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Sample records for molecular potential energy

  1. Potential energy hypersurface and molecular flexibility

    NASA Astrophysics Data System (ADS)

    Koča, Jaroslav

    1993-02-01

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

  2. Molecular Multipole Potential Energy Functions for Water.

    PubMed

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

    2016-03-01

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

  3. Calculation of molecular free energies in classical potentials

    NASA Astrophysics Data System (ADS)

    Farhi, Asaf; Singh, Bipin

    2016-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2006-04-01

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

  5. Molecular understanding of mutagenicity using potential energy methods

    SciTech Connect

    Broyde, S.; Shapiro, R.

    1992-07-01

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

  6. (Molecular understanding of mutagenicity using potential energy methods)

    SciTech Connect

    Broyde, S.

    1990-01-01

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

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

    PubMed

    Kowalewski, Markus; Larsson, Elisabeth; Heryudono, Alfa

    2016-08-28

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

  8. Electronic structure, molecular bonding and potential energy surfaces

    SciTech Connect

    Ruedenberg, K.

    1993-12-01

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

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

    PubMed

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

    2012-11-21

    We present a stochastic, swarm intelligence-based optimization algorithm for the prediction of global minima on potential energy surfaces of molecular cluster structures. Our optimization approach is a modification of the artificial bee colony (ABC) algorithm which is inspired by the foraging behavior of honey bees. We apply our modified ABC algorithm to the problem of global geometry optimization of molecular cluster structures and show its performance for clusters with 2-57 particles and different interatomic interaction potentials. PMID:23181297

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

    NASA Astrophysics Data System (ADS)

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

    2012-11-01

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

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

    PubMed

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

    2016-09-01

    We report precise manipulation of the potential-energy surfaces (PESs) of a series of butterfly-like pyrazolate-bridged platinum binuclear complexes, by synthetic control of the electronic structure of the cyclometallating ligand and the steric bulkiness of the pyrazolate bridging ligand. Color tuning of dual emission from blue/red, to green/red and red/deep red were achieved for these phosphorescent molecular butterflies, which have two well-controlled energy minima on the PESs. The environmentally dependent photoluminescence of these molecular butterflies enabled their application as self-referenced luminescent viscosity sensor. PMID:27500886

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

    SciTech Connect

    Ho, T.; Rabitz, H.

    1996-02-01

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

  13. Molecular electrostatic potentials by systematic molecular fragmentation

    SciTech Connect

    Reid, David M.; Collins, Michael A.

    2013-11-14

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

  14. 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

  15. 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

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

    PubMed

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

    2013-11-01

    A systematic vibrational spectroscopic assignment and analysis of pramipexole [(S)-N(6)-propyl-4,5,6,7-tetrahydro-1,3-benzothiazole-2,6-diamine] has been carried out using FT-IR and FT-Raman spectral data. The vibrational analysis was aided by an electronic structure calculation based on the hybrid density functional method B3LYP using a 6-311G(d, p) and cc-pVTZ basis sets. Molecular equilibrium geometries, electronic energies, IR and Raman intensities, harmonic vibrational frequencies have been computed. The assignments are based on the experimental IR and Raman spectra, and a complete assignment of the observed spectra has been proposed. The UV-visible spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies and the maximum absorption λmax were determined by time-dependent DFT (TD-DFT) method. The geometrical parameters, vibrational frequencies and absorption wavelengths were compared with the experimental data. The complete vibrational assignments are performed on the basis of the potential energy distributions (PEDs) of the vibrational modes in terms of natural internal coordinates. The simulated FT-IR, FT-Raman, and UV spectra of the title compound have been constructed. In addition, the potential energy surface, HOMO and LUMO energies, the molecular electrostatic potential and the first-order hyperpolarizability have been computed. The magnitude of the first-order hyperpolarizability is 5 times larger than that of urea and the title compound may be a potential applicant for the development of NLO materials. PMID:23831980

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

    SciTech Connect

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

    2015-08-15

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

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

    PubMed

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

    2016-07-13

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

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

    PubMed Central

    Wang, Jiyao; Deng, Yuqing; Roux, Benoît

    2006-01-01

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

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

    ScienceCinema

    Sayre, Richard [LANL

    2013-01-22

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

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

    SciTech Connect

    Sayre, Richard

    2012-03-22

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

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

    NASA Astrophysics Data System (ADS)

    Jacobson, Daniel; Stratt, Richard M.

    2014-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2005-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-03-01

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

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

    NASA Astrophysics Data System (ADS)

    Alikacem, A.; Aubert-Frécon, M.

    1985-05-01

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

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

    PubMed

    Bhattacharjee, Rituparna; Roy, Ram Kinkar

    2013-11-14

    The relative contribution of the sum of kinetic [(10/9)CFρ(r)2/3] and exchange energy [(4/9)CXρ(r)1/3] terms to that of the electronic part of the molecular electrostatic potential [Vel(r)] in the variants of hardness potential is investigated to assess the proposed definition of Δ+h(k) = −[VelN+1(k) – VelN(k)] and Δ–h(k) = −[VelN(k) – VelN–1(k)] (Saha; et al. J. Comput. Chem. 2013, 34, 662). Some substituted benzenes and polycyclic aromatic hydrocarbons (PAHs) (undergoing electrophilic aromatic substitution), carboxylic acids, and their derivatives are chosen to carry out the theoretical investigation as stated above. Intra- and intermolecular reactivity trends generated by Δ+h(k) and Δ–h(k) are found to be satisfactory and are correlated reasonably well with experimental results. PMID:24083374

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

    SciTech Connect

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

    2014-10-03

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

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

    ERIC Educational Resources Information Center

    Becker, Nicole M.; Cooper, Melanie M.

    2014-01-01

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

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

    PubMed

    Alishahi, Marzieh; Kamali, Reza; Abouali, Omid

    2016-04-01

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

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

    EPA Science Inventory

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

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

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

    EPA Science Inventory

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

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

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

    NASA Technical Reports Server (NTRS)

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

    1982-01-01

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

  13. 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.

  14. 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.

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

    PubMed

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

    2016-03-21

    We present an extension of various free-energy methodologies to determine the chemical potential of the solid and liquid phases of a fully-flexible molecule using classical simulation. The methods are applied to the Smith-Bharadwaj atomistic potential representation of cyclotrimethylene trinitramine (RDX), a well-studied energetic material, to accurately determine the solid and liquid phase Gibbs free energies, and the melting point (Tm). We outline an efficient technique to find the absolute chemical potential and melting point of a fully-flexible molecule using one set of simulations to compute the solid absolute chemical potential and one set of simulations to compute the solid-liquid free energy difference. With this combination, only a handful of simulations are needed, whereby the absolute quantities of the chemical potentials are obtained, for use in other property calculations, such as the characterization of crystal polymorphs or the determination of the entropy. Using the LAMMPS molecular simulator, the Frenkel and Ladd and pseudo-supercritical path techniques are adapted to generate 3rd order fits of the solid and liquid chemical potentials. Results yield the thermodynamic melting point Tm = 488.75 K at 1.0 atm. We also validate these calculations and compare this melting point to one obtained from a typical superheated simulation technique. PMID:26661376

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

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

    The origin and strength of intra- and inter-molecular vibrational coupling is difficult to probe by direct experimental observations. However, explicitly including or not including some specific intramolecular vibrational modes to study intermolecular interaction provides a precise theoretical way to examine the effects of anharmonic coupling between modes. In this work, a full-dimension intra- and inter-molecular ab initio potential energy surface (PES) for H2O-Ar, which explicitly incorporates interdependence on the intramolecular (Q1, Q2, Q3) normal-mode coordinates of the H2O monomer, has been calculated. In addition, four analytic vibrational-quantum-state-specific PESs are obtained by least-squares fitting vibrationally averaged interaction energies for the (v1, v2, v3) = (0, 0, 0), (0, 0, 1), (1, 0, 0), (0, 1, 0) states of H2O to the three-dimensional Morse/long-range potential function. Each vibrationally averaged PES fitted to 442 points has root-mean-square (rms) deviation smaller than 0.15 cm-1, and required only 58 parameters. With the 3D PESs of H2O-Ar dimer system, we employed the combined radial discrete variable representation/angular finite basis representation method and Lanczos algorithm to calculate rovibrational energy levels. This showed that the resulting vibrationally averaged PESs provide good representations of the experimental infrared data, with rms discrepancies smaller than 0.02 cm-1 for all three rotational branches of the asymmetric stretch fundamental transitions. The infrared band origin shifts associated with three fundamental bands of H2O in H2O-Ar complex are predicted for the first time and are found to be in good agreement with the (extrapolated) experimental values. Upon introduction of additional intramolecular degrees of freedom into the intermolecular potential energy surface, there is clear spectroscopic evidence of intra- and intermolecular vibrational couplings.

  17. Molecular potentials and relaxation dynamics

    NASA Astrophysics Data System (ADS)

    Karo, A. M.

    1981-03-01

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

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

    PubMed

    Bordner, Andrew J

    2012-12-01

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

  19. Molecular potentials and relaxation dynamics

    SciTech Connect

    Karo, A.M.

    1981-03-27

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

  20. 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

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

    NASA Astrophysics Data System (ADS)

    Zhang, Yan; Lin, Hai

    2009-05-01

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

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

    PubMed

    Zhang, Yan; Lin, Hai

    2009-10-29

    Testosterone hydroxylation is a prototypical reaction of human cytochrome P450 3A4, which metabolizes about 50% of oral drugs on the market. Reaction dynamics calculations were carried out for the testosterone 6beta-hydrogen abstraction and the 6beta-d(1)-testosterone 6beta-duterium abstraction employing a model that consists of the substrate and the active oxidant compound I. The calculations were performed at the level of canonical variational transition state theory with multidimensional tunneling and were based on a semiglobal full-dimensional potential energy surface generated by the multiconfiguration molecular mechanics technique. The tunneling coefficients were found to be around 3, indicating substantial contributions by quantum tunneling. However, the tunneling made only modest contributions to the kinetic isotope effects. The kinetic isotope effects were computed to be about 2 in the doublet spin state and about 5 in the quartet spin state. PMID:19480428

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

    PubMed

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

    2016-01-01

    The origin and strength of intra- and inter-molecular vibrational coupling is difficult to probe by direct experimental observations. However, explicitly including or not including some specific intramolecular vibrational modes to study intermolecular interaction provides a precise theoretical way to examine the effects of anharmonic coupling between modes. In this work, a full-dimension intra- and inter-molecular ab initio potential energy surface (PES) for H2O-Ar, which explicitly incorporates interdependence on the intramolecular (Q1,  Q2,  Q3) normal-mode coordinates of the H2O monomer, has been calculated. In addition, four analytic vibrational-quantum-state-specific PESs are obtained by least-squares fitting vibrationally averaged interaction energies for the (v1,  v2,  v3) =  (0,  0,  0), (0,  0,  1), (1,  0,  0), (0,  1,  0) states of H2O to the three-dimensional Morse/long-range potential function. Each vibrationally averaged PES fitted to 442 points has root-mean-square (rms) deviation smaller than 0.15 cm(-1), and required only 58 parameters. With the 3D PESs of H2O-Ar dimer system, we employed the combined radial discrete variable representation/angular finite basis representation method and Lanczos algorithm to calculate rovibrational energy levels. This showed that the resulting vibrationally averaged PESs provide good representations of the experimental infrared data, with rms discrepancies smaller than 0.02 cm(-1) for all three rotational branches of the asymmetric stretch fundamental transitions. The infrared band origin shifts associated with three fundamental bands of H2O in H2O-Ar complex are predicted for the first time and are found to be in good agreement with the (extrapolated) experimental values. Upon introduction of additional intramolecular degrees of freedom into the intermolecular potential energy surface, there is clear spectroscopic evidence of intra- and intermolecular vibrational couplings. PMID:26747800

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

    NASA Technical Reports Server (NTRS)

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

    1975-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  6. Alaska's renewable energy potential.

    SciTech Connect

    Not Available

    2009-02-01

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

  7. Molecular energies from an incremental fragmentation method

    NASA Astrophysics Data System (ADS)

    Meitei, Oinam Romesh; Heßelmann, Andreas

    2016-02-01

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

  8. Molecular Electrostatic Potentials from Invariom Point Charges.

    PubMed

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

    2016-07-18

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

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

    PubMed

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

    2010-01-14

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

  10. An ab initio method for locating potential energy minima

    SciTech Connect

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

    2009-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2006-01-01

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

  12. 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.

  13. 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

  14. 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

  15. 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

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

    SciTech Connect

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

    1999-02-20

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

  17. 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.

  18. 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.

  19. Molecular dynamics simulations of solutions at constant chemical potential

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  20. California Industrial Energy Efficiency Potential

    SciTech Connect

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

    2005-06-01

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

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

    PubMed

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

    2015-12-28

    An effective way to accelerate rare events in molecular dynamics simulations is to apply a bias potential which destabilizes minima without biasing the transitions between stable states. This approach, called hyperdynamics, is limited by our ability to construct general bias potentials without having to understand the reaction mechanisms available to the system, a priori. Current bias potentials are typically constructed in terms of a metric which quantifies the distance that a trajectory deviates from the reactant state minimum. Such metrics include detection of negative curvatures of the potential, an energy increase, or deviations in bond lengths from the minimum. When one of these properties exceeds a critical value, the bias potentials are constructed to approach zero. A problem common to each of these schemes is that their effectiveness decreases rapidly with system size. We attribute this problem to a diminishing volume defined by the metrics around a reactant minimum as compared to the total volume of the reactant state basin. In this work, we mitigate the dimensionality scaling problem by constructing bias potentials that are based upon the distance to the boundary of the reactant basin. This distance is quantified in two ways: (i) by following the minimum mode direction to the reactant boundary and (ii) by training a machine learning algorithm to give an analytic expression for the boundary to which the distance can be calculated. Both of these ridge-based bias potentials are demonstrated to scale qualitatively better with dimensionality than the existing methods. We attribute this improvement to a greater filling fraction of the reactant state using the ridge-based bias potentials as compared to the standard potentials. PMID:26723648

  2. On the ionization potential of molecular oxygen

    NASA Technical Reports Server (NTRS)

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

    1974-01-01

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

  3. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  5. Extracting molecular potentials from incomplete spectroscopic information

    NASA Astrophysics Data System (ADS)

    Li, Xuan; Dutta, Sourav

    2015-12-01

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

  6. Molecular dynamics simulation of threshold displacement energies in zircon

    SciTech Connect

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

    2009-10-15

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

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

    PubMed

    Lesiuk, Michał; Zachara, Janusz

    2013-02-21

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

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

    NASA Astrophysics Data System (ADS)

    Lesiuk, Michał; Zachara, Janusz

    2013-02-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

    Challis, K J; Jack, Michael W

    2013-10-01

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

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

    NASA Astrophysics Data System (ADS)

    Diaf, Ahmed

    2015-01-01

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

  13. 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…

  14. 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 ...

  15. Potential energy of a dinuclear system

    SciTech Connect

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

    1994-11-01

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

  16. 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.

  17. 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

  18. 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)

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  20. 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

  1. 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

  2. On the potential for molecular imaging with Cerenkov luminescence

    PubMed Central

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

    2011-01-01

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

  3. 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.

  4. 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.

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

    PubMed

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

    2006-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2006-09-01

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

  7. 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.

  8. 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)

  9. 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.

  10. A molecularly based theory for electron transfer reorganization energy

    NASA Astrophysics Data System (ADS)

    Zhuang, Bilin; Wang, Zhen-Gang

    2015-12-01

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

  11. 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

  12. 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.

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

    SciTech Connect

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

    2015-10-28

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

  14. Theoretical studies of potential energy surfaces

    SciTech Connect

    Harding, L.B.

    1995-07-01

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

  15. Potential of energy production from conserved forages

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  16. 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.

  17. Scalable Quantum Simulation of Molecular Energies

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  18. Potential function and dissociation energy of alkali halide

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  19. Economic Energy Savings Potential in Federal Buildings

    SciTech Connect

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

    2000-09-04

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

  20. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

  2. 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

  3. Nondynamical correlation energy in model molecular systems

    NASA Astrophysics Data System (ADS)

    Chojnacki, Henryk

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

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

    PubMed

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

    2012-05-25

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

  5. 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.

  6. Molecular thermometers for potential applications in thermal ablation procedures

    NASA Astrophysics Data System (ADS)

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

    2013-02-01

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

  7. MOLECULAR ALTERATIONS IN GLIOBLASTOMA: POTENTIAL TARGETS FOR IMMUNOTHERAPY

    PubMed Central

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

    2015-01-01

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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Geothermal energy and its potential. [Utah

    SciTech Connect

    Berge, C.W.

    1980-06-01

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

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

    PubMed Central

    Stuker, Florian; Ripoll, Jorge; Rudin, Markus

    2011-01-01

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

  14. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

  16. 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.

  17. 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.

  18. Potential energy studies on silane dimers

    NASA Astrophysics Data System (ADS)

    Mahlanen, Riina; Pakkanen, Tapani A.

    2011-04-01

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

  19. 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

  20. 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)

  1. 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.

  2. 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

  3. 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.

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

    PubMed

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

    2016-01-01

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

  6. 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

  7. 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.

  8. 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

  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. 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).

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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

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

    NASA Astrophysics Data System (ADS)

    Price, David Wilson, Jr.

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

  18. 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.

  19. 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.

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

    NASA Astrophysics Data System (ADS)

    Geng, Hua Y.

    2015-02-01

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

  1. 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.

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

    EPA Science Inventory

    Introduction

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

  3. 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

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

    PubMed

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

    2013-10-01

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

  5. 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.

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

    NASA Astrophysics Data System (ADS)

    Wu, Xiangyang

    1999-07-01

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

  7. 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.

  8. 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.

  9. The wind energy potential of western Greece

    SciTech Connect

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

    1992-12-01

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

  10. 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.

  11. Potential energy curves and collision integrals of air components

    NASA Technical Reports Server (NTRS)

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

    1995-01-01

    Collision integrals are fundamental quantities required to determine the transport properties of the environment surrounding aerospace vehicles in the upper atmosphere. These collision integrals can be determined as a function of temperature from the potential energy curves describing the atomic and molecular collisions. Ab initio calculations provide a practical method of computing the required interaction potentials. In this work we will discuss recent advances with an emphasis on the accuracy that is obtainable. Results for interactions, e.g. N+N, N+O, O+O, and H+N2 will be reviewed and their application to the determination of transport properties, such as diffusion and viscosity coefficients, will be examined.

  12. Assessment of wind energy potential in Poland

    NASA Astrophysics Data System (ADS)

    Starosta, Katarzyna; Linkowska, Joanna; Mazur, Andrzej

    2014-05-01

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

  13. Energy potential of sugarcane and sweet sorghum

    SciTech Connect

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

    1980-01-01

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

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

    PubMed Central

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

    2010-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1985-01-01

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

  16. 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.

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

    NASA Astrophysics Data System (ADS)

    Melnikov, V. V.

    2015-06-01

    The structural and energy characteristics of interstitial molecular hydrogen in single-crystal silicon are theoretically studied. The dependence of the potential energy of the system on the position and orientation of the interstitial defect is investigated, and the mechanism of interaction of a hydrogen molecule with a silicon crystal is considered. A three-dimensional model is employed to calculate the energy spectrum of H2 in Si, and the obtained dispersion law is analyzed.

  18. 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.

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

    PubMed

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

    2015-08-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-02-01

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

  1. 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.

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

    PubMed

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

    2012-02-01

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

  3. 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

  4. 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.

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

    NASA Technical Reports Server (NTRS)

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

    1976-01-01

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

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

    PubMed

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

    2015-01-13

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

  7. Energy resource potential of natural gas hydrates

    USGS Publications Warehouse

    Collett, T.S.

    2002-01-01

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

  8. 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

  9. 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.

  10. 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

  11. Potential Molecular and Cellular Mechanism of Psychotropic Drugs

    PubMed Central

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

    2014-01-01

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

  12. 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.

  13. 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

  14. Free energy calculations for molecular solids using GROMACS

    NASA Astrophysics Data System (ADS)

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

    2013-07-01

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

  15. 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.

  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. 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.

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

    NASA Astrophysics Data System (ADS)

    Jiang, Bin; Guo, Hua

    2013-08-01

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

  20. ASSESSMENT OF ENERGY RECOVERY POTENTIAL OF INDUSTRIAL COMBUSTION EQUIPMENT

    EPA Science Inventory

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

  1. 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

  2. Determination of Multidimensional Intermolecular Potential Energy Surfaces

    NASA Astrophysics Data System (ADS)

    Cohen, Ronald Carl

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

  3. 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)

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

    PubMed

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

    2016-04-01

    Pinocembrin is a natural flavonoid compound extracted from honey, propolis, ginger roots, wild marjoram, and other plants. In preclinical studies, it has shown anti-inflammatory and neuroprotective effects as well as the ability to reduce reactive oxygen species, protect the blood-brain barrier, modulate mitochondrial function, and regulate apoptosis. Considering these pharmaceutical characteristics, pinocembrin has potential as a drug to treat ischemic stroke and other clinical conditions. In this review, we summarize its pharmacologic characteristics and discuss its mechanisms of action and potential therapeutic applications. PMID:25744566

  5. Molecular and Therapeutic Potential and Toxicity of Valproic Acid

    PubMed Central

    Chateauvieux, Sébastien; Morceau, Franck; Dicato, Mario; Diederich, Marc

    2010-01-01

    Valproic acid (VPA), a branched short-chain fatty acid, is widely used as an antiepileptic drug and a mood stabilizer. Antiepileptic properties have been attributed to inhibition of Gamma Amino Butyrate (GABA) transaminobutyrate and of ion channels. VPA was recently classified among the Histone Deacetylase Inhibitors, acting directly at the level of gene transcription by inhibiting histone deacetylation and making transcription sites more accessible. VPA is a widely used drug, particularly for children suffering from epilepsy. Due to the increasing number of clinical trials involving VPA, and interesting results obtained, this molecule will be implicated in an increasing number of therapies. However side effects of VPA are substantially described in the literature whereas they are poorly discussed in articles focusing on its therapeutic use. This paper aims to give an overview of the different clinical-trials involving VPA and its side effects encountered during treatment as well as its molecular properties. PMID:20798865

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

    PubMed Central

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

    2013-01-01

    Summary Tea is the most popular beverage in the world, second only to water. Tea contains an infusion of the leaves from the Camellia sinensis plant rich in polyphenolic compounds known as catechins, the most abundant of which is (−)-EGCG. Although tea has been consumed for centuries, it has only recently been studied extensively as a health-promoting beverage that may act to prevent a number of chronic diseases and cancers. The results of several investigations indicate that green tea consumption may be of modest benefit in reducing the plasma concentration of cholesterol and preventing atherosclerosis. Additionally, the cancer-preventive effects of green tea are widely supported by results from epidemiological, cell culture, animal and clinical studies. In vitro cell culture studies show that tea polyphenols potently induce apoptotic cell death and cell cycle arrest in tumor cells but not in their normal cell counterparts. Green tea polyphenols were shown to affect several biological pathways, including growth factor-mediated pathway, the mitogen-activated protein (MAP) kinase-dependent pathway, and ubiquitin/proteasome degradation pathways. Various animal studies have revealed that treatment with green tea inhibits tumor incidence and multiplicity in different organ sites such as skin, lung, liver, stomach, mammary gland and colon. Recently, phase I and II clinical trials have been conducted to explore the anticancer effects of green tea in humans. A major challenge of cancer prevention is to integrate new molecular findings into clinical practice. Therefore, identification of more molecular targets and biomarkers for tea polyphenols is essential for improving the design of green tea trials and will greatly assist in a better understanding of the mechanisms underlying its anti-cancer activity. PMID:18228206

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

    NASA Astrophysics Data System (ADS)

    Sakai, Y.; Huzinaga, S.

    1982-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  9. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2008-12-01

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

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

    PubMed

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

    2015-11-01

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

  12. Energy Transformation in Molecular Electronic Systems

    SciTech Connect

    Kasha, Michael

    1999-05-17

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

  13. 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

  14. Molecular Approaches to Understand Nutritional Potential of Coarse Cereals.

    PubMed

    Singh, Amit Kumar; Singh, Rakesh; Subramani, Rajkumar; Kumar, Rajesh; Wankhede, Dhammaprakash P

    2016-06-01

    Coarse grains are important group of crops that constitutes staple food for large population residing primarily in the arid and semi-arid regions of the world. Coarse grains are designated as nutri-cereals as they are rich in essential amino acids, minerals and vitamins. In spite of having several nutritional virtues in coarse grain as mentioned above, there is still scope for improvement in quality parameters such as cooking qualities, modulation of nutritional constituents and reduction or elimination of anti-nutritional factors. Besides its use in traditional cooking, coarse grains have been used mainly in the weaning food preparation and other malted food production. Improvement in quality parameters will certainly increase consumer's preference for coarse grains and increase their demand. The overall genetic gain in quality traits of economic importance in the cultivated varieties will enhance their industrial value and simultaneously increase income of farmers growing these varieties. The urgent step for improvement of quality traits in coarse grains requires a detailed understanding of molecular mechanisms responsible for varied level of different nutritional contents in different genotypes of these crops. In this review we have discussed the progresses made in understanding of coarse grain biology with various omics tool coupled with modern breeding approaches and the current status with regard to our effort towards dissecting traits related to improvement of quality and nutritional constituents of grains. PMID:27252585

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

    PubMed Central

    Krengel, Ute; Bousquet, Paula A.

    2014-01-01

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

  16. 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.

  17. 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

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

    EPA Science Inventory

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

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

    PubMed

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

    2014-01-01

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

  20. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2008-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-08-01

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

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

    PubMed

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

    2011-01-01

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

  4. 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

  5. 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

  6. 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.

  7. 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..

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

    PubMed

    Snellman, Erick A; Colwell, Rita R

    2004-10-01

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

  9. 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.

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

    PubMed

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

    2016-02-01

    Smaller semiconductors require shallow, low energy ion implantation, resulting space charge effects, which reduced beam currents and production rates. To increase production rates, molecular ions are used. Boron and phosphorous (or arsenic) implantation is needed for P-type and N-type semiconductors, respectively. Carborane, which is the most stable molecular boron ion leaves unacceptable carbon residue on extraction grids. A self-cleaning carborane acid compound (C4H12B10O4) was synthesized and utilized in the ITEP Bernas ion source resulting in large carborane ion output, without carbon residue. Pure gaseous processes are desired to enable rapid switch among ion species. Molecular phosphorous was generated by introducing phosphine in dissociators via 4PH3 = P4 + 6H2; generated molecular phosphorous in a pure gaseous process was then injected into the HCEI Calutron-Bernas ion source, from which P4(+) ion beams were extracted. Results from devices and some additional concepts are described. PMID:26932065

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

  12. Energy dissipation in an adaptive molecular circuit

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  13. The Potential Energy of an Autoencoder.

    PubMed

    Kamyshanska, Hanna; Memisevic, Roland

    2015-06-01

    Autoencoders are popular feature learning models, that are conceptually simple, easy to train and allow for efficient inference. Recent work has shown how certain autoencoders can be associated with an energy landscape, akin to negative log-probability in a probabilistic model, which measures how well the autoencoder can represent regions in the input space. The energy landscape has been commonly inferred heuristically, by using a training criterion that relates the autoencoder to a probabilistic model such as a Restricted Boltzmann Machine (RBM). In this paper we show how most common autoencoders are naturally associated with an energy function, independent of the training procedure, and that the energy landscape can be inferred analytically by integrating the reconstruction function of the autoencoder. For autoencoders with sigmoid hidden units, the energy function is identical to the free energy of an RBM, which helps shed light onto the relationship between these two types of model. We also show that the autoencoder energy function allows us to explain common regularization procedures, such as contractive training, from the perspective of dynamical systems. As a practical application of the energy function, a generative classifier based on class-specific autoencoders is presented. PMID:26357347

  14. 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.

  15. 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.

  16. 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,…

  17. Evaluating Molecular Mechanical Potentials for Helical Peptides and Proteins

    PubMed Central

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

    2010-01-01

    Multiple variants of the AMBER all-atom force field were quantitatively evaluated with respect to their ability to accurately characterize helix-coil equilibria in explicit solvent simulations. Using a global distributed computing network, absolute conformational convergence was achieved for large ensembles of the capped A21 and Fs helical peptides. Further assessment of these AMBER variants was conducted via simulations of a flexible 164-residue five-helix-bundle protein, apolipophorin-III, on the 100 ns timescale. Of the contemporary potentials that had not been assessed previously, the AMBER-99SB force field showed significant helix-destabilizing tendencies, with beta bridge formation occurring in helical peptides, and unfolding of apolipophorin-III occurring on the tens of nanoseconds timescale. The AMBER-03 force field, while showing adequate helical propensities for both peptides and stabilizing apolipophorin-III, (i) predicts an unexpected decrease in helicity with ALA→ARG+ substitution, (ii) lacks experimentally observed 310 helical content, and (iii) deviates strongly from average apolipophorin-III NMR structural properties. As is observed for AMBER-99SB, AMBER-03 significantly overweighs the contribution of extended and polyproline backbone configurations to the conformational equilibrium. In contrast, the AMBER-99φ force field, which was previously shown to best reproduce experimental measurements of the helix-coil transition in model helical peptides, adequately stabilizes apolipophorin-III and yields both an average gyration radius and polar solvent exposed surface area that are in excellent agreement with the NMR ensemble. PMID:20418937

  18. Photoinduced charge and energy transfer in molecular wires.

    PubMed

    Gilbert, Mélina; Albinsson, Bo

    2015-02-21

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

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

    PubMed

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

    2016-06-01

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

  20. Stretching the inflaton potential with kinetic energy

    SciTech Connect

    Lidsey, James E.

    2007-08-15

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

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. Energy functions for rubber from microscopic potentials

    NASA Astrophysics Data System (ADS)

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

    2007-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-01-01

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

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

    EPA Science Inventory

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

  8. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

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

  10. 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.

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

    NASA Astrophysics Data System (ADS)

    Brown, W. Michael; Yamada, Masako

    2013-12-01

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

  12. 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.

  13. Molecular mechanisms underlying the potential antiobesity-related diseases effect of cocoa polyphenols.

    PubMed

    Ali, Faisal; Ismail, Amin; Kersten, Sander

    2014-01-01

    Obesity and related metabolic diseases (e.g., type 2 diabetes, cardiovascular diseases, and hypertension) are the most prevailing nutrition-related issues in the world. An emerging feature of obesity is their relationship with chronic inflammation that begins in white adipose tissue and eventually becomes systemic. One potential dietary strategy to reduce glucose intolerance and inflammation is consumption of polyphenol-rich cocoa-like cocoa or their by-products. In vitro as well as in vivo data indicate that cocoa polyphenols (CPs) may exhibit antioxidant and anti-inflammatory properties. Polyphenols commonly found in cocoa have been reported to regulate lipid metabolism via inducing metabolic gene expression or activating transcription factors that regulate the expression of numerous genes, many of which play an important role in energy metabolism. Currently, several molecular targets (e.g., nuclear factor Kappa B, activated protein-1, peroxisome proliferator-activated receptors, liver X receptors, and adiponectin gene) have been identified, which may explain potential beneficial obesity-associated diseases effects of CPs. Further studies have been performed regarding the protective effects of CPs against metabolic diseases by suppressing transcription factors that antagonize lipid accumulation. Thus, polyphenols-rich cocoa products may diminish obesity-mediated metabolic diseases by multiple mechanisms, thereby attenuating chronic inflammation. PMID:24259381

  14. 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

  15. 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

  16. Molecular hydrogen as a preventive and therapeutic medical gas: initiation, development and potential of hydrogen medicine.

    PubMed

    Ohta, Shigeo

    2014-10-01

    Molecular hydrogen (H2) has been accepted to be an inert and nonfunctional molecule in our body. We have turned this concept by demonstrating that H2 reacts with strong oxidants such as hydroxyl radical in cells, and proposed its potential for preventive and therapeutic applications. H2 has a number of advantages exhibiting extensive effects: H2 rapidly diffuses into tissues and cells, and it is mild enough neither to disturb metabolic redox reactions nor to affect signaling reactive oxygen species; therefore, there should be no or little adverse effects of H2. There are several methods to ingest or consume H2; inhaling H2 gas, drinking H2-dissolved water (H2-water), injecting H2-dissolved saline (H2-saline), taking an H2 bath, or dropping H2-saline into the eyes. The numerous publications on its biological and medical benefits revealed that H2 reduces oxidative stress not only by direct reactions with strong oxidants, but also indirectly by regulating various gene expressions. Moreover, by regulating the gene expressions, H2 functions as an anti-inflammatory and anti-apoptotic, and stimulates energy metabolism. In addition to growing evidence obtained by model animal experiments, extensive clinical examinations were performed or are under investigation. Since most drugs specifically act to their targets, H2 seems to differ from conventional pharmaceutical drugs. Owing to its great efficacy and lack of adverse effects, H2 has promising potential for clinical use against many diseases. PMID:24769081

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

    PubMed

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

    2012-08-23

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

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

    PubMed

    Cawkwell, M J; Niklasson, Anders M N

    2012-10-01

    Born-Oppenheimer molecular dynamics simulations with long-term conservation of the total energy and a computational cost that scales linearly with system size have been obtained simultaneously. Linear scaling with a low pre-factor is achieved using density matrix purification with sparse matrix algebra and a numerical threshold on matrix elements. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] yields microcanonical trajectories with the approximate forces obtained from the linear scaling method that exhibit no systematic drift over hundreds of picoseconds and which are indistinguishable from trajectories computed using exact forces. PMID:23039583

  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. 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.

  1. 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.

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

    PubMed

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

    2013-04-01

    Biomass utilization is increasingly considered as a practical way for sustainable energy supply and long-term environment care around the world. In concerns with food security, starch or sugar-based bioethanol and edible-oilderived biodiesel are severely restricted for large scale production. Alternatively, conversion of lignocellulosic residues from food crops could be considered, but due to its recalcitrance, the current biomass process is unacceptably expensive. In this context, genetic breeding of energy crops appears as a promising solution. To fulfil the global world need as both food and biofuel sources, energy crops are expected to be produced with higher yields and especially in marginal lands. This review focus on recent progress and patents dealing with energy plants and the challenges associated with bioenergy development. We also discuss the potential use of molecular approaches including genome sequencing, molecular markers, and genetic transformation for improving specific traits or generating new cultivars of energy plants. PMID:22779438

  3. Potential Energy Sources Pose Mining Problem

    ERIC Educational Resources Information Center

    Chemical and Engineering News, 1974

    1974-01-01

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

  4. 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.

  5. 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.

  6. 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

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

    PubMed

    McCreery, Richard L

    2016-01-01

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

  8. 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.

  9. 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.

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

    PubMed

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

    2016-01-01

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