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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. Advanced Potential Energy Surfaces for Molecular Simulation.

    PubMed

    Albaugh, Alex; Boateng, Henry A; Bradshaw, Richard T; Demerdash, Omar N; Dziedzic, Jacek; Mao, Yuezhi; Margul, Daniel T; Swails, Jason; Zeng, Qiao; Case, David A; Eastman, Peter; Wang, Lee-Ping; Essex, Jonathan W; Head-Gordon, Martin; Pande, Vijay S; Ponder, Jay W; Shao, Yihan; Skylaris, Chris-Kriton; Todorov, Ilian T; Tuckerman, Mark E; Head-Gordon, Teresa

    2016-09-22

    Advanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models and algorithmic improvements that can ameliorate their cost, underdeveloped interfaces and limited dissemination in computational code bases that are widely used in the computational chemistry community, and software implementations that have not kept pace with modern high-performance computing (HPC) architectures, such as multicore CPUs and modern graphics processing units (GPUs). In this Feature Article we review recent progress made in these areas, including well-defined polarization approximations and new multipole electrostatic formulations, novel methods for solving the mutual polarization equations and increasing the MD time step, combining linear-scaling electronic structure methods with new QM/MM methods that account for mutual polarization between the two regions, and the greatly improved software deployment of these models and methods onto GPU and CPU hardware platforms. We have now approached an era where multipole-based polarizable force fields can be routinely used to obtain computational results comparable to state-of-the-art density functional theory while reaching sampling statistics that are acceptable when compared to that obtained from simpler fixed partial charge force fields.

  3. Advanced Potential Energy Surfaces for Molecular Simulation.

    PubMed

    Albaugh, Alex; Boateng, Henry A; Bradshaw, Richard T; Demerdash, Omar N; Dziedzic, Jacek; Mao, Yuezhi; Margul, Daniel T; Swails, Jason; Zeng, Qiao; Case, David A; Eastman, Peter; Wang, Lee-Ping; Essex, Jonathan W; Head-Gordon, Martin; Pande, Vijay S; Ponder, Jay W; Shao, Yihan; Skylaris, Chris-Kriton; Todorov, Ilian T; Tuckerman, Mark E; Head-Gordon, Teresa

    2016-09-22

    Advanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models and algorithmic improvements that can ameliorate their cost, underdeveloped interfaces and limited dissemination in computational code bases that are widely used in the computational chemistry community, and software implementations that have not kept pace with modern high-performance computing (HPC) architectures, such as multicore CPUs and modern graphics processing units (GPUs). In this Feature Article we review recent progress made in these areas, including well-defined polarization approximations and new multipole electrostatic formulations, novel methods for solving the mutual polarization equations and increasing the MD time step, combining linear-scaling electronic structure methods with new QM/MM methods that account for mutual polarization between the two regions, and the greatly improved software deployment of these models and methods onto GPU and CPU hardware platforms. We have now approached an era where multipole-based polarizable force fields can be routinely used to obtain computational results comparable to state-of-the-art density functional theory while reaching sampling statistics that are acceptable when compared to that obtained from simpler fixed partial charge force fields. PMID:27513316

  4. (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.

  5. Nonequilibrium molecular transport photoinduced by potential energy fluctuations

    NASA Astrophysics Data System (ADS)

    Dekhtyar, Marina L.; Rozenbaum, Viktor M.

    2011-01-01

    The mechanism of directed substrate-parallel motion of molecules caused by photoinduced potential energy fluctuations is investigated. Unlike simplistic models (e.g., an on-off ratchet), the approach suggested implies that the necessary asymmetry of the potential energy can arise not only from the asymmetry of the substrate potential but also from an asymmetric distribution of the fluctuating charge density in the molecule. The thus induced asymmetry of the potential energy governs the direction motion and enables, under certain conditions, its reversal at some frequencies of resonant laser pulses or temperature. These inferences are exemplified by the model charge distributions in the molecule and substrate, and the charge density fluctuations which are obtained by quantum chemical calculations for the realistic molecule of a substituted phenylpyrene compound on a model substrate.

  6. An adaptive interpolation scheme for molecular potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Kowalewski, Markus; Larsson, Elisabeth; Heryudono, Alfa

    2016-08-01

    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.

  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. 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.

  9. 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.

  10. Application of potential constants: Empirical determination of molecular energy components for diatomic molecules—II

    NASA Astrophysics Data System (ADS)

    Ohwada, Ken

    The harmonic and anharmonic potential (force) constants which are usually available from a normal coordinate analysis for a diatomic molecule are applied to determine the molecular energy components such as the electronic kinetic energy, the total electrostatic potential energy, the electron—nuclear attraction energy, the electron—electron repulsion energy, the nuclear—nuclear repulsion energy, and the Hartree—Fock eigen-value sum. The method developed here is based on an inhomogeneous linear third-order differential equation derived from the quantum mechanical virial theorem, and a homogeneity hypothesis of the molecular energy with respect to the atomic number. To confirm the utility of the method, the calculated molecular energy components of diatomic molecules are compared with available Hartree—Fock data. It is concluded from this data that the present method is simple and useful for evaluating the molecular energy components of various diatomic molecules.

  11. Molecular spinless energies of the modified Rosen-Morse potential energy model in higher spatial dimensions

    NASA Astrophysics Data System (ADS)

    Jia, Chun-Sheng; Dai, Jian-Wei; Zhang, Lie-Hui; Liu, Jian-Yi; Zhang, Guang-Dong

    2015-01-01

    We solve the Klein-Gordon equation with the modified Rosen-Morse potential energy model in D spatial dimensions. The bound state energy equation has been obtained by using the supersymmetric WKB approximation approach. We find that the inter-dimensional degeneracy symmetry exists for the molecular system represented by the modified Rosen-Morse potential. For fixed vibrational and rotational quantum numbers, the relativistic energies for the 61Πu state of the 7Li2 molecule and the X3Π state of the SiC radical increase as D increases. We observe that the behavior of the relativistic vibrational energies in higher dimensions remains similar to that of the three-dimensional system.

  12. 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

  13. 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.

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

    PubMed

    Cheung, Ngaam J; Shen, Hong-Bin

    2014-11-01

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

  15. 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

  16. 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.

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

    PubMed

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

    2006-06-28

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

  18. 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

  19. 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

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. Computation of methodology-independent ionic solvation free energies from molecular simulations. I. The electrostatic potential in molecular liquids

    NASA Astrophysics Data System (ADS)

    Kastenholz, M. A.; Hünenberger, Philippe H.

    2006-03-01

    The computation of ionic solvation free energies from atomistic simulations is a surprisingly difficult problem that has found no satisfactory solution for more than 15years. The reason is that the charging free energies evaluated from such simulations are affected by very large errors. One of these is related to the choice of a specific convention for summing up the contributions of solvent charges to the electrostatic potential in the ionic cavity, namely, on the basis of point charges within entire solvent molecules (M scheme) or on the basis of individual point charges (P scheme). The use of an inappropriate convention may lead to a charge-independent offset in the calculated potential, which depends on the details of the summation scheme, on the quadrupole-moment trace of the solvent molecule, and on the approximate form used to represent electrostatic interactions in the system. However, whether the M or P scheme (if any) represents the appropriate convention is still a matter of on-going debate. The goal of the present article is to settle this long-standing controversy by carefully analyzing (both analytically and numerically) the properties of the electrostatic potential in molecular liquids (and inside cavities within them). Restricting the discussion to real liquids of "spherical" solvent molecules (represented by a classical solvent model with a single van der Waals interaction site), it is concluded that (i) for Coulombic (or straight-cutoff truncated) electrostatic interactions, the M scheme is the appropriate way of calculating the electrostatic potential; (ii) for non-Coulombic interactions deriving from a continuously differentiable function, both M and P schemes generally deliver an incorrect result (for which an analytical correction must be applied); and (iii) finite-temperature effects, including intermolecular orientation correlations and a preferential orientational structure in the neighborhood of a liquid-vacuum interface, must be taken

  6. Systematic Fragmentation Method and the Effective Fragment Potential: An Efficient Method for Capturing Molecular Energies

    NASA Astrophysics Data System (ADS)

    Mullin, Jonathan M.; Roskop, Luke B.; Pruitt, Spencer R.; Collins, Michael A.; Gordon, Mark S.

    2009-08-01

    The systematic fragmentation method fragments a large molecular system into smaller pieces, in such a way as to greatly reduce the computational cost while retaining nearly the accuracy of the parent ab initio electronic structure method. In order to attain the desired (sub-kcal/mol) accuracy, one must properly account for the nonbonded interactions between the separated fragments. Since, for a large molecular species, there can be a great many fragments and therefore a great many nonbonded interactions, computations of the nonbonded interactions can be very time-consuming. The present work explores the efficacy of employing the effective fragment potential (EFP) method to obtain the nonbonded interactions since the EFP method has been shown previously to capture nonbonded interactions with an accuracy that is often comparable to that of second-order perturbation theory. It is demonstrated that for nonbonded interactions that are not high on the repulsive wall (generally >2.7 Å), the EFP method appears to be a viable approach for evaluating the nonbonded interactions. The efficacy of the EFP method for this purpose is illustrated by comparing the method to ab initio methods for small water clusters, the ZOVGAS molecule, retinal, and the α-helix. Using SFM with EFP for nonbonded interactions yields an error of 0.2 kcal/mol for the retinal cis-trans isomerization and a mean error of 1.0 kcal/mol for the isomerization energies of five small (120-170 atoms) α-helices.

  7. 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.

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

    ScienceCinema

    Sayre, Richard [LANL

    2016-07-12

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

  9. Reaction mechanism of naphthyl radicals with molecular oxygen. 1. Theoretical study of the potential energy surface.

    PubMed

    Zhou, Chong-Wen; Kislov, Vadim V; Mebel, Alexander M

    2012-02-16

    Potential energy surfaces (PESs) of the reactions of 1- and 2-naphthyl radicals with molecular oxygen have been investigated at the G3(MP2,CC)//B3LYP/6-311G** level of theory. Both reactions are shown to be initiated by barrierless addition of O(2) to the respective radical sites of C(10)H(7). The end-on O(2) addition leading to 1- and 2-naphthylperoxy radicals exothermic by 45-46 kcal/mol is found to be more preferable thermodynamically than the side-on addition. At the subsequent reaction step, the chemically activated 1- and 2-C(10)H(7)OO adducts can eliminate an oxygen atom leading to the formation of 1- and 2-naphthoxy radical products, respectively, which in turn can undergo unimolecular decomposition producing indenyl radical + CO via the barriers of 57.8 and 48.3 kcal/mol and with total reaction endothermicities of 14.5 and 10.2 kcal/mol, respectively. Alternatively, the initial reaction adducts can feature an oxygen atom insertion into the attacked C(6) ring leading to bicyclic intermediates a10 and a10' (from 1-naphthyl + O(2)) or b10 and b10' (from 2-naphthyl + O(2)) composed from two fused six-member C(6) and seven-member C(6)O rings. Next, a10 and a10' are predicted to decompose to C(9)H(7) (indenyl) + CO(2), 1,2-C(10)H(6)O(2) (1,2-naphthoquinone) + H, and 1-C(9)H(7)O (1-benzopyranyl) + CO, whereas b10 and b10' would dissociate to C(9)H(7) (indenyl) + CO(2), 2-C(9)H(7)O (2-benzopyranyl) + CO, and 1,2-C(10)H(6)O(2) (1,2-naphthoquinone) + H. On the basis of this, the 1-naphthyl + O(2) reaction is concluded to form the following products (with the overall reaction energies given in parentheses): 1-naphthoxy + O (-15.5 kcal/mol), indenyl + CO(2) (-123.9 kcal/mol), 1-benzopyranyl + CO (-97.2 kcal/mol), and 1,2-naphthoquinone + H (-63.5 kcal/mol). The 2-naphthyl + O(2) reaction is predicted to produce 2-naphthoxy + O (-10.9 kcal/mol), indenyl + CO(2) (-123.7 kcal/mol), 2-benzopyranyl + CO (-90.7 kcal/mol), and 1,2-naphthoquinone + H (-63.2 kcal

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

    PubMed

    Losilla, S A; Sundholm, D

    2012-06-01

    A computational scheme to perform accurate numerical calculations of electrostatic potentials and interaction energies for molecular systems has been developed and implemented. Molecular electron and energy densities are divided into overlapping atom-centered atomic contributions and a three-dimensional molecular remainder. The steep nuclear cusps are included in the atom-centered functions making the three-dimensional remainder smooth enough to be accurately represented with a tractable amount of grid points. The one-dimensional radial functions of the atom-centered contributions as well as the three-dimensional remainder are expanded using finite element functions. The electrostatic potential is calculated by integrating the Coulomb potential for each separate density contribution, using our tensorial finite element method for the three-dimensional remainder. We also provide algorithms to compute accurate electron-electron and electron-nuclear interactions numerically using the proposed partitioning. The methods have been tested on all-electron densities of 18 reasonable large molecules containing elements up to Zn. The accuracy of the calculated Coulomb interaction energies is in the range of 10(-3) to 10(-6) E(h) when using an equidistant grid with a step length of 0.05 a(0).

  11. Molecular vibrational energy flow

    NASA Astrophysics Data System (ADS)

    Gruebele, M.; Bigwood, R.

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

  12. Far-Infrared and Microwave Spectroscopic Examination of Weakly Bound Molecular Complexes: Potential Energy Surfaces and Internal Dynamics

    NASA Astrophysics Data System (ADS)

    Reeve, Scott Wayne

    1992-01-01

    High resolution far infrared gas phase absorption experiments on both the Ar-HX (X = F, Cl, Br) and the Ar -NH_3 systems are described. All of the spectroscopic measurements were obtained with a tunable far infrared difference frequency sideband (TuFIRS) spectrometer which was coupled to a continuous free jet expansion. In each system the low frequency bending and stretching vibrations, corresponding to the van der Waals coordinates, were observed and measured. The experimental measurements allow basic physical properties (e.g., rotational and centrifugal distortion constants) for these systems to be determined which are sensitive to the global topology of the intermolecular potential energy surface, and thus, provide critical tests for the physical models used to construct potential energy surfaces. A high resolution rotational spectroscopic study of the gas phase complex HCN-BF_3, done as a collaborative effort with scientists at the National Institute for Standards and Technology (NIST), is also described. Here, a Fourier transform microwave spectrometer is used to determine the molecular structure and basic physical properties of the HCN-BF_3 complex. We find the molecular structure to be that of an incipiently bonded molecule. In addition, we interpret the molecular structure, and the other measured molecular properties, within the generalized reaction path framework for BF_3 + nitrogen adducts discussed previously by Dvorak, et. al.^1 ftn^1M. A. Dvorak, R. S. Ford, R. D. Suenram, F. J. Lovas, and K. R. Leopold, J. Amer. Chem. Soc., 114, 108 (1992).

  13. Computational prediction of antibody binding sites on tetracycline antibiotics: electrostatic potentials and average local ionization energies on molecular surfaces.

    PubMed

    Kulshrestha, Pankaj; Sukumar, N; Murray, Jane S; Giese, Rossman F; Wood, Troy D

    2009-01-29

    Enzyme linked immunosorbent assay (ELISA) was used for the analysis of tetracycline, chlortetracycline, oxytetracycline, and their transformed compounds in environmental water samples. The antibodies employed in ELISA showed high relative affinity for tetracycline, epitetracycline, chlortetracycline, and epichlortetracycline as compared to anhydrotetracycline, epianhydrotetracycline, and anhydrochlortetracycline. The specificity and crossreactivity of these antibodies are discussed in relation to the electrostatic potentials and average local ionization energies computed on the molecular surfaces of tetracycline antibiotics and their transformed compounds with an objective of identifying common features as well as differences that may be related to the experimentally observed variation in cross-reactivity values. The computations were performed at both the HF/STO-3G and HF/6-31+G* levels using the Gaussian 98 program. The results in this study are based upon molecular electrostatic potentials and local ionization energies computed on isodensity molecular surfaces. The surface electrostatic potentials are characterized in terms of a group of statistically defined quantities, which include the average deviation, the positive, negative, and total variances, positive and negative surface extrema, and a parameter indicating the degree of electrostatic balance.

  14. 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…

  15. 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.

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

    PubMed

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

    2014-11-17

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

  17. The torsion space nucleic acids molecular mechanics program DUPLEX: Surveying conformation space by potential energy minimization. Progress report

    SciTech Connect

    Hingerty, B.E.; Broyde, S.

    1993-11-01

    It has been 21 years since the inception of the program DUPLEX. Now that ``molecular modeling`` (encompassing quantum mechanics, molecular mechanics and dynamics, and computer graphics) has become something of a trade, the time seems ripe for us to offer a brief perspective of our efforts since the beginnings of the field. The purpose in writing the program was to solve the crystal structure of Ca{sup +2}-GpC, an RNA subunit for which x-ray diffraction data had been collected by T. Sato. No trial structure was available to aid in solving the phase problem in the Fall of 1972 and we hoped to generate one by potential energy minimization. We hoped to compute not only the conformation of the GpC molecule, but also its packing scheme in the unit cell, a feat that had never before been performed for a nucleic acid subunit. Indeed, only one dinucleoside monophosphate crystal structure, that of UpA, had been previously solved and its structure was very different from that of GpC.

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

    PubMed

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

    2014-08-01

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

  19. 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...

  20. 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 ...

  1. 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.

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

    PubMed

    Paesani, Francesco

    2016-09-20

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

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

    PubMed

    Paesani, Francesco

    2016-09-20

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

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

    PubMed

    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.

  5. 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.

  6. 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

  7. 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.

  8. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. Testing time-dependent density functional theory with depopulated molecular orbitals for predicting electronic excitation energies of valence, Rydberg, and charge-transfer states and potential energies near a conical intersection

    SciTech Connect

    Li, Shaohong L.; Truhlar, Donald G.

    2014-09-14

    Kohn-Sham (KS) time-dependent density functional theory (TDDFT) with most exchange-correlation functionals is well known to systematically underestimate the excitation energies of Rydberg and charge-transfer excited states of atomic and molecular systems. To improve the description of Rydberg states within the KS TDDFT framework, Gaiduk et al. [Phys. Rev. Lett. 108, 253005 (2012)] proposed a scheme that may be called HOMO depopulation. In this study, we tested this scheme on an extensive dataset of valence and Rydberg excitation energies of various atoms, ions, and molecules. It is also tested on a charge-transfer excitation of NH{sub 3}-F{sub 2} and on the potential energy curves of NH{sub 3} near a conical intersection. We found that the method can indeed significantly improve the accuracy of predicted Rydberg excitation energies while preserving reasonable accuracy for valence excitation energies. However, it does not appear to improve the description of charge-transfer excitations that are severely underestimated by standard KS TDDFT with conventional exchange-correlation functionals, nor does it perform appreciably better than standard TDDFT for the calculation of potential energy surfaces.

  15. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  17. 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.

  18. Accuracy of recent potential energy surfaces for the He-N2 interaction. II. Molecular beam scattering and bulk gas relaxation phenomena

    NASA Astrophysics Data System (ADS)

    Sanchez-Fortún Stoker, Jamie; Dham, Ashok K.; McCourt, Frederick R. W.; Dickinson, Alan S.

    2008-06-01

    A new semiempirical exchange-Coulomb model potential energy surface for the N2-He interaction was reported recently [A. K. Dham et al., J. Chem. Phys. 127, 054302 (2007)] and, using it, the temperature dependence of bulk gas properties of N2-He mixtures, such as the second virial coefficient and traditional transport phenomena, most of which depend primarily on the isotropic component of the interaction potential energy surface, was determined. Values of these properties, along with values calculated using two high-quality ab initio potential energy surfaces [C.-H. Hu and A. J. Thakkar, J. Chem. Phys. 104, 2541 (1996); K. Patel et al., ibid 119, 909 (2003)] were compared critically to available experimental data. The present paper reports on the ability of the same three potential energy surfaces to predict state-to-state and total differential cross sections, total integral cross sections, and the temperature dependence of bulk gas relaxation phenomena (including magnetic field effects on transport coefficients). While all three potential energy surfaces give total differential and higher speed integral scattering results that fall within the experimental uncertainties, integral scattering results and state-to-state differential cross section measurements consistently exceed the calculated values. All three surfaces give similar agreement with the relaxation properties of N2-He binary mixtures, with the semiempirical exchange-Coulomb model potential energy surface giving slightly better overall agreement with experiment than the two ab initio potential energy surfaces.

  19. ATOMIC AND MOLECULAR PHYSICS: High order correlation-polarization potential for vibrational excitation scattering of diatomic molecules by low-energy electrons

    NASA Astrophysics Data System (ADS)

    Feng, Hao; Sun, Wei-Guo; Zeng, Yang-Yang

    2009-11-01

    This paper introduces a correlation-polarization potential with high order terms for vibrational excitation in electron-molecule scattering. The new polarization potential generalizes the two-term approximation so that it can better reflect the dependence of correlation and polarization effects on the position coordinate of the scattering electron. It applies the new potential on the vibrational excitation scattering from N2 in an energy range which includes the 2Πg shape resonance. The good agreement of theoretical resonant peaks with experiments shows that polarization potentials with high order terms are important and should be included in vibrational excitation scattering.

  20. Two-potential approach for electron-molecular collisions at intermediate and high energies - Application to e-N2 scatterings

    NASA Technical Reports Server (NTRS)

    Choi, B. H.; Poe, R. T.; Sun, J. C.; Shan, Y.

    1979-01-01

    A general theoretical approach is proposed for the calculation of elastic, vibrational, and rotational transitions for electron-molecule scattering at intermediate and high-electron-impact energies. In this formulation, contributions to the scattering process come from the incoherent sum of two dominant potentials: a short-range shielded nuclear Coulomb potential from individual atomic centers, and a permanent/induced long-range potential. Application to e-N2 scattering from 50-500 eV incident electron energies has yielded good agreement with absolutely calibrated experiments. Comparisons with other theoretical approaches are made. The physical picture as well as the general features of electron-molecule scattering process are discussed within the framework of the two-potential approach.

  1. 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.

  2. LHC Physics Potential versus Energy

    SciTech Connect

    Quigg, Chris; /Fermilab

    2009-08-01

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

  3. 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

  4. 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.

  5. Sparse representation for a potential energy surface

    NASA Astrophysics Data System (ADS)

    Seko, Atsuto; Takahashi, Akira; Tanaka, Isao

    2014-07-01

    We propose a simple scheme to estimate the potential energy surface (PES) for which the accuracy can be easily controlled and improved. It is based on model selection within the framework of linear regression using the least absolute shrinkage and selection operator (LASSO) technique. Basis functions are selected from a systematic large set of candidate functions. The sparsity of the PES significantly reduces the computational cost of evaluating the energy and force in molecular dynamics simulations without losing accuracy. The usefulness of the scheme for describing the elemental metals Na and Mg is clearly demonstrated.

  6. Relativity, potential energy, and mass

    NASA Astrophysics Data System (ADS)

    Hecht, Eugene

    2016-11-01

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

  7. 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.

  8. The potential of renewable energy

    NASA Astrophysics Data System (ADS)

    1990-03-01

    On June 27 and 28, 1989, the U.S. DOE national labs 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 labs. As a result of that meeting, interlabor teams were formed to produce analytic white papers on key topics, and a lead lab was designated for each core lab 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. The results are presented of the intensive activity initiated by the June 1989 meeting to produce a white paper on renewable energy.

  9. Energies of Screened Coulomb Potentials.

    ERIC Educational Resources Information Center

    Lai, C. S.

    1979-01-01

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

  10. 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

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Molecular Recognition and Free Energy Simulations

    NASA Astrophysics Data System (ADS)

    Cannon, William Robert

    This dissertation describes the study of molecular recognition processes by free energy computer simulations. The introductory chapter briefly outlines the scientific development and significance of molecular recognition, and then describes statistical thermodynamic approaches to computer simulations. Chapter 1 analyzes the relationship of small guest molecules to a synthetic host in which one guest molecule is preorganized to be structurally complementary to the host while the second guest molecule must organize itself in order to obtain the same complementarity. The preferential recognition of imidazolidone over N,N^' -dimethylurea to the host is described in terms of the energetic cost of preorganizing the N,N^' -dimethylurea which can exist in several rotationally isomeric states. Chapter 2 describes the development of potential functions for molecular simulations and analyzes the structural, dynamic and thermodynamic aspects of sulfate anion solvation. Finally, chapter 3 describes the binding of sulfate anion to a periplasmic receptor and analyzes three mutants that have anomalous binding affinities for sulfate. Two of the mutants that have a greater than expected affinity for the anion are proposed to recognize and bind a water-anion complex rather than the anion alone, and the third mutant is proposed to have a dramatically decreased affinity for the anion due to steric and polarization effects.

  17. Potential Energy Curves for CO

    NASA Technical Reports Server (NTRS)

    Tobias, Irwin; Fallon, Robert J.; Vanderslice, Joseph T.

    1960-01-01

    Potential energy curves for the Chi (sup 1) Epsilon (sup plus), alpha (sup 3) II (sub r), alpha prime (sup 3) epsilon (sup plus), d (sup 3) delta, e (sup 3) Epsilon (sup minus), Alpha (sup 1) II, and Beta (sup 1) Epsilon (sup plus), electronic states of the CO molecule have been calculated by the Rydberg-Klein-Rees method. The curve for the A III state will have to bend sharply in the range between 1.9 and 2.1 angstroms or it will have to pass through a maximum to reach the proper dissociation limit.

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

    PubMed

    Karthick, T; Balachandran, V; Perumal, S

    2015-04-15

    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.

  19. 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.

  20. Dynamic parameterization and ladder operators for the Kratzer molecular potential

    NASA Astrophysics Data System (ADS)

    Babynanda Devi, O.; Amuba Singh, C.

    2014-09-01

    Introducing independent parameters k and \\delta to represent the strength of the attractive and repulsive components, respectively, we write the Kratzer molecular potential as V\\left( k,\\delta \\right)=({{\\hbar }^{2}}/2\\;m)(-k/r+\\delta (\\delta -1)/{{r}^{2}}). This parameterisation is not only natural, but also convenient for the construction of ladder operators for the system. Adopting the straightforward method of deriving recurrence relations among confluent hypergeometric functions, we construct seven pairs of ladder operators for the Kratzer potential system. Detailed analysis of the laddering actions of these operators is given to show that they connect eigenstates of equal energy but belong to a hierarchy of Kratzer potential systems corresponding to different values of the parameters k and \\delta . Significantly, it is pointed out that it may not be possible to construct, in the position representation, a ladder operator which would connect different eigenstates belonging to the same potential V(k,\\delta ). Transition to the hydrogen atom case is discussed. A number (14 altogether) of functional relations among the confluent hypergeometric functions have been derived and reported separately in an appendix.

  1. Nonintuitive Diabatic Potential Energy Surfaces for Thioanisole.

    PubMed

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

    2015-09-01

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

  2. 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…

  3. 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

  4. Reaction Pathway and Free Energy Profile for Pre-Chemical Reaction Step of Human Butyrylcholinesterase-Catalyzed Hydrolysis of (−)-Cocaine by Combined Targeted Molecular Dynamics and Potential of Mean Force Simulations

    PubMed Central

    Huang, Xiaoqin; Pan, Yongmei; Zheng, Fang; Zhan, Chang-Guo

    2010-01-01

    Combined targeted molecular dynamics (TMD) and potential of mean force (PMF) simulations have been carried out to uncover the detailed pathway and determine the corresponding free energy profile for the structural transformation from the nonprereactive butyrylcholinesterase (BChE)-(−)-cocaine binding to the prereactive BChE-(−)-cocaine binding associated with the (−)-cocaine rotation in the binding pocket of BChE. It has been shown that the structural transformation involves two transition states (TS1rot and TS2rot). TS1rot is mainly associated with the deformation of the nonprereactive complex, whereas TS2rot is mainly associated with the formation of the prereactive complex. It has also been demonstrated that the A328W/Y332G mutation significantly reduces the steric hindrance for (−)-cocaine rotation in the binding pocket of BChE and, thus, decreases the free energy barrier for the structural transformation from the nonprereactive binding to the prereactive binding. The calculated relative free energy barriers are all consistent with available experimental kinetic data. The new mechanistic insights obtained and the novel computational protocol tested in this study should be valuable for future computational design of high-activity mutants of BChE. The general computational strategy and approach based on the combined TMD and PMF simulations may be also valuable in computational studies of detailed pathways and free energy profiles for other similar mechanistic problems involving ligand rotation or another type of structural transformation in the binding pocket of a protein. PMID:20883001

  5. 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.

  6. Potential Energy Surface Database of Group II Dimer

    National Institute of Standards and Technology Data Gateway

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  8. 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.

  9. 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

  10. 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)

  11. 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

  12. Potential Water and Energy Savings from Showerheads

    SciTech Connect

    Biermayer, Peter J.

    2005-09-28

    This paper estimates the benefits and costs of six water reduction scenarios. Benefits and costs of showerhead scenarios are ranked in this paper by an estimated water reduction percentage. To prioritize potential water and energy saving scenarios regarding showerheads, six scenarios were analyzed for their potential water and energy savings and the associated dollar savings to the consumer.

  13. 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)

  14. 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.

  15. 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.

  16. 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

  17. 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 ...

  18. 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.

  19. 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.

  20. ATOMIC AND MOLECULAR PHYSICS: Splitting of Spectra in Anharmonic Oscillators Described by Kratzer Potential Function

    NASA Astrophysics Data System (ADS)

    Petreska, Irina; Sandev, Trifce; Ivanovski, Gjorgji; Pejov, Ljupco

    2010-07-01

    A perturbation theory model that describes splitting of the spectra in highly symmetrical molecular species in electrostatic field is proposed. An anahrmonic model of a two-dimensional oscillator having Kratzer potential energy function is used to model the molecular species and to represent the unperturbed system. A selection rule for the radial quantum number of the oscillator is derived. The eigenfunctions of a two-dimensional anharmonic oscillator in cylindrical coordinates are used for the matrix elements representing the probability for energy transitions in dipole approximation to be calculated. Several forms of perturbation operators are proposed to model the interaction between the polyatomic molecular species and an electrostatic field. It is found that the degeneracy is removed in the presence of the electric field and spectral splitting occurs. Anharmonic approximation for the unperturbed system is more accurate and reliable representation of a real polyatomic molecular species.

  1. Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations

    PubMed Central

    2011-01-01

    Molecular dynamics (MD) is one of the most common tools in computational chemistry. Recently, our group has employed accelerated molecular dynamics (aMD) to improve the conformational sampling over conventional molecular dynamics techniques. In the original aMD implementation, sampling is greatly improved by raising energy wells below a predefined energy level. Recently, our group presented an alternative aMD implementation where simulations are accelerated by lowering energy barriers of the potential energy surface. When coupled with thermodynamic integration simulations, this implementation showed very promising results. However, when applied to large systems, such as proteins, the simulation tends to be biased to high energy regions of the potential landscape. The reason for this behavior lies in the boost equation used since the highest energy barriers are dramatically more affected than the lower ones. To address this issue, in this work, we present a new boost equation that prevents oversampling of unfavorable high energy conformational states. The new boost potential provides not only better recovery of statistics throughout the simulation but also enhanced sampling of statistically relevant regions in explicit solvent MD simulations. PMID:22241967

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

    PubMed Central

    M’Koma, Amosy E

    2014-01-01

    Accurate diagnosis of predominantly colonic inflammatory bowel disease (IBD) is not possible in 30% of patients. For decades, scientists have worked to find a solution to improve diagnostic accuracy for IBD, encompassing Crohn’s colitis and ulcerative colitis. Evaluating protein patterns in surgical pathology colectomy specimens of colonic mucosal and submucosal compartments, individually, has potential for diagnostic medicine by identifying integrally independent, phenotype-specific cellular and molecular characteristics. Mass spectrometry (MS) and imaging (I) MS are analytical technologies that directly measure molecular species in clinical specimens, contributing to the in-depth understanding of biological molecules. The biometric-system complexity and functional diversity is well suited to proteomic and diagnostic studies. The direct analysis of cells and tissues by Matrix-Assisted-Laser Desorption/Ionization (MALDI) MS/IMS has relevant medical diagnostic potential. MALDI-MS/IMS detection generates molecular signatures obtained from specific cell types within tissue sections. Herein discussed is a perspective on the use of MALDI-MS/IMS and bioinformatics technologies for detection of molecular-biometric patterns and identification of differentiating proteins. I also discuss a perspective on the global challenge of transferring technologies to clinical laboratories dealing with IBD issues. The significance of serologic-immunometric advances is also discussed. PMID:25429322

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

    PubMed

    M'Koma, Amosy E

    2014-11-27

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

  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. 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.

  6. 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.

  7. 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.

  8. 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.

  9. Applying supersymmetry to energy dependent potentials

    SciTech Connect

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

    2013-11-15

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

  10. Extended Lagrangian free energy molecular dynamics.

    PubMed

    Niklasson, Anders M N; Steneteg, Peter; Bock, Nicolas

    2011-10-28

    Extended free energy Lagrangians are proposed for first principles molecular dynamics simulations at finite electronic temperatures for plane-wave pseudopotential and local orbital density matrix-based calculations. Thanks to the extended Lagrangian description, the electronic degrees of freedom can be integrated by stable geometric schemes that conserve the free energy. For the local orbital representations both the nuclear and electronic forces have simple and numerically efficient expressions that are well suited for reduced complexity calculations. A rapidly converging recursive Fermi operator expansion method that does not require the calculation of eigenvalues and eigenfunctions for the construction of the fractionally occupied density matrix is discussed. An efficient expression for the Pulay force that is valid also for density matrices with fractional occupation occurring at finite electronic temperatures is also demonstrated.

  11. 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.

  12. Energy conservation in Kenya: progress, potentials, problems

    SciTech Connect

    Schipper, L.; Hollander, J.M.; Milukas, M.; Alcamo, J.; Meyers, S.; Noll, S.

    1981-09-01

    A study was carried out of the flows of commercial energy in the economy of Kenya. Indications were sought of the extent to which energy conservation, (i.e., increase in efficiency of energy use) has reduced the ratio of energy inputs to economic outputs, in the post-1973 years. An assessment was made of the potential for energy conservation to reduce the growth of Kenyan energy use in the future and of significant barriers to increasing energy efficiency. Consideration was given to the role of government policy and of international assistance in fostering energy conservation in Kenya and other developing countries. The study was performed by analyzing available energy data and statistics from the largest oil companies, the Kenyan electric utility, and the government. These sources were supplemented by conducting personal interviews with personnel of nearly 50 commercial firms in Kenya. Direct consumption of fuel accounts for 94% of the commercial energy use in Kenya, while electricity accounts for 6%. The sectoral division of fuel use is: transportation 53%, industry 21%, energy production 11%, agriculture 9%, buildings and residences 5%, and construction 1%. For electricity the division is: buildings and residences 48%, industry 45%, energy production 4%, agriculture 2%, and construction 1%. Recent progress in conservation is reported.

  13. Saddles on the potential energy landscape of a Lennard-Jones liquid

    NASA Astrophysics Data System (ADS)

    Broderix, Kurt; Bhattacharya, Kamal K.; Cavagna, Andrea; Zippelius, Annette; Giardina, Irene

    2001-02-01

    By means of molecular dynamics simulations, we study the stationary points of the potential energy in a Lennard-Jones liquid, giving a purely geometric characterization of the energy landscape of the system. We find a linear relation between the degree of instability of the stationary points and their potential energy, and we locate the energy where the instability vanishes. This threshold energy marks the border between saddle-dominated and minima-dominated regions of the energy landscape. The temperature where the potential energy of the Stillinger-Weber minima becomes equal to the threshold energy turns out to be very close to the mode-coupling transition temperature Tc.

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. Energy transformation in molecular electronic systems

    SciTech Connect

    Kasha, M.

    1985-07-25

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

  20. Energy transformation in molecular electronic systems

    NASA Astrophysics Data System (ADS)

    Kasha, M.

    1985-07-01

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

  1. 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.

  2. Electro-magnetic free energy transduction by molecular motors

    NASA Astrophysics Data System (ADS)

    Yakovlev, V. V.

    2009-02-01

    It is generally accepted that molecular motors are utilizing the chemical energy of adenosine triphosphate (ATP) hydrolysis to convert it to the mechanical energy. A set of preliminary data demonstrates that the periodic electric field can induce transport as well, thus providing the energy to the molecular system.

  3. 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.

  4. Molecular Mechanisms of Diabetic Retinopathy: Potential Therapeutic Targets

    PubMed Central

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

    2015-01-01

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

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

    PubMed

    Pickup, Barry T; Fowler, Patrick W; 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.

  6. 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.

  7. 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.

  8. 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

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

    PubMed

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

    2013-12-01

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

  10. 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.

  11. 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.

  12. Accurate global potential energy surface for the H + OH+ collision

    NASA Astrophysics Data System (ADS)

    Gannouni, M. A.; Jaidane, N. E.; Halvick, P.; Stoecklin, T.; Hochlaf, M.

    2014-05-01

    We mapped the global three-dimensional potential energy surface (3D-PES) of the water cation at the MRCI/aug-cc-pV5Z including the basis set superposition (BSSE) correction. This PES covers the molecular region and the long ranges close to the H + OH+(X3Σ-), the O + H2+(X2Σg+), and the hydrogen exchange channels. The quality of the PES is checked after comparison to previous experimental and theoretical results of the spectroscopic constants of H2O+(tilde X2B1) and of the diatomic fragments, the vibronic spectrum, the dissociation energy, and the barrier to linearity for H2O+(tilde X2B1). Our data nicely approach those measured and computed previously. The long range parts reproduce quite well the diatomic potentials. In whole, a good agreement is found, which validates our 3D-PES.

  13. 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)

  14. 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.

  15. Biomedical applications and potential health risks of nanomaterials: molecular mechanisms.

    PubMed

    Lanone, Sophie; Boczkowski, Jorge

    2006-09-01

    Nanotechnologies, defined as techniques aimed to conceive, characterize and produce material at the nanometer scale, represent a fully expanding domain, and one can predict without risk that production and utilization of nanomaterials will increase exponentially in the coming years. Applications of nanotechnologies are numerous, in constant development, and their potential use in the medical field as diagnosis and therapeutics tools is very attractive. The size particularity of these nanomaterials gives them novel properties, allowing them to adopt new comportments because of the laws of quantum physics that exist at this scale. However, worries are expressed regarding the exact properties that make these nanomaterials attractive, and questions are raised regarding their potential toxicity, their long-term secondary effects or their biodegradability, particularly when thinking of their use in the (nano)medical field. These questions are justified by the knowledge of the toxic effects of atmospheric pollution micrometric particles on health, and the fear to get an amplification of these effects because of the size of the materials blamed. In this paper, we first expose the sensed medical applications of nanomaterials, and the physicochemical and molecular determinants potentially responsible for nanomaterials biological effects. Finally, we present a synthesis of the actual knowledge regarding toxicological effects of nanomaterials. It is clear that, in regard to the almost empty field of what is known on the subject, there's an urge to better understand biological effects of nanomaterials, which will allow their safe use, in particular in the nanomedicine field.

  16. Computed potential energy surfaces for chemical reactions

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.

    1994-01-01

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

  17. Computed potential energy surfaces for chemical reactions

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.

    1990-01-01

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

  18. Search for dark energy potentials in quintessence

    NASA Astrophysics Data System (ADS)

    Muromachi, Yusuke; Okabayashi, Akira; Okada, Daiki; Hara, Tetsuya; Itoh, Yutaka

    2015-09-01

    The time evolution of the equation of state w for quintessence models with a scalar field as dark energy is studied up to the third derivative big (d^3w/da^3big ) with respect to the scale factor a, in order to predict future observations and specify the scalar potential parameters with the observables. The third derivative of w for general potential V is derived and applied to several types of potentials. They are the inverse power law big (V=M^{4+α }/Q^{α }big ), the exponential big (V=M^4exp {β M/Q}big ), the mixed big (V=M^{4+γ }exp {β M/Q}/Q^{γ }big ), the cosine big (V=M^4[cos (Q/f)+1]big ), and the Gaussian types big (V=M^4exp big {-Q^2/σ ^2big }big ), which are prototypical potentials for the freezing and thawing models. If the parameter number for a potential form is n, it is necessary to find at least n+2 independent observations to identify the potential form and the evolution of the scalar field (Q and dot {Q}). Such observations would be the values of Ω _Q, w, dw/da,ldots , dw^n/da^n. From these specific potentials, we can predict the n+1 and higher derivatives of w: dw^{n+1}/da^{n+1},ldots . Since four of the abovementioned potentials have two parameters, it is necessary to calculate the third derivative of w for them to estimate the predicted values. If they are tested observationally, it will be understood whether the dark energy can be described by a scalar field with this potential. At least it will satisfy the necessary conditions. Numerical analysis for d^3w/da^3 is performed with some specified parameters in the investigated potentials, except for the mixed one. It becomes possible to distinguish the potentials by accurately observing dw/da and d^2w/da^2 for some parameters.

  19. 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.

  20. 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.

  1. 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

  2. New estimates of ionization potentials of four DIB molecular carriers.

    PubMed

    Sonnentrucker, P; Foing, B H; Ehrenfreund, P

    1999-01-01

    We present a study of the behaviour and ionization properties of four Diffuse Interstellar Bands (DIBs) at lambda lambda 5780, 5797, 6379 and 6613 angstroms. In the lambda lambda 5797, 6379 and 6613 angstrom DIBs, substructures have recently been detected, indicating large gaseous molecular carriers. Studying DIBs in regions with different physical properties in terms of UV flux and density enables us to monitor the behaviour of the carriers and hence to constrain their nature. As a follow-up of Sonnentrucker et al. (1997), we add new lines of sight and generalize the results for lines of sight with 2 or 3 clouds. This refines the Ionization Potential estimates which are between 10 and 13 eV, hence reminiscent of PAH or fullerene cations for those DIBs.

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. 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.

  8. Photodissociation of methane: Exploring potential energy surfaces

    NASA Astrophysics Data System (ADS)

    van Harrevelt, Rob

    2006-09-01

    The potential energy surface for the first excited singlet state (S1) of methane is explored using multireference singles and doubles configuration interaction calculations, employing a valence triple zeta basis set. A larger valence quadruple zeta basis is used to calculate the vertical excitation energy and dissociation energies. All stationary points found on the S1 surface are saddle points and have imaginary frequencies for symmetry-breaking vibrations. By studying several two-dimensional cuts through the potential energy surfaces, it is argued that CH4 in the S1 state will distort to planar structures. Several conical intersection seams between the ground state surface S0 and the S1 surface have been identified at planar geometries. The conical intersections provide electronically nonadiabatic pathways towards products CH3(X˜A2″2)+H, CH2(ãA11)+H2, or CH2(X˜B13)+H +H. The present results thereby make it plausible that the CH3(X˜A2″2)+H and CH2(ãA11)+H2 channels are major dissociation channels, as has been observed experimentally.

  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. Computing molecular correlation energies with guaranteed precision

    NASA Astrophysics Data System (ADS)

    Bischoff, Florian A.; Valeev, Edward F.

    2013-09-01

    We present an approach to compute accurate correlation energies for atoms and molecules in the framework of multiresolution analysis (MRA), using an adaptive discontinuous multiresolution spectral-element representation for the six-dimensional (two-electron) pair function. The key features of our approach that make it feasible, namely (1) low-rank tensor approximations of functions and operators and (2) analytic elimination of operator singularities via explicit correlation, were retained from the previous work [F. A. Bischoff, R. J. Harrison, and E. F. Valeev, J. Chem. Phys. 137, 104103 (2012)]. Here we generalized the working equations to handle general (non-symmetric) many-electron systems at the MP2 level. The numerical performance is shown for the beryllium atom and the water molecule where literature data for the basis set limits could be reproduced to a few tens of μEh. The key advantages of molecular MRA-MP2 are the absence of bias and arbitrariness in the choice of the basis set, high accuracy, and low scaling with respect to the system size.

  11. 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.

  12. 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

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

    PubMed

    Durrant, James R

    2013-08-13

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

  14. 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

  15. 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.

  16. 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.

  17. California's biomass and its energy potential

    SciTech Connect

    Lucarelli, F.B. Jr.

    1980-04-01

    The potentials for using California's biomass for energy have been assessed. The study relies on the recent work of Amory Lovins and Lawrence Berkeley Laboratory's (LBL) Distributed Energy System's Project to specify an energy future for Californians. These works identify transportation fuels as the most valuable energy conversion for biomass. Within this context, the extent of five categories of terrestial biomass is estimated, in addition to the environmental impacts and monetary cost of collecting and transporting each biomass category. Estimates of the costs of transforming biomass into different fuels as well as a survey of government's role in a biomass energy program are presented. The major findings are summarized below. (1) California's existing biomass resources are sufficient to provide only 20 percent of its future liquid fuel requirements. (2) Meeting the full transportation demand with biomass derived fuels will require the development of exotic biomass sources such as kelp farms and significant reductions in automobile travel in the State. (3) Under assumptions of moderate increases in gasoline prices and without major new government incentives, the cost of transforming biomass into transport fuels will be competitive with the price of gasoline on a Btu basis by the year 1990. (4) The environmental impacts of collecting most forms of biomass are beneficial and should reduce air pollution from agricultural burning and water pollution from feedlot and dairy farm runoff. Moreover, the collection of logging residues should improve timber stand productivity and the harvest of chaparral should reduce the risk of wildfire in the State. (5) The institutional context for implementing biomass energy projects is complex and fragmented.

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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

  4. 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

  5. Potential energy surfaces of superheavy nuclei

    SciTech Connect

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

    1998-10-01

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

  6. 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.

  7. 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.

  8. 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.

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

    PubMed

    Cheng, Jun; Sulpizi, Marialore; Sprik, Michiel

    2009-10-21

    The density functional theory based molecular dynamics (DFTMD) method for the computation of redox free energies presented in previous publications and the more recent modification for computation of acidity constants are reviewed. The method uses a half reaction scheme based on reversible insertion/removal of electrons and protons. The proton insertion is assisted by restraining potentials acting as chaperones. The procedure for relating the calculated deprotonation free energies to Brønsted acidities (pK(a)) and the oxidation free energies to electrode potentials with respect to the normal hydrogen electrode is discussed in some detail. The method is validated in an application to the reduction of aqueous 1,4-benzoquinone. The conversion of hydroquinone to quinone can take place via a number of alternative pathways consisting of combinations of acid dissociations, oxidations, or dehydrogenations. The free energy changes of all elementary steps (ten in total) are computed. The accuracy of the calculations is assessed by comparing the energies of different pathways for the same reaction (Hess's law) and by comparison to experiment. This two-sided test enables us to separate the errors related with the restrictions on length and time scales accessible to DFTMD from the errors introduced by the DFT approximation. It is found that the DFT approximation is the main source of error for oxidation free energies. PMID:20568869

  10. 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.

  11. Molecular dynamics studies of sticking and reflection of low-energy deuterium on single crystal tungsten

    NASA Astrophysics Data System (ADS)

    Maya, P. N.

    2016-11-01

    Molecular dynamics simulations have been performed to study deuterium sticking and reflection properties of single crystal tungsten surfaces using two different Tersoff-type tungsten-hydrogen potentials. Single crystal tungsten surfaces of (001) and (110) orientations were bombarded with deuterium atoms up to 100 eV energy at 300 K sample temperature. The potentials show differences in the nature of sticking as well as in the sticking coefficient. In order to understand the variation in the observed sticking coefficient, detailed potential energy analysis has been carried out using both the potentials. The analysis is able to explain the nature of the sticking for various surfaces as well as the observed minima in sticking coefficient in both the potentials. The variation in the sticking and reflection coefficients with energy can be explained from the local variation of the repulsive and attractive potential energy in the near-surface region which are considerably different in both the potentials.

  12. 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.

  13. 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.

  14. 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.

  15. Molecular adaptations in psychrophilic bacteria: potential for biotechnological applications.

    PubMed

    Russell, N J

    1998-01-01

    Bacteria which live in cold conditions are known as psychrophiles. Since so much of our planet is generally cold, i.e. below 5 degrees C, it is not surprising that they are very common amongst a wide variety of habitats. To enable them to survive and grow in cold environments, psychrophilic bacteria have evolved a complex range of adaptations to all of their cellular components, including their membranes, energy-generating systems, protein synthesis machinery, biodegradative enzymes and the components responsible for nutrient uptake. Whilst such a systems approach to the topic has its advantages, all of the changes can be described in terms of adaptive alterations in the proteins and lipids of the bacterial cell. The present review adopts the latter approach and, following a brief consideration of the definition of psychrophiles and description of their habitats, focuses on those adaptive changes in proteins and lipids, especially those which are either currently being explored for their biotechnological potential or might be so in the future. Such applications for proteins range from the use of cold-active enzymes in the detergent and food industries, in specific biotransformations and environmental bioremediations, to specialised uses in contact lens cleaning fluids and reducing the lactose content of milk; ice-nucleating proteins have potential uses in the manufacture of ice cream or artificial snow; for lipids, the uses include dietary supplements in the form of polyunsaturated fatty acids from some Antarctic marine psychrophiles.

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

    PubMed

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

    2012-12-21

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

  17. 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.

  18. 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

  19. Communication: Certifying the potential energy landscape

    NASA Astrophysics Data System (ADS)

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

    2013-05-01

    It is highly desirable for numerical approximations to stationary points for a potential energy landscape to lie in the corresponding quadratic convergence basin. However, it is possible that an approximation may lie only in the linear convergence basin, or even in a chaotic region, and hence not converge to the actual stationary point when further optimization is attempted. Proving that a numerical approximation will quadratically converge to the associated stationary point is termed certification. Here, we apply Smale's α-theory to stationary points, providing a certification serving as a mathematical proof that the numerical approximation does indeed correspond to an actual stationary point, independent of the precision employed. As a practical example, employing recently developed certification algorithms, we show how the α-theory can be used to certify all the known minima and transition states of Lennard-Jones LJN atomic clusters for N = 7, …, 14.

  20. Certification and the potential energy landscape

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

    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.

  1. Tensor decomposition in potential energy surface representations.

    PubMed

    Ostrowski, Lukas; Ziegler, Benjamin; Rauhut, Guntram

    2016-09-14

    In order to reduce the operation count in vibration correlation methods, e.g., vibrational configuration interaction (VCI) theory, a tensor decomposition approach has been applied to the analytical representations of multidimensional potential energy surfaces (PESs). It is shown that a decomposition of the coefficients within the individual n-mode coupling terms in a multimode expansion of the PES is feasible and allows for convenient contractions of one-dimensional integrals with these newly determined factor matrices. Deviations in the final VCI frequencies of a set of small molecules were found to be negligible once the rank of the factors matrices is chosen appropriately. Recommendations for meaningful ranks are provided and different algorithms are discussed. PMID:27634247

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. Thermophotovoltaic energy conversion: Technology and market potential

    NASA Astrophysics Data System (ADS)

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

    1996-02-01

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

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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

  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.

  13. 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.

  14. Adaptively biased molecular dynamics: An umbrella sampling method with a time-dependent potential

    NASA Astrophysics Data System (ADS)

    Babin, Volodymyr; Karpusenka, Vadzim; Moradi, Mahmoud; Roland, Christopher; Sagui, Celeste

    We discuss an adaptively biased molecular dynamics (ABMD) method for the computation of a free energy surface for a set of reaction coordinates. The ABMD method belongs to the general category of umbrella sampling methods with an evolving biasing potential. It is characterized by a small number of control parameters and an O(t) numerical cost with simulation time t. The method naturally allows for extensions based on multiple walkers and replica exchange mechanism. The workings of the method are illustrated with a number of examples, including sugar puckering, and free energy landscapes for polymethionine and polyproline peptides, and for a short β-turn peptide. ABMD has been implemented into the latest version (Case et al., AMBER 10; University of California: San Francisco, 2008) of the AMBER software package and is freely available to the simulation community.

  15. 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.

  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. Molecular and chemical engineering of bacteriophages for potential medical applications.

    PubMed

    Hodyra, Katarzyna; Dąbrowska, Krystyna

    2015-04-01

    Recent progress in molecular engineering has contributed to the great progress of medicine. However, there are still difficult problems constituting a challenge for molecular biology and biotechnology, e.g. new generation of anticancer agents, alternative biosensors or vaccines. As a biotechnological tool, bacteriophages (phages) offer a promising alternative to traditional approaches. They can be applied as anticancer agents, novel platforms in vaccine design, or as target carriers in drug discovery. Phages also offer solutions for modern cell imaging, biosensor construction or food pathogen detection. Here we present a review of bacteriophage research as a dynamically developing field with promising prospects for further development of medicine and biotechnology.

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

    PubMed

    Babin, Volodymyr; Leforestier, Claude; Paesani, Francesco

    2013-12-10

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

  20. 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.

  1. 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.

  2. Accelerating chemical reactions: Exploring reactive free-energy surfaces using accelerated ab initio molecular dynamics

    PubMed Central

    Pierce, Levi C. T.; Markwick, Phineus R. L.; McCammon, J. Andrew; Doltsinis, Nikos L.

    2011-01-01

    A biased potential molecular dynamics simulation approach, accelerated molecular dynamics (AMD), has been implemented in the framework of ab initio molecular dynamics for the study of chemical reactions. Using two examples, the double proton transfer reaction in formic acid dimer and the hypothetical adiabatic ring opening and subsequent rearrangement reactions in methylenecyclopropane, it is demonstrated that ab initio AMD can be readily employed to efficiently explore the reactive potential energy surface, allowing the prediction of chemical reactions and the identification of metastable states. An adaptive variant of the AMD method is developed, which additionally affords an accurate representation of both the free-energy surface and the mechanism associated with the chemical reaction of interest and can also provide an estimate of the reaction rate. PMID:21548673

  3. 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

  4. 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.

  5. Molecular docking of potential inhibitors for influenza H7N9.

    PubMed

    Liu, Zekun; Zhao, Junpeng; Li, Weichen; Wang, Xinkun; Xu, Jingxuan; Xie, Jin; Tao, Ke; Shen, Li; Zhang, Ran

    2015-01-01

    As a new strain of virus emerged in 2013, avian influenza A (H7N9) virus is a threat to the public health, due to its high lethality and pathogenicity. Furthermore, H7N9 has already generated various mutations such as neuraminidase R294K mutation which could make the anti-influenza oseltamivir less effective or ineffective. In this regard, it is urgent to develop new effective anti-H7N9 drug. In this study, we used the general H7N9 neuraminidase and oseltamivir-resistant influenza virus neuraminidase as the acceptors and employed the small molecules including quercetin, chlorogenic acid, baicalein, and oleanolic acid as the donors to perform the molecular docking for exploring the binding abilities between these small molecules and neuraminidase. The results showed that quercetin, chlorogenic acid, oleanolic acid, and baicalein present oseltamivir-comparable high binding potentials with neuraminidase. Further analyses showed that R294K mutation in neuraminidase could remarkably decrease the binding energies for oseltamivir, while other small molecules showed stable binding abilities with mutated neuraminidase. Taken together, the molecular docking studies identified four potential inhibitors for neuraminidase of H7N9, which might be effective for the drug-resistant mutants.

  6. 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.

  7. High hopes: can molecular electronics realise its potential?

    PubMed

    Coskun, Ali; Spruell, Jason M; Barin, Gokhan; Dichtel, William R; Flood, Amar H; Botros, Youssry Y; Stoddart, J Fraser

    2012-07-21

    Manipulating and controlling the self-organisation of small collections of molecules, as an alternative to investigating individual molecules, has motivated researchers bent on processing and storing information in molecular electronic devices (MEDs). Although numerous ingenious examples of single-molecule devices have provided fundamental insights into their molecular electronic properties, MEDs incorporating hundreds to thousands of molecules trapped between wires in two-dimensional arrays within crossbar architectures offer a glimmer of hope for molecular memory applications. In this critical review, we focus attention on the collective behaviour of switchable mechanically interlocked molecules (MIMs)--specifically, bistable rotaxanes and catenanes--which exhibit reset lifetimes between their ON and OFF states ranging from seconds in solution to hours in crossbar devices. When these switchable MIMs are introduced into high viscosity polymer matrices, or self-assembled as monolayers onto metal surfaces, both in the form of nanoparticles and flat electrodes, or organised as tightly packed islands of hundreds and thousands of molecules sandwiched between two electrodes, the thermodynamics which characterise their switching remain approximately constant while the kinetics associated with their reset follow an intuitively predictable trend--that is, fast when they are free in solution and sluggish when they are constrained within closely packed monolayers. The importance of seamless interactions and constant feedback between the makers, the measurers and the modellers in establishing the structure-property relationships in these integrated functioning systems cannot be stressed enough as rationalising the many different factors that impact device performance becomes more and more demanding. The choice of electrodes, as well as the self-organised superstructures of the monolayers of switchable MIMs employed in the molecular switch tunnel junctions (MSTJs) associated

  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. 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,…

  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. 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.

  12. 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.

  13. 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.

  14. 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..

  15. 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.

  16. 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

  17. 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

  18. Nutraceuticals: potential for chondroprotection and molecular targeting of osteoarthritis.

    PubMed

    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

  19. Efficient characterization of stationary points on potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Deglmann, Peter; Furche, Filipp

    2002-12-01

    Traditional methods for characterizing an optimized molecular structure as a minimum or as a saddle point on the nuclear potential energy surface require the full Hessian. However, if f denotes the number of nuclear degrees of freedom, a full Hessian calculation is more expensive than a single point geometry optimization step by the order of magnitude of f. Here we present a method which allows to determine the lowest vibrational frequencies of a molecule at significantly lower cost. Our approach takes advantage of the fact that only a few perturbed first-order wave functions need to be computed in an iterative diagonalization scheme instead of f ones in a full Hessian calculation. We outline an implementation for Hartree-Fock and density functional methods. Applications indicate a scaling similar to that of a single point energy or gradient calculation, but with a larger prefactor. Depending on the number of soft vibrational modes, the iterative method becomes effective for systems with more than 30-50 atoms.

  20. 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.

  1. 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.

  2. 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.

  3. Potential energy surface of H2O on Al{111} and Rh{111} from theoretical methods

    NASA Astrophysics Data System (ADS)

    Ranea, Víctor A.

    2012-11-01

    The potential energy surfaces of molecular water on the Al{111} and on the Rh{111} metal surfaces have been investigated using density functional theory. Similar landscapes were found on both surfaces. In the only minimum found, the water molecule is monocoordinated to the surface via the oxygen atom (top configuration) with its plane nearly parallel to the surface. The maxima are around the bridge and hollow configurations and no local minima or maxima were found. Along the investigated minimum energy pathways, no strong preferential orientation of the water dipole was found, as long as the molecular plane is nearly parallel to the surface.

  4. 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.

  5. 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.

  6. 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.

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

    PubMed

    Durgun, E; Grossman, Jeffrey C

    2013-03-21

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

  8. Advances in carcinogenic metal toxicity and potential molecular markers.

    PubMed

    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

  9. 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.

  10. Plant adaptation to low atmospheric pressures: potential molecular responses.

    PubMed

    Ferl, Robert J; Schuerger, Andrew C; Paul, Anna-Lisa; Gurley, William B; Corey, Kenneth; Bucklin, Ray

    2002-01-01

    There is an increasing realization that it may be impossible to attain Earth normal atmospheric pressures in orbital, lunar, or Martian greenhouses, simply because the construction materials do not exist to meet the extraordinary constraints imposed by balancing high engineering requirements against high lift costs. This equation essentially dictates that NASA have in place the capability to grow plants at reduced atmospheric pressure. Yet current understanding of plant growth at low pressures is limited to just a few experiments and relatively rudimentary assessments of plant vigor and growth. The tools now exist, however, to make rapid progress toward understanding the fundamental nature of plant responses and adaptations to low pressures, and to develop strategies for mitigating detrimental effects by engineering the growth conditions or by engineering the plants themselves. The genomes of rice and the model plant Arabidopsis thaliana have recently been sequenced in their entirety, and public sector and commercial DNA chips are becoming available such that thousands of genes can be assayed at once. A fundamental understanding of plant responses and adaptation to low pressures can now be approached and translated into procedures and engineering considerations to enhance plant growth at low atmospheric pressures. In anticipation of such studies, we present here the background arguments supporting these contentions, as well as informed speculation about the kinds of molecular physiological responses that might be expected of plants in low-pressure environments. PMID:11987308

  11. 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

  12. 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

  13. Nonadiabatic molecular dynamics simulations of the energy transfer between building blocks in a phenylene ethynylene dendrimer.

    PubMed

    Fernandez-Alberti, Sebastian; Kleiman, Valeria D; Tretiak, Sergei; Roitberg, Adrian E

    2009-07-01

    The ultrafast dynamics of electronic and vibrational energy transfer between two- and three-ring linear poly(phenylene ethynylene) units linked by meta-substitution is studied by nonadiabatic molecular dynamics simulations. The molecular dynamics with quantum transitions (1, 2) method is used including an "on the fly" calculation of the potential energy surfaces and electronic couplings. The results show that during the first 40 fs after a vertical photoexcitation to the S(2) state, the nonadiabatic coupling between S(2) and S(1) states causes a fast transfer of the electronic populations. A rapid decrease of the S(1)-S(2) energy gap is observed, reaching a first conical intersection at approximately 5 fs. Therefore, the first hopping events take place, and the S(2) state starts to depopulate. The analysis of the structural and energetic properties of the molecule during the jumps reveals the main role that the ethynylene triple bond plays in the unidirectional energy transfer process. PMID:19378966

  14. 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.

  15. Basal cell carcinoma — molecular biology and potential new therapies

    PubMed Central

    Kasper, Maria; Jaks, Viljar; Hohl, Daniel; Toftgård, Rune

    2012-01-01

    Basal cell carcinoma (BCC) of the skin, the most common malignancy in individuals of mixed European descent, is increasing in incidence due to an aging population and sun exposure habits. The realization that aberrant activation of Hedgehog signaling is a pathognomonic feature of BCC development has opened the way for exciting progress toward understanding BCC biology and translation of this knowledge to the clinic. Genetic mouse models closely mimicking human BCCs have provided answers about the tumor cell of origin, and inhibition of Hedgehog signaling is emerging as a potentially useful targeted therapy for patients with advanced or multiple BCCs that have hitherto lacked effective treatment. PMID:22293184

  16. 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

  17. 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

  18. 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.

  19. 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.

  20. Realizing the potential of nuclear energy. [Monograph

    SciTech Connect

    Walske, C.

    1982-01-01

    The future of nuclear power, just as the future of America, can be viewed with optimism. There is hope in America's record of overcoming obstacles, but growth is essential for that hope to be realized. Despite the downturn in energy demand made possible by conservation, we will need a 35% growth in total energy for new workers and production. Electricity generated by nuclear or coal can make US production more cost-competitive, and it can power mass-transit systems, electric heat pumps, and communications and information systems. Changes in electricity and gross national product (GNP) have been more closely in step since 1973 than have total energy and GNP. The nuclear power units now under construction will add 80,000 megawatts to the 56,000 now on line. It is important to note that, while utilities are cancelling plans for nuclear plants, they aren't ordering new coal plants, which shows the impact of the high cost of money. Interest rates must come down and public-relations efforts to sell electricity must improve to change the situation. Although capital shortages are real, waste disposal is a problem of perception that was politically induced because the government failed to provide a demonstration of safety as the French are doing. Streamlined regulatory and insurance procedures can help to justify optimism in the nuclear option. 4 figures. (DCK)

  1. Harnessing Reversible Electronic Energy Transfer: From Molecular Dyads to Molecular Machines.

    PubMed

    Denisov, Sergey A; Yu, Shinlin; Pozzo, Jean-Luc; Jonusauskas, Gediminas; McClenaghan, Nathan D

    2016-06-17

    Reversible electronic energy transfer (REET) may be instilled in bi-/multichromophoric molecule-based systems, following photoexcitation, upon judicious structural integration of matched chromophores. This leads to a new set of photophysical properties for the ensemble, which can be fully characterized by steady-state and time-resolved spectroscopic methods. Herein, we take a comprehensive look at progress in the development of this type of supermolecule in the last five years, which has seen systems evolve from covalently tethered dyads to synthetic molecular machines, exemplified by two different pseudorotaxanes. Indeed, REET holds promise in the control of movement in molecular machines, their assembly/disassembly, as well as in charge separation.

  2. Combined 3D-QSAR, molecular docking, and molecular dynamics study of tacrine derivatives as potential acetylcholinesterase (AChE) inhibitors of Alzheimer's disease.

    PubMed

    Zhou, An; Hu, Jianping; Wang, Lirong; Zhong, Guochen; Pan, Jian; Wu, Zeyu; Hui, Ailing

    2015-10-01

    Acetylcholinesterase (AChE) is one of the key targets of drugs for treating Alzheimer's disease (AD). Tacrine is an approved drug with AChE-inhibitory activity. In this paper, 3D-QSAR, molecular docking, and molecular dynamics were carried out in order to study 60 tacrine derivatives and their AChE-inhibitory activities. 3D-QSAR modeling resulted in an optimal CoMFA model with q(2) = 0.552 and r(2) = 0.983 and an optimal CoMSIA model with q(2) = 0.581 and r(2) = 0.989. These QSAR models also showed that the steric and H-bond fields of these compounds are important influences on their activities. The interactions between these inhibitors and AChE were further explored through molecular docking and molecular dynamics simulation. A few key residues (Tyr70, Trp84, Tyr121, Trp279, and Phe330) at the binding site of AChE were identified. The results of this study improve our understanding of the mechanisms of AChE inhibitors and afford valuable information that should aid the design of novel potential AChE inhibitors. Graphical Abstract Superposition of backbone atoms of the lowest-energy structure obtained from MD simulation (magenta) onto those of the structure of the initial molecular docking model (green).

  3. 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.

  4. 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

  5. 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.

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

    SciTech Connect

    Coe, B.A.

    1980-01-01

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

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

    SciTech Connect

    Hiester, T.R.

    1980-06-01

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

  8. 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. 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.

  10. 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.

  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. 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.

  13. Quorum sensing inhibitory potential and molecular docking studies of sesquiterpene lactones from Vernonia blumeoides.

    PubMed

    Aliyu, Abubakar Babando; Koorbanally, Neil Anthony; Moodley, Brenda; Singh, Parvesh; Chenia, Hafizah Yousuf

    2016-06-01

    The increasing incidence of multidrug-resistant Gram-negative bacterial pathogens has focused research on the suppression of bacterial virulence via quorum sensing inhibition strategies, rather than the conventional antimicrobial approach. The anti-virulence potential of eudesmanolide sesquiterpene lactones previously isolated from Vernonia blumeoides was assessed by inhibition of quorum sensing and in silico molecular docking. Inhibition of quorum sensing-controlled violacein production in Chromobacterium violaceum was quantified using violacein inhibition assays. Qualitative modulation of quorum sensing activity and signal synthesis was investigated using agar diffusion double ring assays and C. violaceum and Agrobacterium tumefaciens biosensor systems. Inhibition of violacein production was concentration-dependent, with ⩾90% inhibition being obtained with ⩾2.4 mg ml(-1) of crude extracts. Violacein inhibition was significant for the ethyl acetate extract with decreasing inhibition being observed with dichloromethane, hexane and methanol extracts. Violacein inhibition ⩾80% was obtained with 0.071 mg ml(-1) of blumeoidolide B in comparison with ⩾3.6 mg ml(-1) of blumeoidolide A. Agar diffusion double ring assays indicated that only the activity of the LuxI synthase homologue, CviI, was modulated by blumeoidolides A and B, and V. blumeoides crude extracts, suggesting that quorum sensing signal synthesis was down-regulated or competitively inhibited. Finally, molecular docking was conducted to explore the binding conformations of sesquiterpene lactones into the binding sites of quorum sensing regulator proteins, CviR and CviR'. The computed binding energy data suggested that the blumeoidolides have a tendency to inhibit both CviR and CviR' with varying binding affinities. Vernonia eudesmanolide sesquiterpene lactones have the potential to be novel therapeutic agents, which might be important in reducing virulence and pathogenicity of drug-resistant bacteria

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Potential for energy recovery from solid wastes

    SciTech Connect

    Velzy, C.O.

    1983-01-01

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

  6. 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.

  7. 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.

  8. Using operators to expand the block matrices forming the Hessian of a molecular potential.

    PubMed

    Carlsen, Martin

    2014-06-01

    We derive compact expressions of the second-order derivatives of bond length, bond angle, and proper and improper torsion angle potentials, in terms of operators represented in two orthonormal bases. Hereby, simple rules to generate the Hessian of an internal coordinate or a molecular potential can be formulated. The algorithms we provide can be implemented efficiently in high-level programming languages using vectorization. Finally, the method leads to compact expressions for a second-order expansion of an internal coordinate or a molecular potential.

  9. 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.

  10. Field-dependent molecular ionization and excitation energies: Implications for electrically insulating liquids

    NASA Astrophysics Data System (ADS)

    Davari, N.; Åstrand, P.-O.; Unge, M.; Lundgaard, L. E.; Linhjell, D.

    2014-03-01

    The molecular ionization potential has a relatively strong electric-field dependence as compared to the excitation energies which has implications for electrical insulation since the excited states work as an energy sink emitting light in the UV/VIS region. At some threshold field, all the excited states of the molecule have vanished and the molecule is a two-state system with the ground state and the ionized state, which has been hypothesized as a possible origin of different streamer propagation modes. Constrained density-functional theory is used to calculate the field-dependent ionization potential of different types of molecules relevant for electrically insulating liquids. The low singlet-singlet excitation energies of each molecule have also been calculated using time-dependent density functional theory. It is shown that low-energy singlet-singlet excitation of the type n → π* (lone pair to unoccupied π* orbital) has the ability to survive at higher fields. This type of excitation can for example be found in esters, diketones and many color dyes. For alkanes (as for example n-tridecane and cyclohexane) on the other hand, all the excited states, in particular the σ → σ* excitations vanish in electric fields higher than 10 MV/cm. Further implications for the design of electrically insulating dielectric liquids based on the molecular ionization potential and excitation energies are discussed.

  11. 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.

  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. 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.

  14. 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

  15. 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…

  16. 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

  17. 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

  18. Potential energy stored by planets and grand minima events

    NASA Astrophysics Data System (ADS)

    Cionco, Rodolfo G.

    2012-07-01

    Recently, Wolff & Patrone (2010), have developed a simple but very interesting model by which the movement of the Sun around the barycentre of the Solar system could create potential energy that could be released by flows pre-existing inside the Sun. The authors claim that it is the first mechanism showing how planetary movements can modify internal structure in the Sun that can be related to solar cycle. In this work we point out limitations of mentioned mechanism (which is based on interchange arguments), which could be inapplicable to a real star. Then, we calculate the temporal evolution of potential energy stored in zones of Sun's interior in which the potential energy could be most efficiently stored taking into account detailed barycentric Sun dynamics. We show strong variations of potential energy related to Maunder Minimum, Dalton Minimum and the maximum of Cycle 22, around 1990. We discuss briefly possible implications of this putative mechanism to solar cycle specially Grand Minima events.

  19. 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.

  20. Quantitative assessment of substituent effects on cation-π interactions using molecular electrostatic potential topography.

    PubMed

    Sayyed, Fareed Bhasha; Suresh, Cherumuttathu H

    2011-08-25

    A molecular electrostatic potential (MESP) topography based approach has been proposed to quantify the substituent effects on cation-π interactions in complexes of mono-, di-, tri-, and hexasubstituted benzenes with Li(+), Na(+), K(+), and NH(4)(+). The MESP minimum (V(min)) on the π-region of C(6)H(5)X showed strong linear dependency to the cation-π interaction energy, E(M(+)). Further, cation-π distance correlated well with V(min)-π distance. The difference between V(min) of C(6)H(5)X and C(6)H(6) (ΔV(min)) is proposed as a good parameter to quantify the substituent effect on cation-π interaction. Compared to benzene, electron-donating groups stabilize the di-, tri-, and hexasubstituted cation-π complexes while electron-withdrawing groups destabilize them. In multiple substituted complexes, E(M(+)) is almost equal (∼95%) to the sum of the individual substituent contributions (E(M(+)) ≈ Σ(ΔE(M(+)))), suggesting that substituent effect on cation-π interactions is largely additive. The ΔV(min) of C(6)H(5)X systems and additivity feature have been used to make predictions on the interaction energies of 80 multiple substituted cation-π complexes with above 97% accuracy. The average mean absolute deviation of the V(min)-predicted interaction energy, E(M(+))(V) from the calculated E(M(+)) is -0.18 kcal/mol for Li(+), -0.09 kcal/mol for Na(+), -0.43 kcal/mol for K(+), and -0.67 kcal/mol for NH(4)(+), which emphasize the predictive power of V(min) as well as the additive feature of the substituent effect.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Permutationally invariant polynomial basis for molecular energy surface fitting via monomial symmetrization.

    SciTech Connect

    Xie, Z.; Bowman, J. M.; Mathematics and Computer Science; Emory Univ.

    2010-01-01

    We describe a procedure to develop a fitting basis for molecular potential energy surfaces (PESs) that is invariant with respect to permutation of like atoms. The method is based on a straightforward symmetrization of a primitive monomial basis and illustrated for several classes of molecules. A numerically efficient method to evaluate the resulting expression for the PES is also described. The fitting basis is used to obtain a new PES for H{sub 3}O{sup +} based on roughly 62000 ab initio energies.

  6. Exploring potential energy surfaces for chemical reactions: an overview of some practical methods.

    PubMed

    Schlegel, H Bernhard

    2003-09-01

    Potential energy surfaces form a central concept in the application of electronic structure methods to the study of molecular structures, properties, and reactivities. Recent advances in tools for exploring potential energy surfaces are surveyed. Methods for geometry optimization of equilibrium structures, searching for transition states, following reaction paths and ab initio molecular dynamics are discussed. For geometry optimization, topics include methods for large molecules, QM/MM calculations, and simultaneous optimization of the wave function and the geometry. Path optimization methods and dynamics based techniques for transition state searching and reaction path following are outlined. Developments in the calculation of ab initio classical trajectories in the Born-Oppenheimer and Car-Parrinello approaches are described. PMID:12868114

  7. 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.

  8. 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.

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

    SciTech Connect

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

    2013-02-01

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

  10. 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.

  11. Discovery of Potential Inhibitors of Aldosterone Synthase from Chinese Herbs Using Pharmacophore Modeling, Molecular Docking, and Molecular Dynamics Simulation Studies

    PubMed Central

    Lu, Fang; Qiao, Liansheng; Chen, Xi; Li, Gongyu

    2016-01-01

    Aldosterone synthase (CYP11B2) is a key enzyme for the biosynthesis of aldosterone, which plays a significant role for the regulation of blood pressure. Excess aldosterone can cause the dysregulation of the renin-angiotensin-aldosterone system (RAAS) and lead to hypertension. Therefore, research and development of CYP11B2 inhibitor are regarded as a novel approach for the treatment of hypertension. In this study, the pharmacophore models of CYP11B2 inhibitors were generated and the optimal model was used to identify potential CYP11B2 inhibitors from the Traditional Chinese Medicine Database (TCMD, Version 2009). The hits were further refined by molecular docking and the interactions between compounds and CYP11B2 were analyzed. Compounds with high Fitvalue, high docking score, and expected interactions with key residues were selected as potential CYP11B2 inhibitors. Two most promising compounds, ethyl caffeate and labiatenic acid, with high Fitvalue and docking score were reserved for molecular dynamics (MD) study. All of them have stability of ligand binding which suggested that they might perform the inhibitory effect on CYP11B2. This study provided candidates for novel drug-like CYP11B2 inhibitors by molecular simulation methods for the hypertension treatment. PMID:27781210

  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. 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.

  14. Fusion at deep subbarrier energies: potential inversion revisited

    NASA Astrophysics Data System (ADS)

    Hagino, K.; Rowley, N.

    2009-03-01

    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 16O+144Sm and 16O+208Pb 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.

  15. 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.

  16. 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

  17. Electrical energy and cost savings potential at DOD facilities

    SciTech Connect

    Konopacki, S.; Akbari, H.; Lister, L.; DeBaille, L.

    1996-06-01

    The US Department of Defense (DOD) has been mandated to reduce energy consumption and costs by 20% from 1985 to 2000 and by 30% from 1985 to 2005. Reduction of electrical energy consumption at DOD facilities requires a better understanding of energy consumption patterns and energy and financial savings potential. This paper utilizes two independent studies--EDA (End-Use Disaggregation Algorithm) and MEIP (Model Energy Installation Program)--and whole-installation electricity use data obtained from a state utility to estimate electrical energy conservation potential (ECP) and cost savings potential (CSP) at the Fort Hood, Texas, military installation and at DOD nationwide. At Fort Hood, the authors estimated an annual electricity savings of 62.2 GWh/yr (18%), a peak demand savings of 10.1 MW (14%), and an annual energy cost savings of $6.5 million per year. These savings could be attained with an initial investment of $41.1 million, resulting in a simple payback of 6.3 years. Across the DOD, they estimated an annual electricity savings of 4,900 GWh/yr, a peak demand savings of 694 MW, and an annual energy cost savings of $316 million per year. The estimated cost savings is 16% of the total nationwide DOD 1993 annual energy costs. These savings could be attained with an initial investment of $1.23 billion, resulting in a simple payback of 3.9 years.

  18. 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.

  19. Potential of energy farms in the Dominican Republic

    SciTech Connect

    Newman, L.C.; Park, W.R.; Trehan, R.K.

    1980-12-01

    This report assesses the potential of biomass energy farms to supply feedstock for electrical energy needs in the Dominican Republic. That part of the dry forest area not used for agriculture production (1.3 million acres) is found to have a production potential of 200 MW to 1400 MW, depending upon the level of management and choice of species. A biomass energy farm design and conversion facility is described and the economics of operating a wood fired facility of 50 MW, 20 MW, 5 MW, and 2 MW is compared to 50 MW and 20 MW.

  20. A triangular element based on generalized potential energy concepts

    NASA Technical Reports Server (NTRS)

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

    1976-01-01

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

  1. 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

  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. 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.

  4. 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.

  5. 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

  6. Identification of Potential Herbal Inhibitor of Acetylcholinesterase Associated Alzheimer's Disorders Using Molecular Docking and Molecular Dynamics Simulation

    PubMed Central

    Seniya, Chandrabhan; Khan, Ghulam Jilani; Uchadia, Kuldeep

    2014-01-01

    Cholinesterase inhibitors (ChE-Is) are the standard for the therapy of AD associated disorders and are the only class of approved drugs by the Food and Drug Administration (FDA). Additionally, acetylcholinesterase (AChE) is the target for many Alzheimer's dementia drugs which block the function of AChE but have some side effects. Therefore, in this paper, an attempt was made to elucidate cholinesterase inhibition potential of secondary metabolite from Cannabis plant which has negligible or no side effect. Molecular docking of 500 herbal compounds, against AChE, was performed using Autodock 4.2 as per the standard protocols. Molecular dynamics simulations have also been carried out to check stability of binding complex in water for 1000 ps. Our molecular docking and simulation have predicted high binding affinity of secondary metabolite (C28H34N2O6) to AChE. Further, molecular dynamics simulations for 1000 ps suggest that ligand interaction with the residues Asp72, Tyr70-121-334, and Phe288 of AChE, all of which fall under active site/subsite or binding pocket, might be critical for the inhibitory activity of AChE. This approach might be helpful to understand the selectivity of the given drug molecule in the treatment of Alzheimer's disease. The study provides evidence for consideration of C28H34N2O6 as a valuable small ligand molecule in treatment and prevention of AD associated disorders and further in vitro and in vivo investigations may prove its therapeutic potential. PMID:25054066

  7. 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.

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

    NASA Astrophysics Data System (ADS)

    Hratchian, Hrant P.

    2010-06-01

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

  9. 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.

  10. 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.)

  11. Prediction of Dyke Propagation using the Minimum Potential Energy Principle

    NASA Astrophysics Data System (ADS)

    Heimisson, Elías; Hooper, Andrew; Sigmundsson, Freysteinn

    2015-04-01

    An important aspect of eruption forecasting is the prediction and monitoring of dyke propagation. Eruptions occur where dykes propagate to the surface, with lava flows causing a major threat. When such eruption occur under ice, as is common in Iceland, they become explosive and often cause hazardous and destructive floods. Dykes have also been known to trigger explosive eruption when hot basaltic magma comes in contact with more developed volatile saturated magma. Such explosive eruptions pose a danger to both lives and property. At divergent plate boundaries new crust is formed primarily by dyke injections. These injections usually grow laterally away from a central volcano. Lateral growth of a dyke is expected to follow the minimum potential energy principle. Assuming a closed system, a dyke will tend to be emplaced such that it minimizes the total potential energy, ΦT, given by: ΦT = Φs + Φg (1) where Φs is the strain potential and Φg the gravitational energy potential. Assuming that the elastic medium behaves linearly the strain potential can be calculated by numerically integrating the strain energy density over a large volume. If the dyke is assumed to be propagating at a constant depth with respect to sea level the gravitational potential energy can be turned into a two dimensional integral. We do this by integrating the predicted vertical displacements multiplied by the local topographic load above a reference surface and the acceleration of gravity. We approximate strain and stress due to plate movements and then consider strain changes induced by the dyke formation. Opening of a dyke is energetically favourable when it releases strain energy built up at a divergent plate boundary, but once deviatoric stress in the crust adjacent to a segment is released it becomes favourable to propagate laterally. Dyke formation is associated with uplift on their flanks; the lower the topographic load over the flanks, the less energy it costs. For any given

  12. 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}.

  13. 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.

  14. Molecular road ecology: exploring the potential of genetics for investigating transportation impacts on wildlife.

    PubMed

    Balkenhol, Niko; Waits, Lisette P

    2009-10-01

    Transportation infrastructures such as roads, railroads and canals can have major environmental impacts. Ecological road effects include the destruction and fragmentation of habitat, the interruption of ecological processes and increased erosion and pollution. Growing concern about these ecological road effects has led to the emergence of a new scientific discipline called road ecology. The goal of road ecology is to provide planners with scientific advice on how to avoid, minimize or mitigate negative environmental impacts of transportation. In this review, we explore the potential of molecular genetics to contribute to road ecology. First, we summarize general findings from road ecology and review studies that investigate road effects using genetic data. These studies generally focus only on barrier effects of roads on local genetic diversity and structure and only use a fraction of available molecular approaches. Thus, we propose additional molecular applications that can be used to evaluate road effects across multiple scales and dimensions of the biodiversity hierarchy. Finally, we make recommendations for future research questions and study designs that would advance molecular road ecology. Our review demonstrates that molecular approaches can substantially contribute to road ecology research and that interdisciplinary, long-term collaborations will be particularly important for realizing the full potential of molecular road ecology.

  15. 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

  16. 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.

  17. 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.

  18. Emerging role of lncRNA in cancer: a potential avenue in molecular medicine

    PubMed Central

    Jariwala, Nidhi

    2016-01-01

    Hepatocellular carcinoma (HCC) accounts for the second largest number of cancer related deaths globally with limited management options for the advanced disease. Although substantial research has identified molecular targets, with strong validation in pre-clinical in vivo studies, translation of therapeutics to clinics has shown modest success. In a recent manuscript in Hepatology, Zhou and Yang et al. unravel a novel p53 associated long non-coding RNA (PRAL) as a potential prognostic marker and molecular target in HCC. Their work provides a promising approach at capitalizing the tumor suppressive role of p53 protein in fighting HCC. More importantly, it emphasizes the evolving significance of long non-coding RNAs (lncRNA) in molecular medicine. Current research trends focus on identifying and understanding roles of lncRNA in regulation of gene expression relevant to multiple disease pathophysiologies thereby presenting a new avenue of research in molecular and translational medicine. PMID:27569205

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

    PubMed

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

    2015-10-26

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

  20. 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.

  1. The metabolic energy cost of action potential velocity

    NASA Astrophysics Data System (ADS)

    Crotty, Patrick; Sangrey, Thomas; Levy, William

    2006-03-01

    Voltage changes in neurons and other active cells are caused by the passage of ions across the cell membrane. These ionic currents depend on the transmembrane ion concentration gradients, which in unmyelinated axons are maintained during rest and restored after electrical activity by an ATPase sodium-potassium exchanger in the membrane. The amount of ATP consumed by this exchanger can be taken as the metabolic energy cost of any electrical activity in the axon. We use this measure, along with biophysical models of voltage-gated sodium and potassium ion channels, to quantify the energy cost of action potentials propagating in squid giant axons. We find that the energy of an action potential can be naturally divided into three separate components associated with different aspects of the action potential. We calculate these energy components as functions of the ion channel densities and axon diameters and find that the component associated with the rising phase and velocity of the action potential achieves a minimum near the biological values of these parameters. This result, which is robust with respect to other parameters such as temperature, suggests that evolution has optimized the axon for the energy of the action potential wavefront.

  2. 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.

  3. 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...

  4. Molecular dynamics in lipid bilayers. Anisotropic diffusion in an odd restoring potential.

    PubMed Central

    Alam, T M

    1993-01-01

    Recent 2H nuclear magnetic resonance spin relaxation studies have questioned the influence of restoring potential parity on the description of lipid or molecular reorientational dynamics. In biomembranes the polar head groups of lipid and sterol constituents are expected to associate with the aqueous interface; therefore, realistic descriptions of molecular reorientation in bilayer systems should use an odd restoring potential. The multiexponential correlation functions and related spectral density functions for small-step anisotropic diffusion in a pseudo-restoring potential of the form U(beta) = -lambda cos beta are evaluated as a function of molecular ordering . From analysis of these results the single exponential approximation used in previous investigations is found to overestimate the decay rate at lower order, but is reliable for > 0.6. The exception to this trend is the decay constant for the G11 (omega; t) correlation function, which is not accurately portrayed by the first-order approximations. A second-order single exponential approximation is presented, and is shown to be equivalent to the weighted sum of the multidecay constants. In general, the potential parity is found to have only minor effects on the spin relaxation rates obtained to describe molecular reorientation in lipid bilayers. PMID:8369401

  5. Acousto-optically generated potential energy landscapes: potential mapping using colloids under flow.

    PubMed

    Juniper, Michael P N; Besseling, Rut; Aarts, Dirk G A L; Dullens, Roel P A

    2012-12-17

    Optical potential energy landscapes created using acousto-optical deflectors are characterized via solvent-driven colloidal particles. The full potential energy of both single optical traps and complex landscapes composed of multiple overlapping traps are determined using a simple force balance argument. The potential of a single trap is shown to be well described by a Gaussian trap with stiffness found to be consistent with those obtained by a thermal equilibrium method. We also obtain directly the depth of the well, which (as with stiffness) varies with laser power. Finally, various complex systems ranging from double-well potentials to random landscapes are generated from individually controlled optical traps. Predictions of these landscapes as a sum of single Gaussian wells are shown to be a good description of experimental results, offering the potential for fully controlled design of optical landscapes, constructed from single optical traps.

  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. 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.

  8. 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.

  9. 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%.

  10. 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

  11. 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

  12. 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.

  13. 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.

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

    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

  15. Potential energy functions for atomic-level simulations of water and organic and biomolecular systems.

    PubMed

    Jorgensen, William L; Tirado-Rives, Julian

    2005-05-10

    An overview is provided on the development and status of potential energy functions that are used in atomic-level statistical mechanics and molecular dynamics simulations of water and of organic and biomolecular systems. Some topics that are considered are the form of force fields, their parameterization and performance, simulations of organic liquids, computation of free energies of hydration, universal extension for organic molecules, and choice of atomic charges. The discussion of water models covers some history, performance issues, and special topics such as nuclear quantum effects.

  16. 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.

  17. 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

  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. Collisionless Plasma Modeling in an Arbitrary Potential Energy Distribution

    NASA Technical Reports Server (NTRS)

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

    1997-01-01

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

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

    PubMed

    Jacobson, Mark Z; Archer, Cristina L

    2012-09-25

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

  1. Solutions of the Klein-Gordon equation with the Morse potential energy model in higher spatial dimensions

    NASA Astrophysics Data System (ADS)

    Xie, Xiang-Jun; Jia, Chun-Sheng

    2015-03-01

    We solve the Klein-Gordon equation with the Morse potential energy model to obtain the relativistic bound state energy equation in D spatial dimensions. We find that the inter-dimensional degeneracy symmetry exists for the molecular system represented by the Morse potential model. For a fixed vibrational quantum number and various rotational quantum numbers, the relativistic energies for the X1Σ+ state of the ScI molecule diverge as D increases. We observe that the behavior of the relativistic vibrational energies in higher dimensions remains similar to that of the three-dimensional system.

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

    NASA Astrophysics Data System (ADS)

    Pham, Tri T.; Shirts, Michael R.

    2011-07-01

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

  3. ATOMIC AND MOLECULAR PHYSICS: Four-parameter analytical local model potential for atoms

    NASA Astrophysics Data System (ADS)

    Yu, Fei; Sun, Jiu-Xun; Tian, Rong-Gang; Yang, Wei

    2009-10-01

    Analytical local model potential for modeling the interaction in an atom reduces the computational effort in electronic structure calculations significantly. A new four-parameter analytical local model potential is proposed for atoms Li through Lr, and the values of four parameters are shell-independent and obtained by fitting the results of Xa method. At the same time, the energy eigenvalues, the radial wave functions and the total energies of electrons are obtained by solving the radial Schrödinger equation with a new form of potential function by Numerov's numerical method. The results show that our new form of potential function is suitable for high, medium and low Z atoms. A comparison among the new potential function and other analytical potential functions shows the greater flexibility and greater accuracy of the present new potential function.

  4. Potential structural material problems in a hydrogen energy system

    NASA Technical Reports Server (NTRS)

    Gray, H. R.; Nelson, H. G.; Johnson, R. E.; Mcpherson, 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.

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. Energy and water potential of the Southeastern Anatolia Project (GAP)

    SciTech Connect

    Kaygusuz, K.

    1999-12-01

    This article gives an overview of energy and water potential of the Southeastern Anatolia Project (GAP) in Turkey. This integrated socioeconomic development project is one of the largest of its kind in the world. The GAP region is rich in water and soil resources. The Euphrates and Tigris Rivers represent over 28% of the nation's water supply by rivers, and the economically irrigatable areas in the region make up 20% of those for the entire country. On the other hand, the GAP region is the richest region of the country in terms of its hydroelectric potential as well as its oil and asphalt reserves. The GAP region has a 22% share of the country's total hydroelectric potential, with plans for 22 dams and 19 hydropower plants. Once completed, 27 billion kWh of electricity will be generated. In addition to this hydropower and oil potential, the GAP region is also the richest region of Turkey as far as solar energy production is concerned. In meeting the energy requirements of the developing regions worldwide and in Turkey, solar energy is being taken into account as an important renewable source of energy.

  10. 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.

  11. 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.

  12. 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.

  13. Low-energy potential scattering in two and three dimensions

    SciTech Connect

    Khuri, N. N.; Martin, Andre; Richard, J.-M.; Wu, T. T.

    2009-07-15

    Conditions are established for the existence of a scattering length and an effective range in the low-energy expansion of the S-wave phase shift of a central potential in two and three dimensions. The behavior of the phase shift as a function of the momentum is also derived for longer-range power-law potentials which do not fulfill these conditions.

  14. 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.

  15. 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.

  16. 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

  17. 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/.

  18. 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.

  19. Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space.

    PubMed

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

    2015-06-18

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

  20. 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.

  1. 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

  2. Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space

    PubMed Central

    2015-01-01

    Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. In addition, the same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies. PMID:26113956

  3. 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.

  4. 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.

  5. Criticality of the electron-nucleus cusp condition to local effective potential-energy theories

    SciTech Connect

    Pan Xiaoyin; Sahni, Viraht

    2003-01-01

    Local(multiplicative) effective potential energy-theories of electronic structure comprise the transformation of the Schroedinger equation for interacting Fermi systems to model noninteracting Fermi or Bose systems whereby the equivalent density and energy are obtained. By employing the integrated form of the Kato electron-nucleus cusp condition, we prove that the effective electron-interaction potential energy of these model fermions or bosons is finite at a nucleus. The proof is general and valid for arbitrary system whether it be atomic, molecular, or solid state, and for arbitrary state and symmetry. This then provides justification for all prior work in the literature based on the assumption of finiteness of this potential energy at a nucleus. We further demonstrate the criticality of the electron-nucleus cusp condition to such theories by an example of the hydrogen molecule. We show thereby that both model system effective electron-interaction potential energies, as determined from densities derived from accurate wave functions, will be singular at the nucleus unless the wave function satisfies the electron-nucleus cusp condition.

  6. 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.

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

    PubMed Central

    Roux, B

    1997-01-01

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

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

    PubMed

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

    2011-06-01

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

  9. 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

  10. 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

  11. 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.

  12. 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)

  13. 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…

  14. Identification of Potential PPAR γ Agonists as Hypoglycemic Agents: Molecular Docking Approach.

    PubMed

    Mishra, Ganesh Prasad; Sharma, Rajesh

    2016-09-01

    Peroxisome proliferator-activated receptor gamma (PPAR γ) has become an attractive molecular target for drugs that aim to treat hyperglycemia. The object of our study is to identify the required molecular descriptor and essential amino acid residues for effective PPAR γ agonistic activity. In this work, we employed Molegro Virtual Docker program in all molecular docking simulations. Accuracy of receptor-compound docking was validated on a set of 15 PPAR γ-compound complexes for which crystallographic structures were available. The reliability of the docking results was acceptable with good root-mean-square deviation value (<2 Å). A significant correlation between different data derived from docking calculations and experimental data was revealed. Our results allowed identification of compounds with potential to become drugs against hyperglycemia.

  15. Identification of Potential PPAR γ Agonists as Hypoglycemic Agents: Molecular Docking Approach.

    PubMed

    Mishra, Ganesh Prasad; Sharma, Rajesh

    2016-09-01

    Peroxisome proliferator-activated receptor gamma (PPAR γ) has become an attractive molecular target for drugs that aim to treat hyperglycemia. The object of our study is to identify the required molecular descriptor and essential amino acid residues for effective PPAR γ agonistic activity. In this work, we employed Molegro Virtual Docker program in all molecular docking simulations. Accuracy of receptor-compound docking was validated on a set of 15 PPAR γ-compound complexes for which crystallographic structures were available. The reliability of the docking results was acceptable with good root-mean-square deviation value (<2 Å). A significant correlation between different data derived from docking calculations and experimental data was revealed. Our results allowed identification of compounds with potential to become drugs against hyperglycemia. PMID:26374652

  16. Tests of potential functional barriers for laminated multilayer food packages. Part II: Medium molecular weight permeants.

    PubMed

    Simal-Gándara, J; Sarria-Vidal, M; Rijk, R

    2000-09-01

    Experiments were performed to characterize the kinetics of the permeation of different medium molecular weight model permeants: bisphenol A, warfarin and anthracene, from liquid paraffin, through a surrogate potential functional barrier (25 microns-thick orientated polypropylene--OPP) into the food simulants olive oil and 3% (w/v) acetic acid. The characterization of permeation kinetics generally observed the permeation models previously reported to explain the experimental permeation results obtained for a low molecular weight group of model permeants. In general, the model permeants exhibited behaviour consistent with their relative molecular weights with respect to (a) the time taken to attain steady-state permeation into the food simulant in which they were more soluble, (b) their subsequent steady-state permeation rates, and (c) their partition between liquid paraffin and the OPP membrane. PMID:11091796

  17. 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).

  18. 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

  19. 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.

  20. 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.

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

    NASA Astrophysics Data System (ADS)

    Bilgin, Ö.

    2012-04-01

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

  3. 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.

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

    NASA Technical Reports Server (NTRS)

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

    1985-01-01

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

  5. 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.

  6. 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

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

    PubMed

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

    2015-02-01

    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.

  8. 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.

  9. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  11. 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.

  12. 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

  13. Potential of hydrogen bond in water. Comparison of the theory with vibrational spectra and results of molecular dynamics simulations.

    PubMed

    Efimov, Yuri Ya; Naberukhin, Yuri I

    2011-02-01

    Potential of hydrogen bond is the function which relates its energy to geometrical parameters of hydrogen bridge: its length R(O…O) and angles between direction O…O and OH group [φ (H-O…O)] and/or lone pair of proton accepting oxygen atom [χ(-O…O)]. Previously we have suggested an approach to design such potentials based on the approximate numerical solution of a reverse problem of the spectrum band shape in the frames of the fluctuation theory of hydrogen bonding. In the given work this method is applied to construction of the two-parameter potentials that depend on parameters {R(O…O), φ (H-O…O} or {φ (H-O…O), χ (-O…O)}. Using them, the spectra of OH vibrations of HOD molecules in a liquid phase are calculated theoretically in good agreement with experiment in the temperature range up to 200 °C. Distributions of angles P(φ, T), P(χ, T), and energies P(E) are calculated also. The same distributions and spectra are independently calculated on the basis of the geometrical parameters of the hydrogen bridges obtained from molecular dynamics models of water. The shapes of the spectral contours and their temperature evolution calculated for computer models turned out to be similar to experimental ones only for the potential that includes the length of H-bond R(O…O).

  14. 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.

  15. The potential role of aerobic exercise to modulate cardiotoxicity of molecularly targeted cancer therapeutics.

    PubMed

    Scott, Jessica M; Lakoski, Susan; Mackey, John R; Douglas, Pamela S; Haykowsky, Mark J; Jones, Lee W

    2013-01-01

    Molecularly targeted therapeutics (MTT) are the future of cancer systemic therapy. They have already moved from palliative therapy for advanced solid malignancies into the setting of curative-intent treatment for early-stage disease. Cardiotoxicity is a frequent and potentially serious adverse complication of some targeted therapies, leading to a broad range of potentially life-threatening complications, therapy discontinuation, and poor quality of life. Low-cost pleiotropic interventions are therefore urgently required to effectively prevent and/or treat MTT-induced cardiotoxicity. Aerobic exercise therapy has the unique capacity to modulate, without toxicity, multiple gene expression pathways in several organ systems, including a plethora of cardiac-specific molecular and cell-signaling pathways implicated in MTT-induced cardiac toxicity. In this review, we examine the molecular signaling of antiangiogenic and HER2-directed therapies that may underpin cardiac toxicity and the hypothesized molecular mechanisms underlying the cardioprotective properties of aerobic exercise. It is hoped that this knowledge can be used to maximize the benefits of small molecule inhibitors, while minimizing cardiac damage in patients with solid malignancies.

  16. Potential human cholesterol esterase inhibitor design: benefits from the molecular dynamics simulations and pharmacophore modeling studies.

    PubMed

    John, Shalini; Thangapandian, Sundarapandian; Lee, Keun Woo

    2012-01-01

    Human pancreatic cholesterol esterase (hCEase) is one of the lipases found to involve in the digestion of large and broad spectrum of substrates including triglycerides, phospholipids, cholesteryl esters, etc. The presence of bile salts is found to be very important for the activation of hCEase. Molecular dynamic simulations were performed for the apoform and bile salt complexed form of hCEase using the co-ordinates of two bile salts from bovine CEase. The stability of the systems throughout the simulation time was checked and two representative structures from the highly populated regions were selected using cluster analysis. These two representative structures were used in pharmacophore model generation. The generated pharmacophore models were validated and used in database screening. The screened hits were refined for their drug-like properties based on Lipinski's rule of five and ADMET properties. The drug-like compounds were further refined by molecular docking simulation using GOLD program based on the GOLD fitness score, mode of binding, and molecular interactions with the active site amino acids. Finally, three hits of novel scaffolds were selected as potential leads to be used in novel and potent hCEase inhibitor design. The stability of binding modes and molecular interactions of these final hits were re-assured by molecular dynamics simulations. PMID:22292952

  17. 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).

  18. 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.

  19. Molecular mechanism of antiproliferation potential of Acacia honey on NCI-H460 cell line.

    PubMed

    Aliyu, Muhammad; Odunola, Oyeronke A; Farooq, Ahsana D; Rasheed, Huma; Mesaik, Ahmed M; Choudhary, Muhammad I; Channa, Iffat S; Khan, Salman A; Erukainure, Ochuko L

    2013-01-01

    Lung cancer is one of the leading causes of death worldwide. We investigated the molecular mechanism of antiproliferation potential of Acacia honey on NCI-H460 cells by cell cycle, viability, cytokines, calcium ion and gene expression analysis. Acacia honey inhibited cells proliferation, arrested G0/G1 phase, stimulated cytokines, calcium ion release as well as suppressed p53 and Bcl-2 expression in a dose-dependent manner. We proposed that the molecular mechanism of the antiproliferation potential of Acacia honey on NCI-H460 cell line is due to cell cycle arrest, stimulation of cytokines and calcium ion as well as downregulation of Bcl-2 and p53 genes.

  20. Plasmodium falciparum kelch 13: a potential molecular marker for tackling artemisinin-resistant malaria parasites.

    PubMed

    Mita, Toshihiro; Tachibana, Shin-Ichiro; Hashimoto, Muneaki; Hirai, Makoto

    2016-01-01

    Although artemisinin combination therapies have been deployed as a first-line treatment for uncomplicated malaria in almost all endemic countries, artemisinin-resistant parasites have emerged and have gradually spread across the Greater Mekong subregions. There is growing concern that the resistant parasites may migrate to or emerge indigenously in sub-Saharan Africa, which might provoke a global increase in malaria-associated morbidity and mortality. Therefore, development of molecular markers that enable identification of artemisinin resistance with high sensitivity is urgently required to combat this issue. In 2014, a potential artemisinin-resistance responsible gene, Plasmodium falciparum kelch13, was discovered. Here, we review the genetic features of P. falciparum kelch13 and discuss its related resistant mechanisms and potential as a molecular marker.

  1. 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

  2. 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.

  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. 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. 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.

  6. 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.

  7. Spectroscopic features of dual fluorescence/luminescence resonance energy-transfer molecular beacons.

    PubMed

    Tsourkas, Andrew; Behlke, Mark A; Xu, Yangqing; Bao, Gang

    2003-08-01

    Molecular beacons have the potential to become a powerful tool in gene detection and quantification in living cells. Here we report a novel dual molecular beacons approach to reduce false-positive signals in detecting target nucleic acids in homogeneous assays. A pair of molecular beacons, each containing a fluorescence quencher and a reporter fluorophore, one with a donor and a second with an acceptor fluorophore, hybridize to adjacent regions on the same target resulting in fluorescence resonance energy transfer (FRET). The detection of a FRET signal leads to a substantially increased signal-to-background ratio compared with that seen in single molecular beacon assays and enables discrimination between fluorescence due to specific probe/target hybridization and a variety of possible false-positive events. Further, when a lanthanide chelate is used as a donor in a dual-probe assay, extremely high signal-to-background ratios can be achieved owing to the long lifetime and sharp emission peaks of the donor and the time-gated detection of acceptor fluorescence emission. These new approaches allow for the ultrasensitive detection of target molecules in a way that could be readily applied to real-time imaging of gene expression in living cells.

  8. 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

  9. 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

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

    NASA Astrophysics Data System (ADS)

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

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

  11. 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.

  12. 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

  13. Molecular evolution of aerobic energy metabolism in primates.

    PubMed

    Grossman, L I; Schmidt, T R; Wildman, D E; Goodman, M

    2001-01-01

    As part of our goal to reconstruct human evolution at the DNA level, we have been examining changes in the biochemical machinery for aerobic energy metabolism. We find that protein subunits of two of the electron transfer complexes, complex III and complex IV, and cytochrome c, the protein carrier that connects them, have all undergone a period of rapid protein evolution in the anthropoid lineage that ultimately led to humans. Indeed, subunit IV of cytochrome c oxidase (COX; complex IV) provides one of the best examples of positively selected changes of any protein studied. The rate of subunit IV evolution accelerated in our catarrhine ancestors in the period between 40 to 18 million years ago and then decelerated in the descendant hominid lineages, a pattern of rate changes indicative of positive selection of adaptive changes followed by purifying selection acting against further changes. Besides clear evidence that adaptive evolution occurred for cytochrome c and subunits of complexes III (e.g., cytochrome c(1)) and IV (e.g., COX2 and COX4), modest rate accelerations in the lineage that led to humans are seen for other subunits of both complexes. In addition the contractile muscle-specific isoform of COX subunit VIII became a pseudogene in an anthropoid ancestor of humans but appears to be a functional gene in the nonanthropoid primates. These changes in the aerobic energy complexes coincide with the expansion of the energy-dependent neocortex during the emergence of the higher primates. Discovering the biochemical adaptations suggested by molecular evolutionary analysis will be an exciting challenge.

  14. Molecular mimicry of photosynthetic energy and electron transfer

    SciTech Connect

    Gust, D.; Moore, T.A.; Moore, A.L. )

    1993-04-01

    Proper application of reaction design considerations can yield artificial photosynthetic devices which credibility mimic the three natural photochemical processes. One approach is to use pigments and electron donors and acceptors related to those found in natural photosynthesis (and thus presumably optimal for that system), but to replace the protein with covalent bonds as an organizing precept. Molecular pentads described herein exemplify the success of this approach. At the heart of these molecules, are two covalently linked synthetic porphyrin moieties (P-P). One of these models for chlorophyll is attached to a carotenoid polyene (C), whereas the other is linked to a rigid diquinone (Q-Q). As discussed later in this paper, excitation of such a pentad is followed by photoinitiated electron transfer steps which ultimately give a C[sup [center dot]+]-P-P-Q-Q[sup [center dot]-] charge-separated state. Depending upon the structure of the pentad and the conditions, these states are formed with quantum yields of up to 0.83, have lifetimes approaching 0.5 ms, and store about one-half of the energy of the exciting singlet state. Related photosynthesis mimics display singlet-singlet energy transfer from carotenoid polyenes to porphyrins and among porphyrin chromophores, and rapid quenching of porphyrin triplet states by attached carotenoids. How have the structures of these and other successful artificial reaction centers evolved, and what will be the next steps in their development The authors will address these questions from the point of view of photoinitiated electron transfer, and then singlet and triplet energy transfer will briefly be considered. 37 refs., 4 figs.

  15. Bridging the momentum distribution and the potential energy surface of protons in hydrogen bonds

    NASA Astrophysics Data System (ADS)

    Morrone, Joseph; Lin, Lin; Car, Roberto; Parrinello, Michele

    2010-03-01

    Open path integral Car-Parrinello molecular dynamics studies have uncovered the proton momentum distribution in various phases of ice [1,2]. These systems exhibit a wide range of behavior, including symmetric hydrogen bonds and quantum tunneling. In this work, we provide an in-depth statistical analysis of the simulation results. This analysis reveals a direct relation between the open path formalism of quantum particles and their underlying potential energy surface. Application of this analysis to ice systems provides quantitative information about the principle axes of the potential energy surface that the proton experiences, and indicates that the oxygen-oxygen distance is a proper reaction coordinate for such systems. Our analysis also facilitates a direct observation of anharmonic effects along the principle axes. [1] J. A. Morrone and R. Car, Phys. Rev. Lett. 101, 17801, 2008. [2] J. A. Morrone, L. Lin and R. Car, J. Chem. Phys. 130, 204511, 2009.

  16. 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.

  17. A potential for Th from inversion of cohesive energy: Elastic constants

    NASA Astrophysics Data System (ADS)

    Jaroszewicz, S.; Mosca, H. O.; Garcés, J. E.

    2012-08-01

    An interatomic pair potential for Th was derived by using the Chen-Mobius lattice inversion of cohesive energy for fcc Th as a starting point to develop a free-parameter potential suitable to be used in molecular dynamic calculations for predicting microstructure evolution and thermal properties in multicomponent nuclear fuel. The cohesive energy versus lattice parameter of Th was computed from first principles electronic structure calculations. The elastic constants for fcc Th were calculated by applying different types of strain to the starting crystal. Based on this information, the shear modulus, the Youngs modulus and the Poissons ratio were obtained. The computed elastic constants of fcc Th are found to be in a good agreement with experiments and previous theoretical results.

  18. 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.

  19. A global potential energy surface for ArH2

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.; Walch, Stephen P.; Taylor, Peter R.

    1993-01-01

    We describe a simple analytic representation of the ArH2 potential energy surface which well reproduces the results of extensive ab initio electronic structure calculations. The analytic representation smoothly interpolates between the dissociated H2 and strong bonding limits. In the fitting process, emphasis is made on accurately reproducing regions of the potential expected to be important for high temperature (ca. 3000 K) collision processes. Overall, the anisotropy and H2 bond length dependence of the analytic representation well reproduce the input data.

  20. CRC handbook of agricultural energy potential of developing countries

    SciTech Connect

    Duke, J.A.

    1986-01-01

    This book provides background information on the agroenergetic potential of 65 countries and offers summaries of major crops planted, total area planted, yield per hectare, and total production. Total land area is categorized as to agriculture, forest, and woodland, and is discussed with demographic statistics for each country. The potential for agricultural by-products and biomass to contribute to energy availability is explored, with reference to each major crop. Vegetation and/or economic activity, or soil maps are presented for most countries, as are climatic data, with crop yields and residues which are compared with production elsewhere.

  1. Free molecular collision cross section calculation methods for nanoparticles and complex ions with energy accommodation

    SciTech Connect

    Larriba, Carlos Hogan, Christopher J.

    2013-10-15

    The structures of nanoparticles, macromolecules, and molecular clusters in gas phase environments are often studied via measurement of collision cross sections. To directly compare structure models to measurements, it is hence necessary to have computational techniques available to calculate the collision cross sections of structural models under conditions matching measurements. However, presently available collision cross section methods contain the underlying assumption that collision between gas molecules and structures are completely elastic (gas molecule translational energy conserving) and specular, while experimental evidence suggests that in the most commonly used background gases for measurements, air and molecular nitrogen, gas molecule reemission is largely inelastic (with exchange of energy between vibrational, rotational, and translational modes) and should be treated as diffuse in computations with fixed structural models. In this work, we describe computational techniques to predict the free molecular collision cross sections for fixed structural models of gas phase entities where inelastic and non-specular gas molecule reemission rules can be invoked, and the long range ion-induced dipole (polarization) potential between gas molecules and a charged entity can be considered. Specifically, two calculation procedures are described detail: a diffuse hard sphere scattering (DHSS) method, in which structures are modeled as hard spheres and collision cross sections are calculated for rectilinear trajectories of gas molecules, and a diffuse trajectory method (DTM), in which the assumption of rectilinear trajectories is relaxed and the ion-induced dipole potential is considered. Collision cross section calculations using the DHSS and DTM methods are performed on spheres, models of quasifractal aggregates of varying fractal dimension, and fullerene like structures. Techniques to accelerate DTM calculations by assessing the contribution of grazing gas

  2. 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

  3. 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.

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

    PubMed

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

    2004-07-22

    Intramolecular vibrational energy flow in excited bridged azulene-anthracene compounds is investigated by time-resolved pump-probe laser spectroscopy. The bridges consist of molecular chains and are of the type (CH(2))(m) with m up to 6 as well as (CH(2)OCH(2))(n) (n=1,2) and CH(2)SCH(2). After light absorption into the azulene S(1) band and subsequent fast internal conversion, excited molecules are formed where the vibrational energy is localized at the azulene side. The vibrational energy transfer through the molecular bridge to the anthracene side and, finally, to the surrounding medium is followed by probing the red edge of the azulene S(3) absorption band at 300 nm and/or the anthracene S(1) absorption band at 400 nm. In order to separate the time scales for intramolecular and intermolecular energy transfer, most of the experiments were performed in supercritical xenon where vibrational energy transfer to the bath is comparably slow. The intramolecular equilibration proceeds in two steps. About 15%-20% of the excitation energy leaves the azulene side within a short period of 300 fs. This component accompanies the intramolecular vibrational energy redistribution (IVR) within the azulene chromophore and it is caused by dephasing of normal modes contributing to the initial local excitation of the azulene side and extending over large parts of the molecule. Later, IVR in the whole molecule takes place transferring vibrational energy from the azulene through the bridge to the anthracene side and thereby leading to microcanonical equilibrium. The corresponding time constants tau(IVR) for short bridges increase with the chain length. For longer bridges consisting of more than three elements, however, tau(IVR) is constant at around 4-5 ps. Comparison with molecular dynamics simulations suggests that the coupling of these chains to the two chromophores limits the rate of intramolecular vibrational energy transfer. Inside the bridges the energy transport is essentially

  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. 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

  7. A common molecular basis for exogenous and endogenous cannabinoid potentiation of glycine receptors.

    PubMed

    Xiong, Wei; Wu, Xiongwu; Li, Fuying; Cheng, Kejun; Rice, Kenner C; Lovinger, David M; Zhang, Li

    2012-04-11

    Both exogenous and endogenous cannabinoids can allosterically modulate glycine receptors (GlyRs). However, little is known about the molecular basis of cannabinoid-GlyR interactions. Here we report that sustained incubation with the endocannabinoid anandamide (AEA) substantially increased the amplitude of glycine-activated current in both rat cultured spinal neurons and in HEK-293 cells expressing human α1, rat α2 and α3 GlyRs. While the α1 and α3 subunits were highly sensitive to AEA-induced potentiation, the α2 subunit was relatively insensitive to AEA. Switching a serine at 296 and 307 in the TM3 (transmembrane domain 3) of the α1 and α3 subunits with an alanine (A) at the equivalent position in the α2 subunit converted the α1/α3 AEA-sensitive receptors to sensitivity resembling that of α2. The S296 residue is also critical for exogenous cannabinoid-induced potentiation of I(Gly). The magnitude of AEA potentiation decreased with removal of either the hydroxyl or oxygen groups on AEA. While desoxy-AEA was significantly less efficacious in potentiating I(Gly), desoxy-AEA inhibited potentiation produced by both Δ(9)-tetrahydrocannabinol (THC), a major psychoactive component of marijuana, and AEA. Similarly, didesoxy-THC, a modified THC with removal of both hydroxyl/oxygen groups, did not affect I(Gly) when applied alone but inhibited the potentiation of I(Gly) induced by AEA and THC. These findings suggest that exogenous and endogenous cannabinoids potentiate GlyRs via a hydrogen bonding-like interaction. Such a specific interaction likely stems from a common molecular basis involving the S296 residue in the TM3 of the α1 and α3 subunits. PMID:22496565

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Comprehensive molecular pathology analysis of small bowel adenocarcinoma reveals novel targets with potential for clinical utility

    PubMed Central

    Kelly, Paul; Fuchs, Marc-Aurel; Alderdice, Matthew; McCabe, Clare M.; Bingham, Victoria; McGready, Claire; Tripathi, Shailesh; Emmert-Streib, Frank; Loughrey, Maurice B.; McQuaid, Stephen; Maxwell, Perry; Hamilton, Peter W.; Turkington, Richard; James, Jacqueline A.; Wilson, Richard H.; Salto-Tellez, Manuel

    2015-01-01

    Small bowel accounts for only 0.5% of cancer cases in the US but incidence rates have been rising at 2.4% per year over the past decade. One-third of these are adenocarcinomas but little is known about their molecular pathology and no molecular markers are available for clinical use. Using a retrospective 28 patient matched normal-tumor cohort, next-generation sequencing, gene expression arrays and CpG methylation arrays were used for molecular profiling. Next-generation sequencing identified novel mutations in IDH1, CDH1, KIT, FGFR2, FLT3, NPM1, PTEN, MET, AKT1, RET, NOTCH1 and ERBB4. Array data revealed 17% of CpGs and 5% of RNA transcripts assayed to be differentially methylated and expressed respectively (p < 0.01). Merging gene expression and DNA methylation data revealed CHN2 as consistently hypermethylated and downregulated in this disease (Spearman −0.71, p < 0.001). Mutations in TP53 which were found in more than half of the cohort (15/28) and Kazald1 hypomethylation were both were indicative of poor survival (p = 0.03, HR = 3.2 and p = 0.01, HR = 4.9 respectively). By integrating high-throughput mutational, gene expression and DNA methylation data, this study reveals for the first time the distinct molecular profile of small bowel adenocarcinoma and highlights potential clinically exploitable markers. PMID:26315110

  13. 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

  14. 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

  15. 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.

  16. Comprehensive molecular pathology analysis of small bowel adenocarcinoma reveals novel targets with potential for clinical utility.

    PubMed

    Alvi, Muhammad A; McArt, Darragh G; Kelly, Paul; Fuchs, Marc-Aurel; Alderdice, Matthew; McCabe, Clare M; Bingham, Victoria; McGready, Claire; Tripathi, Shailesh; Emmert-Streib, Frank; Loughrey, Maurice B; McQuaid, Stephen; Maxwell, Perry; Hamilton, Peter W; Turkington, Richard; James, Jacqueline A; Wilson, Richard H; Salto-Tellez, Manuel

    2015-08-28

    Small bowel accounts for only 0.5% of cancer cases in the US but incidence rates have been rising at 2.4% per year over the past decade. One-third of these are adenocarcinomas but little is known about their molecular pathology and no molecular markers are available for clinical use. Using a retrospective 28 patient matched normal-tumor cohort, next-generation sequencing, gene expression arrays and CpG methylation arrays were used for molecular profiling. Next-generation sequencing identified novel mutations in IDH1, CDH1, KIT, FGFR2, FLT3, NPM1, PTEN, MET, AKT1, RET, NOTCH1 and ERBB4. Array data revealed 17% of CpGs and 5% of RNA transcripts assayed to be differentially methylated and expressed respectively (p < 0.01). Merging gene expression and DNA methylation data revealed CHN2 as consistently hypermethylated and downregulated in this disease (Spearman -0.71, p < 0.001). Mutations in TP53 which were found in more than half of the cohort (15/28) and Kazald1 hypomethylation were both were indicative of poor survival (p = 0.03, HR = 3.2 and p = 0.01, HR = 4.9 respectively). By integrating high-throughput mutational, gene expression and DNA methylation data, this study reveals for the first time the distinct molecular profile of small bowel adenocarcinoma and highlights potential clinically exploitable markers.

  17. 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

  18. 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.

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

    NASA Astrophysics Data System (ADS)

    Asiaee, Alireza; Benjamin, Kenneth M.

    2016-08-01

    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.

  20. 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

  1. 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.

  2. 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.

  3. 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.

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

    PubMed

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

    2013-09-28

    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.

  5. 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.

  6. 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.

  7. 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.

  8. Spectroscopic constants and potential energy curves of yttrium carbide (YC).

    PubMed

    Suo, Bingbing; Balasubramanian, Krishnan

    2007-06-14

    The potential energy curves of the low-lying electronic states of yttrium carbide (YC) and its cation are calculated at the complete active space self-consistent field and the multireference single and double excitation configuration interaction (MRSDCI) levels of theory. Fifteen low-lying electronic states of YC with different spin and spatial symmetries were identified. The X (4)Sigma- state prevails as the ground state of YC, and a low-lying excited A (4)Pi state is found to be 1661 cm(-1) higher at the MRSDCI level. The computations of the authors support the assignment of the observed spectra to a B (4)Delta(Omega=72)<--A (4)Pi(Omega=52) transition with a reinterpretation that the A (4)Pi state is appreciably populated under the experimental conditions as it is less than 2000 cm(-1) of the X (4)Sigma- ground state, and the previously suggested (4)Pi ground state is reassigned to the first low-lying excited state of YC. The potential energy curves of YC+ confirm a previous prediction by Seivers et al. [J. Chem. Phys. 105, 6322 (1996)] that the ground state of YC+ is formed through a second pathway at higher energies. The calculated ionization energy of YC is 6.00 eV, while the adiabatic electron affinity is 0.95 eV at the MRSDCI level. The computed ionization energy of YC and dissociation energy of YC+ confirm the revised experimental estimates provided by Seivers et al. although direct experimental measurements yielded results with greater errors due to uncertainty in collisional cross sections for YC+ formation.

  9. Characterization of the potential energy landscape of an antiplasticized polymer

    NASA Astrophysics Data System (ADS)

    Riggleman, Robert A.; Douglas, Jack F.; de Pablo, Juan J.

    2007-07-01

    The nature of the individual transitions on the potential energy landscape (PEL) associated with particle motion are directly examined for model fragile glass-forming polymer melts, and the results are compared to those of an antiplasticized polymer system. In previous work, we established that the addition of antiplasticizer reduces the fragility of glass formation so that the antiplasticized material is a stronger glass former. In the present work, we find that the antiplasticizing molecules reduce the energy barriers for relaxation compared to the pure polymer, implying that the antiplasticized system has smaller barriers to overcome in order to explore its configuration space. We examine the cooperativity of segmental motion in these bulk fluids and find that more extensive stringlike collective motion enables the system to overcome larger potential energy barriers, in qualitative agreement with both the Stillinger-Weber and Adam-Gibbs views of glass formation. Notably, the stringlike collective motion identified by our PEL analysis corresponds to incremental displacements that occur within larger-scale stringlike particle displacement processes associated with PEL metabasin transitions that mediate structural relaxation. These “substrings” nonetheless seem to exhibit changes in relative size with antiplasticization similar to those observed in “superstrings” that arise at elevated temperatures. We also study the effects of confinement on the energy barriers in each system. Film confinement makes the energy barriers substantially smaller in the pure polymer, while it has little effect on the energy barriers in the antiplasticized system. This observation is qualitatively consistent with our previous studies of stringlike motion in these fluids at higher temperatures and with recent experimental measurements by Torkelson and co-workers.

  10. Spectroscopic constants and potential energy curves of yttrium carbide (YC)

    NASA Astrophysics Data System (ADS)

    Suo, Bingbing; Balasubramanian, Krishnan

    2007-06-01

    The potential energy curves of the low-lying electronic states of yttrium carbide (YC) and its cation are calculated at the complete active space self-consistent field and the multireference single and double excitation configuration interaction (MRSDCI) levels of theory. Fifteen low-lying electronic states of YC with different spin and spatial symmetries were identified. The XΣ-4 state prevails as the ground state of YC, and a low-lying excited AΠ4 state is found to be 1661cm-1 higher at the MRSDCI level. The computations of the authors support the assignment of the observed spectra to a BΔ4(Ω =7/2)←AΠ4(Ω=5/2) transition with a reinterpretation that the AΠ4 state is appreciably populated under the experimental conditions as it is less than 2000cm-1 of the XΣ-4 ground state, and the previously suggested Π4 ground state is reassigned to the first low-lying excited state of YC. The potential energy curves of YC + confirm a previous prediction by Seivers et al. [J. Chem. Phys. 105, 6322 (1996)] that the ground state of YC+ is formed through a second pathway at higher energies. The calculated ionization energy of YC is 6.00eV, while the adiabatic electron affinity is 0.95eV at the MRSDCI level. The computed ionization energy of YC and dissociation energy of YC+ confirm the revised experimental estimates provided by Seivers et al. although direct experimental measurements yielded results with greater errors due to uncertainty in collisional cross sections for YC+ formation.

  11. 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.

  12. Nuclear momentum distribution and potential energy surface in hexagonal ice

    NASA Astrophysics Data System (ADS)

    Lin, Lin; Morrone, Joseph; Car, Roberto; Parrinello, Michele

    2011-03-01

    The proton momentum distribution in ice Ih has been recently measured by deep inelastic neutron scattering and calculated from open path integral Car-Parrinello simulation. Here we report a detailed investigation of the relation between momentum distribution and potential energy surface based on both experiment and simulation results. The potential experienced by the proton is largely harmonic and characterized by 3 principal frequencies, which can be associated to weighted averages of phonon frequencies via lattice dynamics calculations. This approach also allows us to examine the importance of quantum effects on the dynamics of the oxygen nuclei close to the melting temperature. Finally we quantify the anharmonicity that is present in the potential acting on the protons. This work is supported by NSF and by DOE.

  13. Energy aspects and potential energy savings of the new DASI process for milk sterilization

    SciTech Connect

    Frey, B.C.; Stewart, L.E.; Chandarana, D.; Wolfson, R.P.

    1981-01-01

    An experimental study was conducted to determine the difference in total processing energy required by the DASI ultra-high temperature (UHT) system and a conventional high temperature short time (HTST) fluid milk system. Data available in the literature were used to develop an energy use profile for the current US fluid milk system from processor to consumer. The energy data measured and the profile developed were used to estimate the potential energy savings resulting from the introduction of sterile milk in the US fluid milk market. Savings of energy resulting from the introduction of sterile milk were estimated to be 12 million barrels of oil annually.

  14. Mass, charge, and energy separation by selective acceleration with a traveling potential hill

    NASA Astrophysics Data System (ADS)

    Tung, L. Schwager; Barr, W. L.; Lowder, R. S.; Post, R. F.

    1996-10-01

    A traveling electric potential hill has been used to generate an ion beam with an energy distribution that is mass dependent from a monoenergetic ion beam of mixed masses. This effect can be utilized as a novel method for mass separation applied to identification or enrichment of ions (e.g., of elements, isotopes, or molecules). This theory for mass-selective acceleration is presented here and is shown to be confirmed by experiment and by a time-dependent particle-in-cell computer simulation. Results show that monoenergetic ions with the particular mass of choice are accelerated by controlling the hill potential and the hill velocity. The hill velocity is typically 20%-30% faster than the ions to be accelerated. The ability of the hill to pickup a particular mass uses the fact that small kinetic energy differences in the lab frame appear much larger in the moving hill frame. Ions will gain energy from the approaching hill if their relative energy in the moving hill frame is less than the peak potential of the hill. The final energy of these accelerated ions can be several times the source energy, which facilitates energy filtering for mass purification or identification. If the hill potential is chosen to accelerate multiple masses, the heaviest mass will have the greatest final energy. Hence, choosing the appropriate hill potential and collector retarding voltage will isolate ions with the lightest, heaviest, or intermediate mass. In the experimental device, called a Solitron, purified 20Ne and 22Ne are extracted from a ribbon beam of neon that is originally composed of 20Ne:22Ne in the natural ratio of 91:9. The isotopic content of the processed beam is determined by measuring the energy distribution of the detected current. These results agree with the theory. In addition to mass selectivity, our theory can also be applied to the filtration of an ion beam according to charge state or energy. Because of this variety of properties, the Solitron is envisioned to

  15. 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.

  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. Confining interparticle potential makes both heat transport and energy diffusion anomalous in one-dimensional phononic systems

    NASA Astrophysics Data System (ADS)

    Kosevich, Yuriy A.; Savin, Alexander V.

    2016-10-01

    We provide molecular dynamics simulation of heat transport and energy diffusion in one-dimensional molecular chains with different interparticle pair potentials at zero and non-zero temperature. We model the thermal conductivity (TC) and energy diffusion (ED) in the chain of coupled rotators and in the Lennard-Jones chain either without or with the confining parabolic interparticle potential. The considered chains without the confining potential have normal TC and ED at non-zero temperature, while the corresponding chains with the confining potential are characterized by anomalous (diverging with the system length) TC and superdiffusion of energy. Similar effect is produced by the anharmonic quartic confining pair potential. We confirm in such a way that, surprisingly, the confining pair potential makes both heat transport and energy diffusion anomalous in one-dimensional phononic systems. We show that the normal TC is always accompanied by the normal ED in the thermalized anharmonic chains, while the superdiffusion of energy occurs in the thermalized chains with only anomalous heat transport.

  18. 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).

  19. 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.

  20. 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

  1. 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

  2. Molecular electrostatic potential for exploring π-conjugation: a density-functional investigation.

    PubMed

    Pingale, Subhash S

    2011-09-01

    Molecular electrostatic potentials (MESP) of the most common building blocks of organic π-conjugated systems, viz. ethylene, acetylene, benzene, furan, pyrrole, thiophene and phenylvinylene, are examined at the B3LYP/6-311++G(2d,2p) level. The topography of MESP is employed for mapping the strength of electronic conjugation between these building blocks. When electron-rich molecular regions are connected to each other, the MESP value of the corresponding conjugation critical point (CCP) is able to provide a quantitative measure of the strength of the conjugation. The systems with stronger conjugation are generally seen to possess a larger negative value of CCP and a smaller difference (ΔV(CM-CCP)) between the MESP values of respective conjugated minimum (CM) and the CCP, in agreement with the experimental as well as other theoretical results. The present MESP topography-based approach thus offers a measure of the quantitative strength of π-conjugation in molecules.

  3. 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.

  4. Affine-response model of molecular solvation of ions: Accurate predictions of asymmetric charging free energies

    PubMed Central

    Bardhan, Jaydeep P.; Jungwirth, Pavel; Makowski, Lee

    2012-01-01

    Two mechanisms have been proposed to drive asymmetric solvent response to a solute charge: a static potential contribution similar to the liquid-vapor potential, and a steric contribution associated with a water molecule's structure and charge distribution. In this work, we use free-energy perturbation molecular-dynamics calculations in explicit water to show that these mechanisms act in complementary regimes; the large static potential (∼44 kJ/mol/e) dominates asymmetric response for deeply buried charges, and the steric contribution dominates for charges near the solute-solvent interface. Therefore, both mechanisms must be included in order to fully account for asymmetric solvation in general. Our calculations suggest that the steric contribution leads to a remarkable deviation from the popular “linear response” model in which the reaction potential changes linearly as a function of charge. In fact, the potential varies in a piecewise-linear fashion, i.e., with different proportionality constants depending on the sign of the charge. This discrepancy is significant even when the charge is completely buried, and holds for solutes larger than single atoms. Together, these mechanisms suggest that implicit-solvent models can be improved using a combination of affine response (an offset due to the static potential) and piecewise-linear response (due to the steric contribution). PMID:23020318

  5. 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

  6. Thunderstorm Electric Potential Profiles: Electrical Evolution and Lightning Energy

    NASA Astrophysics Data System (ADS)

    Stolzenburg, M.; Marshall, T. C.

    2005-05-01

    From a balloon sounding of electric field through a thunderstorm, one can calculate the vertical profile of potential, V, within the storm. In this presentation we investigate thunderstorm electrical evolution by examining V profiles through various stages of a storm's life. We present data from New Mexico mountain thunderstorms in which we made a series of 4 to 6 balloon soundings. Several of the successive V profiles in the same storm are quite similar, in spite of the numerous lightning flashes that occurred during the balloon flights. These similarities suggest that the V profiles are reasonable estimates of the in-cloud potential. The similar profiles occur during the mature phase of the storm, and mature phase profiles are even similar from one storm to another. This is true despite different lightning flashing rates and, presumably, different charge generation rates in the different storms. Another result of this work is that potential profiles during the early and late stages of the storm do not resemble those from the mature stage. Recently, Coleman et al. [2003] showed that intra-cloud (IC) flashes connect potential extrema of opposite polarity and that normal (negative) cloud-to-ground (CG) flashes connect a potential minimum to ground. Thus we can use the V profiles to estimate the potential difference spanned by lightning flashes during the evolution of the storm and, with this, estimate the lightning energy. Typical potential differences spanned by IC and CG flashes will be presented from four storms. Reference: Coleman, L.M., T.C. Marshall, M. Stolzenburg, T. Hamlin, P.R. Krehbiel, W. Rison, and R.J. Thomas, Effects of charge and electrostatic potential on lightning propagation, J. Geophys. Res., 108, doi:10.1029/2002JD002718, 2003.

  7. 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

  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. Energy Conversion by Molecular Motors Coupled to Nucleotide Hydrolysis

    NASA Astrophysics Data System (ADS)

    Lipowsky, Reinhard; Liepelt, Steffen; Valleriani, Angelo

    2009-06-01

    Recent theoretical work on the energy conversion by molecular motors coupled to nucleotide hydrolysis is reviewed. The most abundant nucleotide is provided by adenosine triphosphate (ATP) which is cleaved into adenosine diphosphate (ADP) and inorganic phosphate. The motors have several catalytic domains (or active sites), each of which can be empty or occupied by ATP or ADP. The chemical composition of all catalytic domains defines distinct nucleotide states of the motor which form a discrete state space. Each of these motor states is connected to several other states via chemical transitions. For stepping motors such as kinesin, which walk along cytoskeletal filaments, some motor states are also connected by mechanical transitions, during which the motor is displaced along the filament and able to perform mechanical work. The different motor states together with the possible chemical and mechanical transitions provide a network representation for the chemomechanical coupling of the motor molecule. The stochastic motor dynamics on these networks exhibits several distinct motor cycles, which represent the dominant pathways for different regimes of nucleotide concentrations and load force. For the kinesin motor, the competition of two such cycles determines the stall force, at which the motor velocity vanishes and the motor reverses its direction of motion. In general, kinesin is found to be governed by the competition of three distinct chemomechanical cycles. The corresponding network representation provides a unified description for all motor properties that have been determined by single molecule experiments.

  10. Homogeneous connectivity of potential energy network in a solidlike state of water cluster.

    PubMed

    Akimoto, Takuma; Kaneko, Toshihiro; Yasuoka, Kenji; Zeng, Xiao Cheng

    2013-06-28

    A novel route to the exponential trapping-time distribution within a solidlike state in water clusters is described. We propose a simple homogeneous network (SHN) model to investigate dynamics on the potential energy networks of water clusters. In this model, it is shown that the trapping-time distribution in a solidlike state follows the exponential distribution, whereas the trapping-time distribution in local potential minima within the solidlike state is not exponential. To confirm the exponential trapping-time distribution in a solidlike state, we investigate water clusters, (H2O)6 and (H2O)12, by molecular dynamics simulations. These clusters change dynamically from solidlike to liquidlike state and vice versa. We find that the probability density functions of trapping times in a solidlike state are described by the exponential distribution whereas those of interevent times of large fluctuations in potential energy within the solidlike state follow the Weibull distributions. The results provide a clear evidence that transition dynamics between solidlike and liquidlike states in water clusters are well described by the SHN model, suggesting that the exponential trapping-time distribution within a solidlike state originates from the homogeneous connectivity in the potential energy network.

  11. 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.

  12. 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.

  13. 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.

  14. 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).

  15. Electric potential calculation in molecular simulation of electric double layer capacitors

    NASA Astrophysics Data System (ADS)

    Wang, Zhenxing; Olmsted, David L.; Asta, Mark; Laird, Brian B.

    2016-11-01

    For the molecular simulation of electric double layer capacitors (EDLCs), a number of methods have been proposed and implemented to determine the one-dimensional electric potential profile between the two electrodes at a fixed potential difference. In this work, we compare several of these methods for a model LiClO4-acetonitrile/graphite EDLC simulated using both the traditional fixed-charged method (FCM), in which a fixed charge is assigned a priori to the electrode atoms, or the recently developed constant potential method (CPM) (2007 J. Chem. Phys. 126 084704), where the electrode charges are allowed to fluctuate to keep the potential fixed. Based on an analysis of the full three-dimensional electric potential field, we suggest a method for determining the averaged one-dimensional electric potential profile that can be applied to both the FCM and CPM simulations. Compared to traditional methods based on numerically solving the one-dimensional Poisson’s equation, this method yields better accuracy and no supplemental assumptions.

  16. Electric potential calculation in molecular simulation of electric double layer capacitors.

    PubMed

    Wang, Zhenxing; Olmsted, David L; Asta, Mark; Laird, Brian B

    2016-11-23

    For the molecular simulation of electric double layer capacitors (EDLCs), a number of methods have been proposed and implemented to determine the one-dimensional electric potential profile between the two electrodes at a fixed potential difference. In this work, we compare several of these methods for a model LiClO4-acetonitrile/graphite EDLC simulated using both the traditional fixed-charged method (FCM), in which a fixed charge is assigned a priori to the electrode atoms, or the recently developed constant potential method (CPM) (2007 J. Chem. Phys. 126 084704), where the electrode charges are allowed to fluctuate to keep the potential fixed. Based on an analysis of the full three-dimensional electric potential field, we suggest a method for determining the averaged one-dimensional electric potential profile that can be applied to both the FCM and CPM simulations. Compared to traditional methods based on numerically solving the one-dimensional Poisson's equation, this method yields better accuracy and no supplemental assumptions.

  17. Electric potential calculation in molecular simulation of electric double layer capacitors.

    PubMed

    Wang, Zhenxing; Olmsted, David L; Asta, Mark; Laird, Brian B

    2016-11-23

    For the molecular simulation of electric double layer capacitors (EDLCs), a number of methods have been proposed and implemented to determine the one-dimensional electric potential profile between the two electrodes at a fixed potential difference. In this work, we compare several of these methods for a model LiClO4-acetonitrile/graphite EDLC simulated using both the traditional fixed-charged method (FCM), in which a fixed charge is assigned a priori to the electrode atoms, or the recently developed constant potential method (CPM) (2007 J. Chem. Phys. 126 084704), where the electrode charges are allowed to fluctuate to keep the potential fixed. Based on an analysis of the full three-dimensional electric potential field, we suggest a method for determining the averaged one-dimensional electric potential profile that can be applied to both the FCM and CPM simulations. Compared to traditional methods based on numerically solving the one-dimensional Poisson's equation, this method yields better accuracy and no supplemental assumptions. PMID:27624573

  18. 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.

  19. 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.

  20. Control of Electronic Symmetry and Rectification through Energy Level Variations in Bilayer Molecular Junctions.

    PubMed

    Bayat, Akhtar; Lacroix, Jean-Christophe; McCreery, Richard L

    2016-09-21

    Two layers of molecular oligomers were deposited on flat carbon electrode surfaces by electrochemical reduction of diazonium reagents, then a top contact applied to complete a solid-state molecular junction containing a molecular bilayer. The structures and energy levels of the molecular layers included donor molecules with relatively high energy occupied orbitals and acceptors with low energy unoccupied orbitals. When the energy levels of the two molecular layers were similar, the device had electronic characteristics similar to a thick layer of a single molecule, but if the energy levels differed, the current voltage behavior exhibited pronounced rectification. Higher current was observed when the acceptor molecule was biased negatively in eight different bilayer combinations, and the direction of rectification was reversed if the molecular layers were also reversed. Rectification persisted at very low temperature (7 K), and was activationless between 7 and 100 K. The results are a clear example of a "molecular signature" in which electronic behavior is directly affected by molecular structure and orbital energies. The rectification mechanism is discussed, and may provide a basis for rational design of electronic properties by variation of molecular structure.

  1. Control of Electronic Symmetry and Rectification through Energy Level Variations in Bilayer Molecular Junctions.

    PubMed

    Bayat, Akhtar; Lacroix, Jean-Christophe; McCreery, Richard L

    2016-09-21

    Two layers of molecular oligomers were deposited on flat carbon electrode surfaces by electrochemical reduction of diazonium reagents, then a top contact applied to complete a solid-state molecular junction containing a molecular bilayer. The structures and energy levels of the molecular layers included donor molecules with relatively high energy occupied orbitals and acceptors with low energy unoccupied orbitals. When the energy levels of the two molecular layers were similar, the device had electronic characteristics similar to a thick layer of a single molecule, but if the energy levels differed, the current voltage behavior exhibited pronounced rectification. Higher current was observed when the acceptor molecule was biased negatively in eight different bilayer combinations, and the direction of rectification was reversed if the molecular layers were also reversed. Rectification persisted at very low temperature (7 K), and was activationless between 7 and 100 K. The results are a clear example of a "molecular signature" in which electronic behavior is directly affected by molecular structure and orbital energies. The rectification mechanism is discussed, and may provide a basis for rational design of electronic properties by variation of molecular structure. PMID:27563739

  2. 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.

  3. 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.

  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. 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.

  6. 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

  7. 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

  8. The conundrum of inhibitory signaling by ITAM-containing immunoreceptors: potential molecular mechanisms

    PubMed Central

    Waterman, Paul M.; Cambier, John C.

    2010-01-01

    Immunoreceptor signals must be appropriately transduced and regulated to achieve effective immunity while controlling inflammation and autoimmunity. It is generally held that these processes are mediated by the interplay of distinct activating and inhibitory receptors via conserved activating (ITAM) and inhibitory (ITIM) signaling motifs. However, recent evidence indicates that under certain conditions incomplete phosphorylation of ITAM tyrosines leads to inhibitory signals. This new regulatory function of ITAMs has been termed ITAMi (inhibitory ITAM). Here we discuss the potential molecular mechanisms of inhibitory signaling by ITAM-containing receptors. PMID:20875413

  9. 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.

  10. 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.

  11. Picosecond fluctuating protein energy landscape mapped by pressure temperature molecular dynamics simulation.

    SciTech Connect

    Meinhold, Lars; Smith, Jeremy C; Kitao, Akio; Zewail, Ahmed H.

    2007-10-01

    Microscopic statistical pressure fluctuations can, in principle, lead to corresponding fluctuations in the shape of a protein energy landscape. To examine this, nanosecond molecular dynamics simulations of lysozyme are performed covering a range of temperatures and pressures. The well known dynamical transition with temperature is found to be pressure-independent, indicating that the effective energy barriers separating conformational substates are not significantly influenced by pressure. In contrast, vibrations within substates stiffen with pressure, due to increased curvature of the local harmonic potential in which the atoms vibrate. The application of pressure is also shown to selectively increase the damping of the anharmonic, low-frequency collective modes in the protein, leaving the more local modes relatively unaffected. The critical damping frequency, i.e., the frequency at which energy is most efficiently dissipated, increases linearly with pressure. The results suggest that an invariant description of protein energy landscapes should be subsumed by a fluctuating picture and that this may have repercussions in, for example, mechanisms of energy dissipation accompanying functional, structural, and chemical relaxation.

  12. Picosecond Fluctuating Protein Energy Landscape Mapped by Pressure-Temperature Molecular Dynamics Simulation

    SciTech Connect

    Meinhold, Lars; Smith, Jeremy C; Kitao, Akio; Zewail, Ahmed H.

    2007-08-01

    Microscopic statistical pressure fluctuations can, in principle, lead to corresponding fluctuations in the shape of a protein energy landscape. To examine this, nanosecond molecular dynamics simulations of lysozyme are performed covering a range of temperatures and pressures. The well known dynamical transition with temperature is found to be pressure-independent, indicating that the effective energy barriers separating conformational substates are not significantly influenced by pressure. In contrast, vibrations within substates stiffen with pressure, due to increased curvature of the local harmonic potential in which the atoms vibrate. The application of pressure is also shown to selectively increase the damping of the anharmonic, low-frequency collective modes in the protein, leaving the more local modes relatively unaffected. The critical damping frequency, i.e., the frequency at which energy is most efficiently dissipated, increases linearly with pressure. The results suggest that an invariant description of protein energy landscapes should be subsumed by a fluctuating picture and that this may have repercussions in, for example, mechanisms of energy dissipation accompanying functional, structural, and chemical relaxation.

  13. 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.

  14. 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.

  15. The Potential for Energy Efficiency and Renewable Energy in North Carolina

    SciTech Connect

    Hadley, SW

    2003-08-06

    As many states have restructured their electric power industry, they have established a ''systems benefit charge'' to help fund those activities that will no longer be funded by utilities in the new structure. Examples include weatherization of low-income housing, efficiency programs, and renewable energy development. Varying amounts have been collected and allocated depending on state needs and abilities. One question that arises is what are the potential results of funding the different types of programs. What is the potential for energy efficiency or for renewable power, and what would be accomplished given the amount of funding that the system benefit charge may provide? The purpose of this project is to provide an initial estimate of the potential for energy efficiency and renewable energy in North Carolina. This potential could be funded by a public benefits fund resulting from a green power program being considered in the state. It concentrates on electric energy savings and production. Savings in buildings can include improvements to space conditioning as well as improvements to lighting or other appliances. Distributed power potential, through use of combined heat and power and renewables such as photovoltaic, wind, and biomass were examined. The goal is to provide information to decision makers who are developing a green power program in North Carolina. It will not be a complete and detailed study of all efficiency potentials but is more of a scoping exercise to determine the relative impacts and begin the process for a more definitive study at a later date. Statewide energy savings potential cannot be directly measured but must be calculated. First, the word ''potential'' means that the savings have not occurred yet. Second, the savings are often only indirectly measured by estimating what energy use there would have been without the changes in technology or behavior. Calculations through sampling and statistical analysis or by simulation are a necessary

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Stabilized quasi-Newton optimization of noisy potential energy surfaces

    SciTech Connect

    Schaefer, Bastian; Goedecker, Stefan; Alireza Ghasemi, S.; Roy, Shantanu

    2015-01-21

    Optimizations of atomic positions belong to the most commonly performed tasks in electronic structure calculations. Many simulations like global minimum searches or characterizations of chemical reactions require performing hundreds or thousands of minimizations or saddle computations. To automatize these tasks, optimization algorithms must not only be efficient but also very reliable. Unfortunately, computational noise in forces and energies is inherent to electronic structure codes. This computational noise poses a severe problem to the stability of efficient optimization methods like the limited-memory Broyden–Fletcher–Goldfarb–Shanno algorithm. We here present a technique that allows obtaining significant curvature information of noisy potential energy surfaces. We use this technique to construct both, a stabilized quasi-Newton minimization method and a stabilized quasi-Newton saddle finding approach. We demonstrate with the help of benchmarks that both the minimizer and the saddle finding approach are superior to comparable existing methods.