experimentally derived Hammett parameters whereas a convenient theoretical tool to study these effects in π-conjugated molecular systems is molecular electrostatic potential (MESP) analysis. The present study shows that the difference between MESP at the nucleus of the para carbon of substituted benzene and a carbon atom in benzene, designated as ΔVC, is very useful to quantify and classify substituent effects. On the basis of positive and negative ΔVC values, a broad classification of around 381 substituents into electron withdrawing and donating categories is made. Each category is again sorted based on the magnitude of ΔVC into subcategories such as very strong, strong, medium, and weak electron donating/withdrawing. Furthermore, the data are used to show the transferability and additivity of substituent effects in π-conjugated organic molecules such as condensed aromatic, olefinic, acetylenic, and heterocyclic systems. The transferability properties hold good for ΔVC in all these molecular systems. The additive properties of substituent effects are strongly reflected on ΔVC and the predictive power of the data to assign the total substituent effects of multi-substituted systems is verified. The ΔVC data and the present classification of substituents are very useful to design π-conjugated organic molecular systems with desired electron rich/poor character. PMID:27412764

  8. Molecular Insights into the Potential Toxicological Interaction of 2-Mercaptothiazoline with the Antioxidant Enzyme-Catalase.

    PubMed

    Huang, Zhenxing; Huang, Ming; Mi, Chenyu; Wang, Tao; Chen, Dong; Teng, Yue

    2016-01-01

    2-mercaptothiazoline (2-MT) is widely used in many industrial fields, but its residue is potentially harmful to the environment. In this study, to evaluate the biological toxicity of 2-MT at protein level, the interaction between 2-MT and the pivotal antioxidant enzyme-catalase (CAT) was investigated using multiple spectroscopic techniques and molecular modeling. The results indicated that the CAT fluorescence quenching caused by 2-MT should be dominated by a static quenching mechanism through formation of a 2-MT/CAT complex. Furthermore, the identifications of the binding constant, binding forces, and the number of binding sites demonstrated that 2-MT could spontaneously interact with CAT at one binding site mainly via Van der Waals' forces and hydrogen bonding. Based on the molecular docking simulation and conformation dynamic characterization, it was found that 2-MT could bind into the junctional region of CAT subdomains and that the binding site was close to enzyme active sites, which induced secondary structural and micro-environmental changes in CAT. The experiments on 2-MT toxicity verified that 2-MT significantly inhibited CAT activity via its molecular interaction, where 2-MT concentration and exposure time both affected the inhibitory action. Therefore, the present investigation provides useful information for understanding the toxicological mechanism of 2-MT at the molecular level. PMID:27537873

  9. Interaction potential for aluminum nitride: a molecular dynamics study of mechanical and thermal properties of crystalline and amorphous aluminum nitride

    SciTech Connect

    Vashishta, Priya; Kalia, Rajiv K.; Nakano, Aiichiro; Rino, Jose Pedro

    2011-01-01

    An effective interatomic interaction potential for AlN is proposed. The potential consists of two-body and three-body covalent interactions. The two-body potential includes steric repulsions due to atomic sizes, Coulomb interactions resulting from charge transfer between atoms, charge-induced dipole-interactions due to the electronic polarizability of ions, and induced dipole–dipole (van der Waals) interactions. The covalent characters of the Al–N–Al and N–Al–N bonds are described by the three-body potential. The proposed three-body interaction potential is a modification of the Stillinger–Weber form proposed to describe Si. Using the molecular dynamics method, the interaction potential is used to study structural, elastic, and dynamical properties of crystalline and amorphous states of AlN for several densities and temperatures. The structural energy for wurtzite (2H) structure has the lowest energy, followed zinc-blende and rock-salt (RS) structures. The pressure for the structural transformation from wurtzite-to-RS from the common tangent is found to be 24 GPa. For AlN in the wurtzite phase, our computed elastic constants ( C{sub 11} , C{sub 12} , C{sub 13} , C{sub 33} , C{sub 44} , and C{sub 66} ), melting temperature, vibrational density-of-states, and specific heat agree well with the experiments. Predictions are made for the elastic constant as a function of density for the crystalline and amorphous phase. Structural correlations, such as pair distribution function and neutron and x-ray static structure factors are calculated for the amorphous and liquid state.

  10. 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).

  11. Molecular simulation of aqueous electrolytes: Water chemical potential results and Gibbs-Duhem equation consistency tests

    NASA Astrophysics Data System (ADS)

    Moučka, Filip; Nezbeda, Ivo; Smith, William R.

    2013-09-01

    This paper deals with molecular simulation of the chemical potentials in aqueous electrolyte solutions for the water solvent and its relationship to chemical potential simulation results for the electrolyte solute. We use the Gibbs-Duhem equation linking the concentration dependence of these quantities to test the thermodynamic consistency of separate calculations of each quantity. We consider aqueous NaCl solutions at ambient conditions, using the standard SPC/E force field for water and the Joung-Cheatham force field for the electrolyte. We calculate the water chemical potential using the osmotic ensemble Monte Carlo algorithm by varying the number of water molecules at a constant amount of solute. We demonstrate numerical consistency of these results in terms of the Gibbs-Duhem equation in conjunction with our previous calculations of the electrolyte chemical potential. We present the chemical potential vs molality curves for both solvent and solute in the form of appropriately chosen analytical equations fitted to the simulation data. As a byproduct, in the context of the force fields considered, we also obtain values for the Henry convention standard molar chemical potential for aqueous NaCl using molality as the concentration variable and for the chemical potential of pure SPC/E water. These values are in reasonable agreement with the experimental values.

  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. Calculation of Molecular Shape Resonances Using Grid Based Exterior Complex Scaling and N2-Term Separable Potentials

    NASA Astrophysics Data System (ADS)

    Abeln, Brant; Rescigno, Thomas N.; McCurdy, C. William

    2015-05-01

    A novel approach employing Exterior Complex Scaling (ECS) and discrete grid methods is used to calculate molecular resonance energies and widths for the 2Πg shape resonance state of N2-and 2Πu shape resonance of CO2-.These calculations are performed using a Finite Element Discrete Variable Representation (FE-DVR) in prolate spheroidal coordinates with an atomic center placed at each of the foci of the coordinate system, thereby preserving the cusp condition at those sites. A separable approximation to the interaction potential is made from the matrices of the nuclear attraction, direct and exchange operators generated by an existing quantum chemistry structure code in a Gaussian basis. These potentials are then represented on our ECS FE-DVR grid allowing the calculation of complex-valued resonance energies. The method is demonstrated here in the static-exchange approximation. Work supported by NSFGRF DGE1148897, USDOE, Office of Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division.

  14. Weakly coupled molecular photonic wires: synthesis and excited-state energy-transfer dynamics.

    PubMed

    Ambroise, Arounaguiry; Kirmaier, Christine; Wagner, Richard W; Loewe, Robert S; Bocian, David F; Holten, Dewey; Lindsey, Jonathan S

    2002-05-31

    Molecular photonic wires, which absorb light and undergo excited-state energy transfer, are of interest as biomimetic models for photosynthetic light-harvesting systems and as molecular devices with potential applications in materials chemistry. We describe the stepwise synthesis of four molecular photonic wires. Each wire consists of an input unit, transmission element, and output unit. The input unit consists of a boron-dipyrrin dye or a perylene-monoimide dye (linked either at the N-imide or the C9 position); the transmission element consists of one or three zinc porphyrins affording short or long wires, respectively; and the output unit consists of a free base (Fb) porphyrin. The components in the arrays are joined in a linear architecture via diarylethyne linkers (an ethynylphenyl linker is attached to the C9-linked perylene). The wires have been examined by static absorption, static fluorescence, and time-resolved absorption spectroscopy. Each wire (with the exception of the C9-linked perylene wire) exhibits a visible absorption spectrum that is the sum of the spectra of the component parts, indicating the relatively weak electronic coupling between the components. Excitation of each wire at the wavelength where the input unit absorbs preferentially (typically 480-520 nm) results in emission almost exclusively from the Fb porphyrin. The static emission and time-resolved data indicate that the overall rate constants and quantum efficiencies for end-to-end (i.e., input to output) energy transfer are as follows: perylene-(N-imide)-linked short wire, (33 ps)(-1) and >99%; perylene-(C9)-linked short wire, (26 ps)(-1) and >99%; boron-dipyrrin-based long wire, (190 ps)(-1) and 81%; perylene-(N-imide)-linked long wire, (175 ps)(-1) and 86%. Collectively, the studies provide valuable insight into the singlet-singlet excited-state energy-transfer properties in weakly coupled molecular photonic wires. PMID:12027698

  15. Calculation of free energies and chemical potentials for gas hydrates using Monte Carlo simulations.

    PubMed

    Wierzchowski, S J; Monson, P A

    2007-06-28

    We describe a method for calculating free energies and chemical potentials for molecular models of gas hydrate systems using Monte Carlo simulations. The method has two components: (i) thermodynamic integration to obtain the water and guest molecule chemical potentials as functions of the hydrate occupancy; (ii) calculation of the free energy of the zero-occupancy hydrate system using thermodynamic integration from an Einstein crystal reference state. The approach is applicable to any classical molecular model of a hydrate. We illustrate the methodology with an application to the structure-I methane hydrate using two molecular models. Results from the method are also used to assess approximations in the van der Waals-Platteeuw theory and some of its extensions. It is shown that the success of the van der Waals-Platteeuw theory is in part due to a cancellation of the error arising from the assumption of a fixed configuration of water molecules in the hydrate framework with that arising from the neglect of methane-methane interactions. PMID:17530795

  16. Molecular simulation of CO chemisorption on Co(0001) in presence of supercritical fluid solvent: A potential of mean force study.

    PubMed

    Asiaee, Alireza; Benjamin, Kenneth M

    2016-08-28

    For several decades, heterogeneous catalytic processes have been improved through utilizing supercritical fluids (SCFs) as solvents. While numerous experimental studies have been established across a range of chemistries, such as oxidation, pyrolysis, amination, and Fischer-Tropsch synthesis, still there is little fundamental, molecular-level information regarding the role of the SCF on elementary heterogeneous catalytic steps. In this study, the influence of hexane solvent on the adsorption of carbon monoxide on Co(0001), as the first step in the reaction mechanism of many processes involving syngas conversion, is probed. Simulations are performed at various bulk hexane densities, ranging from ideal gas conditions (no SCF hexane) to various near- and super-critical hexane densities. For this purpose, both density functional theory and molecular dynamics simulations are employed to determine the adsorption energy and free energy change during CO chemisorption. Potential of mean force calculations, utilizing umbrella sampling and the weighted histogram analysis method, provide the first commentary on SCF solvent effects on the energetic aspects of the chemisorption process. Simulation results indicate an enhanced stability of CO adsorption on the catalyst surface in the presence of supercritical hexane within the reduced pressure range of 1.0-1.5 at a constant temperature of 523 K. Furthermore, it is shown that the maximum stability of CO in the adsorbed state as a function of supercritical hexane density at 523 K nearly coincides with the maximum isothermal compressibility of bulk hexane at this temperature. PMID:27586934

  17. Intermolecular potential functions and high resolution molecular spectroscopy of weakly bound complexes. Final progress report

    SciTech Connect

    Muenter, J.S.

    1997-04-01

    This report describes accomplishments over the past year in research supported by this grant. Two papers published in this period are briefly discussed. The general goal of the work is to consolidate the understanding of experimental results through a theoretical model of intermolecular potential energy surfaces. Progress in the experimental and theoretical phases of the program are presented and immediate goals outlined. The ability to construct analytic intermolecular potential functions that accurately predict the energy of interaction between small molecules will have great impact in many areas of chemistry, biochemistry, and biology.

  18. 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.

  19. An exploration of the ozone dimer potential energy surface

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

    The (O3)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 O3 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-1. In addition to the five minima, 11 higher-order stationary points are identified.

  20. An exploration of the ozone dimer potential energy surface.

    PubMed

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

    2014-06-28

    The (O3)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 O3 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(-1). In addition to the five minima, 11 higher-order stationary points are identified. PMID:24985642

  1. Lanthanide nano-drums: a new class of molecular nanoparticles for potential biomedical applications†

    PubMed Central

    Gnanam, Annie J.; Arambula, Jonathan F.; Jones, Jessica N.; Swaminathan, Jagannath; Yang, Xiaoping; Schipper, Desmond; Hall, Justin W.; DePue, Lauren J.; Dieye, Yakhya; Vadivelu, Jamuna; Chandler, Don J.; Marcotte, Edward M.; Sessler, Jonathan L.; Ehrlich, Lauren I. R.; Brown, Katherine A.

    2015-01-01

    We are developing a new class of lanthanide-based self-assembling molecular nanoparticles as potential reporter molecules for imaging, and as multi-functional nanoprobes or nanosensors in diagnostic systems. These lanthanide “nano-drums” are homogeneous 4d–4f clusters approximately 25 to 30 Å in diameter that can emit from the visible to near-infrared (NIR) wavelengths. Here, we present syntheses, crystal structures, photophysical properties, and comparative cytotoxicity data for six nano-drums containing either Eu, Tb, Lu, Er, Yb or Ho. Imaging capabilities of these nano-drums are demonstrated using epifluorescence, total internal reflection fluorescence (TIRF), and two-photon microscopy. We discuss how these molecular nanoparticles can to be adapted for a range of assays, particularly by taking advantage of functionalization strategies with chemical moieties to enable conjugation to protein or nucleic acids. PMID:25284181

  2. Regularizing the molecular potential in electronic structure calculations. II. Many-body methods

    SciTech Connect

    Bischoff, Florian A.

    2014-11-14

    In Paper I of this series [F. A. Bischoff, “Regularizing the molecular potential in electronic structure calculations. I. SCF methods,” J. Chem. Phys. 141, 184105 (2014)] a regularized molecular Hamilton operator for electronic structure calculations was derived and its properties in SCF calculations were studied. The regularization was achieved using a correlation factor that models the electron-nuclear cusp. In the present study we extend the regularization to correlated methods, in particular the exact solution of the two-electron problem, as well as second-order many body perturbation theory. The nuclear and electronic correlation factors lead to computations with a smaller memory footprint because the singularities are removed from the working equations, which allows coarser grid resolution while maintaining the precision. Numerical examples are given.

  3. Meningiomas and Proteomics: Focus on New Potential Biomarkers and Molecular Pathways.

    PubMed

    Abbritti, Rosaria Viola; Polito, Francesca; Cucinotta, Maria; Lo Giudice, Claudio; Caffo, Maria; Tomasello, Chiara; Germanò, Antonino; Aguennouz, Mohammed

    Meningiomas are one of the most common tumors affecting the central nervous system, exhibiting a great heterogeneity in grading, treatment and molecular background. This article provides an overview of the current literature regarding the molecular aspect of meningiomas. Analysis of potential biomarkers in serum, cerebrospinal fluid (CSF) and pathological tissues was reported. Applying bioinformatic methods and matching the common proteic profile, arising from different biological samples, we highlighted the role of nine proteins, particularly related to tumorigenesis and grading of meningiomas: serpin peptidase inhibitor alpha 1, ceruloplasmin, hemopexin, albumin, C3, apolipoprotein, haptoglobin, amyloid-P-component serum and alpha-1-beta-glycoprotein. These proteins and their associated pathways, including complement and coagulation cascades, plasma lipoprotein particle remodeling and lipid metabolism could be considered possible diagnostic, prognostic biomarkers, and eventually therapeutic targets. Further investigations are needed to better characterize the role of these proteins and pathways in meningiomas. The role of new therapeutic strategies are also discussed. PMID:27566655

  4. 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.

  5. Comparison of Quantum Mechanics and Molecular Mechanics Dimerization Energy Landscapes for Pairs of Ring-Containing Amino Acids in Proteins

    SciTech Connect

    Morozov, Alexandre V.; Misura M. S., Kira; Tsemekhman, Kiril; Baker, David

    2004-06-17

    A promising approach to developing improved potential functions for modeling macromolecular interactions consists of combining protein structural analysis, quantum mechanical calculations on small molecule models, and molecular mechanics potential decomposition. Here we apply this approach to the interactions of pairs of ring-containing amino acids in proteins. We find reasonable qualitative agreement between molecular mechanics and quantum chemistry calculations, both over one-dimensional projections of the binding free energy landscape for amino acid homodimers and over a set of homodimers and heterodimers from experimentally observed protein crystal structures. The molecular mechanics landscapes are a sum of charge-charge and Lennard-Jones contributions; short-range quantum mechanical effects such as charge transfer appear not to be significant in ring side chain interactions. We also find a reasonable degree of correlation between the molecular mechanics energy landscapes and the distributions of dimer geometries observed in protein structures, suggesting that the intrinsic dimer interaction energies do contribute to packing of side chains in proteins rather than being overwhelmed by the numerous interactions with other protein atoms and solvent. These results demonstrate that interactions involving aromatic residues and proline can be fairly well modeled using current molecular mechanics force fields, but there is still room for improvement, particularly for interactions involving proline and tyrosine.

  6. Through-Space Effects of Substituents Dominate Molecular Electrostatic Potentials of Substituted Arenes

    PubMed Central

    Wheeler, Steven E.; Houk, K. N.

    2009-01-01

    Model systems have been studied using density functional theory to assess the contributions of π-resonance and through-space effects on electrostatic potentials of substituted arenes. The results contradict the widespread assumption that changes in molecular ESPs reflect only local changes in the electron density. Substituent effects on the ESP above the molecular plane are commonly attributed to changes in the aryl π-system. We show that ESP changes for a collection of substituted benzenes and more complex aromatic systems can be accounted for mostly by through-space effects, with no change in the aryl π-electron density. Only when π-resonance effects are substantial do they influence changes in the ESP above the aromatic ring to any extent. Examples of substituted arenes studied here are taken from the fields of drug design, host-guest chemistry, and crystal engineering. These findings emphasize the potential pitfalls of assuming ESP changes reflect changes in the local electron density. Since ESP changes are frequently used to rationalize and predict intermolecular interactions, these findings have profound implications for our understanding of substituent effects in countless areas of chemistry and molecular biology. Specifically, in many non-covalent interactions there are significant, often neglected, through-space interactions with the substituents. Finally, the present results explain the perhaps unexpectedly good performance of many molecular mechanics force-fields applied to supramolecular assembly phenomena and π-π interactions in biological systems despite the neglect of the polarization of the aryl π-system by substituents. PMID:20161573

  7. Saturn Magnetospheric Impact on Surface Molecular Chemistry and Astrobiological Potential of Enceladus

    NASA Technical Reports Server (NTRS)

    Cooper, Paul D.; Cooper, John F.; Sittler, Edward C.; Burger, Matthew H.; Sturner, Steven J.; Rymer, Abigail M.

    2008-01-01

    The active south polar surface of Enceladus is exposed to strong chemical processing by direct interaction with charged plasma and energetic particles in the local magnetospheric environment of this icy moon. Chemical oxidation activity is suggested by detection of H202 at the surface in this region and less directly by substantial presence of C02, CO, and N2 in the plume gases. Molecular composition of the uppermost surface, including ejecta from plume activity, is radiolytically transformed mostly by penetrating energetic electrons with lesser effects from more depleted populations of energetic protons. The main sources of molecular plasma ions and E-ring dust grains in the magnetospheric environment are the cryovolcanic plume emissions from Enceladus. These molecular ions and the dust grains are chemically processed by magnetospheric interactions that further impact surface chemistry on return to Enceladus. For example, H20 neutrals dominating the emitted plume gas return to the surface mostly as H30+ ions after magnetospheric processing. Surface oxidant loading is further increased by return of radiolytically processed ice grains from the E-ring. Plume frost deposition and micrometeoroid gardening protect some fraction of newly produced molecular species from destruction by further irradiation. The evident horizontal and vertical mobility of surface ices in the south polar region drive mixing of these processed materials into the moon interior with potential impacts on deep ice molecular chemistry and plume gas production. Similarly as suggested previously for Europa, the externally driven source of radiolytic oxidants could affect evolution of life in any subsurface liquid water environments of Enceladus.

  8. 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.

  9. Theoretical Study of FH2– Electron Photodetachment Spectra on New Ab Initio Potential Energy Surfaces.

    PubMed

    Yu, Dequan; Chen, Jun; Cong, Shulin; Sun, Zhigang

    2015-12-17

    The FH2– anion has a stable structure that resembles a configuration in the vicinity of the transition state for neutral reaction F + H2 → HF + H. Electron photodetachment spectra of the FH2– anion reveal the neutral reaction dynamics in the critical transition-state region. Accurate quantum dynamics simulations of the photodetachment spectra using highly accurate new ab initio potential energy surfaces for both anionic and neutral FH2 are performed and compared with all available experimental results. The results provide reliable interpretations for the experimental observations of FH2– photoelectron detachment and reveal a detailed picture of the molecular dynamics around the transition state of the F + H2 reaction. The latest high-resolution photoelectron detachment spectra [Kim et al. Science, 2015, 349, 510-513] confirm the high accuracy of our new potential energy surface for describing the resonance-enhanced reactivity of the neutral F + H2 reaction. PMID:26550683

  10. Quantum transition state dynamics of the cyclooctatetraene unimolecular reaction on ab initio potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Tokizaki, Chihiro; Yoshida, Takahiko; Takayanagi, Toshiyuki

    2016-05-01

    The cyclooctatetraene (COT) anion has a stable D4h structure that is similar to the transition state configurations of the neutral C-C bond-alternation (D4h ↔ D8h ↔ D4h) and ring-inversion (D2d ↔ D4h ↔ D2d) unimolecular reactions. The previously measured photodetachment spectrum of COT- revealed the reaction dynamics in the vicinity of the two transition states on the neutral potential energy surface. In this work, the photodetachment spectrum is calculated quantum mechanically on ab initio-level potential energy surfaces within a three degree-of-freedom reduced-dimensionality model. Very good agreement has been obtained between theory and experiment, providing reliable interpretations for the experimental spectrum. A detailed picture of the reactive molecular dynamics of the COT unimolecular reaction in the transition state region is also discussed.

  11. The ground-state potential energy curve of the radium dimer from relativistic coupled cluster calculations

    NASA Astrophysics Data System (ADS)

    Teodoro, Tiago Quevedo; Haiduke, Roberto Luiz Andrade; Dammalapati, Umakanth; Knoop, Steven; Visscher, Lucas

    2015-08-01

    The potential energy curve for the ground-state of radium dimer (Ra2) is provided by means of atomic and molecular relativistic coupled cluster calculations. The short-range part of this curve is defined by an equilibrium bond length of 5.324 Å, a dissociation energy of 897 cm-1, and a harmonic vibrational frequency of 20.5 cm-1. The asymptotic behavior at large interatomic distances is characterized by the van der Waals coefficients C6 = 5.090 × 103, C8 = 6.978 × 105, and C10 = 8.786 × 107 atomic units. The two regions are matched in an analytical potential to provide a convenient representation for use in further calculations, for instance, to model cold collisions between radium atoms. This might become relevant in future experiments on ultracold, optically trapped, radioactive radium atoms that are used to search for a permanent electric dipole moment.

  12. 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.

  13. 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.

  14. 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. PMID:22715929

  15. Comparison of molecular dynamics methods and interatomic potentials for calculating the thermal conductivity of silicon

    NASA Astrophysics Data System (ADS)

    Howell, P. C.

    2012-12-01

    We compare the molecular dynamics Green-Kubo and direct methods for calculating thermal conductivity κ, using as a test case crystalline silicon at temperatures T in the range 500-1000 K (classical regime). We pay careful attention to the convergence with respect to simulation size and duration and to the procedures used to fit the simulation data. We show that in the Green-Kubo method the heat current autocorrelation function is characterized by three decay processes, of which the slowest lasts several tens of picoseconds so that convergence requires several tens of nanoseconds of data. Using the Stillinger-Weber potential we find excellent agreement between the two methods. We also use the direct method to calculate κ(T) for the Tersoff potential and find that the magnitude and the temperature-dependence are different for the two potentials and that neither potential agrees with experimental data. We argue that this implies that using the Stillinger-Weber or Tersoff potentials to predict trends in kappa as some system parameter is varied may yield results which are specific to the potential but not intrinsic to Si.

  16. Comparison of molecular dynamics methods and interatomic potentials for calculating the thermal conductivity of silicon.

    PubMed

    Howell, P C

    2012-12-14

    We compare the molecular dynamics Green-Kubo and direct methods for calculating thermal conductivity κ, using as a test case crystalline silicon at temperatures T in the range 500-1000 K (classical regime). We pay careful attention to the convergence with respect to simulation size and duration and to the procedures used to fit the simulation data. We show that in the Green-Kubo method the heat current autocorrelation function is characterized by three decay processes, of which the slowest lasts several tens of picoseconds so that convergence requires several tens of nanoseconds of data. Using the Stillinger-Weber potential we find excellent agreement between the two methods. We also use the direct method to calculate κ(T) for the Tersoff potential and find that the magnitude and the temperature-dependence are different for the two potentials and that neither potential agrees with experimental data. We argue that this implies that using the Stillinger-Weber or Tersoff potentials to predict trends in kappa as some system parameter is varied may yield results which are specific to the potential but not intrinsic to Si. PMID:23248991

  17. Exact energy spectrum for models with equally spaced point potentials

    NASA Astrophysics Data System (ADS)

    Caudrelier, V.; Crampé, N.

    2006-03-01

    We describe a non-perturbative method for computing the energy band structures of one-dimensional models with general point potentials sitting at equally spaced sites. This is done thanks to a Bethe ansatz approach and the method is applicable even when periodicity is broken, that is when Bloch's theorem is not valid any more. We derive the general equation governing the energy spectrum and illustrate its use in various situations. In particular, we get exact results for boundary effects. We also study non-perturbatively the effects of impurities in such systems. Finally, we discuss the possibility of including interactions between the particles of these systems.

  18. Bifurcations on Potential Energy Surfaces of Organic Reactions

    PubMed Central

    Ess, Daniel H.; Wheeler, Steven E.; Iafe, Robert G.; Xu, Lai; Çelebi-Ölçüm, Nihan; Houk, K. N.

    2009-01-01

    A single transition state may lead to multiple intermediates or products if there is a post-transition state reaction path bifurcation. These bifurcations arise when there are sequential transition states with no intervening energy minimum. For such systems, the shape of the potential energy surface and dynamic effects control selectivity rather than transition state energetics. This minireview covers recent investigations of organic reactions exhibiting reaction pathway bifurcations. Such phenomena are surprisingly general and affect experimental observables such as kinetic isotope effects and product distributions. PMID:18767086

  19. Quintom dark energy models with nearly flat potentials

    SciTech Connect

    Setare, M. R.; Saridakis, E. N.

    2009-02-15

    We examine quintom dark energy models, produced by the combined consideration of a canonical and a phantom field, with nearly flat potentials and dark energy equation-of-state parameter w{sub DE} close to -1. We find that all such models converge to a single expression for w{sub DE}(z), depending only on the initial field values and their derivatives. We show that this quintom paradigm allows for a description of the transition through -1 in the near cosmological past. In addition, we provide the necessary conditions for the determination of the direction of the -1 crossing.

  20. 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.

  1. Extending the essential dynamics analysis to investigate molecular properties: application to the redox potential of proteins.

    PubMed

    Zanetti-Polzi, Laura; Corni, Stefano; Daidone, Isabella; Amadei, Andrea

    2016-07-21

    Here, a methodology is proposed to investigate the collective fluctuation modes of an arbitrary set of observables, maximally contributing to the fluctuation of another functionally relevant observable. The methodology, based on the analysis of fully classical molecular dynamics (MD) simulations, exploits the essential dynamics (ED) method, originally developed to analyse the collective motions in proteins. We apply this methodology to identify the residues that are more relevant for determining the reduction potential (E(0)) of a redox-active protein. To this aim, the fluctuation modes of the single-residue electrostatic potentials mostly contributing to the fluctuations of the total electrostatic potential (the main determinant of E(0)) are investigated for wild-type azurin and two of its mutants with a higher E(0). By comparing the results here obtained with a previous study on the same systems [Zanetti-Polzi et al., Org. Biomol. Chem., 2015, 13, 11003] we show that the proposed methodology is able to identify the key sites that determine E(0). This information can be used for a general deeper understanding of the molecular mechanisms on the basis of the redox properties of the proteins under investigation, as well as for the rational design of mutants with a higher or lower E(0). From the results of the present analysis we propose a new azurin mutant that, according to our calculations, shows a further increase of E(0). PMID:27339768

  2. Revealing potential molecular targets bridging colitis and colorectal cancer based on multidimensional integration strategy

    PubMed Central

    Hu, Yongfei; Li, Xiaobo; Wang, Xishan; Fan, Huihui; Wang, Guiyu; Wang, Dong

    2015-01-01

    Chronic inflammation may play a vital role in the pathogenesis of inflammation-associated tumors. However, the underlying mechanisms bridging ulcerative colitis (UC) and colorectal cancer (CRC) remain unclear. Here, we integrated multidimensional interaction resources, including gene expression profiling, protein-protein interactions (PPIs), transcriptional and post-transcriptional regulation data, and virus-host interactions, to tentatively explore potential molecular targets that functionally link UC and CRC at a systematic level. In this work, by deciphering the overlapping genes, crosstalking genes and pivotal regulators of both UC- and CRC-associated functional module pairs, we revealed a variety of genes (including FOS and DUSP1, etc.), transcription factors (including SMAD3 and ETS1, etc.) and miRNAs (including miR-155 and miR-196b, etc.) that may have the potential to complete the connections between UC and CRC. Interestingly, further analyses of the virus-host interaction network demonstrated that several virus proteins (including EBNA-LP of EBV and protein E7 of HPV) frequently inter-connected to UC- and CRC-associated module pairs with their validated targets significantly enriched in both modules of the host. Together, our results suggested that multidimensional integration strategy provides a novel approach to discover potential molecular targets that bridge the connections between UC and CRC, which could also be extensively applied to studies on other inflammation-related cancers. PMID:26461477

  3. A Mechanism for Ion Transport Across the Water/Dichloromethane Interface: A Molecular Dynamics Study Using Polarizable Potential Models

    SciTech Connect

    Dang, Liem X. )

    2001-02-01

    In this work, we used molecular dynamics techniques and mean force approaches to compute the ion transfer free energy for the water/dichloromethane liquid-liquid interface. We used polarizable potential models to describe the interactions among the species, and both forward and reverse directions were carried out to estimate the error bar of the computed free energy results. Based on the results of our calculations, we have proposed a mechanism that describes the transport of a chlorine ion across the interface. The computed ion transfer free energy is 14 & No.177; 2 kcal/mol, which is in reasonable agreement with the experimentally reported value of 10 kcal/mol. A smooth transition from the aqueous phase to the non-aqueous phase on the free energy profile clearly indicates that the ion transfer mechanism is a nonactivated process. The computed hydration number for the chlorine ion indicates that some water molecules are associated with the ion inside the non-aqueous phase. This result is in excellent agreement with the experimental interpretation of the ion transfer mechanism reported recently by Osakai et al. (J. Phys. Chem. 1997, 101, 8341).

  4. The Potential For Energy Efficiency In The State of Iowa

    SciTech Connect

    Hadley, SW

    2001-12-05

    The purpose of this study was to do an initial estimate of the potential for energy savings in the state of Iowa. Several methods for determining savings were examined, including existing programs, surveys, savings calculators, and economic simulation. Each method has advantages and disadvantages, trading off between detail of information, accuracy of results, and scope. This paper concentrated on using economic simulation (the NEMS model (EIA 2000a)) to determine market potential for energy savings for the residential and commercial sectors. The results of surveys were used to calculate the economic potential for savings in the industrial sector. The NEMS model is used by the Energy Information Administration to calculate twenty-year projections of energy use for every region of the country. The results of the Annual Energy Outlook 2000 were used as the Base case (EIA 1999a). Two alternative cases were created to simulate energy savings policies. Voluntary, market-related programs were simulated by lowering the effective discount rates that end-users use when making decisions on equipment purchases. Standards programs in the residential sector were simulated by eliminating the availability of low efficiency equipment in future years. The parameters for these programs were based on the Moderate scenario from the DOE Clean Energy Futures study (Interlaboratory Working Group 2000), which assumed increased concern by society on energy efficiency but not to the point of fiscal policies such as taxes or direct subsidies. The study only considered a subset of the various programs, policies, and technologies that could reduce energy use. The major end-uses in the residential sector affected by the policies were space cooling (20% savings by 2020) and water heating (14% savings by 2020.) Figure S-1 shows the space cooling savings when voluntary programs and minimum efficiency standards were implemented. Refrigerators, freezers, and clothes dryers saw slight improvements

  5. Computed rotational rainbows from realistic potential energy surfaces

    SciTech Connect

    Gianturco, F.A.; Palma, A.

    1985-08-01

    The quantal IOS approximation in here employed to study interference structures in the rotationally inelastic, state-to-state differential cross sections for polar diatomic targets (LiH, FH, and CO) interacting with He atoms. Quite realistic expressions are used to describe the relevant potential energy surfaces (PES) which were taken from previous works that tested them against accurate experimental findings for total and partial differential cross sections. Specific features like short-range anisotropy and well depth, long-range attractive regions and overall range of action for each potential employed are analyzed and discussed in relation to their influence on rotational rainbows appearance and on the possible observation of cross section extrema in rotational energy distributions.

  6. 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

  7. FT-IR and FT-Raman spectra, molecular structure and first-order molecular hyperpolarizabilities of a potential antihistaminic drug, cyproheptadine HCl.

    PubMed

    Sagdinc, Seda G; Erdas, Dilek; Gunduz, Ilknur; Sahinturk, Ayse Erbay

    2015-01-01

    Cyproheptadine hydrochloride (CYP HCl) {4-(5H-dibenzo[a,d]-cyclohepten-5-ylidene)-1-methylpiperidine hydrochloride} is a first-generation antihistamine with additional anticholinergic, antiserotonergic, and local-anesthetic properties. The geometry optimization, Mulliken atomic charges and wavenumber and intensity of the vibrational bands of all of the possible modes of CYP HCl have been calculated using ab initio Hartree-Fock (HF) and density functional theory (DFT) employing the B3LYP functional with the 6-311G(d,p) basis set. We have compared the calculated IR and Raman wavenumbers with experimental data. Quantum-chemical calculations of the geometrical structure, energies, and molecular electrostatic potential and NBO analysis of CYP HCl have been performed using the B3LYP/6-311G(d,p) method. The electric dipole moment (μ), static polarizability (α) and the first hyperpolarizability (β) values of the title compound have been computed using HF and DFT methods. The study reveals that the antihistaminic pharmacological property of CYP HCl has a large β value and, hence, may in general have potential applications in the development of non-linear optical materials. The experimental and calculated results for CYP HCl have also been compared with those for mianserin HCl. PMID:25022508

  8. FT-IR and FT-Raman spectra, molecular structure and first-order molecular hyperpolarizabilities of a potential antihistaminic drug, cyproheptadine HCl

    NASA Astrophysics Data System (ADS)

    Sagdinc, Seda G.; Erdas, Dilek; Gunduz, Ilknur; Sahinturk, Ayse Erbay

    2015-01-01

    Cyproheptadine hydrochloride (CYP HCl) {4-(5H-dibenzo[a,d]-cyclohepten-5-ylidene)-1-methylpiperidine hydrochloride} is a first-generation antihistamine with additional anticholinergic, antiserotonergic, and local-anesthetic properties. The geometry optimization, Mulliken atomic charges and wavenumber and intensity of the vibrational bands of all of the possible modes of CYP HCl have been calculated using ab initio Hartree-Fock (HF) and density functional theory (DFT) employing the B3LYP functional with the 6-311G(d,p) basis set. We have compared the calculated IR and Raman wavenumbers with experimental data. Quantum-chemical calculations of the geometrical structure, energies, and molecular electrostatic potential and NBO analysis of CYP HCl have been performed using the B3LYP/6-311G(d,p) method. The electric dipole moment (μ), static polarizability (α) and the first hyperpolarizability (β) values of the title compound have been computed using HF and DFT methods. The study reveals that the antihistaminic pharmacological property of CYP HCl has a large β value and, hence, may in general have potential applications in the development of non-linear optical materials. The experimental and calculated results for CYP HCl have also been compared with those for mianserin HCl.

  9. Validation of Potential Models for Li2O in Classical Molecular Dynamics Simulation

    SciTech Connect

    Oda, Takuji; Oya, Yasuhisa; Tanaka, Satoru; Weber, William J.

    2007-08-01

    Four Buckingham-type pairwise potential models for Li2O were assessed by molecular static and dynamics simulations. In the static simulation, all models afforded acceptable agreement with experimental values and ab initio calculation results for the crystalline properties. Moreover, the superionic phase transition was realized in the dynamics simulation. However, the Li diffusivity and the lattice expansion were not adequately reproduced at the same time by any model. When using these models in future radiation simulation, these features should be taken into account, in order to reduce the model dependency of the results.

  10. Molecular physiology of cellular glucose transport - a potential area for clinical studies in diabetes mellitus.

    PubMed

    Tatoń, Jan; Piatkiewicz, Paweł; Czech, Anna

    2010-01-01

    The normalization of cellular glucose assimilation is the basic aim of metabolic therapy in type 2 diabetes mellitus (T2DM). It requires parallel changes in the process of cellular glucose transport (CGT). This review presents the pathophysiological and clinical outlines of CGT. Sequentially, the advances in the mechanisms and classification of CGT and their physiological and molecular base are described. The role of CGT pathogenetic significance in diabetes mellitus is stressed. Finally, the opinion is expressed that the CGT study is a potentially important approach to clinical interpretation of glucose metabolism disturbances and their pharmacotherapy. PMID:20602306

  11. Molecular regulation of vasculogenic mimicry in tumors and potential tumor-target therapy

    PubMed Central

    Fan, Yue-Zu; Sun, Wei

    2010-01-01

    “Vasculogenic mimicry (VM)”, is a term that describes the unique ability of highly aggressive tumor cells to express a multipotent, stem cell-like phenotype, and form a pattern of vasculogenic-like networks in three-dimensional culture. As an angiogenesis-independent pathway, VM and/or periodic acid-schiff-positive patterns are associated with poor prognosis in tumor patients. Moreover, VM is resistant to angiogenesis inhibitors. Here, we will review the advances in research on biochemical and molecular signaling pathways of VM in tumors and on potential anti-VM therapy strategy. PMID:21160860

  12. Potential molecular, cellular and microenvironmental mechanism of sorafenib resistance in hepatocellular carcinoma.

    PubMed

    Chen, Jiang; Jin, Renan; Zhao, Jie; Liu, Jinghua; Ying, Hanning; Yan, Han; Zhou, Senjun; Liang, Yuelong; Huang, Diyu; Liang, Xiao; Yu, Hong; Lin, Hui; Cai, Xiujun

    2015-10-10

    Sorafenib, an orally-available kinase inhibitor, is the only standard clinical treatment against advanced hepatocellular carcinoma. However, development of resistance to sorafenib has raised concern in recent years due to the high-level heterogeneity of individual response to sorafenib treatment. The resistance mechanism underlying the impaired sensitivity to sorafenib is still elusive though some researchers have made great efforts. Here, we provide a systemic insight into the potential molecular, cellular and microenvironmental mechanism of sorafenib resistance in hepatocellular carcinoma depending on abundant previous studies and reports. PMID:26170167

  13. The role of the exchange in the embedding electrostatic potential for the fragment molecular orbital method.

    PubMed

    Fedorov, Dmitri G; Kitaura, Kazuo

    2009-11-01

    We have examined the role of the exchange in describing the electrostatic potential in the fragment molecular orbital method and showed that it should be included in the total Fock matrix to obtain an accurate one-electron spectrum; however, adding it to the Fock matrices of individual fragments and pairs leads to very large errors. For the error analysis we have used the virial theorem; numerical tests have been performed for solvated phenol at the Hartree-Fock level with the 6-31G( *) and 6-311G( * *) basis sets. PMID:19894991

  14. 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

  15. Systematic search for molecular clouds near supernova remnants as sources of very-high-energy γ-ray emission

    NASA Astrophysics Data System (ADS)

    Häffner, Stephanie; Stegmann, Christian; Jung-Richardt, Ira

    2015-12-01

    Supernova remnants accelerate particles up to energies of at least 100 TeV as established by observations in very-high-energy γ-ray astronomy. Molecular clouds in their vicinity provide an increased amount of target material for proton-proton interaction and subsequent neutral pion decay into γ-rays of accelerated hadrons escaping the remnant. Therefore, these molecular clouds are potential γ-ray sources. The γ-ray emission from these clouds provides a unique environment to derive information on the propagation of very-high-energy particles through the interstellar medium as well as on the acceleration of hadrons in supernova remnants. Current Imaging Atmospheric Cherenkov Telescope systems are suitable to explore a large parameter space of the propagation properties depending on the age of the supernova remnant and the distance between the remnant and the nearby molecular cloud. In this paper we present our strategy and results of a systematic search for γ-ray emitting molecular clouds near supernova remnants which are potentially detectable with current experiments in the TeV energy range and explore the prospects of future experiments.

  16. 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. PMID:27433628

  17. 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.

  18. 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.

  19. Potential molecular wires by an iterative divergent/convergent approach. Doubling of molecular length at each iteration

    NASA Astrophysics Data System (ADS)

    Pearson, Darren L.; Schumm, Jeffry S.; Jones, Leroy, II; Tour, James M.

    1994-06-01

    We have devised an iterative convergent/divergent approach to conjugated oligomers that might serve as molecular wires. The molecular length doubles with each iteration. The systems prepared are completely monodispersed and based upon oligo(thiophene-ethynylene)s (1) and oligo(phenylene-ethynylene)s at 100 A and 128 A long, respectively. The optical and size exclusion chromatography (SEC) properties are discussed. Methods are outlined to attach end groups that might serve as molecular alligator clips.

  20. Supercell convergence of charge-transfer energies in pentacene molecular crystals from constrained DFT

    NASA Astrophysics Data System (ADS)

    Turban, David H. P.; Teobaldi, Gilberto; O'Regan, David D.; Hine, Nicholas D. M.

    2016-04-01

    Singlet fission (SF) is a multiexciton generation process that could be harnessed to improve the efficiency of photovoltaic devices. Experimentally, systems derived from the pentacene molecule have been shown to exhibit ultrafast SF with high yields. Charge-transfer (CT) configurations are likely to play an important role as intermediates in the SF process in these systems. In molecular crystals, electrostatic screening effects and band formation can be significant in lowering the energy of CT states, enhancing their potential to effectively participate in SF. In order to simulate these, it desirable to adopt a computational approach which is acceptably accurate, relatively inexpensive, and which scales well to larger systems, thus enabling the study of screening effects. We propose an electrostatically corrected constrained density functional theory (cDFT) approach as a low-cost solution to the calculation of CT energies in molecular crystals such as pentacene. Here we consider an implementation in the context of the onetep linear-scaling DFT code, but our electrostatic correction method is in principle applicable in combination with any constrained DFT implementation, also outside the linear-scaling framework. Our newly developed method allows us to estimate CT energies in the infinite crystal limit, and with these to validate the accuracy of the cluster approximation.

  1. 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.

  2. 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. PMID:26723619

  3. 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.

  4. 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.

  5. 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

  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.

    PubMed

    Samanta, Amit; Morales, Miguel A; Schwegler, Eric

    2016-04-28

    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. PMID:27131525

  9. 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.

  10. Characterisation of bacteria in ascites--reporting the potential of culture-independent, molecular analysis.

    PubMed

    Rogers, G B; Russell, L E; Preston, P G; Marsh, P; Collins, J E; Saunders, J; Sutton, J; Fine, D; Bruce, K D; Wright, M

    2010-05-01

    Spontaneous bacterial peritonitis (SBP) is a severe complication of liver disease. A significant proportion of patients have culture-negative ascites, despite having similar signs, symptoms and mortality to those with SBP. Therefore, empirical antibiotic treatment for infection is often started without knowledge of the causative organisms. Here, we investigated the potential of molecular techniques to provide rapid and accurate characterisation of the bacteria present in ascitic fluid. Ascites samples were obtained from 29 cirrhotic patients undergoing clinically indicated therapeutic paracentesis. Bacterial content was determined by terminal restriction fragment length polymorphism (T-RFLP) analysis, quantitative polymerase chain reaction (PCR) and 16S ribosomal clone sequence analysis. Bacterial signal was detected in all samples, compared to three out of ten using standard methods. Bacterial loads ranged from 5.5 x 10(2) to 5.4 x 10(7) cfu/ml, with a mean value of 1.9 x 10(6) cfu/ml (standard deviation +/- 9.6 x 10(6) cfu/ml). In all but one instance, bacterial species identified by culture were also confirmed by molecular analyses. Preliminary data presented here suggests that culture-independent, molecular analyses could provide rapid characterisation of the bacterial content of ascites fluid, providing a basis for the investigation of SBP development and allowing early and targeted antibiotic intervention. PMID:20238135

  11. Market potential for optical fiber sensors in the energy sector

    NASA Astrophysics Data System (ADS)

    Bosselmann, T.

    2007-07-01

    For a long time electric power was taken as a natural unlimited resource. With globalisation the demand for energy has risen. This has brought rising prices for fossil fuels, as well as a diversification of power generation. Besides conventional fossil, nuclear plants are coming up again. Renewable energy sources are gaining importance resulting in recent boom of wind energy plants. In the past reliability and availability and an extremely long lifetime were of paramount importance. Today this has been added by cost, due to the global competition and the high fuel costs. New designs of power components have increased efficiency using lesser material. Higher efficiency causes inevitably higher stress on the materials, of which the machines are built. As a reduction of lifetime is not acceptable and maintenance costs are expected to be at a minimum, condition monitoring systems are going to being used now. This offers potentials for fibre optic sensor application.

  12. 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.

  13. Potential energy surface of triplet N2O2

    NASA Astrophysics Data System (ADS)

    Varga, Zoltan; Meana-Pañeda, Rubén; Song, Guoliang; Paukku, Yuliya; Truhlar, Donald G.

    2016-01-01

    We present a global ground-state triplet potential energy surface for the N2O2 system that is suitable for treating high-energy vibrational-rotational energy transfer and collision-induced dissociation. The surface is based on multi-state complete-active-space second-order perturbation theory/minimally augmented correlation-consistent polarized valence triple-zeta electronic structure calculations plus dynamically scaled external correlation. In the multireference calculations, the active space has 14 electrons in 12 orbitals. The calculations cover nine arrangements corresponding to dissociative diatom-diatom collisions of N2, O2, and nitric oxide (NO), the interaction of a triatomic molecule (N2O and NO2) with the fourth atom, and the interaction of a diatomic molecule with a single atom (i.e., the triatomic subsystems). The global ground-state potential energy surface was obtained by fitting the many-body interaction to 54 889 electronic structure data points with a fitting function that is a permutationally invariant polynomial in terms of bond-order functions of the six interatomic distances.

  14. Potential energy surface of triplet N2O2.

    PubMed

    Varga, Zoltan; Meana-Pañeda, Rubén; Song, Guoliang; Paukku, Yuliya; Truhlar, Donald G

    2016-01-14

    We present a global ground-state triplet potential energy surface for the N2O2 system that is suitable for treating high-energy vibrational-rotational energy transfer and collision-induced dissociation. The surface is based on multi-state complete-active-space second-order perturbation theory/minimally augmented correlation-consistent polarized valence triple-zeta electronic structure calculations plus dynamically scaled external correlation. In the multireference calculations, the active space has 14 electrons in 12 orbitals. The calculations cover nine arrangements corresponding to dissociative diatom-diatom collisions of N2, O2, and nitric oxide (NO), the interaction of a triatomic molecule (N2O and NO2) with the fourth atom, and the interaction of a diatomic molecule with a single atom (i.e., the triatomic subsystems). The global ground-state potential energy surface was obtained by fitting the many-body interaction to 54 889 electronic structure data points with a fitting function that is a permutationally invariant polynomial in terms of bond-order functions of the six interatomic distances. PMID:26772574

  15. Molecular dynamics simulation of nano-indentation of (111) cubic boron nitride with optimized Tersoff potential

    NASA Astrophysics Data System (ADS)

    Zhao, Yinbo; Peng, Xianghe; Fu, Tao; Huang, Cheng; Feng, Chao; Yin, Deqiang; Wang, Zhongchang

    2016-09-01

    We conduct molecular dynamics simulation of nanoindentation on (111) surface of cubic boron nitride and find that shuffle-set dislocations slip along <112> direction on {111} plane at the initial stage of the indentation. The shuffle-set dislocations are then found to meet together, forming surfaces of a tetrahedron. We also find that the surfaces are stacking-fault zones, which intersect with each other, forming edges of stair-rod dislocations along <110> direction. Moreover, we also calculate the generalized stacking fault (GSF) energies along various gliding directions on several planes and find that the GSF energies of the <112>{111} and <110>{111} systems are relatively smaller, indicating that dislocations slip more easily along <110> and <112> directions on the {111} plane.

  16. Angular dependent potential for α-boron and large-scale molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Pokatashkin, P.; Kuksin, A.; Yanilkin, A.

    2015-06-01

    Both quantum mechanical and molecular-dynamics (MD) simulations of α-boron are done at this work. Angular dependent interatomic potential (ADP) for boron is obtained using force-matching technique. Fitting data are based on ab initio results within  -20..100 GPa pressure range and temperatures up to 2000 K. Characteristics of α-boron, obtained using ADP potential such as bond lengths at equilibrium condition, bulk modulus, pressure-volume relations, Gruneisen coefficient, thermal expansion coefficient are in good agreement with both ab initio data, obtained in this work and known experimental data. As an example of application, the propagation of shock waves through a single crystal of α-boron is also explored by large-scale MD simulations.

  17. Immunohistochemical detection of a potential molecular therapeutic target for canine hemangiosarcoma

    PubMed Central

    ADACHI, Mami; HOSHINO, Yuki; IZUMI, Yusuke; TAKAGI, Satoshi

    2015-01-01

    Canine hemangiosarcoma (HSA) is a progressive malignant neoplasm of dogs for which there is currently no effective treatment. A recent study suggested that receptor tyrosine kinases (RTKs), the PI3K/Akt/m-TOR and MAPK pathways are all activated in canine and human HSA. The aim of the present study was to investigate the overexpression of these proteins by immunohistochemistry in canine splenic HSA to identify potential molecular therapeutic targets. A total of 10 splenic HSAs and two normal splenic samples surgically resected from dogs were sectioned and stained with hematoxylin and eosin for histological diagnosis or analyzed using immunohistochemistry. The expression of RTKs, c-kit, VEGFR-2 and PDGFR-2, as well as PI3K/Akt/m-TOR and MEK was higher in canine splenic HSAs compared to normal spleens. These proteins may therefore be potential therapeutic targets in canine splenic HSA. PMID:26685984

  18. Identification of NbME MITE families: potential molecular markers in the microsporidia Nosema bombycis.

    PubMed

    Xu, Jinshan; Wang, Min; Zhang, Xiaoyan; Tang, Fahui; Pan, Guoqing; Zhou, Zeyang

    2010-01-01

    Six novel families of miniature inverted-repeat transposable elements (MITEs) were characterized in the microsporidia Nosema bombycis and were named NbMEs. The structural characteristics and the distribution of NbME copies in the N. bombycis genome were investigated, and it was found that portions of NbMEs are associated with gene sections. Potential molecular markers for various N. bombycis strains were identified in this study through utilization of the MITE-AFLP technique. Three distinct pathogenic isolates collected from different areas were distinguished, and polymorphisms were detected using the NbME5 marker, thereby establishing this NbME as a potential marker for studying isolate variation in N. bombycis. PMID:19861130

  19. Immunohistochemical detection of a potential molecular therapeutic target for canine hemangiosarcoma.

    PubMed

    Adachi, Mami; Hoshino, Yuki; Izumi, Yusuke; Takagi, Satoshi

    2016-05-01

    Canine hemangiosarcoma (HSA) is a progressive malignant neoplasm of dogs for which there is currently no effective treatment. A recent study suggested that receptor tyrosine kinases (RTKs), the PI3K/Akt/m-TOR and MAPK pathways are all activated in canine and human HSA. The aim of the present study was to investigate the overexpression of these proteins by immunohistochemistry in canine splenic HSA to identify potential molecular therapeutic targets. A total of 10 splenic HSAs and two normal splenic samples surgically resected from dogs were sectioned and stained with hematoxylin and eosin for histological diagnosis or analyzed using immunohistochemistry. The expression of RTKs, c-kit, VEGFR-2 and PDGFR-2, as well as PI3K/Akt/m-TOR and MEK was higher in canine splenic HSAs compared to normal spleens. These proteins may therefore be potential therapeutic targets in canine splenic HSA. PMID:26685984

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

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

    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.

  1. Ranking protein-protein docking results using steered molecular dynamics and potential of mean force calculations.

    PubMed

    Kingsley, Laura J; Esquivel-Rodríguez, Juan; Yang, Ying; Kihara, Daisuke; Lill, Markus A

    2016-07-01

    Crystallization of protein-protein complexes can often be problematic and therefore computational structural models are often relied on. Such models are often generated using protein-protein docking algorithms, where one of the main challenges is selecting which of several thousand potential predictions represents the most near-native complex. We have developed a novel technique that involves the use of steered molecular dynamics (sMD) and umbrella sampling to identify near-native complexes among protein-protein docking predictions. Using this technique, we have found a strong correlation between our predictions and the interface RMSD (iRMSD) in ten diverse test systems. On two of the systems, we investigated if the prediction results could be further improved using potential of mean force calculations. We demonstrated that a near-native (<2.0 Å iRMSD) structure could be identified in the top-1 ranked position for both systems. © 2016 Wiley Periodicals, Inc. PMID:27232548

  2. Artificial Bee Colony Optimization of Capping Potentials for Hybrid Quantum Mechanical/Molecular Mechanical Calculations.

    PubMed

    Schiffmann, Christoph; Sebastiani, Daniel

    2011-05-10

    We present an algorithmic extension of a numerical optimization scheme for analytic capping potentials for use in mixed quantum-classical (quantum mechanical/molecular mechanical, QM/MM) ab initio calculations. Our goal is to minimize bond-cleavage-induced perturbations in the electronic structure, measured by means of a suitable penalty functional. The optimization algorithm-a variant of the artificial bee colony (ABC) algorithm, which relies on swarm intelligence-couples deterministic (downhill gradient) and stochastic elements to avoid local minimum trapping. The ABC algorithm outperforms the conventional downhill gradient approach, if the penalty hypersurface exhibits wiggles that prevent a straight minimization pathway. We characterize the optimized capping potentials by computing NMR chemical shifts. This approach will increase the accuracy of QM/MM calculations of complex biomolecules. PMID:26610125

  3. Development of empirical potential functions for the study of molecular geometry, and applications to chlorophyll a dimers

    SciTech Connect

    Oie, Tetsuro

    1980-07-28

    A purpose of the present studies is twofold: (1) development of an empirical potential function (EDF) and (2) application of it to the studies of photoreaction center chlorophyll a dimer. The reliable estimate of geometric structures and energies of large molecules by quantum mechanical methods is not possible at the present time. An alternative method is, therefore, needed for the studies of large molecular systems, and Chapter I is dedicated to the development of this tool, i.e., an empirical potential function, which could suffice this purpose. Because of a large number of variable chemical compositions and functional groups characteristically present in a large molecule, it is important to include a large number of structurally diverse molecules in the development of the EPF. In Chapter II, the EPF is applied to study the geometrical structure of a chlorophyll a (Ch1 a) dimer, which is believed to exist at the photoreaction center of green plants and is known to play an essential role in photosynthetic energy conversion. Although various models have been proposed for this dimer structure, there is still a great need for information concerning the detailed geometric structure of this dimer. Therefore, in this chapter the structural stabilities of various dimer models are examined by the EPF, and detailed and quantitative information on the structure and stability of these models is provided.

  4. Development of empirical potential functions for the study of molecular geometry, and applications to chlorophyll a dimers. [Dissertation

    SciTech Connect

    Oie, Tetsuro

    1980-01-01

    A purpose of the present studies is twofold: (1) development of an empirical potential function (EPF) and (2) application of it to the studies of photoreaction center chlorophyll a dimer. The reliable estimate of geometric structures and energies of large molecules by quantum mechanical methods is not possible at the present time. An alternative method is, therefore, needed for the studies of large molecular systems, and Chapter I is dedicated to the development of this tool, i.e., an empirical potential function, which could suffice this purpose. Because of a large number of variable chemical compositions and functional groups characteristically present in a large molecule, it is important to include a large number of structurally diverse molecules in the development of the EPF. In Chapter II, the EPF is applied to study the geometrical structure of a chlorophyll a (Chl a) dimer, which is believed to exist at the photoreaction center of green plants and is known to play an essential role in photosynthetic energy conversion. Although various models have been proposed for this dimer structure, there is still a great need for information concerning the detailed geometric structure of this dimer. Therefore, in this chapter the structural stabilities of various dimer models are examined by the EPF, and detailed and quantitative information on the structure and stability of these models is provided.

  5. Quantitative proteomic analysis of amniocytes reveals potentially dysregulated molecular networks in Down syndrome

    PubMed Central

    2013-01-01

    Background Down syndrome (DS), caused by an extra copy of chromosome 21, affects 1 in 750 live births and is characterized by cognitive impairment and a constellation of congenital defects. Currently, little is known about the molecular pathogenesis and no direct genotype-phenotype relationship has yet been confirmed. Since DS amniocytes are expected to have a distinct biological behaviour compared to normal amniocytes, we hypothesize that relative quantification of proteins produced from trisomy and euploid (chromosomally normal) amniocytes will reveal dysregulated molecular pathways. Results Chromosomally normal- and Trisomy 21-amniocytes were quantitatively analyzed by using Stable Isotope Labeling of Amino acids in Cell culture and tandem mass spectrometry. A total of 4919 unique proteins were identified from the supernatant and cell lysate proteome. More specifically, 4548 unique proteins were identified from the lysate, and 91% of these proteins were quantified based on MS/MS spectra ratios of peptides containing isotope-labeled amino acids. A total of 904 proteins showed significant differential expression and were involved in 25 molecular pathways, each containing a minimum of 16 proteins. Sixty of these proteins consistently showed aberrant expression from trisomy 21 affected amniocytes, indicating their potential role in DS pathogenesis. Nine proteins were analyzed with a multiplex selected reaction monitoring assay in an independent set of Trisomy 21-amniocyte samples and two of them (SOD1 and NES) showed a consistent differential expression. Conclusions The most extensive proteome of amniocytes and amniotic fluid has been generated and differentially expressed proteins from amniocytes with Trisomy 21 revealed molecular pathways that seem to be most significantly affected by the presence of an extra copy of chromosome 21. PMID:23394617

  6. Role of electrostatic potential in the in silico prediction of molecular bioactivation and mutagenesis.

    PubMed

    Ford, Kevin A

    2013-04-01

    Electrostatic potential (ESP) is a useful physicochemical property of a molecule that provides insights into inter- and intramolecular associations, as well as prediction of likely sites of electrophilic and nucleophilic metabolic attack. Knowledge of sites of metabolic attack is of paramount importance in DMPK research since drugs frequently fail in clinical trials due to the formation of bioactivated metabolites which are often difficult to measure experimentally due to their reactive nature and relatively short half-lives. Computational chemistry methods have proven invaluable in recent years as a means to predict and study bioactivated metabolites without the need for chemical syntheses, or testing on experimental animals. Additional molecular properties (heat of formation, heat of solvation and E(LUMO) - E(HOMO)) are discussed in this paper as complementary indicators of the behavior of metabolites in vivo. Five diverse examples are presented (acetaminophen, aniline/phenylamines, imidacloprid, nefazodone and vinyl chloride) which illustrate the utility of this multidimensional approach in predicting bioactivation, and in each case the predicted data agreed with experimental data described in the scientific literature. A further example of the usefulness of calculating ESP, in combination with the molecular properties mentioned above, is provided by an examination of the use of these parameters in providing an explanation for the sites of nucleophilic attack of the nucleic acid cytosine. Exploration of sites of nucleophilic attack of nucleic acids is important as adducts of DNA have the potential to result in mutagenesis. PMID:23323940

  7. Molecular Expression Profile Reveals Potential Biomarkers and Therapeutic Targets in Canine Endometrial Lesions

    PubMed Central

    Voorwald, Fabiana Azevedo; Marchi, Fabio Albuquerque; Villacis, Rolando Andre Rios; Alves, Carlos Eduardo Fonseca; Toniollo, Gilson Hélio; Amorim, Renee Laufer

    2015-01-01

    Cystic endometrial hyperplasia (CEH), mucometra, and pyometra are common uterine diseases in intact dogs, with pyometra being a life threatening disease. This study aimed to determine the gene expression profile of these lesions and potential biomarkers for closed-cervix pyometra, the most severe condition. Total RNA was extracted from 69 fresh endometrium samples collected from 21 healthy female dogs during diestrus, 16 CEH, 15 mucometra and 17 pyometra (eight open and nine closed-cervixes). Global gene expression was detected using the Affymetrix Canine Gene 1.0 ST Array. Unsupervised analysis revealed two clusters, one mainly composed of diestrus and CEH samples and the other by 12/15 mucometra and all pyometra samples. When comparing pyometra with other groups, 189 differentially expressed genes were detected. SLPI, PTGS2/COX2, MMP1, S100A8, S100A9 and IL8 were among the top up-regulated genes detected in pyometra, further confirmed by external expression data. Notably, a particular molecular profile in pyometra from animals previously treated with exogenous progesterone compounds was observed in comparison with pyometra from untreated dogs as well as with other groups irrespective of exogenous hormone treatment status. In addition to S100A8 and S100A9 genes, overexpression of the inflammatory cytokines IL1B, TNF and IL6 as well as LTF were detected in the pyometra from treated animals. Interestingly, closed pyometra was more frequently detected in treated dogs (64% versus 33%), with IL1B, TNF, LBP and CXCL10 among the most relevant overexpressed genes. This molecular signature associated with potential biomarkers and therapeutic targets, such as CXCL10 and COX2, should guide future clinical studies. Based on the gene expression profile we suggested that pyometra from progesterone treated dogs is a distinct molecular entity. PMID:26222498

  8. Molecular Expression Profile Reveals Potential Biomarkers and Therapeutic Targets in Canine Endometrial Lesions.

    PubMed

    Voorwald, Fabiana Azevedo; Marchi, Fabio Albuquerque; Villacis, Rolando Andre Rios; Alves, Carlos Eduardo Fonseca; Toniollo, Gilson Hélio; Amorim, Renee Laufer; Drigo, Sandra Aparecida; Rogatto, Silvia Regina

    2015-01-01

    Cystic endometrial hyperplasia (CEH), mucometra, and pyometra are common uterine diseases in intact dogs, with pyometra being a life threatening disease. This study aimed to determine the gene expression profile of these lesions and potential biomarkers for closed-cervix pyometra, the most severe condition. Total RNA was extracted from 69 fresh endometrium samples collected from 21 healthy female dogs during diestrus, 16 CEH, 15 mucometra and 17 pyometra (eight open and nine closed-cervixes). Global gene expression was detected using the Affymetrix Canine Gene 1.0 ST Array. Unsupervised analysis revealed two clusters, one mainly composed of diestrus and CEH samples and the other by 12/15 mucometra and all pyometra samples. When comparing pyometra with other groups, 189 differentially expressed genes were detected. SLPI, PTGS2/COX2, MMP1, S100A8, S100A9 and IL8 were among the top up-regulated genes detected in pyometra, further confirmed by external expression data. Notably, a particular molecular profile in pyometra from animals previously treated with exogenous progesterone compounds was observed in comparison with pyometra from untreated dogs as well as with other groups irrespective of exogenous hormone treatment status. In addition to S100A8 and S100A9 genes, overexpression of the inflammatory cytokines IL1B, TNF and IL6 as well as LTF were detected in the pyometra from treated animals. Interestingly, closed pyometra was more frequently detected in treated dogs (64% versus 33%), with IL1B, TNF, LBP and CXCL10 among the most relevant overexpressed genes. This molecular signature associated with potential biomarkers and therapeutic targets, such as CXCL10 and COX2, should guide future clinical studies. Based on the gene expression profile we suggested that pyometra from progesterone treated dogs is a distinct molecular entity. PMID:26222498

  9. 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

  10. 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).

  11. 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.

  12. Theoretical prediction of the potential curves for the lowest-lying states of the C2 + molecular ion

    NASA Astrophysics Data System (ADS)

    Petrongolo, Carlo; Bruna, Pablo J.; Peyerimhoff, Sigrid D.; Buenker, Robert J.

    1981-04-01

    Ab initio MRD-CI potential curves have been calculated for C2+ in its first 16 electronic states and vertical transition energies Tv have been computed for a number of higher-lying species, all of which correlate with the first dissociation limit C(3Pg)+C+(2Pu). The ground state of this molecular ion is found to be X 4Σg- while the first excited state is 1 2Πu, with a calculated Te value of 0.84 eV. On the basis of this work the C2 I.P. value known experimentally is ascribed to the a 3Πu→1 2Πu process while the transition involving both ground states appears to be difficult to detect experimentlly. Thus, the measured De value for C+2 should involve fragmentation of the 1 2Πu states as well. A comparison with previous calculations which attempt to estimate the correlation energies of the various C+2 states in a semiempirical manner shows very large discrepancies, both in the transition energies themselves and in the ordering of these states. Finally the assignment for the Meinel experimental band system at 4.98 eV as a 2Σ-g←2Πu transition in C+2 is not supported by the present theoretical study.

  13. 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.

  14. Molecular links between early energy metabolism alterations and Alzheimer's disease.

    PubMed

    Pedros, Ignacio; Patraca, Ivan; Martinez, Nohora; Petrov, Dmitry; Sureda, Francesc X; Auladell, Carme; Beas-Zarate, Carlos; Folch, Jaume

    2016-01-01

    Recent studies suggest that the neurobiology of Alzheimer's disease (AD) pathology could not be explained solely by an increase in beta-amyloid levels. In fact, success with potential therapeutic drugs that inhibit the generation of beta amyloid has been low. Therefore, due to therapeutic failure in recent years, the scientists are looking for alternative hypotheses to explain the causes of the disease and the cognitive loss. Accordingly, alternative hypothesis propose a link between AD and peripheral metabolic alteration. Then, we review in depth changes related to insulin signalling and energy metabolism in the context of the APPSwe/PS1dE9 (APP/PS1) mice model of AD. We show an integrated view of the changes that occur in the early stages of the amyloidogenic process in the APP/PS1 double transgenic mice model. These early changes affect several key metabolic processes related to glucose uptake and insulin signalling, cellular energy homeostasis, mitochondrial biogenesis and increased Tau phosphorylation by kinase molecules like mTOR and Cdk5. PMID:26709757

  15. Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP\\H-REMD) for absolute ligand binding free energy calculations.

    SciTech Connect

    Jiang, W.; Roux, B.

    2010-09-01

    Free Energy Perturbation with Replica Exchange Molecular Dynamics (FEP/REMD) offers a powerful strategy to improve the convergence of free energy computations. In particular, it has been shown previously that a FEP/REMD scheme allowing random moves within an extended replica ensemble of thermodynamic coupling parameters '{lambda}' can improve the statistical convergence in calculations of absolute binding free energy of ligands to proteins [J. Chem. Theory Comput. 2009, 5, 2583]. In the present study, FEP/REMD is extended and combined with an accelerated MD simulations method based on Hamiltonian replica-exchange MD (H-REMD) to overcome the additional problems arising from the existence of kinetically trapped conformations within the protein receptor. In the combined strategy, each system with a given thermodynamic coupling factor {lambda} in the extended ensemble is further coupled with a set of replicas evolving on a biased energy surface with boosting potentials used to accelerate the interconversion among different rotameric states of the side chains in the neighborhood of the binding site. Exchanges are allowed to occur alternatively along the axes corresponding to the thermodynamic coupling parameter {lambda} and the boosting potential, in an extended dual array of coupled {lambda}- and H-REMD simulations. The method is implemented on the basis of new extensions to the REPDSTR module of the biomolecular simulation program CHARMM. As an illustrative example, the absolute binding free energy of p-xylene to the nonpolar cavity of the L99A mutant of the T4 lysozyme was calculated. The tests demonstrate that the dual {lambda}-REMD and H-REMD simulation scheme greatly accelerates the configurational sampling of the rotameric states of the side chains around the binding pocket, thereby improving the convergence of the FEP computations.

  16. 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.

  17. 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.

  18. Intermolecular potential energy surface and thermophysical properties of ethylene oxide.

    PubMed

    Crusius, Johann-Philipp; Hellmann, Robert; Hassel, Egon; Bich, Eckard

    2014-10-28

    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. PMID:25362314

  19. 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.

  20. 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.

  1. Comparing the accuracy of high-dimensional neural network potentials and the systematic molecular fragmentation method: A benchmark study for all-trans alkanes

    NASA Astrophysics Data System (ADS)

    Gastegger, Michael; Kauffmann, Clemens; Behler, Jörg; Marquetand, Philipp

    2016-05-01

    Many approaches, which have been developed to express the potential energy of large systems, exploit the locality of the atomic interactions. A prominent example is the fragmentation methods in which the quantum chemical calculations are carried out for overlapping small fragments of a given molecule that are then combined in a second step to yield the system's total energy. Here we compare the accuracy of the systematic molecular fragmentation approach with the performance of high-dimensional neural network (HDNN) potentials introduced by Behler and Parrinello. HDNN potentials are similar in spirit to the fragmentation approach in that the total energy is constructed as a sum of environment-dependent atomic energies, which are derived indirectly from electronic structure calculations. As a benchmark set, we use all-trans alkanes containing up to eleven carbon atoms at the coupled cluster level of theory. These molecules have been chosen because they allow to extrapolate reliable reference energies for very long chains, enabling an assessment of the energies obtained by both methods for alkanes including up to 10 000 carbon atoms. We find that both methods predict high-quality energies with the HDNN potentials yielding smaller errors with respect to the coupled cluster reference.

  2. Comparing the accuracy of high-dimensional neural network potentials and the systematic molecular fragmentation method: A benchmark study for all-trans alkanes.

    PubMed

    Gastegger, Michael; Kauffmann, Clemens; Behler, Jörg; Marquetand, Philipp

    2016-05-21

    Many approaches, which have been developed to express the potential energy of large systems, exploit the locality of the atomic interactions. A prominent example is the fragmentation methods in which the quantum chemical calculations are carried out for overlapping small fragments of a given molecule that are then combined in a second step to yield the system's total energy. Here we compare the accuracy of the systematic molecular fragmentation approach with the performance of high-dimensional neural network (HDNN) potentials introduced by Behler and Parrinello. HDNN potentials are similar in spirit to the fragmentation approach in that the total energy is constructed as a sum of environment-dependent atomic energies, which are derived indirectly from electronic structure calculations. As a benchmark set, we use all-trans alkanes containing up to eleven carbon atoms at the coupled cluster level of theory. These molecules have been chosen because they allow to extrapolate reliable reference energies for very long chains, enabling an assessment of the energies obtained by both methods for alkanes including up to 10 000 carbon atoms. We find that both methods predict high-quality energies with the HDNN potentials yielding smaller errors with respect to the coupled cluster reference. PMID:27208939

  3. Potential molecular mechanisms underlying muscle fatigue mediated by reactive oxygen and nitrogen species

    PubMed Central

    Debold, Edward P.

    2015-01-01

    Intense contractile activity causes a dramatic decline in the force and velocity generating capacity of skeletal muscle within a few minutes, a phenomenon that characterizes fatigue. Much of the research effort has focused on how elevated levels of the metabolites of ATP hydrolysis might inhibit the function of the contractile proteins. However, there is now growing evidence that elevated levels of reactive oxygen and nitrogen species (ROS/RNS), which also accumulate in the myoplasm during fatigue, also play a causative role in this type of fatigue. The most compelling evidence comes from observations demonstrating that pre-treatment of intact muscle with a ROS scavenger can significantly attenuate the development of fatigue. A clear advantage of this line of inquiry is that the molecular targets and protein modifications of some of the ROS scavengers are well-characterized enabling researchers to begin to identify potential regions and even specific amino acid residues modified during fatigue. Combining this knowledge with assessments of contractile properties from the whole muscle level down to the dynamic motions within specific contractile proteins enable the linking of the structural modifications to the functional impacts, using advanced chemical and biophysical techniques. Based on this approach at least two areas are beginning emerge as potentially important sites, the regulatory protein troponin and the actin binding region of myosin. This review highlights some of these recent efforts which have the potential to offer uniquely precise information on the underlying molecular basis of fatigue. This work may also have implications beyond muscle fatigue as ROS/RNS mediated protein modifications are also thought to play a role in the loss of muscle function with aging and in some acute pathologies like cardiac arrest and ischemia. PMID:26388779

  4. Nuclear binding energy and symmetry energy of nuclear matter with modern nucleon-nucleon potentials

    SciTech Connect

    Hassaneen, Kh.S.A.; Abo-Elsebaa, H.M.; Sultan, E.A.; Mansour, H.M.M.

    2011-03-15

    Research Highlights: > The nuclear matter is studied within the Brueckner-Hartree-Fock (BHF) approach employing the most recent accurate nucleon-nucleon potentials. > The results come out by approximating the single particle self-consistent potential with a parabolic form. > We discuss the current status of the Coester line, i.e., density and energy of the various saturation points being strongly linearly correlated. > The nuclear symmetry energy is calculated as the difference between the binding energy of pure neutron matter and that of symmetric nuclear matter. - Abstract: The binding energy of nuclear matter at zero temperature in the Brueckner-Hartree-Fock approximation with modern nucleon-nucleon potentials is studied. Both the standard and continuous choices of single particle energies are used. These modern nucleon-nucleon potentials fit the deuteron properties and are phase shifts equivalent. Comparison with other calculations is made. In addition we present results for the symmetry energy obtained with different potentials, which is of great importance in astrophysical calculation.

  5. A new measure of molecular attractions between nanoparticles near kT adhesion energy.

    PubMed

    Kendall, Kevin; Dhir, Aman; Du, Shangfeng

    2009-07-01

    The weak molecular attractions of nanoparticles are important because they drive self-assembly mechanisms, allow processing in dispersions e.g. of pigments, catalysts or device structures, influence disease through the attraction of viruses to cells and also cause potential toxic effects through nanoparticle interference with biomolecules and organs. The problem is to understand these small forces which pull nanoparticles into intimate contact; forces which are comparable with 3kT/2z the thermal impact force experienced by an average Brownian particle hitting a linear repulsive potential of range z. Here we describe a new method for measuring the atomic attractions of nanoparticles based on the observation of aggregates produced by these small forces. The method is based on the tracking of individual monosize nanoparticles whose diameter can be calculated from the Stokes-Einstein analysis of the tracks in aqueous suspensions. Then the doublet aggregates are distinguished because they move slower and are also very much brighter than the dispersed nanoparticles. By finding the ratio of doublets to singlets, the adhesive energy between the particles can be calculated from known statistical thermodynamic theory using assumptions about the shape of the interaction potential. In this way, very small adhesion energies of 2kT have been measured, smaller than those seen previously by atomic force microscopy (AFM) and scanning tunneling microscopy (STM). PMID:19531867

  6. Synthesis, characterisation, spectral, thermal, XRD, molecular modelling and potential antibacterial study of metal complexes containing octadentate azodye ligands

    NASA Astrophysics Data System (ADS)

    Mahapatra, Bipin Bihari; Chaulia, Satyanarayan; Sarangi, Ashish Kumar; Dehury, Satyanarayan; Panda, Jnyanaranjan

    2015-05-01

    Twelve tetrametallic complexes of Co(II), Ni(II), Cu(II), Zn(II), Cd(II) and Hg(II) with two new octadentate azodye ligands, 4,4‧-bis(2‧,4‧-dihydroxy-5‧carboxyphenylazo) diphenylether (LH6) and 4,4‧-bis(2‧,4‧-dihydroxy-5‧-acylphenylazo) diphenylether (L‧H4) have been synthesised. The structural elucidation of the complexes was made basing upon analytical, conductance, magnetic susceptibility, IR, electronic spectra, ESR, NMR, ESI-MS, TG, DTG, DTA and X-ray diffraction (powder pattern) data. The cobalt (II) and nickel (II) complexes are found to be octahedral, copper (II) complexes are distorted octahedral and a tetrahedral stereochemistry has been suggested to zinc (II), cadmium (II) and mercury (II) complexes. The thermal analysis data provided the kinetic parameters as order of decomposition reaction, activation energy and frequency factor. The geometry of the ligands and their Co(II), Ni(II), Cu(II) and Zn(II) complexes were optimised and their physicochemical properties were calculated by using molecular modelling procedure. The ESI-MS determination supports the molecular formula and molecular weight of the ligands and the complexes. The Ni(II) complex is found to have a triclinic crystal system. The potential antibacterial study of the two ligands and eight metal complexes was made by cup-plate method against one gram positive and one gram negative bacteria. The results showed increase in the activity of some metal complexes as compare with azodye ligands.

  7. Potential for energy savings in old and new auto engines

    NASA Astrophysics Data System (ADS)

    Reitz, John R.

    1985-11-01

    This paper disucsses the potential for energy savings in the transportation sector through the use of both improved and entirely new automotive engines. Although spark-ignition and diesel internal combustion engines will remain the dominant choices for passenger-car use throughout the rest of this century, improved versions of these engines (lean-burn, low-friction spark-ignition and adiabatic, low-friction diesel engines) could, in the long term, provide a 20-30 percent improvement in fuel economy over what is currently available. The use of new materials, and modifications to both vehicle structure and vehicle transmissions may yield further improvements. Over a longer time frame, the introduction of the high-temperature gas-turbine engine and the use of new synfuels may provide further opportunities for energy conservation.

  8. Ab initio potential energy surface and rovibrational states of HBO

    NASA Astrophysics Data System (ADS)

    Ha, Tae-Kyu; Makarewicz, Jan

    1999-01-01

    The potential energy surface describing the large-amplitude motion of H around the BO core in the HBO molecule has been determined from ab initio calculations. This surface has been sampled by a set of 170 grid points from a two-dimensional space defined by the stretching and the bending coordinates of the H nucleus. At each grid point, the BO bond length has been optimized using the second-order Møller-Plesset perturbation theory with the basis set aug-cc-pVTZ. The surface has a local minimum for the linear as well as the bent configuration of HBO. A low energy barrier to the linear configuration BOH causes a large-amplitude motion and a strong rovibrational interaction in the molecule. Its rovibrational dynamics is different from the dynamics in bent or quasilinear triatomic molecules.

  9. Finite field-energy and interparticle potential in logarithmic electrodynamics

    NASA Astrophysics Data System (ADS)

    Gaete, Patricio; Helayël-Neto, José

    2014-03-01

    We pursue an investigation of logarithmic electrodynamics, for which the field energy of a point-like charge is finite, as happens in the case of the usual Born-Infeld electrodynamics. We also show that, contrary to the latter, logarithmic electrodynamics exhibits the feature of birefringence. Next, we analyze the lowest-order modifications for both logarithmic electrodynamics and for its non-commutative version, within the framework of the gauge-invariant path-dependent variables formalism. The calculation shows a long-range correction (-type) to the Coulomb potential for logarithmic electrodynamics. Interestingly enough, for its non-commutative version, the interaction energy is ultraviolet finite. We highlight the role played by the new quantum of length in our analysis.

  10. 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.

  11. 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.

  12. 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.

  13. Dark Energy:. the Absolute Electric Potential of the Universe

    NASA Astrophysics Data System (ADS)

    Jiménez, Jose Beltrán; Maroto, Antonio L.

    Is there an absolute cosmic electric potential? The recent discovery of the accelerated expansion of the universe could be indicating that this is certainly the case. In this essay we show that the consistency of the covariant and gauge-invariant theory of electromagnetism is truly questionable when considered on cosmological scales. Out of the four components of the electromagnetic field, Maxwell's theory contains only two physical degrees of freedom. However, in the presence of gravity, one of the "unphysical" states cannot be consistently eliminated, thus becoming real. This third polarization state is completely decoupled from charged matter, but can be excited gravitationally, thus breaking gauge invariance. On large scales the new state can be seen as a homogeneous cosmic electric potential, whose energy density behaves as a cosmological constant.

  14. 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.

  15. Two-center interference in molecular photoelectron energy spectra with intense attosecond circularly polarized XUV laser pulses

    NASA Astrophysics Data System (ADS)

    Yuan, Kai-Jun; Bian, Xue-Bin; Bandrauk, André D.

    2014-08-01

    We study two-center electron interference in molecular photoionization processes by intense attosecond circularly polarized extreme ultraviolet (XUV) laser pulses in both symmetric H2+ and nonsymmetric HHe2+ one-electron diatomic systems. Simulations from numerical solutions of time-dependent Schrödinger equations for the oriented symmetric molecular ion H2+ exhibit a signature of interference with double peaks (minima) in molecular attosecond photoelectron energy spectra (MAPES) at critical angles ϑc between the continuum electron momentum pe and the molecular internuclear R axis. The interference patterns are shown to be influenced by the molecular Coulomb potential, leading to a shift of the critical angle ϑc. Dependence of the two-center interference on the pulse ellipticity is also investigated. Furthermore, it is found that the interference phenomena are critically sensitive to the molecular orbital symmetry. For the nonsymmetric molecular ion HHe2+, such double peaks in MAPES also occur, thus suggesting a method for imaging orbitals in molecules by intense ultrashort circularly polarized XUV pulses on the attosecond time scale.

  16. 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. PMID:26476072

  17. 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 .

  18. Influence of rotational energy barriers to the conformational search of protein loops in molecular dynamics and ranking the conformations.

    PubMed

    Tappura, K

    2001-08-15

    An adjustable-barrier dihedral angle potential was added as an extension to a novel, previously presented soft-core potential to study its contribution to the efficacy of the search of the conformational space in molecular dynamics. As opposed to the conventional soft-core potential functions, the leading principle in the design of the new soft-core potential, as well as of its extension, the soft-core and adjustable-barrier dihedral angle (SCADA) potential (referred as the SCADA potential), was to maintain the main equilibrium properties of the original force field. This qualifies the methods for a variety of a priori modeling problems without need for additional restraints typically required with the conventional soft-core potentials. In the present study, the different potential energy functions are applied to the problem of predicting loop conformations in proteins. Comparison of the performance of the soft-core and SCADA potential showed that the main hurdles for the efficient sampling of the conformational space of (loops in) proteins are related to the high-energy barriers caused by the Lennard-Jones and Coulombic energy terms, and not to the rotational barriers, although the conformational search can be further enhanced by lowering the rotational barriers of the dihedral angles. Finally, different evaluation methods were studied and a few promising criteria found to distinguish the near-native loop conformations from the wrong ones. PMID:11455590

  19. Combined-hyperbolic-inverse-power-representation of potential energy surfaces: A preliminary assessment for H_3 and HO_2

    NASA Astrophysics Data System (ADS)

    Varandas, A. J. C.

    2013-02-01

    The purpose is to fit an accurate smooth function of the many-body expansion type to a multidimensional large data set using a basis-set type method. By adopting a combined-hyperbolic-inverse-power-representation for the basis, the novel approach is tested in detail for the ground electronic state of tri-hydrogen and hydroperoxyl systems, assuming that their potential energy surfaces are single-sheeted representable. It is also shown that the method can be easily applicable to potential energy curves by considering as prototypes molecular oxygen and the hydroxyl radical.

  20. Combined-hyperbolic-inverse-power-representation of potential energy surfaces: a preliminary assessment for H3 and HO2.

    PubMed

    Varandas, A J C

    2013-02-01

    The purpose is to fit an accurate smooth function of the many-body expansion type to a multidimensional large data set using a basis-set type method. By adopting a combined-hyperbolic-inverse-power-representation for the basis, the novel approach is tested in detail for the ground electronic state of tri-hydrogen and hydroperoxyl systems, assuming that their potential energy surfaces are single-sheeted representable. It is also shown that the method can be easily applicable to potential energy curves by considering as prototypes molecular oxygen and the hydroxyl radical. PMID:23406111